From dmb at mrc-dunn.cam.ac.uk Wed Oct 1 04:53:17 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Wed, 01 Oct 2003 09:53:17 +0100 Subject: [BiO BB] searching information References: <20030930214908.66913.qmail@web41905.mail.yahoo.com> Message-ID: <3F7A95FD.304@mrc-dunn.cam.ac.uk> Where did the peer to peer journal sharing discussion leave off? pablo gonzalez wrote: > Mr. Jeff W. Bizzarro: > thank you for aswer my letter. I?m working with pseudomonas and I > would like to ask you about how can i do to reduce the number of > hypothetical proteins ( if it?s possible) and obtein more information > about known proteins, when i use BLAST program. > > Yours sincerely Pablo J. Gonzalez > Universidad Nacional de Rio Cuarto - C?rdoba - ARGENTINA > > > > > > "J.W. Bizzaro" wrote: > > Hi Pablo. > > You're probably looking for sequence alignment tools such as BLAST or > Clustal. You may want to post the question with more detail (what > specifically do you want to do) to the > bio_bulletin_board at bioinformatics.org > > Cheers. > Jeff > > Pablo J.Gonzalez wrote: > > I am argentinian and i am studing microbiology and i want > > information about how to use the bioinformatics tools,(for > > search homologies between microorganism sequences and > > proteins) becausse the bad economic situation i can?t buy a > > book for learn the keys for a good handling of the tools > > that offer internet, so, i will be gratefull for > > information about free sites for consult the information > > what i want. > > Thank you for your time. > > PABLO J. GONZALEZ > > > -- > J.W. Bizzaro jeff at bioinformatics.org > Pr esident, Bioinformatics.Org http://bioinformatics.org/~jeff > "As we enjoy great advantages from the inventions of others, we > should be glad of an opportunity to serve others by any invention > of ours; and this we should do freely and generously." > -- Benjamin Franklin > -- > > > ------------------------------------------------------------------------ > Internet GRATIS es Yahoo! Conexi?n. > Usuario: yahoo; contrase?a: yahoo > Desde Buenos Aires: 4004-1010 > M?s ciudades: clic aqu? > . -------------- next part -------------- An HTML attachment was scrubbed... URL: From deletto at unisa.it Wed Oct 1 06:44:40 2003 From: deletto at unisa.it (deletto at unisa.it) Date: Wed, 1 Oct 2003 12:44:40 +0200 Subject: [BiO BB] pcr oligo design tool In-Reply-To: <3F7A95FD.304@mrc-dunn.cam.ac.uk> References: <20030930214908.66913.qmail@web41905.mail.yahoo.com> <3F7A95FD.304@mrc-dunn.cam.ac.uk> Message-ID: <1065005080.3f7ab018f2a4c@webmail.unisa.it> Sorry for bothering all cause I have got a very simple question :) Can anyone of you is so kind to give me a good suggestion about a "sharp" online tool for pcr oligo design? I will appreciate any helps too much. Thanks in advance, davide ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/ From vesko_baev at abv.bg Wed Oct 1 08:07:53 2003 From: vesko_baev at abv.bg (Vesko Baev) Date: Wed, 1 Oct 2003 15:07:53 +0300 (EEST) Subject: [BiO BB] bioinformatics/cell biology Message-ID: <1716712619.1065010073939.JavaMail.nobody@app1.ni.bg> Hello All, Can you help me with one question? I'm looking for a themes where the intrests of bioinformatics and cell biology are one. Can you tell me some ideas for bioinformatics in cell biology? Thanks to all! ----------------------------------------------------------------- http://club.abv.bg/jsp/abvCard.jsp - ???? ??? - ??????? ? ?????? ????? ? ???? ! From nlevenkov at wistar.upenn.edu Wed Oct 1 12:37:36 2003 From: nlevenkov at wistar.upenn.edu (N. Levenkov) Date: Wed, 1 Oct 2003 12:37:36 -0400 Subject: [BiO BB] program to generate Venn diagram Message-ID: <200310011237.AA42926694@mail.wistar.upenn.edu> Hi, Does anybody know a program for Unix that would create a Venn diagram? Thank you, Natasha From dmb at mrc-dunn.cam.ac.uk Wed Oct 1 13:10:02 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Wed, 01 Oct 2003 18:10:02 +0100 Subject: [BiO BB] program to generate Venn diagram References: <200310011237.AA42926694@mail.wistar.upenn.edu> Message-ID: <3F7B0A6A.4070105@mrc-dunn.cam.ac.uk> If you find one let me know! I have found some interesting leads... http://www.csr.uvic.ca/~fruskey/Publications/VennArea/VennArea.pdf http://www.cs.kent.ac.uk/pubs/2003/1652/ http://www.it.bton.ac.uk/research/vmg/papers/D2K2FH.pdf http://www.it.bton.ac.uk/Research/vmg/papers/algorithm.pdf http://www.cs.kent.ac.uk/pubs/2003/1652/content.pdf Venn euler diagrams are a powerful and overlooked tool in bioinformatics. N. Levenkov wrote: >Hi, > >Does anybody know a program for Unix that would create a Venn diagram? > > >Thank you, > >Natasha >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From dmb at mrc-dunn.cam.ac.uk Wed Oct 1 13:13:01 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Wed, 01 Oct 2003 18:13:01 +0100 Subject: [BiO BB] bioinformatics/cell biology References: <1716712619.1065010073939.JavaMail.nobody@app1.ni.bg> Message-ID: <3F7B0B1D.6010407@mrc-dunn.cam.ac.uk> protein localization! Vesko Baev wrote: >Hello All, >Can you help me with one question? I'm looking for a themes where the intrests of bioinformatics and cell biology are one. Can you tell me some ideas for bioinformatics in cell biology? > >Thanks to all! > >----------------------------------------------------------------- >http://club.abv.bg/jsp/abvCard.jsp - ???? ??? - ??????? ? ?????? ????? ? ???? ! >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From dmb at mrc-dunn.cam.ac.uk Wed Oct 1 13:17:36 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Wed, 01 Oct 2003 18:17:36 +0100 Subject: [BiO BB] program to generate Venn diagram References: <200310011237.AA42926694@mail.wistar.upenn.edu> <3F7B0A6A.4070105@mrc-dunn.cam.ac.uk> Message-ID: <3F7B0C30.1080309@mrc-dunn.cam.ac.uk> if you just need some very simple diagrams, you can use M$ Word! Dan Bolser wrote: > If you find one let me know! > > I have found some interesting leads... > > http://www.csr.uvic.ca/~fruskey/Publications/VennArea/VennArea.pdf > > http://www.cs.kent.ac.uk/pubs/2003/1652/ > > http://www.it.bton.ac.uk/research/vmg/papers/D2K2FH.pdf > > http://www.it.bton.ac.uk/Research/vmg/papers/algorithm.pdf > > http://www.cs.kent.ac.uk/pubs/2003/1652/content.pdf > > > Venn euler diagrams are a powerful and overlooked tool in bioinformatics. > > > N. Levenkov wrote: > >> Hi, >> >> Does anybody know a program for Unix that would create a Venn diagram? >> >> >> Thank you, >> >> Natasha >> _______________________________________________ >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >> > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From drjohn08318 at yahoo.com Wed Oct 1 14:19:34 2003 From: drjohn08318 at yahoo.com (John G. Hoey, Ph.D.) Date: Wed, 1 Oct 2003 11:19:34 -0700 (PDT) Subject: [BiO BB] pcr oligo design tool In-Reply-To: <1065005080.3f7ab018f2a4c@webmail.unisa.it> Message-ID: <20031001181934.35349.qmail@web14410.mail.yahoo.com> Try primer3 at the following link: www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi drjohn deletto at unisa.it wrote: Sorry for bothering all cause I have got a very simple question :) Can anyone of you is so kind to give me a good suggestion about a "sharp" online tool for pcr oligo design? I will appreciate any helps too much. Thanks in advance, davide ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/ _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board --------------------------------- Do you Yahoo!? The New Yahoo! Shopping - with improved product search -------------- next part -------------- An HTML attachment was scrubbed... URL: From Eitan.Rubin at weizmann.ac.il Thu Oct 2 06:23:25 2003 From: Eitan.Rubin at weizmann.ac.il (Eitan Rubin) Date: Thu, 2 Oct 2003 13:23:25 +0300 Subject: [BiO BB] Re: Primer design In-Reply-To: <20031001160120.1E4D3D280A@www.bioinformatics.org> Message-ID: <74E070C7-F4C2-11D7-8B12-000A957756C0@weizmann.ac.il> Hi, What do you mean "sharp"? I had very good experience with Washu's Primer3. The interface is not great but works, and the primers it produces are reliable. Eitan -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 226 bytes Desc: not available URL: From dig at bioinformatics.org Thu Oct 2 07:32:22 2003 From: dig at bioinformatics.org (Dmitri I GOULIAEV) Date: Thu, 2 Oct 2003 06:32:22 -0500 Subject: [BiO BB] program to generate Venn diagram In-Reply-To: <200310011237.AA42926694@mail.wistar.upenn.edu>; from nlevenkov@wistar.upenn.edu on Wed, Oct 01, 2003 at 12:37:36PM -0400 References: <200310011237.AA42926694@mail.wistar.upenn.edu> Message-ID: <20031002063222.A6227@lifebook> Hi, Natasha! On Wed, Oct 01, 2003 at 12:37:36PM -0400, N. Levenkov wrote: > Does anybody know a program for Unix that would create a Venn diagram? It depends of what kind of diagram you are talking about. You might want to take a look at venn.mp [1] -- it is a MetaPost generator of Venn diagramms. I put some examples on-line [2], generated with the help of this package (MetaPost -> PostScript -> PNG). Another possibility is Create-A-Venn [3] -- it is on-line generator of Venn diagram. It produces a ~450x550px GIF-file. [1] http://www.ctan.org/tex-archive/graphics/metapost/contrib/macros/venn/ [2] http://www.bioinformatics.org/~dig/other/venn-diagram/ [3] http://www.venndiagram.com/venn01.html Best regards, -- DIG (Dmitri I GOULIAEV) http://www.bioinformatics.org/~dig/ 1024D/63A6C649: 26A0 E4D5 AB3F C2D4 0112 66CD 4343 C0AF 63A6 C649 From dmb at mrc-dunn.cam.ac.uk Thu Oct 2 09:03:02 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 02 Oct 2003 14:03:02 +0100 Subject: [BiO BB] program to generate Venn diagram References: <200310011237.AA42926694@mail.wistar.upenn.edu> <3F7B0A6A.4070105@mrc-dunn.cam.ac.uk> <3F7B0C30.1080309@mrc-dunn.cam.ac.uk> <20031002063341.B6227@lifebook> Message-ID: <3F7C2206.4070502@mrc-dunn.cam.ac.uk> Dmitri I GOULIAEV wrote: >Hi, Dan Bolser ! > > On Wed, Oct 01, 2003 at 06:17:36PM +0100, Dan Bolser wrote: > > > >>if you just need some very simple diagrams, you can use M$ Word! >> >> >Cruel joke. > Heh heh heh.... > >Regards, > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dgs70190 at cmsu2.cmsu.edu Wed Oct 1 14:24:26 2003 From: dgs70190 at cmsu2.cmsu.edu (dgs70190 at cmsu2.cmsu.edu) Date: Wed, 01 Oct 2003 13:24:26 -0500 (CDT) Subject: [BiO BB] Biotechnology Competency Project. Message-ID: <1065032666.3f7b1bda3ec64@mulemail.cmsu.edu> Dear Sir or Madam, A Delphi study is currently being conducted to develop biotechnology competencies. This is a cooperative project of the Internaltional Technology Education Association (ITEA)-Council on Technology Teacher Education (CTTE), Central Missouri State University (Warrensburg, Mo.), and Illinois State University (Normal, Illinois) for technology teacher education programs as they prepare technology education teachers. This modified Delphi technique provides two rounds of feedback from industry professionals, technology and biotechnology educators, and those with a vested interest in the content area of biotechnology. The first-round will include participant feedback on a pre-developed list of Biotechnology competencies. The second-round will attempt to arrive at a consensus based on the committee's first-round responses. I am seeking participants to serve as the panel members for this study. The study will be performed electronically, no travel will be required. Please contact me at dgs70190 at cmsu2.cmsu.edu if you will be able to serve on this committee. The results of the study will be presented at the next ITEA conference in Albuquerque. Sincerely, Donald Scott (Researcher) Dr. Barton Waher (CMSU Advisor, ITEA/CTTE) Dr. Chris Merrill (ISU Advisor, ITEA/CTTE) ------------------------------------------------- This mail sent through MuleMail: http://mulemail.cmsu.edu/ From lucifer at chiark.greenend.org.uk Wed Oct 1 20:54:16 2003 From: lucifer at chiark.greenend.org.uk (Lucy McWilliam) Date: Thu, 2 Oct 2003 01:54:16 +0100 (BST) Subject: [BiO BB] Re: pcr oligo design tool In-Reply-To: <20031001160120.1E4D3D280A@www.bioinformatics.org> Message-ID: deletto at unisa.it wrote: > Can anyone of you is so kind to give me a good suggestion about a > "sharp" online tool for pcr oligo design? Primer3: http://www-genome.wi.mit.edu/cgi-bin/primer/primer3.cgi/primer3_www.cgi Hope that helps, -- Lucy McWilliam Department of Genetics University of Cambridge http://www.flychip.org.uk/ From letondal at pasteur.fr Thu Oct 2 14:17:04 2003 From: letondal at pasteur.fr (Catherine Letondal) Date: Thu, 02 Oct 2003 20:17:04 +0200 Subject: [BiO BB] Re: pcr oligo design tool In-Reply-To: Your message of "Thu, 02 Oct 2003 01:54:16 BST." Message-ID: <200310021817.h92IH4bs045671@electre.pasteur.fr> Lucy McWilliam wrote: > > deletto at unisa.it wrote: > > > Can anyone of you is so kind to give me a good suggestion about a > > "sharp" online tool for pcr oligo design? > > Primer3: > http://www-genome.wi.mit.edu/cgi-bin/primer/primer3.cgi/primer3_www.cgi > You can also look at these resource: http://www.pasteur.fr/cgi-bin/biology/bnb_s.pl?english=1&query=primer&rsc=online+analysis+tools Best, -- Catherine Letondal -- Pasteur Institute Computing Center From lhaifeng at dso.org.sg Thu Oct 2 21:51:55 2003 From: lhaifeng at dso.org.sg (Liu Haifeng) Date: Fri, 3 Oct 2003 09:51:55 +0800 Subject: [BiO BB] Blast comparison References: Message-ID: <000801c38950$ecd559e0$706712ac@GENETHON> Hi, I need to do comparisons between pairs of protein sequences. I have installed standalone Blast locally and would like to call it from my bioperl program. For using blastp, I am wondering if I can avoid to perform formatdb first since I am comparing one sequence against another rather than searching one sequence against a set of sequences? I guess it must be stupid to format a single sequence into a blast DB whenever I want to perform a comparison. I will appreciate your any advices and help on the matter. Thank you! Sincerely Haifeng Liu From stefan.grzybek at pharma.novartis.com Fri Oct 3 02:43:14 2003 From: stefan.grzybek at pharma.novartis.com (stefan.grzybek at pharma.novartis.com) Date: Fri, 3 Oct 2003 08:43:14 +0200 Subject: [BiO BB] Blast comparison Message-ID: Dear Haifeng, you might want to use bl2seq. It is part of the NCBI blast distribution and allows you to compare just two sequences by any one of the blast algorithms (blast[npx], tblast[nx]). Best regards, Stefan "Liu Haifeng" To: Sent by: cc: bio_bulletin_board-admin at bioinfo Subject: [BiO BB] Blast comparison rmatics.org Category: |-------------------------| | ( ) Action needed | 03-10-2003 03:51 | ( ) Decision needed | Please respond to | ( ) General Information | bio_bulletin_board |-------------------------| Hi, I need to do comparisons between pairs of protein sequences. I have installed standalone Blast locally and would like to call it from my bioperl program. For using blastp, I am wondering if I can avoid to perform formatdb first since I am comparing one sequence against another rather than searching one sequence against a set of sequences? I guess it must be stupid to format a single sequence into a blast DB whenever I want to perform a comparison. I will appreciate your any advices and help on the matter. Thank you! Sincerely Haifeng Liu _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From madhavi at cs.cmu.edu Fri Oct 3 16:49:14 2003 From: madhavi at cs.cmu.edu (Madhavi Ganapathiraju) Date: Fri, 03 Oct 2003 16:49:14 -0400 Subject: [BiO BB] Update: Biological Language Conference Message-ID: <5.2.0.9.2.20031003162439.020a0e28@128.2.254.145> BLC2003: Biological Language Conference : Final Call for papers UPDATE: The conference is being held in cooperation with American Association for Artificial Intelligence (AAAI). Selected papers will be published in J. Applied Bioinformatics. http://flan.blm.cs.cmu.edu/meeting2003/ Scope: Integration of language technologies in bioinformatics/computational biology research Protein sequences from different organisms may be viewed as texts written in different languages. The mapping of protein sequence to their structure, dynamics and function then becomes analogous to the mapping of words to meaning in natural languages. This analogy can be exploited by application of statistical language modeling and text classification techniques to biological sequences, thereby generating testable hypotheses regarding the fundamental building blocks of "protein sequence language". The biology-language analogy enables novel applications of language technologies to the biology domain, but is to a great extent overlapping with existing other computational biology/bioinformatics applications. The purpose of the Biological Language Conference is to facilitate scientific exchange between researchers using the language analogy approach directly and researchers using other approaches. We invite papers in the following areas of interest: ------------------------------------------------------------ secondary structure prediction tertiary structure prediction repetitive fold prediction membrane protein-specific prediction challenges protein folding/misfolding conformational changes genome evolution/comparison sequence alignment protein family classification immune system protein-protein interactions protein/gene networks and pathways Because of the challenge in bioinformatics research of involvement of non-biology domain experts in biology research, we also encourage submission of papers describing new approaches to cross-disciplinary education. Venue and dates: November 20-21, 2003 at Carnegie Mellon University in Pittsburgh, USA The conference is organized by: Profs. Raj Reddy and Judith Klein-Seetharaman of the NSF-funded Center for Biological Language Modeling (http://www.cs.cmu.edu/~blmt). Papers should be a maximum of 15 pages and will be peer-reviewed. All accepted papers will appear in the conference proceedings a selection of best papers will be published in J. Applied Bioinformatics. Papers should be prepared according to the guidelines (http://flan.blm.cs.cmu.edu/meeting2003/template.doc) and submitted online here. Further information on the conference will be available at http://flan.blm.cs.cmu.edu/meeting2003/. September 20th, 2003 (Optional) White-paper abstract and indication of intention to submit a paper by email to judithks at cs.cmu.edu October 20th, 2003 Deadline for electronic paper submission November 1st, 2003 Notification of acceptance November 10th, 2003 Final camera-ready manuscript due November 10th, 2003 Registration deadline Contact Judith Klein-Seetharaman, Language Technologies Institute, School of Computer Science, Carnegie Melon University, Pittsburgh 15213 PA USA email: judithks at cs.cmu.edu, phone: 412 383 7325, fax: 412 648 1945. From rnet_myousef at bezeqint.net Sat Oct 4 17:25:27 2003 From: rnet_myousef at bezeqint.net (Malik Yousef) Date: Sat, 4 Oct 2003 14:25:27 -0700 Subject: [BiO BB] DNA Promoter Message-ID: <005601c38abe$07c49950$0101c80a@privaten9kaszw> Hello Could one explain to me what is the meaning of Promoter? Where one find explanation of Bioinformatics expressions? ================================================================== Dr Malik Yousef (10/2003- Center for Bioinformatics , University of Pennsylvania Philadelphia, PA 19104-6021) CRI- The Caesarea Edmond Benjamin de Rothschild Foundation Institute for Interdisciplinary Applications of Computer Science University of Haifa Mount Carmel 31905 Haifa, Israel -------------- next part -------------- An HTML attachment was scrubbed... URL: From boris.steipe at utoronto.ca Sat Oct 4 12:39:29 2003 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Sat, 04 Oct 2003 12:39:29 -0400 Subject: [BiO BB] DNA Promoter References: <005601c38abe$07c49950$0101c80a@privaten9kaszw> Message-ID: <3F7EF7C1.25C647CE@utoronto.ca> > Malik Yousef wrote: > > Hello > > Could one explain to me what is the meaning of Promoter? > Where one find > explanation of Bioinformatics expressions? > One of the most useful tools is the Google Web search service: a search for "promoter" yields six results among the top ten, that are relevant for the biological meaning: a DNA sequence pattern that binds RNA-polymerase to allow transcription of the downstream sequence. Best regards, Boris --- Boris Steipe University of Toronto Program in Proteomics & Bioinformatics Departments of Biochemistry & Molecular and Medical Genetics http://biochemistry.utoronto.ca/steipe From drjohn08318 at yahoo.com Sat Oct 4 19:50:44 2003 From: drjohn08318 at yahoo.com (John G. Hoey, Ph.D.) Date: Sat, 4 Oct 2003 16:50:44 -0700 (PDT) Subject: [BiO BB] DNA Promoter In-Reply-To: <005601c38abe$07c49950$0101c80a@privaten9kaszw> Message-ID: <20031004235044.92692.qmail@web14409.mail.yahoo.com> ..I would strongly suggest "Molecular Biology of the Cell"....it's a wonderful reference text. JGH Malik Yousef wrote: Hello Could one explain to me what is the meaning of Promoter? Where one find explanation of Bioinformatics expressions? ================================================================== Dr Malik Yousef (10/2003- Center for Bioinformatics , University of Pennsylvania Philadelphia, PA 19104-6021) CRI- The Caesarea Edmond Benjamin de Rothschild Foundation Institute for Interdisciplinary Applications of Computer Science University of Haifa Mount Carmel 31905 Haifa, Israel --------------------------------- Do you Yahoo!? The New Yahoo! Shopping - with improved product search -------------- next part -------------- An HTML attachment was scrubbed... URL: From Bill_A_Nussbaumer at bd.com Mon Oct 6 09:37:27 2003 From: Bill_A_Nussbaumer at bd.com (Bill_A_Nussbaumer at bd.com) Date: Mon, 6 Oct 2003 09:37:27 -0400 Subject: [BiO BB] DNA Promoter Message-ID: And what's wonderful is that you can read and search it online (along with many others) on NCBI's web page. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books - Bill "John G. Hoey, Ph.D." To: bio_bulletin_board at bioinformatics.org Sent by: cc: bio_bulletin_board-admin at bioinfor Subject: Re: [BiO BB] DNA Promoter matics.org 10/04/2003 07:50 PM Please respond to bio_bulletin_board ..I would strongly suggest "Molecular Biology of the Cell"....it's a wonderful reference text. JGH Malik Yousef wrote: Hello Could one explain to me what is the meaning of Promoter? Where one find explanation of Bioinformatics expressions? From j.u.wang at dundee.ac.uk Mon Oct 6 10:12:44 2003 From: j.u.wang at dundee.ac.uk (WANG Jun) Date: Mon, 06 Oct 2003 15:12:44 +0100 Subject: [BiO BB] reference manage software in linux? Message-ID: <20031006150923.FECD.J.U.WANG@dundee.ac.uk> Hi everybody, Is there any free software in Linux can organize the references like Endnote in windows? Thanks for your help! WANG, Jun 06-10-2003 15:09:23 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ Division of Cell and Developmental Biology Wellcome Trust Biocentre University of Dundee Dundee DD1 5EH United Kingdom http://www.dundee.ac.uk/biocentre @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ From steletch at biomedicale.univ-paris5.fr Mon Oct 6 10:30:09 2003 From: steletch at biomedicale.univ-paris5.fr (=?ISO-8859-1?Q?Teletch=E9a_St=E9phane?=) Date: 06 Oct 2003 16:30:09 +0200 Subject: [BiO BB] reference manage software in linux? In-Reply-To: <20031006150923.FECD.J.U.WANG@dundee.ac.uk> References: <20031006150923.FECD.J.U.WANG@dundee.ac.uk> Message-ID: <1065450609.19011.3.camel@pcumr70.biomedicale.univ-paris5.fr> Le lun 06/10/2003 ? 16:12, WANG Jun a ?crit : > Hi everybody, > > Is there any free software in Linux can organize the references like > Endnote in windows? > > Thanks for your help! > One only answer : pybliographer, available at : http://pybliographer.org/ Stef -- -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 189 bytes Desc: not available URL: From sadiqr at yahoo.com Mon Oct 6 10:35:46 2003 From: sadiqr at yahoo.com (Rehan Sadiq) Date: Mon, 6 Oct 2003 07:35:46 -0700 (PDT) Subject: [BiO BB] Bio Informatics Grad Programs? In-Reply-To: <1065450609.19011.3.camel@pcumr70.biomedicale.univ-paris5.fr> Message-ID: <20031006143546.82972.qmail@web20416.mail.yahoo.com> Hi Everyone. I am in the software industry. However, I would like to know if anyone has any recommendations of schools or programs to learn more regarding Bio Informatics. Thanks, -R __________________________________ Do you Yahoo!? The New Yahoo! Shopping - with improved product search http://shopping.yahoo.com From rouellette at umuc.edu Mon Oct 6 11:04:30 2003 From: rouellette at umuc.edu (Robert Ouellette) Date: Mon, 06 Oct 2003 11:04:30 -0400 Subject: [BiO BB] Bio Informatics Grad Programs? References: <20031006143546.82972.qmail@web20416.mail.yahoo.com> Message-ID: <3F81847E.D6DB2182@umuc.edu> I recommend UMUC. We have an extensive Biotechnology Studies Program and A Bioinformatics Practice Track. One of the great advantage is all all classes are offered face-to-face and online. Classes are supported by virtual laboratories. I am the program director for both. You can find the details online at www.umuc.edu/gsmt. Click on degree programs. Click on biotechnology. welcome bob Rehan Sadiq wrote: > Hi Everyone. > > I am in the software industry. However, I would like > to know if anyone has any recommendations of schools > or programs to learn more regarding Bio Informatics. > > Thanks, > > -R > > __________________________________ > Do you Yahoo!? > The New Yahoo! Shopping - with improved product search > http://shopping.yahoo.com > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From hjm at tacgi.com Mon Oct 6 14:30:53 2003 From: hjm at tacgi.com (Harry Mangalam) Date: Mon, 06 Oct 2003 11:30:53 -0700 Subject: [BiO BB] reference manage software in linux? In-Reply-To: <20031006150923.FECD.J.U.WANG@dundee.ac.uk> References: <20031006150923.FECD.J.U.WANG@dundee.ac.uk> Message-ID: <3F81B4DD.1030905@tacgi.com> and sixpack (perl/tk) http://www.santafe.edu/~dirk/sixpack/ http://sourceforge.net/projects/sixpack/ hjm WANG Jun wrote: > Hi everybody, > > Is there any free software in Linux can organize the references like > Endnote in windows? > > Thanks for your help! > > WANG, Jun > 06-10-2003 15:09:23 > @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ > Division of Cell and Developmental Biology > Wellcome Trust Biocentre > University of Dundee > Dundee DD1 5EH > United Kingdom > http://www.dundee.ac.uk/biocentre > @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Cheers, Harry Harry J Mangalam - 949 856 2847 (v&f) - hjm at tacgi.com <> From joel.dudley at asu.edu Tue Oct 7 20:22:16 2003 From: joel.dudley at asu.edu (Joel Dudley) Date: Tue, 7 Oct 2003 17:22:16 -0700 Subject: [BiO BB] Bio Informatics Grad Programs? In-Reply-To: <20031006143546.82972.qmail@web20416.mail.yahoo.com> Message-ID: <78FAEC57-F925-11D7-9F22-0003939F02D0@asu.edu> Arizona State has a nice program and many of the NCBI Human Genome guys set up shop in Phoenix at TGEN (www.tgen.org). Several large Biotech buildings on campus are also nearing completion (http://www.azbio.org/). Arizona State Computational Biosciences Program http://lifesciences.asu.edu/compbiosci/ Joel Dudley Faculty Research Associate Center for Evolutionary Functional Genomics Arizona BioDesign Institute at Arizona State University On Monday, October 6, 2003, at 07:35 AM, Rehan Sadiq wrote: > Hi Everyone. > > I am in the software industry. However, I would like > to know if anyone has any recommendations of schools > or programs to learn more regarding Bio Informatics. > > Thanks, > > -R > > > > __________________________________ > Do you Yahoo!? > The New Yahoo! Shopping - with improved product search > http://shopping.yahoo.com > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From lsrubin at wicc.weizmann.ac.il Sun Oct 5 09:37:56 2003 From: lsrubin at wicc.weizmann.ac.il (Eitan Rubin) Date: Sun, 5 Oct 2003 15:37:56 +0200 Subject: [BiO BB] Is this list moderated? Message-ID: <3F8007E9@wiccweb> Hi, As part of my job, I have to say to people "no, I cannot explain to everything there is to know about bioinformatics through email" three times a day. If we keep this list non-moderated, this is where it is heading. Eitan >===== Original Message From bio_bulletin_board at bioinformatics.org ===== >When replying, PLEASE edit your Subject line so it is more specific >than "Re: BiO_Bulletin_Board digest, Vol..." > > >Today's Topics: > > 1. Update: Biological Language Conference (Madhavi Ganapathiraju) > 2. DNA Promoter (Malik Yousef) > >--__--__-- > >Message: 1 >Date: Fri, 03 Oct 2003 16:49:14 -0400 >To: >From: Madhavi Ganapathiraju >Subject: [BiO BB] Update: Biological Language Conference >Reply-To: bio_bulletin_board at bioinformatics.org > >BLC2003: Biological Language Conference : Final Call for papers >UPDATE: The conference is being held in cooperation with American >Association for Artificial Intelligence (AAAI). Selected papers will be >published in J. Applied Bioinformatics. >http://flan.blm.cs.cmu.edu/meeting2003/ > >Scope: >Integration of language technologies in bioinformatics/computational >biology research >Protein sequences from different organisms may be viewed as texts written >in different languages. The mapping of protein sequence to their structure, >dynamics and function then becomes analogous to the mapping of words to >meaning in natural languages. This analogy can be exploited by application >of statistical language modeling and text classification techniques to >biological sequences, thereby generating testable hypotheses regarding the >fundamental building blocks of "protein sequence language". > >The biology-language analogy enables novel applications of language >technologies to the biology domain, but is to a great extent overlapping >with existing other computational biology/bioinformatics applications. The >purpose of the Biological Language Conference is to facilitate scientific >exchange between researchers using the language analogy approach directly >and researchers using other approaches. > >We invite papers in the following areas of interest: >------------------------------------------------------------ >secondary structure prediction >tertiary structure prediction >repetitive fold prediction >membrane protein-specific prediction challenges >protein folding/misfolding >conformational changes >genome evolution/comparison >sequence alignment >protein family classification >immune system >protein-protein interactions >protein/gene networks and pathways > >Because of the challenge in bioinformatics research of involvement of >non-biology domain experts in biology research, we also encourage >submission of papers describing new approaches to cross-disciplinary education. > >Venue and dates: > >November 20-21, 2003 at Carnegie Mellon University in Pittsburgh, USA > >The conference is organized by: > Profs. Raj Reddy and Judith Klein-Seetharaman > of the NSF-funded Center for Biological Language Modeling >(http://www.cs.cmu.edu/~blmt). > >Papers should be a maximum of 15 pages and will be peer-reviewed. All >accepted papers will appear in the conference proceedings a selection of >best papers will be published in J. Applied Bioinformatics. Papers should >be prepared according to the guidelines >(http://flan.blm.cs.cmu.edu/meeting2003/template.doc) and submitted online >here. Further information on the conference will be available at >http://flan.blm.cs.cmu.edu/meeting2003/. > > > >September 20th, 2003 > (Optional) White-paper abstract and indication of intention to submit a >paper by email to judithks at cs.cmu.edu > >October 20th, 2003 > Deadline for electronic paper submission > >November 1st, 2003 > Notification of acceptance > >November 10th, 2003 > Final camera-ready manuscript due > >November 10th, 2003 > Registration deadline > > >Contact >Judith Klein-Seetharaman, >Language Technologies Institute, >School of Computer Science, >Carnegie Melon University, >Pittsburgh 15213 PA >USA >email: judithks at cs.cmu.edu, >phone: 412 383 7325, >fax: 412 648 1945. > > >--__--__-- > >Message: 2 >From: "Malik Yousef" >To: >Date: Sat, 4 Oct 2003 14:25:27 -0700 >Subject: [BiO BB] DNA Promoter >Reply-To: bio_bulletin_board at bioinformatics.org > >This is a multi-part message in MIME format. > >------=_NextPart_000_0057_01C38A83.5B65C150 >Content-Type: text/plain; > charset="us-ascii" >Content-Transfer-Encoding: 7bit > >Hello > >Could one explain to me what is the meaning of Promoter? Where one find >explanation of Bioinformatics expressions? > > > >================================================================== >Dr Malik Yousef (10/2003- Center for Bioinformatics , University of >Pennsylvania Philadelphia, PA 19104-6021) >CRI- The Caesarea Edmond Benjamin de Rothschild Foundation Institute for >Interdisciplinary Applications of Computer Science >University of Haifa >Mount Carmel >31905 Haifa, Israel > > >------=_NextPart_000_0057_01C38A83.5B65C150 >Content-Type: text/html; > charset="us-ascii" >Content-Transfer-Encoding: quoted-printable > > > >charset=3Dus-ascii"> >Message > > > >
>

Hello

>

Could one explain to me what is the meaning of Promoter? Where one = >find=20 >explanation of Bioinformatics expressions?

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> >------=_NextPart_000_0057_01C38A83.5B65C150-- > > > >--__--__-- > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > >End of BiO_Bulletin_Board Digest From balavijayan_1 at yahoo.com Wed Oct 8 17:07:46 2003 From: balavijayan_1 at yahoo.com (balavijayan thiyagarajan) Date: Wed, 8 Oct 2003 14:07:46 -0700 (PDT) Subject: [BiO BB] i need help regarding bioperl Message-ID: <20031008210746.86097.qmail@web10707.mail.yahoo.com> Hi Iam a student of PGD in bioinformatics in chennai INDIA.. Iam trying to learn about bioperl wich is appart from my sylabus , I have installed active perl In my home pc windows XP its working good , then i downloaded bioperl from internet with all other entire accesory file from CPAN . Iam not able 2 run bioperl programs that is being given as sample programs. If u could help me plzz, reply me ,stating my requirements on the files thst i have to download and how to run bioperl program in windows. While running gome of the programs through dos prompt as perl filename.pl iam not getting the out put iam getting command executable prompt in the next line. Idont know where the out put goes . If u could plzz reply me it will a great help for me to learn bioperl. waiting for ur reply. thanking you, bala vijayan. --------------------------------- Do you Yahoo!? The New Yahoo! Shopping - with improved product search -------------- next part -------------- An HTML attachment was scrubbed... URL: From gary at www.bioinformatics.org Thu Oct 9 18:02:03 2003 From: gary at www.bioinformatics.org (Gary Van Domselaar) Date: Thu, 9 Oct 2003 18:02:03 -0400 (EDT) Subject: [BiO BB] i need help regarding bioperl In-Reply-To: <20031008210746.86097.qmail@web10707.mail.yahoo.com> Message-ID: Hi balavijayan, Bioperl related questions are best directed to the bioperl mailing list. Check out http://www.bioperl.com Regards, g. On Wed, 8 Oct 2003, balavijayan thiyagarajan wrote: > Hi > Iam a student of PGD in bioinformatics in chennai INDIA.. Iam trying to learn about bioperl wich is appart from my sylabus , > I have installed active perl In my home pc windows XP its working good , then i downloaded bioperl from internet with all other entire accesory file from CPAN . > Iam not able 2 run bioperl programs that is being given as sample programs. > > If u could help me plzz, reply me ,stating my requirements on the files thst i have to download and how to run bioperl program in windows. > While running gome of the programs through dos prompt as perl filename.pl iam not getting the out put iam getting command executable prompt in the next line. Idont know where the out put goes . > > If u could plzz reply me it will a great help for me to learn bioperl. > > waiting for ur reply. > > thanking you, > > bala vijayan. > > > --------------------------------- > Do you Yahoo!? > The New Yahoo! Shopping - with improved product search From idoerg at burnham.org Thu Oct 9 18:13:33 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Thu, 09 Oct 2003 15:13:33 -0700 Subject: [BiO BB] i need help regarding bioperl In-Reply-To: References: Message-ID: <3F85DD8D.3030804@burnham.org> That would be: http://bioperl.org Iddo Gary Van Domselaar wrote: > Hi balavijayan, > > Bioperl related questions are best directed to the bioperl mailing list. > Check out > http://www.bioperl.com > > Regards, > > g. > > > On Wed, 8 Oct 2003, balavijayan thiyagarajan wrote: > > >>Hi >> Iam a student of PGD in bioinformatics in chennai INDIA.. Iam trying to learn about bioperl wich is appart from my sylabus , >> I have installed active perl In my home pc windows XP its working good , then i downloaded bioperl from internet with all other entire accesory file from CPAN . >> Iam not able 2 run bioperl programs that is being given as sample programs. >> >> If u could help me plzz, reply me ,stating my requirements on the files thst i have to download and how to run bioperl program in windows. >> While running gome of the programs through dos prompt as perl filename.pl iam not getting the out put iam getting command executable prompt in the next line. Idont know where the out put goes . >> >> If u could plzz reply me it will a great help for me to learn bioperl. >> >>waiting for ur reply. >> >>thanking you, >> >>bala vijayan. >> >> >>--------------------------------- >>Do you Yahoo!? >>The New Yahoo! Shopping - with improved product search > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo From gary at www.bioinformatics.org Thu Oct 9 18:23:45 2003 From: gary at www.bioinformatics.org (Gary Van Domselaar) Date: Thu, 9 Oct 2003 18:23:45 -0400 (EDT) Subject: [BiO BB] i need help regarding bioperl In-Reply-To: <3F85DD8D.3030804@burnham.org> Message-ID: Ooops, I mistyped. Thanks Iddo. Ashamedly, g. On Thu, 9 Oct 2003, Iddo Friedberg wrote: > That would be: > > http://bioperl.org > > Iddo > > Gary Van Domselaar wrote: > > Hi balavijayan, > > > > Bioperl related questions are best directed to the bioperl mailing list. > > Check out > > http://www.bioperl.com > > > > Regards, > > > > g. > > > > > > On Wed, 8 Oct 2003, balavijayan thiyagarajan wrote: > > > > > >>Hi > >> Iam a student of PGD in bioinformatics in chennai INDIA.. Iam trying to learn about bioperl wich is appart from my sylabus , > >> I have installed active perl In my home pc windows XP its working good , then i downloaded bioperl from internet with all other entire accesory file from CPAN . > >> Iam not able 2 run bioperl programs that is being given as sample programs. > >> > >> If u could help me plzz, reply me ,stating my requirements on the files thst i have to download and how to run bioperl program in windows. > >> While running gome of the programs through dos prompt as perl filename.pl iam not getting the out put iam getting command executable prompt in the next line. Idont know where the out put goes . > >> > >> If u could plzz reply me it will a great help for me to learn bioperl. > >> > >>waiting for ur reply. > >> > >>thanking you, > >> > >>bala vijayan. > >> > >> > >>--------------------------------- > >>Do you Yahoo!? > >>The New Yahoo! Shopping - with improved product search > > > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > From jeff at bioinformatics.org Thu Oct 9 19:56:32 2003 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 09 Oct 2003 19:56:32 -0400 Subject: [BiO BB] Is this list moderated? References: <3F8007E9@wiccweb> Message-ID: <3F85F5B0.1090206@bioinformatics.org> Hi Eitan. Posting to the list is restricted to subscribers, but, other than that, there is no moderation. Full moderation would require that all posts be held for approval, which could take hours. I have even seen moderated newsgroups hold up posts for a day. For lists that I have administered in the past and for wich I have chosen this approach, I have received complaints that it takes too long to get a post through. Many people, I have learned, would prefer even to get spam if it meant getting an answer to a question with expedition. Besides, it seems several people were willing to answer Milak's questions. But, I would agree that "help me with my assignment" and "give me an idea" posts are irritating. Cheers. Jeff Eitan Rubin wrote: > Hi, > > As part of my job, I have to say to people "no, I cannot explain to > everything there is to know about bioinformatics through email" three times a > day. If we keep this list non-moderated, this is where it is heading. > > Eitan > > > -- J.W. Bizzaro jeff at bioinformatics.org President, Bioinformatics.Org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From jeff at bioinformatics.org Thu Oct 9 20:06:31 2003 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 09 Oct 2003 20:06:31 -0400 Subject: [BiO BB] CALL FOR PRESENTERS: Bioclusters 2004 Workshop Message-ID: <3F85F807.7060008@bioinformatics.org> ======================================================================= MEETING ANNOUNCEMENT / CALL FOR PRESENTERS ======================================================================= BIOCLUSTERS 2004 Workshop March 30, 2004 Hynes Convention Center, Boston MA USA ======================================================================= * Speakers Wanted - Please Distribute Where Appropriate * Organized by several members of the bioclusters at bioinformatics.org mailing list, the Bioclusters 2004 Workshop is a networking and educational forum for people involved in all aspects of cluster and grid computing within the life sciences. The motivation for organizers of this event was the cancellation of the O'Reilly Bioinformatics Technology Conference series and the general lack of forums for researchers and professionals involved with the applied use of high performance IT and distributed computing techniques in the life sciences. The primary focus of the workshop will be technical presentations from experienced IT professionals and scientific researchers discussing real world systems, solutions, use-cases and best practices. This event is being held onsite at the Hynes Convention Center on the first day of the larger 2004 Bio-IT World Conference+Expo. BioIT-World Magazine is generously providing space and logistical support for the meeting and workshop attendees will have access to the expo floor and keynote addresses. Registration & fees will be finalized in short order. Presentations will be broken down among a few general content areas: 1. Researcher, Application & End user Issues 2. Builder, Scaling & Integration Issues 3. Future Directions The organizing committee is actively soliciting presentation proposals from members of the life science and technical computing communities. Interested parties should contact the committee at bioclusters04 at open- bio.org. Bioclusters 2004 Workshop Committee Members J.W Bizzaro ? Bioinformatics Organization Inc. James Cuff - MIT/Harvard Broad Institute Chris Dwan - The University of Minnesota Chris Dagdigian ? Open Bioinformatics Foundation & BioTeam Inc. Joe Landman ? Scalable Informatics LLC The committee can be reached at: bioclusters04 at open-bio.org About the Bioclusters Mailing List Community The bioclusters at bioinformatics.org mailing list is a 600+ member forum for users, builders and programmers of distributed systems used in life science research and bioinformatics. For more information about the list including the public archives and subscription information please visit http://bioinformatics.org/mailman/listinfo/bioclusters From crasmen at magic.fr Thu Oct 9 21:48:01 2003 From: crasmen at magic.fr (Corentin =?iso-8859-1?Q?Cras=2DM=E9neur?=) Date: Thu, 9 Oct 2003 20:48:01 -0500 Subject: [BiO BB] CALL FOR PRESENTERS: Bioclusters 2004 Workshop In-Reply-To: <3F85F807.7060008@bioinformatics.org> References: <3F85F807.7060008@bioinformatics.org> Message-ID: At 20:06 -0400 on 09/10/2003, you wrote: >======================================================================= > MEETING ANNOUNCEMENT / CALL FOR PRESENTERS >======================================================================= > BIOCLUSTERS 2004 Workshop > March 30, 2004 > Hynes Convention Center, Boston MA USA >======================================================================= > > * Speakers Wanted - Please Distribute Where Appropriate * > > Organized by several members of the bioclusters at bioinformatics.org > mailing list, the Bioclusters 2004 Workshop is a networking and > educational forum for people involved in all aspects of cluster and > grid computing within the life sciences. > > The motivation for organizers of this event was the cancellation of the > O'Reilly Bioinformatics Technology Conference series and the general > lack of forums for researchers and professionals involved with the > applied use of high performance IT and distributed computing techniques > in the life sciences. > > The primary focus of the workshop will be technical presentations from > experienced IT professionals and scientific researchers discussing real > world systems, solutions, use-cases and best practices. > > This event is being held onsite at the Hynes Convention Center on the > first day of the larger 2004 Bio-IT World Conference+Expo. BioIT-World > Magazine is generously providing space and logistical support for the > meeting and workshop attendees will have access to the expo floor and > keynote addresses. Registration & fees will be finalized in short > order. > > Presentations will be broken down among a few general content areas: > > 1. Researcher, Application & End user Issues > 2. Builder, Scaling & Integration Issues > 3. Future Directions > > The organizing committee is actively soliciting presentation proposals > from members of the life science and technical computing communities. > Interested parties should contact the committee at bioclusters04 at open- > bio.org. > > > Bioclusters 2004 Workshop Committee Members > > J.W Bizzaro - Bioinformatics Organization Inc. > James Cuff - MIT/Harvard Broad Institute > Chris Dwan - The University of Minnesota > Chris Dagdigian - Open Bioinformatics Foundation & BioTeam Inc. > Joe Landman - Scalable Informatics LLC > > The committee can be reached at: bioclusters04 at open-bio.org > > > About the Bioclusters Mailing List Community > > The bioclusters at bioinformatics.org mailing list is a 600+ member forum > for users, builders and programmers of distributed systems used in life > science research and bioinformatics. For more information about the > list including the public archives and subscription information please > visit http://bioinformatics.org/mailman/listinfo/bioclusters > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From sravan_111 at rediffmail.com Fri Oct 10 02:49:37 2003 From: sravan_111 at rediffmail.com (sravan sravan) Date: 10 Oct 2003 06:49:37 -0000 Subject: [BiO BB] Re: BiO_BRequest for the suggestions: Message-ID: <20031010064937.4238.qmail@webmail31.rediffmail.com> An HTML attachment was scrubbed... URL: -------------- next part -------------- Sir, I am a postgraduate in Biochemistry , with an Advanced Diploma in Bioinformatics. I looking into the concepts on sequence alignments with affine gap scoring. So I would like to forward my request to all my coulegues . If possible please suggest me the flowchart/algorithm for the alignment and scoring system for the process. Thank you so much. Yours sincerely, P.Sravana Kumar. From twins at info.com.ph Fri Oct 10 03:14:00 2003 From: twins at info.com.ph (Carlo Lapid) Date: Fri, 10 Oct 2003 15:14:00 +0800 Subject: [BiO BB] reply to bala vijayan References: <20031010014622.E4254D287E@www.bioinformatics.org> Message-ID: <008a01c38efe$1920e750$0100a8c0@Lapid3> Hi, I had the same situation as you; I run ActivePerl on my home windows XP, and I had wanted to install Bioperl. You said that you downloaded it from CPAN? If you just downloaded it directly, then the module might not be installed properly in your Perl library files. I suggest you use PPM (Perl Package Manager) which is automatically installed with the ActivePerl package. Just run PPM and you should see a command prompt. To find out if bioperl was properly installed, type "query bioperl", or if you want to see a list of all the packages that have been installed, type "query *". If bioperl is not on the list, then type "install bioperl"; this will tell PPM to automatically download Bioperl from the ActiveState package repository, unzip it, and download it. (You have to be connected to the internet for this to work, of course). Easy! Carlo > Message: 2 > Date: Wed, 8 Oct 2003 14:07:46 -0700 (PDT) > From: balavijayan thiyagarajan > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] i need help regarding bioperl > Reply-To: bio_bulletin_board at bioinformatics.org > > --0-2051315488-1065647266=:85807 > Content-Type: text/plain; charset=us-ascii > > Hi > Iam a student of PGD in bioinformatics in chennai INDIA.. Iam trying to learn about bioperl wich is appart from my sylabus , > I have installed active perl In my home pc windows XP its working good , then i downloaded bioperl from internet with all other entire accesory file from CPAN . > Iam not able 2 run bioperl programs that is being given as sample programs. > > If u could help me plzz, reply me ,stating my requirements on the files thst i have to download and how to run bioperl program in windows. > While running gome of the programs through dos prompt as perl filename.pl iam not getting the out put iam getting command executable prompt in the next line. Idont know where the out put goes . > > If u could plzz reply me it will a great help for me to learn bioperl. > > waiting for ur reply. > > thanking you, > > bala vijayan. > > From sravan_111 at rediffmail.com Fri Oct 10 02:47:28 2003 From: sravan_111 at rediffmail.com (sravan sravan) Date: 10 Oct 2003 06:47:28 -0000 Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #540 - 8 msgs Message-ID: <20031010064728.23848.qmail@webmail9.rediffmail.com> An HTML attachment was scrubbed... URL: -------------- next part -------------- Sir, I am a postgraduate in Biochemistry , with an Advanced Diploma in Bioinformatics. I looking into the concepts on sequence alignments with affine gap scoring. So I would like to forward my request to all my coulegues . If possible please suggest me the flowchart/algorithm for the alignment and scoring system for the process. Thank you so much. Yours sincerely, P.Sravana Kumar. From yqzhou at buffalo.edu Fri Oct 10 08:58:23 2003 From: yqzhou at buffalo.edu (Yaoqi Zhou) Date: Fri, 10 Oct 2003 08:58:23 -0400 Subject: [BiO BB] Protein structure In-Reply-To: <007401c313db$83c1fd40$2046a296@cpmd02> Message-ID: <6E3A9D8B-FB21-11D7-9578-000A956DD572@buffalo.edu> You can try our web server SPARKS on theory.buffalo.edu On Tuesday, May 6, 2003, at 10:26 AM, Luciani Tatsch Piemolini wrote: > ?Hello, > > Can anyone suggest a program to construct a 3D structure of one > protein sequence, that has demonstrated low homology with crystal > structure in > current databases? > ?Sincerely > ? > Luciani Tatsch Piemolini > ? > > Yaoqi Zhou, Assistant Professor Department of Physiology and Biophysics University at Buffalo, State University of New York 124 Sherman Hall, Buffalo, Ny 14214 (716) 829-2985 Fax (716) 829-2344 Email: yqzhou at buffalo.edu Webpage: http://theory.med.buffalo.edu/ From yqzhou at buffalo.edu Fri Oct 10 12:01:04 2003 From: yqzhou at buffalo.edu (Yaoqi Zhou) Date: Fri, 10 Oct 2003 12:01:04 -0400 Subject: [BiO BB] Protein structure In-Reply-To: <20031010092629.A14408@lifebook> Message-ID: Sorry. It should be theory.med.buffalo.edu On Friday, October 10, 2003, at 10:26 AM, Dmitri I GOULIAEV wrote: > Hi, Yaoqi Zhou ! > > On Fri, Oct 10, 2003 at 08:58:23AM -0400, Yaoqi Zhou wrote: > >> You can try our web server SPARKS on theory.buffalo.edu > > [dig at www dig]$ host theory.buffalo.edu > Host theory.buffalo.edu not found: 3(NXDOMAIN) > > [dig at www dig]$ dig -x theory.buffalo.edu > Invalid IP address theory.buffalo.edu > > [dig at www dig]$ ping -c 3 theory.buffalo.edu > ping: unknown host theory.buffalo.edu > > ==> Is this a correct address? > > > Regards, > > -- > DIG (Dmitri I GOULIAEV) http://www.bioinformatics.org/~dig/ > 1024D/63A6C649: 26A0 E4D5 AB3F C2D4 0112 66CD 4343 C0AF 63A6 C649 > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > Yaoqi Zhou, Assistant Professor Department of Physiology and Biophysics University at Buffalo, State University of New York 124 Sherman Hall, Buffalo, Ny 14214 (716) 829-2985 Fax (716) 829-2344 Email: yqzhou at buffalo.edu Webpage: http://theory.med.buffalo.edu/ From deletto at unisa.it Fri Oct 10 13:12:25 2003 From: deletto at unisa.it (deletto at unisa.it) Date: Fri, 10 Oct 2003 19:12:25 +0200 Subject: [BiO BB] PROTEIN WORLD: how to retrieve any information about In-Reply-To: References: Message-ID: <1065805945.3f86e87988f44@webmail.unisa.it> Hi, I am sorry of bothering all with a so trivial question; I hope I will enough clear in order to explain any detail of my question. I would like to retrieve as many detailed information as possible about a protein I wanted to study the NMR profile of. I'd like to know if that protein is already known in each its aspects; the huge amount of informations (from any kind of database available online) doesn't only make this task very hard,but it make me feel very confused. Can anyone (of you) be so kind to help me? I will appreciate any suggestion too much. Thanks in advance, davide ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/ From idoerg at burnham.org Fri Oct 10 13:29:09 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Fri, 10 Oct 2003 10:29:09 -0700 Subject: [BiO BB] Is this list moderated? In-Reply-To: <3F85F5B0.1090206@bioinformatics.org> References: <3F8007E9@wiccweb> <3F85F5B0.1090206@bioinformatics.org> Message-ID: <3F86EC65.6070901@burnham.org> Part of the problem may be solved by including a few ground rules in the email sent to new subscribers, something along the lines of: "Welcome to the BioBB. Please read the following carefully before posting to the list [What is this list about, RTFFAQ. Keep it short, otherwise they won't read it anyway]. Failure to comply with these outline will result in a LART party at your place." ./I J.W. Bizzaro wrote: > Hi Eitan. > > Posting to the list is restricted to subscribers, but, other than that, > there is no moderation. Full moderation would require that all posts be > held for approval, which could take hours. I have even seen moderated > newsgroups hold up posts for a day. > > For lists that I have administered in the past and for wich I have > chosen this approach, I have received complaints that it takes too long > to get a post through. Many people, I have learned, would prefer even > to get spam if it meant getting an answer to a question with expedition. > > Besides, it seems several people were willing to answer Milak's > questions. But, I would agree that "help me with my assignment" and > "give me an idea" posts are irritating. > > Cheers. > Jeff > > Eitan Rubin wrote: > >> Hi, >> >> As part of my job, I have to say to people "no, I cannot explain to >> everything there is to know about bioinformatics through email" three >> times a day. If we keep this list non-moderated, this is where it is >> heading. >> >> Eitan >> >> >> > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo From boris.steipe at utoronto.ca Fri Oct 10 19:49:24 2003 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Fri, 10 Oct 2003 19:49:24 -0400 Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #540 - 8 msgs References: <20031010064728.23848.qmail@webmail9.rediffmail.com> Message-ID: <3F874583.F4EC84C5@utoronto.ca> sravan sravan wrote: > > Sir, > I am a postgraduate in Biochemistry , with an Advanced Diploma in Bioinformatics. I looking into the concepts on sequence alignments with affine gap scoring. So I would like to forward my request to all my coulegues . If possible please suggest me the flowchart/algorithm for the alignment and scoring system for the process. > Affine gap scoring simply means that you have a fixed gap-opening and linear gap-extension penalty. I.e. a penalty p = a + bl, where a and b are parameters that need to be determined empirically to work well with a given scoring matrix and l is the length of an insertion or deletion (indel). Such an affine gap penalty is justified more from computational simplicity than from biological reality. See for example below for an empirical determination of parameters that emphasizes that a constant gap-opening penalty is not a good concept - it should scale with evolutionary distance. All this has no bearing on the fundamental principles of an optimal (e.g. Needleman-Wunsch or Smith-Waterman) or empirical (e.g. BLAST, FASTA) alignment, only on how the algorithm handles penalties for indels. The algorithms are described in standard bioinformatics texts. Best regards, Boris --- Boris Steipe University of Toronto Program in Proteomics & Bioinformatics Departments of Biochemistry & Molecular and Medical Genetics http://biochemistry.utoronto.ca/steipe From letondal at pasteur.fr Sat Oct 11 04:25:11 2003 From: letondal at pasteur.fr (Catherine Letondal) Date: Sat, 11 Oct 2003 10:25:11 +0200 Subject: [BiO BB] Bio Informatics Grad Programs? In-Reply-To: Your message of "Mon, 06 Oct 2003 07:35:46 PDT." <20031006143546.82972.qmail@web20416.mail.yahoo.com> Message-ID: <200310110825.h9B8PBbs427432@electre.pasteur.fr> Rehan Sadiq wrote: > Hi Everyone. > > I am in the software industry. However, I would like > to know if anyone has any recommendations of schools > or programs to learn more regarding Bio Informatics. This is not a recommandation, but you have a listing here: http://www.pasteur.fr/cgi-bin/biology/bnb_s.pl?english=1&rsc=courses+and+tutorials&bio=bio-computing (also includes online courses) > > Thanks, > > -R > > > > __________________________________ > Do you Yahoo!? > The New Yahoo! Shopping - with improved product search > http://shopping.yahoo.com > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Catherine Letondal -- Pasteur Institute Computing Center From drkannanphd at yahoo.com Sat Oct 11 10:06:51 2003 From: drkannanphd at yahoo.com (ram kan) Date: Sat, 11 Oct 2003 07:06:51 -0700 (PDT) Subject: [BiO BB] i need help regarding bioperl In-Reply-To: <20031008210746.86097.qmail@web10707.mail.yahoo.com> Message-ID: <20031011140651.94767.qmail@web13309.mail.yahoo.com> Hi first sure that you had installed perl. The open a notepad (OR click start; run; type notepad; enter) type something. Like Print "My first perl" Keep it as such. open command (Or click start; run; type command; enter) check the folder in the command. Mostly it will be C:/desktop. then save the note pad in desktop and give the any file name XXXXX.pl before giving the name of file change the version from text file to ALL files. now type perl XXXX.pl in command line. your file will open. now after you can do as you like. Kannan Hi Iam a student of PGD in bioinformatics in chennai INDIA.. Iam trying to learn about bioperl wich is appart from my sylabus , I have installed active perl In my home pc windows XP its working good , then i downloaded bioperl from internet with all other entire accesory file from CPAN . Iam not able 2 run bioperl programs that is being given as sample programs. If u could help me plzz, reply me ,stating my requirements on the files thst i have to download and how to run bioperl program in windows. While running gome of the programs through dos prompt as perl filename.pl iam not getting the out put iam getting command executable prompt in the next line. Idont know where the out put goes . If u could plzz reply me it will a great help for me to learn bioperl. waiting for ur reply. thanking you, bala vijayan. --------------------------------- Do you Yahoo!? The New Yahoo! Shopping - with improved product search --------------------------------- Do you Yahoo!? The New Yahoo! Shopping - with improved product search -------------- next part -------------- An HTML attachment was scrubbed... URL: From maria.mirto at unile.it Mon Oct 13 11:02:03 2003 From: maria.mirto at unile.it (Maria Mirto) Date: Mon, 13 Oct 2003 17:02:03 +0200 Subject: [BiO BB] Call for Papers: ITCC2004 Message-ID: <1066057323.3f8abe6bbac07@wm.unile.it> Dear all, please find attached the Call for Papers for: 5th IEEE International Conference on Information Technology: Coding and Computing (ITCC2004) - Special Session on Methodologies, Technologies and Applications in distributed and Grid systems. Las Vegas, Nevada 5-7 April 2004 http://datadog.unile.it/itcc2004/cfp.htm http://www.itcc.info/ sponsored by IEEE Computer Society This Conference Track aims at offering a forum of discussion where young researchers and PhD students could present their research activities, either at an early or mature phase. Best regards, Maria Mirto. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Maria Mirto, CACT/ISUFI (Center for Advanced Computing Technology) Engineering Faculty, Department of Innovation Engineering University of Lecce, Via per Monteroni, 73100 Lecce, Italy phone: +39-0832-297304, fax: +39-0832-297279 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ We apologize if you receive multiple copies of this email. ------------------------------------------------------------------------------- - Special Session on Methodologies, Technologies and Applications in distributed and Grid systems. ITCC 2004: IEEE International Conference on Information Technology: Coding and Computing Sponsored by the IEEE Computer Society April 5-7, 2004 The Orleans, Las Vegas, Nevada ------------------------------------------------------------------------------- - Call for Papers http://datadog.unile.it/itcc2004/cfp.htm http://www.itcc.info ****************** Computational Grids, initially used for the sharing of distributed computation resources in scientific applications, start to be used in different application domains offering basic services for application definition and execution in heterogeneous distributed systems. In health systems, the Grid offers the power and ubiquity needed to the acquisition of biomedical data, processing and delivering of biomedical images (CT, MRI, PET, SPECT, etc) located in different hospitals, within a wide area. So, the Grid acts as a Collaborative Working Environment: doctors often want to aggregate not only medical data, but also human expertise and might want colleague around the world to visualize the examinations in the same way and at the same time so that the group can discuss the diagnosis in real time. The Grid offers a dynamic infrastructure for retrieving and on-demand processing of remote sensing data, for instance, retrieving of SAR metadata related to terabyte of SAR data, starting on-demand processing on raw data, starting on-demand post-processing on focalized data and creating a complex application composing simple tasks. For atmospheric and climate modeling, a Grid offers tools for simulate and forecasting meteorological phenomena, simulate emission and dispersion of pollutants for air quality studies and simulate complex phenomena about the impact of global climate changes. Grid Computing techniques can be used in the motor industry, reducing the optimization process time for improvement of diesel engine emission performance using, for instance, micro-genetic algorithms for engine chamber geometry optimization and Kiva3 code to calculate chamber geometry fitness. In the computer aided medicine, a new research area involves the use of the Grid technologies for surgical simulations. Some simulations could be performed in a distributed system to allow surgeons to practise executing of particular surgical procedures. Analysis of the problems relevant to the use of GRID in medical virtual environments will be appreciated. Finally, bioinformatic applications call for the ability to read large datasets (e.g. protein databases) and to create new datasets (e.g. mass spectrometry proteomic data). They can require the ability to change (updating) existing datasets; consequently a Data Grid, i.e. a distributed infrastructure for storing large datasets, is needed. In the bioinformatic field, a Data Grid could reveal useful to build Electronic Patient Record systems (EPRs) for the management of patient information (data, metadata and images), to support data replication, allowing the integration and sharing of biological databases and, generally, for the developement of efficient bioinformatics (in particular proteomic) applications. The main goal of the Conference Track is to discuss well-known and emerging data-intensive applications in the context of distributed systems and Grid systems, and to analyze technologies and methodologies useful to develop such applications in such environments. In particular, this Conference Track aims at offering a forum of discussion where young researchers and PhD students could present their research activities, either at an early or mature phase. Topics include, but are not limited to: Data intensive applications in distributed and Grid systems: - Grid for biomedical imaging; - Grid for remote sensing and GIS application; - Grid for Atmospheric and Climate Modeling; - Grid for motor industry (diesel engine simulation); - Grid for surgery simulations; - Bioinformatic for: o Biomedical Imaging; o Proteomics and genomics; o Electronic Patient Records; o Medical images, data and metadata management; o Image Recognition, Processing and Analysis. Technologies and methodologies in distributed and grid-based applications: - Grid technologies (Grid portals, Web & Grid services, portlets); - Grid Information and Monitoring services and related (OO,Relational,XML) data models; - Grid Security; - Grid Workload and Data management services; - Grid Resource management; - Parallel and Distributed application (cluster and grid based); - Simulation and Applications of Modeling. IMPORTANT DATES October 17, 2003 Paper Due November 14, 2003 Author Notification December 19, 2003 Camera-Ready Copy Note: The Proceedings will be published by IEEE Computer Society. A special issue of an international journal is being planned consisting of selected papers from this conference. Authors of selected papers will be invited to submit an extended version for the journal. SUBMISSION DETAILS Papers should be original and contain contributions of theoretical or experimental nature. Interested authors should submit a paper (up to 8 pages, formatted in the style of IEEE Proceedings format - http://computer.org/cspress/instruct.htm), including keywords, using a specific form (http://www.softconf.com/start/ITCC2004/submit.html), before October 17, 2003. Instructions about submission are also available (http://www.ee.unlv.edu/%7Eit/Files/start/how-to-submit.html). If any problem occurs during electronic paper submission, please contact track chair. Maria Mirto, CACT/ISUFI (Center for Advanced Computing Technology), c/o Engineering Faculty, Department of Innovation Engineering, University of Lecce, Via per Monteroni, 73100 Lecce, Italy, Voice: +39-0832-297304, Fax: +39-0832-297279, Email: maria.mirto at unile.it Electronic submission (PostScript or PDF) is strongly encouraged. From deepan_3356 at yahoo.co.in Mon Oct 13 11:58:02 2003 From: deepan_3356 at yahoo.co.in (=?iso-8859-1?q?deepan=20chakravarthy=20n?=) Date: Mon, 13 Oct 2003 16:58:02 +0100 (BST) Subject: [BiO BB] cell simulation Message-ID: <20031013155802.1231.qmail@web8207.mail.in.yahoo.com> hello , i am writing algorithm for a cell simulation software. 1) we know complex reactions are involved in cell metabolism. many reversible rxns, non reversible rxns are involved. to calculate the concentration of each component at a given instant we have to use complex differential equations. if someone can suggest me some websites or books to refer for such calculations plz do it. 2) i have taken my reference cell as E.Coli . where can i get the complete set of metabolism rxn involved in EColi .(along with the values of equlibrium constants) plese guide me if possible ===== --------------------------------------------- deepan chakravarthy n 2nd year,(2nd sem), b.tech(biotech), anna university , chennai. ph no: hostel:22354862(044)room no205, home:04287-241199,04287244399, address: ac tech hostel (jh 207), anna university, chennai-25. ________________________________________________________________________ Yahoo! India Matrimony: Find your partner online. Go to http://yahoo.shaadi.com From bader at cbio.mskcc.org Mon Oct 13 12:49:56 2003 From: bader at cbio.mskcc.org (Gary Bader) Date: Mon, 13 Oct 2003 12:49:56 -0400 Subject: [BiO BB] cell simulation In-Reply-To: <20031013155802.1231.qmail@web8207.mail.in.yahoo.com> Message-ID: <006601c391aa$084d3010$1149a8c0@cbio.mskcc.org> Hi Deepan, > -----Original Message----- > From: bio_bulletin_board-admin at bioinformatics.org > [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of deepan > chakravarthy n > Sent: Monday, October 13, 2003 11:58 AM > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] cell simulation > > hello , > i am writing algorithm for a cell simulation > software. > > 1) > we know complex reactions are involved in cell > metabolism. > many reversible rxns, non reversible rxns are > involved. > to calculate the concentration of each component at a > given instant we have to use complex differential > equations. > if someone can suggest me some websites or books to > refer for such calculations plz do it. Many software tools are available for these calculations. Some of these are open source, so you can see how the calculations are done. See http://sbml.org for more details. > 2) > i have taken my reference cell as E.Coli . where can > i get the complete set of metabolism rxn involved in > EColi .(along with > the values of equlibrium constants) > The best resource for E.coli pathways is EcoCyc: http://www.ecocyc.org/ But other resources exist for simulation e.g. http://gcrg.ucsd.edu/organisms/ecoli.html for flux-balance based simulations. > plese guide me if possible > > > > ===== > --------------------------------------------- > deepan chakravarthy n > 2nd year,(2nd sem), > b.tech(biotech), > anna university , > chennai. > ph no: > hostel:22354862(044)room no205, > home:04287-241199,04287244399, > address: > ac tech hostel (jh 207), > anna university, > chennai-25. > > ________________________________________________________________________ > Yahoo! India Matrimony: Find your partner online. > Go to http://yahoo.shaadi.com > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From drjohn08318 at yahoo.com Mon Oct 13 17:16:46 2003 From: drjohn08318 at yahoo.com (John G. Hoey, Ph.D.) Date: Mon, 13 Oct 2003 14:16:46 -0700 (PDT) Subject: [BiO BB] cell simulation In-Reply-To: <20031013155802.1231.qmail@web8207.mail.in.yahoo.com> Message-ID: <20031013211646.23834.qmail@web14403.mail.yahoo.com> Cellular metabolism is extraordinarily complex. Reversible/nonreversible reactions are only a microcosm of the variables you will have to contend with in developing a "model" such as this. I believe you will have little trouble finding numbers to plug into your algoritm for any number of reactions involved in cellular respiration for instance. However, as a cell biologist I would be very skeptical of cell simulation software that attempted to analyze any more than a couple of these reactions simultaneously. John John G. Hoey, Ph.D. deepan chakravarthy n wrote: hello , i am writing algorithm for a cell simulation software. 1) we know complex reactions are involved in cell metabolism. many reversible rxns, non reversible rxns are involved. to calculate the concentration of each component at a given instant we have to use complex differential equations. if someone can suggest me some websites or books to refer for such calculations plz do it. 2) i have taken my reference cell as E.Coli . where can i get the complete set of metabolism rxn involved in EColi .(along with the values of equlibrium constants) plese guide me if possible ===== --------------------------------------------- deepan chakravarthy n 2nd year,(2nd sem), b.tech(biotech), anna university , chennai. ph no: hostel:22354862(044)room no205, home:04287-241199,04287244399, address: ac tech hostel (jh 207), anna university, chennai-25. ________________________________________________________________________ Yahoo! India Matrimony: Find your partner online. Go to http://yahoo.shaadi.com _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board --------------------------------- Do you Yahoo!? The New Yahoo! Shopping - with improved product search -------------- next part -------------- An HTML attachment was scrubbed... URL: From val at vtek.com Mon Oct 13 18:46:03 2003 From: val at vtek.com (val) Date: Mon, 13 Oct 2003 18:46:03 -0400 Subject: [BiO BB] cell simulation References: <20031013155802.1231.qmail@web8207.mail.in.yahoo.com> Message-ID: <168d01c391db$c827e930$6400a8c0@vt1000> hi deepan, i wouldn't rush with your cell simulation. There are few dozens projects around (google eCell and related ones), and even most pretencious ones fail in terms of interesting predictions. it's understandable. Cell is *not* a bag with 10K chemical reactions. So, my suggestion is to think twice and formulate your goal - why you are going to do this and what you expect to obtain? my best for you, val ----- Original Message ----- From: "deepan chakravarthy n" To: Sent: Monday, October 13, 2003 11:58 AM Subject: [BiO BB] cell simulation > hello , > i am writing algorithm for a cell simulation > software. > > 1) > we know complex reactions are involved in cell > metabolism. > many reversible rxns, non reversible rxns are > involved. > to calculate the concentration of each component at a > given instant we have to use complex differential > equations. > if someone can suggest me some websites or books to > refer for such calculations plz do it. > > 2) > i have taken my reference cell as E.Coli . where can > i get the complete set of metabolism rxn involved in > EColi .(along with > the values of equlibrium constants) > > > plese guide me if possible > > > > ===== > --------------------------------------------- > deepan chakravarthy n > 2nd year,(2nd sem), > b.tech(biotech), > anna university , > chennai. > ph no: > hostel:22354862(044)room no205, > home:04287-241199,04287244399, > address: > ac tech hostel (jh 207), > anna university, > chennai-25. > > ________________________________________________________________________ > Yahoo! India Matrimony: Find your partner online. > Go to http://yahoo.shaadi.com > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From adarshramakumar at yahoo.co.uk Tue Oct 14 06:55:21 2003 From: adarshramakumar at yahoo.co.uk (=?iso-8859-1?q?Adarsh=20Ramakumar?=) Date: Tue, 14 Oct 2003 11:55:21 +0100 (BST) Subject: [BiO BB] GC variation in Genome Message-ID: <20031014105521.20277.qmail@web86011.mail.ukl.yahoo.com> Dear all, A warm hello! Based on you expertice, I was interested to ask you guys for some opinions and I would highly appreciate if you could sqeeze in any time you have for me to reply. Basically I am working with a very peculiar prokaryotic genome(yet to be annotated) and I am sure you agree with me that they are all unique in their own ways. I am confronted with a few difficulties and felt I could run by you to have your opinion on it. There is a very high GC variation(as low as 40-67% at some regions) in the so far highly polished genome contig we have. I believe and suspect a lot of lateral gene transfers and funny starts and codon usage statistics. I would like to basically understand these variation and quantify them with respect to their inherent nature of variation. I am looking at finding these regions of variations, first of all to see if they(these variation in geneome) are close to each other in clusters or entirely in random at different regions of genome, then I would like to see the gene's in these regions and study their codon usage(if they are similar or different and how variable are these with amongst themselves), extract such typical funny ones, statistically group them according to their location in genome, and then try to do some similarity searches to fish out if any homologs from other published data, try to build a phyologenitc tree to derive at conclusion of variation, gene families and so on. Could you guys suggest how I could do them or rather best way of doing it? I mean is there any software that you know off where I can graphically see the variations in the contigs with respect to GC? I would be very grateful and highly appreciate of any time you can offer to inform me on these issues. Hoping to hear soon. Have a great day! Thanks and Regards ________________________________________________________________________ Want to chat instantly with your online friends? Get the FREE Yahoo! Messenger http://mail.messenger.yahoo.co.uk From thomas at cbs.dtu.dk Tue Oct 14 06:46:43 2003 From: thomas at cbs.dtu.dk (Thomas Sicheritz-Ponten) Date: Tue, 14 Oct 2003 12:46:43 +0200 Subject: [BiO BB] GC variation in Genome In-Reply-To: <20031014105521.20277.qmail@web86011.mail.ukl.yahoo.com> (Adarsh Ramakumar's message of "Tue, 14 Oct 2003 11:55:21 +0100 (BST)") References: <20031014105521.20277.qmail@web86011.mail.ukl.yahoo.com> Message-ID: Short answers: for visualisation of GC content etc.: Artemis: http://www.sanger.ac.uk/Software/Artemis/ Genome Atlas: http://www.cbs.dtu.dk/services/GenomeAtlas/ for a phylogenomic analysis, mining possible HGT's: PyPhy http://www.cbs.dtu.dk/staff/thomas/pyphy/ cheers -thomas Adarsh Ramakumar writes: > Dear all, > A warm hello! Based on you expertice, I was > interested to ask you guys for some opinions and I > would highly appreciate if you could sqeeze in any > time you have for me to reply. > > Basically I am working with a very peculiar > prokaryotic genome(yet to be annotated) and I am sure > you agree with me that they are all unique in their > own ways. > I am confronted with a few difficulties and felt I > could run by you to have your opinion on it. > > There is a very high GC variation(as low as 40-67% at > some regions) in the so far highly polished genome > contig we have. I believe and suspect a lot of lateral > gene transfers and funny starts and codon usage > statistics. I would like to basically understand these > variation and quantify them with respect to their > inherent nature of variation. > > I am looking at finding these regions of variations, > first of all to see if they(these variation in > geneome) are close to each other in clusters or > entirely in random at different regions of genome, > then I would like to see the gene's in these regions > and study their codon usage(if they are similar or > different and how variable are these with amongst > themselves), extract such typical funny ones, > statistically group them according to their location > in genome, and then try to do some similarity searches > to fish out if any homologs from other published data, > try to build a phyologenitc tree to derive at > conclusion of variation, gene families and so on. > > Could you guys suggest how I could do them or rather > best way of doing it? I mean is there any software > that you know off where I can graphically see the > variations in the contigs with respect to GC? > > I would be very grateful and highly appreciate of any > time you can offer to inform me on these issues. > Hoping to hear soon. Have a great day! > Thanks and Regards > > -- Sicheritz-Ponten Thomas, Ph.D, thomas at biopython.org ( Center for Biological Sequence Analysis \ BioCentrum-DTU, Technical University of Denmark ) CBS: +45 45 252485 Building 208, DK-2800 Lyngby ##-----> Fax: +45 45 931585 http://www.cbs.dtu.dk/thomas ) / ... damn arrow eating trees ... ( From alex at milowski.com Tue Oct 14 11:00:14 2003 From: alex at milowski.com (Alex Milowski) Date: Tue, 14 Oct 2003 08:00:14 -0700 Subject: [BiO BB] GC variation in Genome In-Reply-To: <20031014105521.20277.qmail@web86011.mail.ukl.yahoo.com> Message-ID: <1DC8D244-FE57-11D7-84EF-000393B2B0F4@milowski.com> On Tuesday, October 14, 2003, at 03:55 AM, Adarsh Ramakumar wrote: > Could you guys suggest how I could do them or rather > best way of doing it? I mean is there any software > that you know off where I can graphically see the > variations in the contigs with respect to GC? You could also check out the software that produces Chaos Game Fractals from genome sequences. There are many variations available out there. They "visualize" the sequences and subsequences quite compactly. The nice thing is that if you count on a discrete lattice, each lattice point corresponds to a unique subsequence (or partial subsequence). Thus, you can calculate the fractal and count many different subsequences that contain GC at once. I wrote a paper on using this fractal to calculate CpG islands: http://www.milowski.com/display.jsp?doc=math/cpggame/ ...and I have some software which I can make available on my website. I just haven't gotten around to it... :) There is also a really nice recent article by Almedia et. al titled "Analysis of Genomic Sequences by Chaos Game Representation" that was published in Bioinfomatics. They talk about methods for counting fractional sequences (amongst other things). Ultimately, the original source is an article by Jeffery titled "Chaos Game Representation of Gene Structure" published in Nucleic Acids Research. Depending on what you want, a lattice-based Chaos Game fractal could quickly count GC-containing subsequences and give you a way to visualize them. Alex Milowski FAX: (707) 598-7649 alex at milowski.com "The excellence of grammar as a guide is proportional to the paucity of the inflexions, i.e. to the degree of analysis effected by the language considered." Bertrand Russell in a footnote of Principles of Mathematics From wwhsiao at sfu.ca Tue Oct 14 13:09:19 2003 From: wwhsiao at sfu.ca (William Hsiao) Date: Tue, 14 Oct 2003 10:09:19 -0700 Subject: [BiO BB] GC variation in Genome In-Reply-To: <20031014105521.20277.qmail@web86011.mail.ukl.yahoo.com> Message-ID: <001201c39275$efa60650$a50aa8c0@microbe> Hi Adarsh, Our lab has developed a web service, IslandPath (http://www.pathogenomics.sfu.ca/islandpath) that is useful in looking for horizontally transferred regions. The source code for the application is available if you wish to use it for your in-house analysis. Background in Perl will be required to modify the source code for your own needs. Alternatively, once your genome is published or if the genomic sequence and annotation becomes available, I can put it through IslandPath to produce the output. Cheers Will William Hsiao Graduate Student, Brinkman Laboratory Department of Molecular Biology and Biochemistry Simon Fraser University, 8888 University Dr. Burnaby, BC, Canada V5A 1S6 Phone: 604-291-4206 Fax: 604-291-5583 -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of Adarsh Ramakumar Sent: October 14, 2003 3:55 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] GC variation in Genome Dear all, A warm hello! Based on you expertice, I was interested to ask you guys for some opinions and I would highly appreciate if you could sqeeze in any time you have for me to reply. Basically I am working with a very peculiar prokaryotic genome(yet to be annotated) and I am sure you agree with me that they are all unique in their own ways. I am confronted with a few difficulties and felt I could run by you to have your opinion on it. There is a very high GC variation(as low as 40-67% at some regions) in the so far highly polished genome contig we have. I believe and suspect a lot of lateral gene transfers and funny starts and codon usage statistics. I would like to basically understand these variation and quantify them with respect to their inherent nature of variation. I am looking at finding these regions of variations, first of all to see if they(these variation in geneome) are close to each other in clusters or entirely in random at different regions of genome, then I would like to see the gene's in these regions and study their codon usage(if they are similar or different and how variable are these with amongst themselves), extract such typical funny ones, statistically group them according to their location in genome, and then try to do some similarity searches to fish out if any homologs from other published data, try to build a phyologenitc tree to derive at conclusion of variation, gene families and so on. Could you guys suggest how I could do them or rather best way of doing it? I mean is there any software that you know off where I can graphically see the variations in the contigs with respect to GC? I would be very grateful and highly appreciate of any time you can offer to inform me on these issues. Hoping to hear soon. Have a great day! Thanks and Regards ________________________________________________________________________ Want to chat instantly with your online friends? Get the FREE Yahoo! Messenger http://mail.messenger.yahoo.co.uk _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From sdua at coes.latech.edu Tue Oct 14 18:49:00 2003 From: sdua at coes.latech.edu (Sumeet Dua) Date: Tue, 14 Oct 2003 17:49:00 -0500 Subject: [BiO BB] Call for Papers: IEEE ITCC Track: IT in Bioinformatics and Biomedical Computing Message-ID: <6.0.0.22.0.20031014174435.01b85008@webmail.latech.edu> Apologies for cross-posting ----------- Call for Papers IEEE ITCC 2004: IEEE International Conference on Information Technology: Coding and Computing Special Track on: INFORMATION TECHNOLOGY IN BIOINFORMATICS AND BIOMEDICAL COMPUTING The Orleans, Las Vegas, NV, April 5 -7, 2004 Sponsored by IEEE Computer Society Submission deadline: November 21, 2003. Track Homepage: http://www.latech.edu/~sdua/itcc2004/ Context and Objectives: Biology and Biomedicine have become increasingly data-driven sciences. The researchers in this area are producing vast quantities of data daily from sources such as clinical trials, statistics, population genetics, imaging, gene sequencing, gene expression analysis, and protein identification projects. These data enable the creation of enormous digital libraries. This data is unique in the sense that it combines enormity with fine granularity. The rate of accumulation of this data has far exceeded our capacity to analyze it and discover novel and significant knowledge embedded in it using non-automated means. This has led to the evolution of a new-fangled area of multi-disciplinary research, termed Bioinformatics, defined as the science of storing, extracting, organizing, analyzing, interpreting and utilizing information from biological sequences and molecules. Biomedical Informatics deals with algorithms and routines that have general applicability and that form the basis for the evolving information technology research in biomedical sciences and related disciplines. This track focuses on the techniques and methodologies which give rise to design and development of information technology routines for applications in Bioinformatics and/or Biomedical Informatics. The topics of interest include, but are not limited to the following: Bioinformatics: - Algorithms for Microarray Analysis - Computational Protein Structure prediction and Analysis - Data Mining for Bioinformatics applications - Functional Genomics - High Performance Computing - Machine learning - Pathways, Networks, Systems Biology - Pattern Recognition and Sequence Alignment - Regulatory Networks - String and graph algorithms for Bioinformatics Biomedical Computing: - Mining biomedical databases - Heterogeneous Data Integration - Storage and access structures for biomedical data - Biological and biomedical data modeling - Information Retrieval from Biomedical data Sources - Scientific Visualization - Automated text categorization and authority determination - Mining techniques for emerging imaging types Publication: All submitted papers will be reviewed on the basis of technical quality, relevance, significance and clarity. Authors should submit original, unpublished papers containing contributions of theoretical or experimental nature. Papers will be published in ITCC 2004 Conference Proceedings. Selected papers will be considered for Journal publication. Submit your papers (up to 8 pages, in the IEEE Proceedings format) electronically through http://www.softconf.com/start/ITCC2004/submit.html Further help on submission is available at http://www.ee.unlv.edu/~it/Files/start/how-to-submit.html Track co-chairs: Bioinformatics: Dr. Sumeet Dua (sdua at coes.latech.edu) Biomedical Computing: Dr. Y. Alp Aslandogan (alp at cse.uta.edu ) Important Deadlines: November 21, 2003: Paper submission December 19, 2003: Notification of Acceptance January 9, 2004: Camera-ready Copies Due Dr. Sumeet Dua Computer Science Program, Louisiana Tech University 223 Nethken Hall, 600 W. Arizona Avenue, Ruston, LA 71272 Voice: (318)-257-2830 Fax: (318)-257-4922 Email: sdua at coes.latech.edu URL: http://www.latech.edu/~sdua Dr. Y. Alp Aslandogan Dept. of Computer Science and Engineering University of Texas at Arlington 416 Yates St., 306 Nedderman Hall Arlington, TX 76019-0015 Voice: (817)-272-3334 Fax: (817)-272-3784 Email: alp at cse.uta.edu URL: http://ranger.uta.edu/~alp From johannes.huesing at uni-essen.de Wed Oct 15 05:31:24 2003 From: johannes.huesing at uni-essen.de (=?iso-8859-1?Q?Johannes_H=FCsing?=) Date: Wed, 15 Oct 2003 11:31:24 +0200 Subject: [BiO BB] Google search in Medline Message-ID: <20031015113124.A71844@spi.power.uni-essen.de> Hi all, I found when I google within Medline like this: site:ncbi.nlm.nih.gov some terms specific for an article I get some results, which are obviously the results of somebody else's previous searches within Medline. This might be an interesting hint toward the impact of a certain article. Does anyone have an idea how quickly the availability and number of cached search results varies? Obviously, it is a function of how long the search results are cached, and how often Google bots spider Medline. Greetings Johannes From ngadewal at yahoo.com Wed Oct 15 07:09:48 2003 From: ngadewal at yahoo.com (nikhil gadewal) Date: Wed, 15 Oct 2003 04:09:48 -0700 (PDT) Subject: [BiO BB] Text mining tool Message-ID: <20031015110948.36225.qmail@web40907.mail.yahoo.com> Dear members, I am looking for 'Text mining tool' to search literature database like PubMed which is freely available. If any alternative way of mining is available then please let me know. Thank you in advance. with regards, Nikhil ===== NIKHIL S. GADEWAL Bioinformatics center, ACTREC, Cancer Research Inst., Kharghar, Navi Mumbai, India E-mail: cri3 at soochak.ncst.ernet.in __________________________________ Do you Yahoo!? The New Yahoo! Shopping - with improved product search http://shopping.yahoo.com From pedro.fabre at gen.gu.se Wed Oct 15 07:53:10 2003 From: pedro.fabre at gen.gu.se (Pedro) Date: Wed, 15 Oct 2003 12:53:10 +0100 Subject: [BiO BB] Text mining tool In-Reply-To: <20031015110948.36225.qmail@web40907.mail.yahoo.com> References: <20031015110948.36225.qmail@web40907.mail.yahoo.com> Message-ID: >Dear members, > > I am looking for 'Text mining tool' to search >literature database like PubMed which is freely >available. If any alternative way of mining is >available then please let me know. > Thank you in advance. search on google using keywords "Text mining tool" medline http://www.google.com/search?hl=en&ie=ISO-8859-1&q=%22Text+mining+tool%22+medline&btnG=Google+Search gives you the answer to your question Cheers Pedro From paolo at ist.unige.it Wed Oct 15 09:10:22 2003 From: paolo at ist.unige.it (Paolo Romano) Date: Wed, 15 Oct 2003 15:10:22 +0200 (DFT) Subject: [BiO BB] Text mining tool In-Reply-To: from "Pedro" at Oct 15, 2003 12:53:10 PM Message-ID: <200310151310.PAA19020@ist.unige.it> > > I am looking for 'Text mining tool' to search > >literature database like PubMed which is freely > >available. If any alternative way of mining is > >available then please let me know. > > search on google using keywords "Text mining tool" medline > > http://www.google.com/search?hl=en&ie=ISO-8859-1&q=%22Text+mining+tool%22+medline&btnG=Google+Search well, maybe this list could give some more useful comments including criticisms, appreciations, etc... on the different tools. Paolo -- Paolo Romano (paolo.romano at istge.it) National Cancer Research Institute Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 Fax: +39-010-5737-295 From dmb at mrc-dunn.cam.ac.uk Wed Oct 15 07:20:05 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Wed, 15 Oct 2003 12:20:05 +0100 (BST) Subject: [BiO BB] Text mining tool In-Reply-To: References: <20031015110948.36225.qmail@web40907.mail.yahoo.com> Message-ID: <54133.193.60.81.207.1066216805.squirrel@www.mrc-dunn.cam.ac.uk> Pedro said: > > >>Dear members, >> >> I am looking for 'Text mining tool' to search >>literature database like PubMed which is freely >>available. If any alternative way of mining is >>available then please let me know. >> Thank you in advance. > > search on google using keywords "Text mining tool" medline > > http://www.google.com/search?hl=en&ie=ISO-8859-1&q=%22Text+mining+tool%22+medline&btnG=Google+Search > > gives you the answer to your question Not really. None of the above links (on the first page) return links to software. > Cheers > Pedro > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From deepan_3356 at yahoo.co.in Wed Oct 15 07:32:11 2003 From: deepan_3356 at yahoo.co.in (=?iso-8859-1?q?deepan=20chakravarthy=20n?=) Date: Wed, 15 Oct 2003 12:32:11 +0100 (BST) Subject: [BiO BB] cell simulation In-Reply-To: <168d01c391db$c827e930$6400a8c0@vt1000> Message-ID: <20031015113211.36483.qmail@web8207.mail.in.yahoo.com> hi val, i undestand what u mean , cell metabolism is highly complex. we are a group of students ,we just want to get an insight of the problems and complex nature of cell simulation software . so we have set out to write a simplest model of cell that would mimic very few pathways of cell. deepan --- val wrote: > hi deepan, > > i wouldn't rush with your cell simulation. > There are few dozens projects around (google eCell > and related ones), and even most pretencious ones > fail in terms of interesting predictions. > it's understandable. Cell is *not* a bag with > 10K chemical reactions. So, my suggestion is > to think twice and formulate your goal - why you > are going to do this and what you expect to obtain? > my best for you, > val > > > ----- Original Message ----- > From: "deepan chakravarthy n" > > To: > Sent: Monday, October 13, 2003 11:58 AM > Subject: [BiO BB] cell simulation > > > > hello , > > i am writing algorithm for a cell > simulation > > software. > > > > 1) > > we know complex reactions are involved in cell > > metabolism. > > many reversible rxns, non reversible rxns are > > involved. > > to calculate the concentration of each component > at a > > given instant we have to use complex differential > > equations. > > if someone can suggest me some websites or books > to > > refer for such calculations plz do it. > > > > 2) > > i have taken my reference cell as E.Coli . where > can > > i get the complete set of metabolism rxn involved > in > > EColi .(along with > > the values of equlibrium constants) > > > > > > plese guide me if possible > > > > > > > > ===== > > --------------------------------------------- > > deepan chakravarthy n > > 2nd year,(2nd sem), > > b.tech(biotech), > > anna university , > > chennai. > > ph no: > > hostel:22354862(044)room no205, > > home:04287-241199,04287244399, > > address: > > ac tech hostel (jh 207), > > anna university, > > chennai-25. > > > > > ________________________________________________________________________ > > Yahoo! India Matrimony: Find your partner online. > > Go to http://yahoo.shaadi.com > > _______________________________________________ > > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board ===== --------------------------------------------- deepan chakravarthy n 2nd year,(2nd sem), b.tech(biotech), anna university , chennai. ph no: hostel:22354862(044)room no205, home:04287-241199,04287244399, address: ac tech hostel (jh 207), anna university, chennai-25. ________________________________________________________________________ Yahoo! India Matrimony: Find your partner online. Go to http://yahoo.shaadi.com From drjohn08318 at yahoo.com Wed Oct 15 09:25:03 2003 From: drjohn08318 at yahoo.com (John G. Hoey, Ph.D.) Date: Wed, 15 Oct 2003 06:25:03 -0700 (PDT) Subject: [BiO BB] cell simulation In-Reply-To: <20031015113211.36483.qmail@web8207.mail.in.yahoo.com> Message-ID: <20031015132503.96089.qmail@web14410.mail.yahoo.com> ..Check out www.bio.com. There is an interesting article you may want to read. Mathematical Modeling Predicts Cellular CommunicationMathematical Modeling Predicts Cellular Communication John G. Hoey, Ph.D. deepan chakravarthy n wrote: hi val, i undestand what u mean , cell metabolism is highly complex. we are a group of students ,we just want to get an insight of the problems and complex nature of cell simulation software . so we have set out to write a simplest model of cell that would mimic very few pathways of cell. deepan --- val wrote: > hi deepan, > > i wouldn't rush with your cell simulation. > There are few dozens projects around (google eCell > and related ones), and even most pretencious ones > fail in terms of interesting predictions. > it's understandable. Cell is *not* a bag with > 10K chemical reactions. So, my suggestion is > to think twice and formulate your goal - why you > are going to do this and what you expect to obtain? > my best for you, > val > > > ----- Original Message ----- > From: "deepan chakravarthy n" > > To: > Sent: Monday, October 13, 2003 11:58 AM > Subject: [BiO BB] cell simulation > > > > hello , > > i am writing algorithm for a cell > simulation > > software. > > > > 1) > > we know complex reactions are involved in cell > > metabolism. > > many reversible rxns, non reversible rxns are > > involved. > > to calculate the concentration of each component > at a > > given instant we have to use complex differential > > equations. > > if someone can suggest me some websites or books > to > > refer for such calculations plz do it. > > > > 2) > > i have taken my reference cell as E.Coli . where > can > > i get the complete set of metabolism rxn involved > in > > EColi .(along with > > the values of equlibrium constants) > > > > > > plese guide me if possible > > > > > > > > ===== > > --------------------------------------------- > > deepan chakravarthy n > > 2nd year,(2nd sem), > > b.tech(biotech), > > anna university , > > chennai. > > ph no: > > hostel:22354862(044)room no205, > > home:04287-241199,04287244399, > > address: > > ac tech hostel (jh 207), > > anna university, > > chennai-25. > > > > > ________________________________________________________________________ > > Yahoo! India Matrimony: Find your partner online. > > Go to http://yahoo.shaadi.com > > _______________________________________________ > > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board ===== --------------------------------------------- deepan chakravarthy n 2nd year,(2nd sem), b.tech(biotech), anna university , chennai. ph no: hostel:22354862(044)room no205, home:04287-241199,04287244399, address: ac tech hostel (jh 207), anna university, chennai-25. ________________________________________________________________________ Yahoo! India Matrimony: Find your partner online. Go to http://yahoo.shaadi.com _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board --------------------------------- Do you Yahoo!? The New Yahoo! Shopping - with improved product search -------------- next part -------------- An HTML attachment was scrubbed... URL: From schlitt at ebi.ac.uk Wed Oct 15 09:58:33 2003 From: schlitt at ebi.ac.uk (Thomas Schlitt) Date: Wed, 15 Oct 2003 14:58:33 +0100 (BST) Subject: [BiO BB] Text mining tool In-Reply-To: <20031015110948.36225.qmail@web40907.mail.yahoo.com> Message-ID: Dear Nikhil you can use SRS to search Medline, too. http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+top+-newId Cheers Thomas On Wed, 15 Oct 2003, nikhil gadewal wrote: > Dear members, > > I am looking for 'Text mining tool' to search > literature database like PubMed which is freely > available. If any alternative way of mining is > available then please let me know. > Thank you in advance. > > with regards, > Nikhil > > > ===== > NIKHIL S. GADEWAL > Bioinformatics center, > ACTREC, Cancer Research Inst., > Kharghar, Navi Mumbai, India > E-mail: cri3 at soochak.ncst.ernet.in > > __________________________________ > Do you Yahoo!? > The New Yahoo! Shopping - with improved product search > http://shopping.yahoo.com > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > _____________________________________________________________ Thomas Schlitt Tel.: ++44-1223-494651 EMBL-EBI Hinxton eMail: Schlitt at ebi.ac.uk Wellcome Trust Genome Campus Cambridge CB10 1SD, UK From cmdobson at ucalgary.ca Wed Oct 15 10:21:17 2003 From: cmdobson at ucalgary.ca (Melissa Dobson) Date: Wed, 15 Oct 2003 08:21:17 -0600 Subject: [BiO BB] Text mining tool In-Reply-To: References: <20031015110948.36225.qmail@web40907.mail.yahoo.com> Message-ID: <3F8D57DD.1070302@ucalgary.ca> Another useful tool is Pubcrawler - automated Pubmed search tool that is just wonderful Melissa Pedro wrote: > > >> Dear members, >> >> I am looking for 'Text mining tool' to search >> literature database like PubMed which is freely >> available. If any alternative way of mining is >> available then please let me know. >> Thank you in advance. > > > search on google using keywords "Text mining tool" medline > > http://www.google.com/search?hl=en&ie=ISO-8859-1&q=%22Text+mining+tool%22+medline&btnG=Google+Search > > > gives you the answer to your question > > Cheers > Pedro > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From helge.tippmann at risoe.dk Thu Oct 16 05:53:51 2003 From: helge.tippmann at risoe.dk (helge.tippmann at risoe.dk) Date: Thu, 16 Oct 2003 11:53:51 +0200 Subject: [BiO BB] DNA Promoter Message-ID: <1644C21C399A7B4EBFD7E5224209EFE30AB9F0@EXCHG-VS1.risoe.dk> I know this mail was sent some time ago, but I think similar questions will come up again all the time. It might (not) be interesting for all, but at 2can (EBI) http://www.ebi.ac.uk/cgi-bin/search/glossary.pl there is a nice glossary for most biology & BioIT terms. Of course you should still read a (introductory) book about molecular biology. Helge -----Original Message----- Malik Yousef wrote: Hello Could one explain to me what is the meaning of Promoter? Where one find explanation of Bioinformatics expressions? From moyc at mail.med.upenn.edu Thu Oct 16 12:13:59 2003 From: moyc at mail.med.upenn.edu (Chris Moy) Date: Thu, 16 Oct 2003 11:13:59 -0500 Subject: [BiO BB] Re: DNA Promoter In-Reply-To: <20031016160117.87BCCD2861@www.bioinformatics.org> Message-ID: There are a number of books available online at the ncbi. You will find more detailed information about promoters there. Here is the link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=books On Thursday, October 16, 2003, at 11:01 AM, bio_bulletin_board-request at bioinformatics.org wrote: > When replying, PLEASE edit your Subject line so it is more specific > than "Re: BiO_Bulletin_Board digest, Vol..." > > > Today's Topics: > > 1. RE: DNA Promoter (helge.tippmann at risoe.dk) > > --__--__-- > > Message: 1 > Date: Thu, 16 Oct 2003 11:53:51 +0200 > From: helge.tippmann at risoe.dk > Subject: RE: [BiO BB] DNA Promoter > To: bio_bulletin_board at bioinformatics.org > Reply-To: bio_bulletin_board at bioinformatics.org > > I know this mail was sent some time ago, but I think similar questions > = > will come up again all the time. > It might (not) be interesting for all, but at 2can (EBI) > > http://www.ebi.ac.uk/cgi-bin/search/glossary.pl > > there is a nice glossary for most biology & BioIT terms.=20 > > Of course you should still read a (introductory) book about molecular = > biology.=20 > > Helge > > > -----Original Message----- > Malik Yousef wrote: > > > Hello > > > Could one explain to me what is the meaning of Promoter? Where one > find > explanation of Bioinformatics expressions? > > > > > > --__--__-- > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > End of BiO_Bulletin_Board Digest > From pooja at igc.gulbenkian.pt Thu Oct 16 12:30:58 2003 From: pooja at igc.gulbenkian.pt (pooja at igc.gulbenkian.pt) Date: Thu, 16 Oct 2003 17:30:58 +0100 (WEST) Subject: [BiO BB] Text mining tool In-Reply-To: <3F8D57DD.1070302@ucalgary.ca> References: <20031015110948.36225.qmail@web40907.mail.yahoo.com> <3F8D57DD.1070302@ucalgary.ca> Message-ID: <4416.193.126.26.74.1066321858.squirrel@webmail.igc.gulbenkian.pt> Hi Nikhil, Have a look at the MedMiner following the link below : http://discover.nci.nih.gov/textmining/filters.html I have also heard about PubMatrix and XploreMed for literature mining. But don't know much. You may use google to get some relevant information about them. The Network Browser tool of another web based tool namely, 'PubGene? Gene Database and Tools', displays literature or sequence association networks for a gene. May interest you ! Hope this helps. -Pooja > Another useful tool is Pubcrawler - automated Pubmed search tool that is > just wonderful > Melissa > > Pedro wrote: > >> >> >>> Dear members, >>> >>> I am looking for 'Text mining tool' to search >>> literature database like PubMed which is freely >>> available. If any alternative way of mining is >>> available then please let me know. >>> Thank you in advance. >> >> >> search on google using keywords "Text mining tool" medline >> >> http://www.google.com/search?hl=en&ie=ISO-8859-1&q=%22Text+mining+tool%22+medline&btnG=Google+Search >> >> >> gives you the answer to your question >> >> Cheers >> Pedro >> _______________________________________________ >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From drjohn08318 at yahoo.com Thu Oct 16 13:19:05 2003 From: drjohn08318 at yahoo.com (John G. Hoey, Ph.D.) Date: Thu, 16 Oct 2003 10:19:05 -0700 (PDT) Subject: [BiO BB] Re: DNA Promoter In-Reply-To: Message-ID: <20031016171905.7371.qmail@web14407.mail.yahoo.com> Aren't Bioinformatics folks trained in standard Molecular/Cellular Biology? JGH Chris Moy wrote: There are a number of books available online at the ncbi. You will find more detailed information about promoters there. Here is the link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=books On Thursday, October 16, 2003, at 11:01 AM, bio_bulletin_board-request at bioinformatics.org wrote: > When replying, PLEASE edit your Subject line so it is more specific > than "Re: BiO_Bulletin_Board digest, Vol..." > > > Today's Topics: > > 1. RE: DNA Promoter (helge.tippmann at risoe.dk) > > --__--__-- > > Message: 1 > Date: Thu, 16 Oct 2003 11:53:51 +0200 > From: helge.tippmann at risoe.dk > Subject: RE: [BiO BB] DNA Promoter > To: bio_bulletin_board at bioinformatics.org > Reply-To: bio_bulletin_board at bioinformatics.org > > I know this mail was sent some time ago, but I think similar questions > = > will come up again all the time. > It might (not) be interesting for all, but at 2can (EBI) > > http://www.ebi.ac.uk/cgi-bin/search/glossary.pl > > there is a nice glossary for most biology & BioIT terms.=20 > > Of course you should still read a (introductory) book about molecular = > biology.=20 > > Helge > > > -----Original Message----- > Malik Yousef wrote: > > > Hello > > > Could one explain to me what is the meaning of Promoter? Where one > find > explanation of Bioinformatics expressions? > > > > > > --__--__-- > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > End of BiO_Bulletin_Board Digest > _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board --------------------------------- Do you Yahoo!? The New Yahoo! Shopping - with improved product search -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.d.vanschaik at amc.uva.nl Fri Oct 17 09:59:57 2003 From: b.d.vanschaik at amc.uva.nl (Barbera van Schaik) Date: Fri, 17 Oct 2003 15:59:57 +0200 Subject: [BiO BB] Re: DNA Promoter In-Reply-To: <20031016171905.7371.qmail@web14407.mail.yahoo.com> References: <20031016171905.7371.qmail@web14407.mail.yahoo.com> Message-ID: <3F8FF5DD.7000307@amc.uva.nl> That's the idea, but you have to start somewhere right ;) And besides that, some have an informatics background or so .......... A google search with the term "What is a promotor" gave me this: http://jared.rijah.com/micro_review.txt Regards, Barbera John G. Hoey, Ph.D. wrote: > Aren't Bioinformatics folks trained in standard Molecular/Cellular > Biology? > > JGH > > */Chris Moy /* wrote: > > There are a number of books available online at the ncbi. You will > find > more detailed information about promoters there. Here is the link: > > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=books > > > > > > > On Thursday, October 16, 2003, at 11:01 AM, > bio_bulletin_board-request at bioinformatics.org wrote: > > > When replying, PLEASE edit your Subject line so it is more specific > > than "Re: BiO_Bulletin_Board digest, Vol..." > > > > > > Today's Topics: > > > > 1. RE: DNA Promoter (helge.tippmann at risoe.dk) > > > > --__--__-- > > > > Message: 1 > > Date: Thu, 16 Oct 2003 11:53:51 +0200 > > From: helge.tippmann at risoe.dk > > Subject: RE: [BiO BB] DNA Promoter > > To: bio_bulletin_board at bioinformatics.org > > Reply-To: bio_bulletin_board at bioinformatics.org > > > > I know this mail w as sent some time ago, but I think similar > questions > > = > > will come up again all the time. > > It might (not) be interesting for all, but at 2can (EBI) > > > > http://www.ebi.ac.uk/cgi-bin/search/glossary.pl > > > > there is a nice glossary for most biology & BioIT terms.=20 > > > > Of course you should still read a (introductory) book about > molecular = > > biology.=20 > > > > Helge > > > > > > -----Original Message----- > > Malik Yousef wrote: > > > > > > Hello > > > > > > Could one explain to me what is the meaning of Promoter? Where one > > find > > explanation of Bioinformatics expressions? > > > > > > > > > > > > --__--__-- > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > End of BiO_Bulletin_Board Digest > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > ------------------------------------------------------------------------ > Do you Yahoo!? > The New Yahoo! Shopping > > - with improved product search -- ._._._._._._._._._._._._._._._._._._._._._._. Barbera D.C. van Schaik Academic Medical Center (K2.207) Postbus 22660 1100 DD Amsterdam The Netherlands DivG/BioInformatics Laboratory DivC/Human Genetics Room: K2.207 Phone: (+31) 20 - 566 25 18 Email: B.D.vanSchaik at amc.uva.nl _._._._._._._._._._._._._._._._._._._._._._._ -------------- next part -------------- An HTML attachment was scrubbed... URL: From hra at cs.uga.edu Sat Oct 18 14:03:43 2003 From: hra at cs.uga.edu (Hamid Arabnia) Date: Sat, 18 Oct 2003 14:03:43 -0400 (EDT) Subject: [BiO BB] CFP: 18 Int'l Conferences in CS & CE in 2004; June 21-24, Nevada, USA Message-ID: <200310181803.OAA03657@apollo.cs.uga.edu> C A L L F O R P A P E R S The 2004 International Multiconference in Computer Science and Computer Engineering (18 Joint Int'l Conferences) Monte Carlo Resort, Las Vegas, Nevada, USA June 21-24, 2004 Dear Colleagues: You are invited to submit a draft paper (see instructions below) and/or a proposal to organize a technical session/workshop. All accepted papers will be published in the respective conference proceedings. The names of technical session/workshop organizers/chairs will appear on the cover of the proceedings/books as Associate Editors. Any help in distributing this announcement would be most appreciated. The 2004 International Multiconference in Computer Science and Computer Engineering is composed of the following 18 conferences - each event is the premier conference for presentation of advances in their respective subjects. All conferences will be held simultaneously (same location and dates: June 21-24, 2004, Las Vegas, USA): 1. The 2004 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'04) 2. The 2004 International Conference on Artificial Intelligence (IC-AI'04) 3. The 2004 International Conference on Imaging Science, Systems, and Technology (CISST'04) 4. The 2004 International Conference on Modeling, Simulation and Visualization Methods (MSV'04) 5. The 2004 International Conference on Software Engineering Research and Practice (SERP'04) 6. The 2004 International Conference on Information and Knowledge Engineering (IKE'04) 7. The 2004 International Conference on Embedded Systems and Applications (ESA'04) 8. The 2004 International Conference on Internet Computing (IC'04) 9. The 2004 International Conference on Wireless Networks (ICWN'04) 10. The 2004 International Symposium on Web Services and Applications (ISWS'04) 11. The 2004 International Workshop on Wearable Computers (IWWC'04) 12. The 2004 International Conference on Security and Management (SAM'04) 13. The 2004 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS'04) 14. The 2004 International Conference on Machine Learning; Models, Technologies and Applications (MLMTA'04) 15. The 2004 International Conference on Communications in Computing (CIC'04) 16. The 2004 International Conference on VLSI (VLSI'04) 17. The 2004 International Conference on Engineering of Reconfigurable Systems and Algorithms (ERSA'04) 18. The 2004 International Conference on Algorithmic Mathematics and Computer Science (AMCS'04) (a link to each conference's URL can be found at http://www.world-academy-of-science.org/IMCSE2004 - currently under construction.) Please regard this announcement as General Guidelines. You are requested to send your submission to the Multiconference chair whose address appears below (The chair may be forwarding the papers to respective conference chairs/committees). CONFERENCES CONTACT: H. R. Arabnia, PhD General Chair, The 2004 International Multiconference in Computer Science and Computer Engineering (IMCSE2004) The University of Georgia Department of Computer Science 415 Graduate Studies Research Center Athens, Georgia 30602-7404, U.S.A. Tel: (706) 542-3480 Fax: (706) 542-2966 E-mail: hra at cs.uga.edu HISTORY: The International Multiconference in Computer Science and Computer Engineering is a major annual international research event. It assembles a spectrum of affiliated research conferences, workshops, and symposiums into a coordinated research meeting held in a common place at a common time. This model facilitates communication among researchers in different fields of computer science and computer engineering. The last Multiconference attracted over 1,650 computer science and Engineering researchers from 78 countries. It is anticipated that The 2004 Int'l Multiconference will attract about 2000 participants. The 2004 event is composed of 18 (planned) major conferences - attendees will have full access to all 18 conferences' sessions & tracks. Each conference will have its own proceedings. All conference proceedings/books are considered for inclusion in major database indexes that are designed to provide easy access to the current literature of the sciences (database examples: ISI Thomson Scientific, IEE INSPEC, DBLP, ...). SUBMISSION OF PAPERS: Prospective authors are invited to submit three copies of their draft paper (about 5 pages - single space, font size of 10 to 12) to H. R. Arabnia by the due date (who may be forwarding the papers to respective conference chairs/committees). E-mail submissions in MS document or PDF formats are preferable (Fax submissions are also acceptable.) The length of the Camera-Ready papers (if accepted) will be limited to 7 (IEEE style) pages. Papers must not have been previously published or currently submitted for publication elsewhere. The first page of the draft paper should include: title of the paper, name, affiliation, postal address, E-mail address, telephone number, & Fax number for each author. The first page should also include the name of the author who will be presenting the paper (if accepted) & a maximum of 5 keywords. EVALUATION PROCESS: Papers will be evaluated for originality, significance, clarity, and soundness. Each paper will be refereed by two researchers in the topical area. The Camera-Ready papers will be reviewed by one person. PUBLICATION: The conference proceedings will be published by CSREA Press (ISBN) in hardcopy. The proceedings will be available at the conference. Some accepted papers will also be considered for journal publication (soon after the conference). All conference proceedings published by CSREA Press are considered for inclusion in major database indexes that are designed to provide easy access to the current literature of the sciences (database examples: ISI Thomson Scientific, IEE INSPEC, DBLP, ...). ORGANIZERS/SPONSORS: A number of university faculty members and their staff in cooperation with the Monte Carlo Resort (Conference Division) will be organizing the conference. Technical co-sponsors include: World Academy of Science (non-profit organization - pending); Computer Science Research, Education, & Applications Press (CSREA: USA Federal EIN # 58-2171953); together with research centers, international associations, international research groups, and developers of high-performance machines and systems. The complete list of co-sponsors will be available at a later time. (Previous conferences' sponsors included: CSREA, the National Supercomputing Center for Energy and the Environment - DOE, The International Association for Mathematics and Computers in Simulation, The International Technology Institute (ITI), The Java High Performance Computing research group, World Scientific and Engineering Society, Sundance Digital Signal Processing Inc., Convex, Hewlett-Packard Inc., a number of publishers of books and journals, chapters of computer associations from various countries, ...) LOCATION OF CONFERENCES: The conferences will be held in the Monte Carlo Resort hotel, Las Vegas, Nevada, USA (with any overflows at other near-by hotels). The Monte Carlo Resort is a mega hotel with excellent conference facilities & over 3,000 rooms. The hotel is minutes from the airport with 24-hour shuttle service to & from the airport. This hotel has many recreational attractions, including: waterfalls, spa, pools & kiddie pools, sunning decks, Easy River water ride, wave pool with cascades, lighted tennis courts, health spa (with workout equipment, whirlpool, sauna, ...), arcade virtual reality game rooms, nightly shows, snack bars, a number of restaurants, shopping area, bars, ... Many of these attractions are open 24 hours a day & most are suitable for families & children. The negotiated room rate for conference attendees is very reasonable. The hotel is within walking distance from most other attractions (major shopping areas, recreational destinations, fine dining & night clubs, free street shows, ...). IMPORTANT DATES: Feb. 16, 2004: Draft papers (about 5 pages) due March 22, 2004: Notification of acceptance April 21, 2004: Camera-Ready papers & Prereg. due June 21-24, 2004: 2004 Int'l Multiconference in CS & CE Proposals to organize technical sessions should be submitted as soon as possible. PROPOSAL FOR ORGANIZING TECHNICAL SESSIONS: Each technical session will have at least 6 paper presentations (from different authors). The session chairs will be responsible for all aspects of their sessions; including, soliciting papers, reviewing, selecting, ... The names of session chairs will appear as Associate Editors in the conference proceedings. After the conference, some sessions will be considered for publication in appropriate journals as Special Issues with the session proposer as the Guest Editor of the journal. Proposals to organize technical sessions should include the following information: name and address (+ E-mail) of proposer, title of session, a 100-word description of the topic of the session, and a short description on how the session will be advertised (in most cases, session proposers solicit papers from colleagues and researchers whose work is known to the session proposer). Mail your proposal to H. R. Arabnia (address is given above); E-mail submissions are preferred. MEMBERS OF PROGRAM & ORGANIZING COMMITTEES: The Program Committee includes members of chapters of World Academy of Science (chapters: supercomputing; scientific computing; artificial intelligence; imaging science; databases; simulation; software engineering; embedded systems; internet and web technologies; communications; computer security; and bioinformatics.) The Program Committee for individual conferences is currently being formed. Those interested in joining the Program Committee should email H. R. Arabnia (hra at cs.uga.edu) the following information: Name, affiliation and position, complete mailing address, email address, tel/fax numbers, a short biography together with research interests and the name of the conference offering to help with. EXHIBITION: An exhibition is being planned. Interested parties should contact H. R. Arabnia (hra at cs.uga.edu). All exhibitors will be considered to be the co-sponsors of the conference. TOPICAL SCOPE FOR EACH CONFERENCE APPEARS BELOW (the list of topics that appear below should be regarded as a partial list): SCOPE OF PDPTA'04: (Conference on Parallel and Distributed Processing Techniques and Applications) O Parallel/Distributed applications: Numerical computations, neural networks and fuzzy logic, medicine, remote sensing, bioinformatics, ... O Parallel/Distributed architectures: Clusters, network topologies, supercomputers, shared memory, distributed memory, dedicated systems, ... O Building block processors O Networks and Interconnection networks: Scalable networks, reconfigurable networks, routing issues, network protocols, Optical interconnects, ... O Reliability and fault-tolerance O Performance analysis, evaluation, prediction, ... O Real-time and embedded systems O Parallel/Distributed algorithms O Mobile computation and communication O Object Oriented Technology and related issues O Multimedia Communications, Systems, and Applications O Software tools and environments for parallel and distributed platforms: Operating systems, compilers, languages, debuggers, ... O High-performance computing in Computational Science O Petri Nets: theory, analysis, tools and applications O Web-based simulation and computing O Education: parallel and distributed processing in computer science curriculum O Trends in supercomputing technology O Applications SCOPE OF IC-AI'04: (Conference on Artificial Intelligence) O Intelligent Information Systems O Intelligent Software Engineering O Intelligent Agents O Intelligent Networks O Intelligent Databases O Evolutionary Algorithms O Data mining O Reasoning Strategies O Automated Problem Solving O Distributed AI Algorithms and Techniques O Distributed AI Systems and Architectures O Expert Systems + Fuzzy Logic O Genetic Algorithms O Heuristic Searching O Knowledge Acquisition, Discovery and Representation O Knowledge-Intensive Problem Solving Techniques O Languages and Programming Techniques for AI O Software Tools for AI O Natural Language Processing O Neural Networks and Applications O Multisource Information Fusion: Theory and Applications O Multisource-Multisensor Data and Information Fusion O Learning and Adaptive Sensor Fusion O Integration of AI with other Technologies O Social Impact of AI O Applications (including: Computer Vision, Signal Processing, Military, Surveillance, Robotics, Medicine, Pattern Recognition, Face Recognition, Finger Print Recognition, Finance and Marketing, Stock Market, Education, Emerging Applications, ...) SCOPE OF CISST'04: (Conference on Imaging Science, Systems, and Technology) O Image generation, acquisition, and processing O Image display techniques O Image data structures and databases O Convergence of imaging media (video and computer) O Virtual reality and Haptic technology O Image compression, coding, and encryption O Multimedia / Applications O Tools for multimedia production and services O Digital imaging for film and television O Visualization + scene and object modeling O Knowledge acquisition O Visual inspection O Document image understanding O Image algebra O Optical image processing systems O Mathematical morphology O Architecture of imaging and vision systems O Neural network techniques and fuzzy logic O Performance analysis and evaluation O Software tools and environments for imaging O Animation O Geometric modeling and Fractals O CAD/CAM systems O Rendering techniques O Applications including: medicine, robotic, GIS, remote sensing, industrial inspection (using machine vision), nondestructive evaluation (or NDE), ... O Multi-resolution and multi-spectral image processing O Image sequence processing O Indexing and Retrieval of Images (image databases) O Information fusion O Other aspects and applications relating to imaging science SCOPE OF MSV'04: (Conference on Modeling, Simulation and Visualization Methods) O Simulation languages O Internet, web and security visualization O Modeling and simulation for computer engineering O Modeling and simulation for education and training O Real-time modeling and simulation O Modeling methodologies O Specification issues for modeling and simulation O Visual interactive simulation and modeling O Visualization tools and systems for simulation and modeling O Java-based modelers O Scalability issues O Numerical Methods used in simulation and modeling O Finite and boundary element techniques O Process simulation/modeling O Device simulation/modeling O Circuit simulation/modeling O Multi-level modeling O Prototyping and simulation O Biomedical visualization and applications O Databases and visualization O Information and scientific visualization O Interaction paradigms and human factors O Parallel and distributed simulation O Discrete and numeric simulation O Virtual reality and simulation O Perceptual issues in visualization and modeling O Tools and applications O Virtual environments and data visualization O Object-oriented simulation O Knowledge-based simulation O Simulation of machine architectures O Simulation of wireless systems O Simulation of semiconductors and microelectronics O Simulation and modeling with applications in biotechnology O Simulation and modeling with applications in Nanotechnology O CAD/CAE/CAM SCOPE OF SERP'04: (Conference on Software Engineering Research and Practice) O Software architectures O Object-Oriented technology O Measurement, metrics and analysis O Survivable systems O Requirements engineering O Reverse engineering O Software domain modeling O Software process modeling O Workflow - Computer Supported Cooperative Work (CSCW) O Project management issues O Distributed and parallel systems O Legal issues and standards O Configuration management (issues and tools) O Automated software specification O Automated software design and synthesis O Theoretic approaches (formal methods, graph, ...) O Domain modeling and meta-modeling O Evolution and maintenance O Knowledge acquisition O Reflection and metadata methodologies O AI approaches to Software Engineering O Automated software engineering O Component-based engineering O Interoperability O Intelligent CASE tools O Multimedia in software engineering O Hypermedia O Software reuse O Verification, validation and quality assurance O Performance critical systems O Engineering practices O Programming languages O Program understanding issues O Education (software engineering curriculum design) O Software engineering versus Systems engineering O Software documentation O Technology adoption O Human-Computer Interaction (HCI) O Architecture tradeoff analysis O Novel software tools and environments SCOPE OF IKE'04: (Conference on Information and Knowledge Engineering) O Knowledge and Information Management Techniques O Knowledge Delivery Methods O Knowledge Life Cycle O Knowledge and Information Extraction and Discovery Techniques O Knowledge Classification Tools O Data Warehousing and Data Security O Data Mining Techniques O Database Engineering and Systems O Data and Knowledge Processing O Databanks - issues, methods, and standards O Dataweb Models and Systems O Data Fusion + Data/Information/Knowledge Models O Information Retrieval Systems O Information Reliability and Security O Information and Knowledge Structures O Information Quality (Quality Metrics) O Large-Scale Information Processing Methods O Intelligent Knowledge-Based Systems O Re-usability of Software/Knowledge/Information O Aspect-Oriented Programming O Formal and Visual Specification Languages O Decision Support and Expert Systems O Applications (e-Commerce, Multimedia, Business, Banking, ...) O Managing Copyright Laws O E-Libraries (Digital Libraries) + Electronic Publishing O Digital Typography O Agent-Based Techniques and Systems (Mobile Agents) O Image Processing (Knowledge Extraction) O Workflow Management O Large-Scale Information Processing Methods O Content Management O Privacy Issues O Interoperability Issues O Transaction Systems O Object-Oriented Modeling and Systems O Case-Based Reasoning SCOPE OF ESA'04: (Conference on Embedded Systems and Applications) O Embedded Hardware Support System-on-a-chip, DSPs, hardware specification, synthesis, modeling, simulation, power-aware, verifiable systems, performance modeling, ... O Embedded Software Compilers, assemblers and cross assemblers, virtual machines, scheduling, concurrent software for SoCs, ... O Embedded System Architecture Heterogeneous multiprocessors, reconfigurable platforms, communication, protocols, network-on-chip, embedded microcontrollers, ... O Hardware/Software Co-design Methodologies, test and debug strategies, specification and modeling, design representation, ... O Real-time Systems All real-time related aspects such as software, distributed real-time systems, real-time kernels, ... O Testing Techniques design-for-test, test synthesis, built-in self-test, embedded test, ... O Application-specific Processors and Devices Network processors, real-time processor, application specific hardware accelerators, low power embedded processors, bio/fluidic processors, ... O Industrial Practices and Benchmark Suites emerging technologies, interchange format, tools, copyrights, maintenance, O Embedded Computing Education O Emerging New Topics New challenges for next generation embedded computing systems, arising from new technologies (e.g., nanotechnology), new applications (e.g., pervasive or ubiquitous computing, embedded internet tools), ... SCOPE OF IC'04: (Conference on Internet Computing) O Internet Security O Internet Applications and Appliances O Performance Evaluation of the Internet O Resource Management and Location O Design and Analysis of Internet Protocols O Web based computing O Network Management O Network Architectures O Network Computing O Network Operating Systems O Quality of Service O Wide Area Consistency O Electronic Commerce O The WWW and Intranets O Metacomputing O Grid based Computing and Tools O Languages for Distributed Programming O Cooperative Applications O Tele-Medical and other applications O Internet Telephony O Mobile Computing O Educational Applications O Digital Libraries/Digital Image Collections O Web Interfaces to Databases O User-interface/Multimedia/Video/Audio/User Interaction O Markup Languages/HTML/XML/VRML O Java Applications on Internet O Alternative Web lifestyles, role-playing, chat, ... O Caching Algorithms for the Internet O Traffic Models & Statistics O Server Space/Web Server Performance O Web Monitoring O Web Documents Management O Web Site Design and Coordination O Other aspects & applications relating to internet computing SCOPE OF ICWN'04: (Conference on Wireless Networks) O Mobile wireless QoS, radio resource management O Mobile wireless Internet, IPv6 O Heterogeneous wireless networks, radio access networks O OFDM O W-CDMA, cdma2000, TD-SCDMA, ... O MIMO, adaptive antenna O Software-defined radio, reconfigurable radio networks O Wireless security O Wireless applications, mobile e-commerce, multimedia O Satellite-based systems O Broadcast networks O High altitude platform O GPS, location-based service O Mobile agents O Wireless & mobile applications O Multiple access O Routing, multicasting, ... O Resource management, wireless QoS O Mobile Internet O Transport-layer issues O Wireless security O Wireless network architectures O Mobile computing O Modeling, simulation, ... O Ad hoc networks, sensor networks, ... O 4G, 3.5G, 3G, ... wireless systems O Personal area networks, body wireless networks, Bluetooth O Wireless sensor networks O Coding & modulation O Multi-user detection O Power management & control, low-power protocols O OFDM, ... O Wireless IP networks, interworking O Wireless multimedia, QoS adaptation O WAP, mobile e-commerce O Location-based service, GPS O Distributed algorithms for wireless networks SCOPE OF ISWS'04: (Symposium on Web Services and Applications) O Web service technologies and research directions: - Enhancements to the basic Web services platform (SOAP, WSDL, UDDI) - Grid Computing - Advanced Web service technologies including security, workflow/process management, transactions, mobile and wireless, portals, services management, quality-of-service (QoS) - Novel Web service architectures - Development and modeling frameworks for Web service applications - Composite Web services, enabling technologies and support infrastructure - Data structures and models O Best practices for developing enterprise-class Web services and applications: - Design patterns - Architecting for customization, maintenance, and management - Architecting for easy integration or service "consumption" - Fault-tolerant architectures - Service mediation systems and architectures O Case studies of Web service development and deployment: - E-Commerce applications using Web services - Business-to-Business (B2B) applications using Web services - Mobile and wireless applications using Web services - Utility and on-demand computing using Web services - Government applications using Web services - Applications of Web services in developing countries SCOPE OF IWWC'04: (Workshop on Wearable Computers) O Wearable computing for people with disabilities. O Applications of wearable computers (medical, consumer, industrial, military, ...) O On-body networks O Next generation of wearable computers O Wireless network technology used by wearable computers O New Gadgets O Handheld computers vs wearable computers O Operating systems issues O Wearable system design O Energy / Power management (batteries) O Software architectures for wearable computers O Ergonomic issues O Wearable computers and virtual reality O Human interface systems and issues (I/O devices) O Social ramifications O Wearable computing and AI O Smart clothes O Design of wearability (study on the comfort of wearable computers, ...) O Heat dissipation issues O Wearable displays O Tasks for which wearable computers can be used O User evaluations O System architectures O Advanced textile circuitry O Keyless "keyboards" SCOPE OF SAM'04: (Conference on Security and Management) O Security Protocols O Mobility Management O Security Algorithms O Location Management O QoS Management O Key Management Techniques O Security in E-commerce and M-commerce O Security Policies O Resource Management O Mobile Network Security O Channel Management O AAA O Encryption O Security in Mobile IPv4/IPv6 O VPN O Firewall O IDS (Intrusion Detection System) O Digital contents copyright protection techniques O Watermarking O Secure OS O Honeypot O Virus Issues (Detection, Prevention, ...) O Tracing Techniques in Internet O Active Networks O Security in CDN (Contents Distribution Networks) O Hacking Techniques and Related Issues O Security in GRID O Biological Security Technologies O Surveillance Technologies O High-Tech Systems at Airports O Face Recognition Systems O Signature Recognition Systems O Network Management O System Management O Network Security Management O Management in Network Equipments O SAN (Storage Area Networks) Management O GRID Middleware O GRID Applications O GRID Networks O Security for Protocol Management O Management Protocol (SNMP, CMIP, ...) SCOPE OF METMBS'04: (Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences) O Bioinformatics: This includes informatics techniques in genomics (e.g. gene sequencing, gene pattern discovery, gene pattern-function studies, and other genomics related studies), proteomics, ... O Cheminformatics: All informatics techniques applied to biochemical and chemical processes and analyses. O Data mining in medicine and biological sciences. O Pattern recognition in medicine and biological sciences. O Signal processing in medicine and biological sciences (e.g. biomedical signal processing, ...) O Image processing in medicine and biological sciences (e.g. biomedical image processing, biomedical imaging, ...) O Medical decision-making. O Medical Physics. O Biomedical Engineering. O Biomedical Electronics. O Biosignal interpretation. O Any application of computers in Medicine and biological sciences (protein structure-function analysis, drug and protein design, molecular modeling and simulation, ...) O Application of information technology in biomedicine (e.g. medical database management, information retrieval and use of computers in hospitals.) O Application of Computational Intelligence (artificial neural networks, fuzzy logic, and evolutionary computing) in medicine and biological sciences. O Medical and bio-computing. O High-performance computing as applied to natural and medical sciences. O Computer-based medical systems (automation in medicine, ...) O Recent history (1990-2004) of Mathematics and engineering techniques in medicine and biological sciences, and what to expect during the next decade; New horizons. Review articles.) O Other aspects and applications relating to technological advancements in medicine and biological sciences. SCOPE OF MLMTA'04: (Conference on Machine Learning; Models, Technologies and Applications) O Artificial Neural Networks and Learning O Fuzzy Logic + Fusion and Learning O Information Retrieval and Data Mining O Inductive Learning and Applications O Knowledge Representation and Management O Knowledge Acquisition and Discovery Techniques O Evolutionary Algorithms and Bayesian-Based Methodologies O Reinforcement Learning Methods O Grammatical Inference O Learning Models O Multi-Agent Learning O Cognitive Modeling O Hybrid Techniques + Hierarchical Learning Models O Collaborative Filtering O Case-Based Reasoning O Semantic Indexing O Natural Language Processing O Machine Translation O Markov Decision Processes (including Semi-Markov DM) O ODE Methods and Machine Learning O Multi-Criteria Reinforcement Learning O Temporal Abstractions O Relational Learning Models O Computational Needs of Learning Models O Formal Learning Methods O Graph-Based Learning O Theory Refinement Methodologies O Probabilistic Reasoning O Decision Trees O Learning Based on Adaptive Techniques O Learning Topological Maps O Verification Models O Mobile Robotics O Learning in Planning O Query Learning and Active Learning O Memory-Based Learning O Instance-Based Learning and Self-Adaptation Techniques O Requirements Models O Transformation-Based Learning O Simulated Annealing and Learning O Life-Long Learning and Learning by Examples O Q-Learning O Predictive Learning Models O Text Categorization and Classification O Machine Learning Applications (Medicine, Games, Biology, Industrial Applications, Robotics, Security, ...) SCOPE OF CIC'04: (Conference on Communications in Computing) O High Performance Applications O Distributed Systems and Advanced Applications (e.g. multimedia, cooperative systems) O Grid computing O Scalable and Interoperable Systems and Associated Standards O Software Systems (e.g. operating system support, middleware, ...) O Architecture (e.g. VLSI, SIMD, MIMD, vector, systolic, reconfigurable, ...) O Interconnection networks (e.g. bus-based, optical) O ATM based networks O Communications (e.g. routing, wireless, mobile) O Visualization (e.g. scientific visualization, debugging and load balancing tools) O Photonics and Optical Computing O Performance Issues (e.g. benchmarks, performance measurement, evaluation and prediction) O Modeling and Simulation of High Performance Systems O Advanced Compilation Techniques (e.g. parallelizing compilers) O Programming Languages for Parallel and other High Performance Computing O Parallel/Distributed/Vector Algorithms O Reliability and Fault Tolerance O Embedded and Real Time Systems O Digital Signal Processing O Neural Computing, Genetic Algorithms O Issues in High Performance Computing (e.g. evolving paradigms, ...) O Internet & web based processing, E-commerce, telecommunication network, cluster-based computing SCOPE OF VLSI'04: (Conference on VLSI) O Quantum Computing O Nanoelectronics O Molecular and Biological Computing O MEMS O Circuits and Systems O Novel Design and Methodologies O System-on-a-Chip: Design and Methodology O Low Power VLSI System Design O Complexity Issues O Simulation Tools O Algorithm Design Approaches (AI, Genetic, ...) O High-Level Design Methodologies O ASIC Design and Architectures O Reconfigurable Systems Design O Novel Devices and Circuits O Emerging Trends O High-Performance Circuits O Reusable Architectures O Test and Verification O Synthesis O Mixed-Signal Design and Analysis O Electrical/Packaging Designs and Co-Designs O FPGA-based Design O Applications (all applications will be considered) SCOPE OF ERSA'04: (Conference on Engineering of Reconfigurable Systems and Algorithms) O Theory, Mapping and Parallelization: Theoretical models of computing in space-time and adaptive computing + Mapping algorithms into hardware and synthesis of regular arrays + Parallelization and (space-time) partitioning of algorithms + System architectures using configurable computing platform + Newly developed algorithms for efficient implementation on reconfigurable systems. O Software, CAD and Operating Systems: CAD, specification, partitioning and verification + High-level synthesis, hardware compilation, hardware/software codesign, developing correct circuits + High and low-level languages and compilers, design environments, Java-based environments + Operating systems and run-time reconfiguring, intelligent libraries + IP-based and object oriented models and mapping methods. O Adaptive Hardware Architectures: Adaptive and dynamically reconfigurable systems + Reconfigurable processor architectures, fine and coarse-grained processor arrays + Complex systems using reconfigurable processors + Application-tailored reconfigurable Systems-on-Chip + Low power systems on reconfigurable platform. O Applications: Wireless communication systems: - mobile communication systems, video-phone, software radio, global positioning systems, ... - Multimedia and virtual reality: video imaging, teleconferencing, data compression, image databases, computational geometry and computer graphics, ... - Space-based applications: reconfigurable systems for remote processors, space telescope systems, satellite networks, ... tradeoffs between on-board and ground-based processing, radiation effects mitigation, fault tolerance and reliability. - Numeric processing: floating point operations, fixed and floating point tradeoffs, residue number systems, customizable libraries, solving complex mathematical problems (linear algebra, PDEs etc.), supercomputing experiences, ... - Automotive industry: vehicle guidance, lane and obstacle detection, object recognition, traffic systems, navigation of robots, ... - Security systems: object recognition and tracking, cryptology, Internet and security, ... - Classical image and signal processing: digital filters, edge and line detection, morphological operators, motion and stereo estimation, discrete transformations, linear algebra, radar systems, object recognition, ... SCOPE OF AMCS'04: (Conference on Algorithmic Mathematics and Computer Science) O Computational Mathematics: Combinatorics, Linear Algebra, Commutative Algebra, Symbolic Computation, Computational Geometry, Algebraic Number Theory, Computational Methods for Summations, Computational Methods for Differential Equations, ... O Algorithms: Symbolic, Algebraic, Geometric, Numeric, and Theoretical Complexity; Applications of Symbolic and Algebraic Algorithms in Engineering, Sciences, and Education. O Computer Science: Practical Complexity of Algorithms, Automated Mathematical Reasoning, Automated Differentiation, Theoretical and Practical Problems in Symbolic Computation, Symbolic Computation Systems, Computer-Aided Problem-Solving, User Interfaces and Problem-Solving Environments, O Mathematical Software Design and Implementation: Software, Libraries, and Programming Languages, Parallel and Distributed Mathematical Computations, High Performance Mathematical Computations Using Grid-Computing, Concrete Analysis, Benchmarking, Code Generation, Mathematical Protocols, Internet Accessible Mathematical Computation (IAMC) O Applications From deepan_3356 at yahoo.co.in Mon Oct 20 11:05:34 2003 From: deepan_3356 at yahoo.co.in (=?iso-8859-1?q?deepan=20chakravarthy=20n?=) Date: Mon, 20 Oct 2003 16:05:34 +0100 (BST) Subject: [BiO BB] i need help regarding bioperl In-Reply-To: <20031011140651.94767.qmail@web13309.mail.yahoo.com> Message-ID: <20031020150534.62286.qmail@web8201.mail.in.yahoo.com> hi , u all speak about bio perl i am ug student in biotechnology . how is bioperl use for computational biology? what actually do u people do with perl how is cgi linked with bio perl . please reply --- ram kan wrote: > Hi > first sure that you had installed perl. > The open a notepad (OR click start; run; type > notepad; enter) type something. Like > Print "My first perl" > Keep it as such. > open command (Or click start; run; type command; > enter) > check the folder in the command. Mostly it will be > C:/desktop. > then save the note pad in desktop and give the any > file name XXXXX.pl before giving the name of file > change the version from text file to ALL files. > now type perl XXXX.pl in command line. > your file will open. now after you can do as you > like. > Kannan > > > Hi > Iam a student of PGD in bioinformatics in chennai > INDIA.. Iam trying to learn about bioperl wich is > appart from my sylabus , > I have installed active perl In my home pc > windows XP its working good , then i downloaded > bioperl from internet with all other entire accesory > file from CPAN . > Iam not able 2 run bioperl programs that is being > given as sample programs. > > If u could help me plzz, reply me ,stating my > requirements on the files thst i have to download > and how to run bioperl program in windows. > While running gome of the programs through dos > prompt as perl filename.pl iam not getting the out > put iam getting command executable prompt in the > next line. Idont know where the out put goes . > > If u could plzz reply me it will a great help > for me to learn bioperl. > > waiting for ur reply. > > thanking you, > > bala vijayan. > > > --------------------------------- > Do you Yahoo!? > The New Yahoo! Shopping - with improved product > search > > --------------------------------- > Do you Yahoo!? > The New Yahoo! Shopping - with improved product search ===== --------------------------------------------- deepan chakravarthy n 2nd year,(2nd sem), b.tech(biotech), anna university , chennai. ph no: hostel:22354862(044)room no205, home:04287-241199,04287244399, address: ac tech hostel (jh 207), anna university, chennai-25. ________________________________________________________________________ Yahoo! India Matrimony: Find your partner online. Go to http://yahoo.shaadi.com From rachel.mullen at intertradeireland.com Tue Oct 21 11:33:33 2003 From: rachel.mullen at intertradeireland.com (Rachel Mullen) Date: Tue, 21 Oct 2003 16:33:33 +0100 Subject: [BiO BB] Informatics Companies Message-ID: Hi, I was wondering if you could tell me the names of all of the companies associated with informatics in Ireland (both North and South). Kind Regards Rachel InterTradeIreland The Old Gasworks Business Park Kilmorey Street Newry BT34 2DE * 028 308 34138 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: InterScan_Disclaimer.txt URL: From logan at cacs.louisiana.edu Tue Oct 21 13:50:40 2003 From: logan at cacs.louisiana.edu (Rasiah Loganantharaj) Date: Tue, 21 Oct 2003 12:50:40 -0500 Subject: [BiO BB] call for paper on BioInformatics Session at the IEA/AIE 2004 conference Message-ID: You are invited to submit technical papers to a special session on BioInformatics at the IEA/AIE Conference 2004 to be held in Ottawa, Canada from May 17 through 20, 2004. Electronic version of the paper must be submitted by October 31, 2003 and the authors will be notified on the acceptance / rejection by January 5, 2004. For details of the BioInformatic session is posted at http://www.cacs.louisiana.edu/~logan/cfp-ieaaie2004.htm and the complete call for paper is posted at http://www.iea-aie2004.org/scientific_e.html Raja Loganantharaj Center for Advanced Computer Studies University of Louisiana Lafayette, LA 70504 Voice: 337-482-5345 From alexsub1 at covad.net Thu Oct 23 02:56:14 2003 From: alexsub1 at covad.net (Alex Schilling) Date: Thu, 23 Oct 2003 01:56:14 -0500 Subject: [BiO BB] Informatics Companies References: Message-ID: <20031023065146.509C2D233E@www.bioinformatics.org> Rachel, You might want to look at www.bio-itworld.com to see if there is a country by country listing or if they can direct you to a source for the info. Bio-ItWorld is a free newspaper that tracks the business of bioinformatics. Alex On Tue, 21 Oct 2003 16:33:33 +0100, Rachel Mullen wrote: >Hi, > > > >I was wondering if you could tell me the names of all of the >companies associated with informatics in Ireland (both North and >South). > > > >Kind Regards > >Rachel > > > >InterTradeIreland > >The Old Gasworks Business Park > >Kilmorey Street > >Newry > >BT34 2DE > > > >) 028 308 34138 > > > -- Alex Schilling, alexsub1 at covad.net on 10/23/2003 From prathibha_562 at yahoo.co.in Thu Oct 23 09:06:09 2003 From: prathibha_562 at yahoo.co.in (=?iso-8859-1?q?prathibha=20bharathi?=) Date: Thu, 23 Oct 2003 14:06:09 +0100 (BST) Subject: [BiO BB] about biojava......... In-Reply-To: <54133.193.60.81.207.1066216805.squirrel@www.mrc-dunn.cam.ac.uk> Message-ID: <20031023130609.29007.qmail@web8106.mail.in.yahoo.com> all of u people are seriously talking about bioperl..........what about BioJava???????? Dan Bolser wrote: Pedro said: > > >>Dear members, >> >> I am looking for 'Text mining tool' to search >>literature database like PubMed which is freely >>available. If any alternative way of mining is >>available then please let me know. >> Thank you in advance. > > search on google using keywords "Text mining tool" medline > > http://www.google.com/search?hl=en&ie=ISO-8859-1&q=%22Text+mining+tool%22+medline&btnG=Google+Search > > gives you the answer to your question Not really. None of the above links (on the first page) return links to software. > Cheers > Pedro > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board Yahoo! India Matrimony: Find your partner online.Post your profile. -------------- next part -------------- An HTML attachment was scrubbed... URL: From rah at mrc-dunn.cam.ac.uk Thu Oct 23 11:08:10 2003 From: rah at mrc-dunn.cam.ac.uk (Richard Harrington) Date: Thu, 23 Oct 2003 16:08:10 +0100 (BST) Subject: [BiO BB] stats book Message-ID: <3846.193.60.85.29.1066921690.squirrel@www.mrc-dunn.cam.ac.uk> hi, could anyone recommend a good molecular biology statistics book cheers, richie _______________________________________________ Richard Harrington, HUS Graduate Vice-President, Men's Boat Club Captain, Homerton College. PhD student, Bioinformatics Group, MRC-Dunn Human Nutrition Unit, Cambridge University. e-mail: rah at mrc-dunn.cam.ac.uk telephone: +44 (0) 1223 252861 mobile: 07817 927175 _______________________________________________ From idoerg at burnham.org Thu Oct 23 12:04:57 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Thu, 23 Oct 2003 09:04:57 -0700 Subject: [BiO BB] stats book In-Reply-To: <3846.193.60.85.29.1066921690.squirrel@www.mrc-dunn.cam.ac.uk> References: <3846.193.60.85.29.1066921690.squirrel@www.mrc-dunn.cam.ac.uk> Message-ID: <3F97FC29.8000107@burnham.org> Hi, I am not sure what exactly you are looking for, i.e. what applications of statistics in molecular biology intereset you. A generally good introduction to statistics: Biostatistical Analysis / Jerrold Zar For computational biology, there aer several good statistics books, again that depends on what you want to do. A good book for probabilistic models is: Biological Sequence Analysis / Durbin, Eddy, Krogh & Mitchison Introductory, but gets practical very quick. Another book which people here like but I haven't had a chance to look at: Statistical methods in Bioinformatics / W.J. Ewens & G.R. Grant See also the FAQ: http://bioinformatics.org/faq/#books Iddo Richard Harrington wrote: > hi, > > could anyone recommend a good molecular biology statistics book > > cheers, > > richie > > > _______________________________________________ > > Richard Harrington, > HUS Graduate Vice-President, > Men's Boat Club Captain, > Homerton College. > > PhD student, > Bioinformatics Group, > MRC-Dunn Human Nutrition Unit, > Cambridge University. > > e-mail: rah at mrc-dunn.cam.ac.uk > telephone: +44 (0) 1223 252861 > mobile: 07817 927175 > _______________________________________________ > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo From paolo at ist.unige.it Thu Oct 23 14:01:07 2003 From: paolo at ist.unige.it (Paolo Romano) Date: Thu, 23 Oct 2003 20:01:07 +0200 Subject: [BiO BB] CFP: NETTAB 2003 Message-ID: <200310231801.UAA18192@ist.unige.it> This message is sent to many mailing lists. I apologize for duplications. Paolo Romano --- NETTAB 2003 Call for Papers Bioinformatics for the management, analysis and interpretation of microarray data November 27-28, 2003, Bologna, Italy http://www.nettab.org/2003/ NETTAB workshops are a series of workshops focused on the most promising and innovative ICT tools and to their usefulness in Bioinformatics. Participation is at an internation level, mainly European, and speakers are among the most known researchers in the field. NETTAB workshops: - Focus on a well defined, emerging, promising ICT technology (not on a specific biological research topic) - Introduce the basic knowledge related to the technology under analysis, in a non trivial way - Outline the promising features of the technology in bioinformatics - Show some valuable examples in bioinformatics or different domains - Allow for as much discussion as possible - Demonstrate "how it works" practically, through demos or tutorials Previous editions were devoted to: "CORBA and XML: towards a bioinformatics integrated network environment" (Genova, 17-19 May 2001) and "Agents in Bioinformatics" (Bologna, 12-14 July 2002). You are welcome to visit the workshops' web site at http://www.nettab.org/ . The NETTAB 2003 workshop will be focused on the "Bioinformatics for the management, analysis and interpretation of microarray data". See http://www.nettab.org/2003/ . This edition will be organized also with the help of the Hormone Responsive Breast Cancer (HRBC) Genomics Network (http://www.hrbc-genomics.net/) - about 100 researchers from about 15 different institutions, most of them will be at the NETTAB worskhop. The network has been funded by the Italian Ministry of Research (FIRB project) for a three-years research project on the breast cancer. The network makes large use of microarray technology, and it is going to select common platforms (both experimentals and bioinformatics) to generate comparable results in different labs. In the last years, biomedical research has evolved through the development of new technologies, as the microarray technology, able to assay gene expression for thousands of genes at a time. This "high-throughput" technology gives the researchers the opportunity to investigate with a new and powerful approach the underlying genetic causes of many human diseases, as well as physiological aspects of growth and development. After few years, during which the experimental platforms and protocols have been assessed, microarrays applications are now quickly growing up. In the meantime, bioinformatics is solicited to create the tools of analysis and interpretation to understand the biological phenomena under investigation. Analysis of massive gene expression data requires statistical methods, data mining approaches, and data base storage and searches tools, but most relevant is the standardization of experimental protocols, data format, information describing experimentals, and other experimental and analytical aspects, to be able to exploit data sets from different laboratories in large scale analysis of data. Workshop aims are: - to collect the latest ideas, achievements and proposals in the application of bioinformatics to the microarray data analysis and interpretation, - to strengthen the relationships within bioinformatics community, also in view of a wider sinergical effort towards common scientific aims, - to improve cooperation between bioinformatics and biomedical communities. The worshop is organized in sessions, where invited speakers present the state of art of the session's topic, and open discussions. Open discussions will also be based upon submitted issues and topics. Tutorials are also foreseen. A limited number of submissions will be admitted as oral communication A call for position papers, posters and oral communication is now open. Submitted contributions must address at least one of the following issues: standardization of experiments and data, including: - identification of information requirements, - use cases, - data models, - data structures, - data exchange formats, - submission formats, - comparison of platforms, - etc... analysis and management tools, including: - database management systems, - clustering tools, - etc... applications of bioinformatics to microarray experiments, including: - integrative data analysis, - gene expression analysis, - wide genome analysis, - toxicogenomics, - oncogenomics, - any-omics, - etc.... Authors are encouraged to submit: Position papers: submit a short abstract (max 1 A4 pages in length, size 12pt, in pdf or MS Word format) specifying research interests and issues to be discussed during the workshop. Authors submitting position papers do not engage themselves to present a poster. Instead, they will be invited to introduce the issues during the discussions. Abstracts will be printed in the abstracts book, but won't be inserted in the conference proceedings. Posters: submit an extended abstract (max 3 A4 pages, size 12pt, in pdf or MS Word format). Abstracts will be reviewed and acceptation will be communicated to authors. Posters will be inserted in the abstract book and, only if actually presented at the workshop, in the conference proceedings. Oral Communications: submit an extended abstract (max 5 A4 pages, size 12pt, in pdf or MS Word format) as for posters. Only a very limited number of abstracts will be selected as oral communications. All abstracts submitted as oral communication but not selected will automatically be considered as posters. Abstracts must be sent by email to: papers2003 at nettab.org Deadlines: Abstracts due: November 10, 2003. Notification to authors: November 17, 2003. Early registration: November 17, 2003 On behalf of Organizing and Scientific Committees Paolo Romano --- Paolo Romano (paolo.romano at istge.it) National Cancer Research Institute Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 Fax: +39-010-5737-295 From hjm at tacgi.com Thu Oct 23 12:58:59 2003 From: hjm at tacgi.com (Harry Mangalam) Date: Thu, 23 Oct 2003 09:58:59 -0700 Subject: [BiO BB] stats book In-Reply-To: <3846.193.60.85.29.1066921690.squirrel@www.mrc-dunn.cam.ac.uk> References: <3846.193.60.85.29.1066921690.squirrel@www.mrc-dunn.cam.ac.uk> Message-ID: <3F9808D3.8070105@tacgi.com> For a good intro, Motulsky's book is pretty good. You can read excerpts and other articles on his web page. http://www.graphpad.com/articles/library.cfm There's another website that I use to refresh at: http://davidmlane.com/hyperstat/ which contains lots of stats info in surprisingly easy to digest and understand form. Richard Harrington wrote: > hi, > > could anyone recommend a good molecular biology statistics book > > cheers, > > richie > > > _______________________________________________ > > Richard Harrington, > HUS Graduate Vice-President, > Men's Boat Club Captain, > Homerton College. > > PhD student, > Bioinformatics Group, > MRC-Dunn Human Nutrition Unit, > Cambridge University. > > e-mail: rah at mrc-dunn.cam.ac.uk > telephone: +44 (0) 1223 252861 > mobile: 07817 927175 > _______________________________________________ > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Cheers, Harry Harry J Mangalam - 949 856 2847 (v&f) - hjm at tacgi.com <> From thompson at wadsworth.org Thu Oct 23 13:17:15 2003 From: thompson at wadsworth.org (William Thompson) Date: Thu, 23 Oct 2003 13:17:15 -0400 (EDT) Subject: [BiO BB] stats book Message-ID: <200310231717.h9NHHFe28922@csserv.wadsworth.org> Check out Biological Sequence Analysis by Durbin, Eddy, Krogh and Mitchison Cambridge Univ. Press Also, Statistical Methods in Biuoinformatics by Ewens and Grant pub. Springer. Bill > Date: Thu, 23 Oct 2003 16:08:10 +0100 (BST) > From: "Richard Harrington" > To: > Subject: [BiO BB] stats book > Reply-To: bio_bulletin_board at bioinformatics.org > > hi, > > could anyone recommend a good molecular biology statistics book > > cheers, > > richie > > > _______________________________________________ > > Richard Harrington, > HUS Graduate Vice-President, > Men's Boat Club Captain, > Homerton College. > > PhD student, > Bioinformatics Group, > MRC-Dunn Human Nutrition Unit, > Cambridge University. > > e-mail: rah at mrc-dunn.cam.ac.uk > telephone: +44 (0) 1223 252861 > mobile: 07817 927175 > _______________________________________________ > > > > > --__--__-- > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > End of BiO_Bulletin_Board Digest From Daniel.Chan at Sun.COM Fri Oct 24 19:13:15 2003 From: Daniel.Chan at Sun.COM (Daniel Chan) Date: Fri, 24 Oct 2003 16:13:15 -0700 Subject: [BiO BB] Could you spare 5 minutes to help out the global HPC community? Message-ID: <3F99B20B.1DD17410@Sun.COM> Dear researcher/research staff/faculty/student, We are currently conducting a global survey to identify key HPC applications researchers and engineers in university and government laboratories worldwide are using to conduct their research. We need you to provide some quick feedback specifically on the type of applications that you are currently using for the purpose of your research. This survey is hosted by the Asia-Pacific Science and Technology Center at Nanyang Technological University in Singapore and sponsored by Sun Microsystems, Inc. The information you provide here will remain confidential and will not be used for sales and marketing purposes. The results of this survey will be published to help the High Performance Computing community determine trends and improve the performance and availability of these applications to the scientific community at large. We strongly encourage you to participate in this non-commercial survey. The survey will only take 5 minutes and a few clicks. To participate, click on the following URL: http://apstc.ntu.edu.sg/hpcsurvey/ Kindly forward this e-mail to other individuals whom you know are also involved in HPC research. Thank you so much for your cooperation. Respectfully, Daniel Chan _____________________________ Science & Engineering Computing Global Education and Research Sun Microsystems, Inc. http://www.sun.com/edu/hpc Direct line: (650) 786-0780 -------------- next part -------------- An HTML attachment was scrubbed... URL: From sc_bio_wang at hotmail.com Mon Oct 27 04:11:49 2003 From: sc_bio_wang at hotmail.com (maillist mailist) Date: Mon, 27 Oct 2003 09:11:49 +0000 Subject: [BiO BB] Call For Papers: Soft Computing for Bioinformatics (SOFT COMPUTING Journal - SPR Message-ID: SOFT COMPUTING Journal - SPRINGER Special Issue on Soft Computing for Bioinformatics CALL FOR PAPERS The past few years have witnessed phenomenal growth of bioinformatics, an exciting field devoted to the interpretation and analysis of biological data using computational techniques. Among the large number of computational techniques used, soft computing, which incorporates * neural networks, * evolutionary computation, * fuzzy systems, and * chaos, stands out because of its demonstrated strength in handling imprecise information and providing novel solutions to hard problems. This special issue aims at not only showcasing innovative applications of soft computing techniques to bioinformatics, but also clarifying outstanding issues for future progress. Biological areas of interest include but are not limited to the following: * protein structure and function, * genomics, * proteomics, * molecular sequence analysis, * evolution and phylogenetics, * molecular interactions and structure, * gene expression, * metabolic pathways, * regulatory networks, * developmental control and systems biology. Papers should be submitted in PDF format via email to any of the following guest editors by 30 March 2004: * David Corne (D.W.Corne at exeter.ac.uk) * Gary Fogel (gfogel at natural-selection.com) * Jagath C. Rajapakse (asjagath at ntu.edu.sg) * Lipo Wang (elpwang at ntu.edu.sg) Please include title/abstract and author contact information in text format in the email. More information about the Soft Computing journal, such as Instructions for Authors, may be found at http://link.springer.de/link/service/journals/00500/index.htm _________________________________________________________________ Get MSN Hotmail alerts on your mobile. http://en-asiasms.mobile.msn.com/ From Pignatelli at noraybio.com Wed Oct 29 08:09:23 2003 From: Pignatelli at noraybio.com (Miguel Pignatelli) Date: Wed, 29 Oct 2003 14:09:23 +0100 Subject: [BiO BB] Algoritmos de modelado molecular con UFF Message-ID: <001c01c39e1d$dff1ecc0$2501a8c0@NORAYBIO.COM> Hola a todos, Estamos intentando hacer un programa en C que calcule la energia de una molecula a partir de las (coordenadas cartesianas X,Y,Z) de los ?tomos que la componen. Para ello tenemos como datos de partida cada atomo y sus coordenadas en el espacio. Hemos pensado realizar la aplicacion con los Universal Force Fields (UFF) descritos por Rapp?. A partir de los datos de energ?a calculados se le aplicar? algoritmos de minimizaci?n de energ?a basada en gradientes conjugados. No tengo tanta experiencia en programacion en C como para tener claro como abordar todos los aspectos computacionales. Tengo dudas sobre todo en qu? tipo de estructuras de datos utilizar en la aplicaci?n (debe correr r?pido y eficientemetne). He estado ojeando programas para sacar ideas de como empezar (como Gromacs) pero los que he encontrado que realizan aproximaciones con UFF son de pago o no te dan el codigo fuente. ?Alguien sabe donde puedo encontrar algoritmos que utilicen las Universal Force Fields o algo parecido? El programa s?lo sabra de ?tomos y coordenadas asi que tendra que determinar qu? atomos estan unidos entre si analizando sus distancias ?conoceis algun algoritmo que haga esto de forma eficiente? ?Que tipo de estructura de datos creeis que es m?s apropiadas para manejar? ?Alguna sugerencia de como abordar el problema antes de empezar? ?Alg?n programa donde echar un ojo? Gracias de antemano! Miguel -------------- next part -------------- An HTML attachment was scrubbed... URL: From atari at libero.it Wed Oct 29 10:45:02 2003 From: atari at libero.it (Andrea Franceschini) Date: Wed, 29 Oct 2003 16:45:02 +0100 Subject: [BiO BB] about biojava......... References: <20031023130609.29007.qmail@web8106.mail.in.yahoo.com> Message-ID: <00b001c39e33$9e956f20$43c17b3e@atarippc> I'm too interest in the use of Java to implement bioinformatics algorithms/software. I've made a search over Java Official website (java.sun.com) with the key "bioinformatics" finding 31 results. This is one of the articles i've found: http://java.sun.com/features/2001/10/genome2.html I would be happy if someone could help me understanding better the possible role of Java in the bioinformatic's software (now and on the next few years). Thankyou Andrea Franceschini atari at portalis.it ----- Original Message ----- From: prathibha bharathi To: bio_bulletin_board at bioinformatics.org Sent: Thursday, October 23, 2003 2:06 PM Subject: [BiO BB] about biojava......... all of u people are seriously talking about bioperl..........what about BioJava???????? -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgruenb at gmx.net Wed Oct 29 10:55:08 2003 From: mgruenb at gmx.net (Michael Gruenberger) Date: Wed, 29 Oct 2003 15:55:08 +0000 Subject: [BiO BB] about biojava......... In-Reply-To: <00b001c39e33$9e956f20$43c17b3e@atarippc> References: <20031023130609.29007.qmail@web8106.mail.in.yahoo.com> <00b001c39e33$9e956f20$43c17b3e@atarippc> Message-ID: <1067442908.2668.10.camel@vogel> I haven't followed this thread very closely, so I'm sorry if this has already been posted. Have you had a look at http://www.biojava.org/ yet? Cheers, Michael. On Wed, 2003-10-29 at 15:45, Andrea Franceschini wrote: > I'm too interest in the use of Java to implement bioinformatics > algorithms/software. > I've made a search over Java Official website (java.sun.com) with the > key "bioinformatics" finding 31 results. > This is one of the articles i've found: > http://java.sun.com/features/2001/10/genome2.html > > I would be happy if someone could help me understanding better the > possible role of Java in the bioinformatic's software (now and on the > next few years). > > Thankyou > Andrea Franceschini > atari at portalis.it > > > ----- Original Message ----- > From: prathibha bharathi > To: bio_bulletin_board at bioinformatics.org > Sent: Thursday, October 23, 2003 2:06 PM > Subject: [BiO BB] about biojava......... > > all of u people are seriously talking about > bioperl..........what about BioJava???????? -- Michael Gruenberger Computer Officer, University of Cambridge Webmaster, European Late Effects Project, http://www.eulep.org Developer, Pathbase, http://www.pathbase.net PGP-Public Key ID: 278E1DFF -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: From peri at wseas.org Sun Oct 26 21:17:50 2003 From: peri at wseas.org (Katerina Tsironi) Date: Mon, 27 Oct 2003 04:17:50 +0200 Subject: [BiO BB] 4th WSEAS International Conference on MATHEMATICS AND COMPUTERS IN BIOLOGY AND CHEMISTRY (MCBC'03) with special emphasis on: BIOENGINEERING, MOLECULAR BIOLOGY, MATHEMATICAL BIOLOGY, BIOCHEMISTRY, BIOPHYSICS, COMPUTER BIOLOGY, BIOLOGICAL DYNAMICAL SYSTEMS, Message-ID: <200310270217.h9R2HqN8011889@forthnet.gr> WSEAS will reply to you only if you write the word: WSEAS somewhere in the Subject of your message, In case that you forgot it, unfortunately, there is not any automatic reply or warning! ----------------------------------------------------------------------------------- EXTENDED DEADLINE: Nov.15, 2003 CALL FOR PAPERS: http://www.wseas.org Tenerife, Canary Islands, Spain, December 19-21, 2003 4th WSEAS International Conference on MATHEMATICS AND COMPUTERS IN BIOLOGY AND CHEMISTRY (MCBC'03) with special emphasis on: BIOENGINEERING, MOLECULAR BIOLOGY, MATHEMATICAL BIOLOGY, BIOCHEMISTRY, BIOPHYSICS, COMPUTER BIOLOGY, BIOLOGICAL DYNAMICAL SYSTEMS, IN THIS WSEAS CONFERENCE ALL THE ACCEPTED PAPERS WILL BE PUBLISHED TWICE (different publications, different ISSN/ISBN), (a) as papers in the conference proceedings AS WELL AS (b) chapters in WSEAS Books DEADLINE FOR YOU: NOVEMBER 15, 2003 http://www.wseas.org From Pignatelli at noraybio.com Thu Oct 30 04:43:03 2003 From: Pignatelli at noraybio.com (Miguel Pignatelli) Date: Thu, 30 Oct 2003 10:43:03 +0100 Subject: [BiO BB] Molecular Mechanics (Universal Force Fields models) Message-ID: <003601c39eca$36c21fa0$2501a8c0@NORAYBIO.COM> Hi, I'm trying to make a program in C that calculates the energy of a molecule from the coordinates X,Y,Z of its atoms. We want to apply the Universal Force Fields (UFF) described by Rappe. Once we have the total energy of the molecule (contribution from each chemical bond (bond stretching), angle bending, torsional terms, improper torsions, out of plane bending motions and non-bonded interactions (electrostatic and Van der Waals forces)) we will look for energy minimisation through the conjugate gradient minimisation method. I am looking for a similar software to look at or any algorithm that could help me. First of all I would like to know what is the best data structure to use in this kind of software and if there is any similar software to look at its code or any algorithm that implements the UFF. The software imput will be atoms and coordinates, so it will determine which atoms are bonded. Is there any efficient algorithm for that? Any suggestions? Thanks all -------------- next part -------------- An HTML attachment was scrubbed... URL: From denis_aubin at canada.com Thu Oct 30 15:30:09 2003 From: denis_aubin at canada.com (denis_aubin at canada.com) Date: Thu, 30 Oct 2003 12:30:09 -0800 (PST) Subject: [BiO BB] Best Bioinformatics and Database Education Message-ID: <20031030123010.29779.h020.c009.wm@mail.canada.com.criticalpath.net> Hi Group, As a C++, VB, .NET programer, also experienced in SQL I'm very interested to get into the bioinformatics either in programming or in database architecture, administration. What are the modules I should get used to (I've heard of Bioperl) ? Is a certification in Biology or similar mandatory? Thank you Denis On Thu, 30 Oct 2003 12:01:33 -0500 (EST), bio_bulletin_board-request at bioinformatics.org wrote: > > When replying, PLEASE edit your Subject line so it is > more specific > than "Re: BiO_Bulletin_Board digest, Vol..." > > > Today's Topics: > > 1. Molecular Mechanics (Universal Force Fields > models) (Miguel Pignatelli) > > --__--__-- > > Message: 1 > From: "Miguel Pignatelli" > To: > Date: Thu, 30 Oct 2003 10:43:03 +0100 > Subject: [BiO BB] Molecular Mechanics (Universal Force > Fields models) > Reply-To: bio_bulletin_board at bioinformatics.org > > This is a multi-part message in MIME format. > > ------=_NextPart_000_0033_01C39ED2.984F9920 > Content-Type: text/plain; > charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > Hi, > > I'm trying to make a program in C that calculates the > energy of a = > molecule from the coordinates X,Y,Z of its atoms. We > want to apply the = > Universal Force Fields (UFF) described by Rappe. Once > we have the total = > energy of the molecule (contribution from each chemical > bond (bond = > stretching), angle bending, torsional terms, improper > torsions, out of = > plane bending motions and non-bonded interactions > (electrostatic and Van = > der Waals forces)) we will look for energy minimisation > through the = > conjugate gradient minimisation method. > > I am looking for a similar software to look at or any > algorithm that = > could help me. First of all I would like to know what > is the best data = > structure to use in this kind of software and if there > is any similar = > software to look at its code or any algorithm that > implements the UFF. > =20 > The software imput will be atoms and coordinates, so it > will determine = > which atoms are bonded. Is there any efficient > algorithm for that? > =20 > Any suggestions? > > Thanks all > > ------=_NextPart_000_0033_01C39ED2.984F9920 > Content-Type: text/html; > charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > Transitional//EN"> > > http-equiv=3DContent-Type> > name=3DGENERATOR> > > > >
>
Hi,
>
 
>
I'm trying to make a > program in C=20 > that calculates the energy of a molecule from the > coordinates X,Y,Z = > of its=20 > atoms. We want to apply the Universal Force Fields > (UFF) described by = > Rappe.=20 > Once we have the total energy of the molecule > (contribution from each = > chemical=20 > bond (bond stretching), angle bending, torsional terms, > improper=20 > torsions, out of plane bending motions and > non-bonded interactions=20 > (electrostatic and Van der Waals forces)) we will look > for energy = > minimisation=20 > through the conjugate gradient minimisation > method.
>
 
>
I am looking for a > similar software to = > look at or=20 > any algorithm that could help me. First of all I would > like to know what = > is the=20 > best data structure to use in this kind of software and > if there is any = > similar=20 > software to look at its code or any algorithm that > implements the=20 > UFF.
>
 
>
The software imput > will be atoms and = > coordinates,=20 > so it will determine which atoms are bonded. Is there > any efficient = > algorithm=20 > for that?
>
 
>
Any > suggestions?
>
 
>
Thanks=20 > all
> > ------=_NextPart_000_0033_01C39ED2.984F9920-- > > > > --__--__-- > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > End of BiO_Bulletin_Board Digest From dmb at mrc-dunn.cam.ac.uk Fri Oct 31 03:37:46 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 31 Oct 2003 08:37:46 -0000 (GMT) Subject: [BiO BB] Best Bioinformatics and Database Education In-Reply-To: <20031030123010.29779.h020.c009.wm@mail.canada.com.criticalpath.net> References: <20031030123010.29779.h020.c009.wm@mail.canada.com.criticalpath.net> Message-ID: <2355.143.248.30.114.1067589466.squirrel@www.mrc-dunn.cam.ac.uk> > Hi Group, > > As a C++, VB, .NET programer, also experienced in SQL > I'm very interested to get into the bioinformatics > either in programming or in database architecture, > administration. > > What are the modules I should get used to (I've heard > of Bioperl) ? > > Is a certification in Biology or similar mandatory? This is an interesting question. I think the process of data modeling is like domain modeling, so in this respect I think a good understanding of the concepts underlying the data is important. I.e. You need a certain amount of domain knowledge. Naturally this doesn't affect the techical aspects of data normalization given a good data model, but often normalization is a pain for end users, who have clear ideas about what data is conceptually related, and don't want to have to manually link such data over several tables. However, if your end users are screened from the underlying data it is no problem, but then I think you are in the field of application developement. This may be associated with bioinformatics, but isn't really any different from any other kind of engineering work. I think some really important developement would be to allow individual (domain experts) to create individual domain models, which could then be openly shared / linked etc. Cheers, Dan. > Thank you > > Denis > > On Thu, 30 Oct 2003 12:01:33 -0500 (EST), > bio_bulletin_board-request at bioinformatics.org wrote: > >> >> When replying, PLEASE edit your Subject line so it is >> more specific >> than "Re: BiO_Bulletin_Board digest, Vol..." >> >> >> Today's Topics: >> >> 1. Molecular Mechanics (Universal Force Fields >> models) (Miguel Pignatelli) >> >> --__--__-- >> >> Message: 1 >> From: "Miguel Pignatelli" >> To: >> Date: Thu, 30 Oct 2003 10:43:03 +0100 >> Subject: [BiO BB] Molecular Mechanics (Universal Force >> Fields models) >> Reply-To: bio_bulletin_board at bioinformatics.org >> >> This is a multi-part message in MIME format. >> >> ------=_NextPart_000_0033_01C39ED2.984F9920 >> Content-Type: text/plain; >> charset="iso-8859-1" >> Content-Transfer-Encoding: quoted-printable >> >> Hi, >> >> I'm trying to make a program in C that calculates the >> energy of a = >> molecule from the coordinates X,Y,Z of its atoms. We >> want to apply the = >> Universal Force Fields (UFF) described by Rappe. Once >> we have the total = >> energy of the molecule (contribution from each > chemical >> bond (bond = >> stretching), angle bending, torsional terms, improper >> torsions, out of = >> plane bending motions and non-bonded interactions >> (electrostatic and Van = >> der Waals forces)) we will look for energy > minimisation >> through the = >> conjugate gradient minimisation method. >> >> I am looking for a similar software to look at or any >> algorithm that = >> could help me. First of all I would like to know what >> is the best data = >> structure to use in this kind of software and if there >> is any similar = >> software to look at its code or any algorithm that >> implements the UFF. >> =20 >> The software imput will be atoms and coordinates, so > it >> will determine = >> which atoms are bonded. Is there any efficient >> algorithm for that? >> =20 >> Any suggestions? >> >> Thanks all >> >> ------=_NextPart_000_0033_01C39ED2.984F9920 >> Content-Type: text/html; >> charset="iso-8859-1" >> Content-Transfer-Encoding: quoted-printable >> >> > Transitional//EN"> >> >> > http-equiv=3DContent-Type> >> > name=3DGENERATOR> >> >> >> >>
>>
Hi,
>>
 
>>
I'm trying to make a >> program in C=20 >> that calculates the energy of a molecule from the >> coordinates X,Y,Z = >> of its=20 >> atoms. We want to apply the Universal Force Fields >> (UFF) described by = >> Rappe.=20 >> Once we have the total energy of the molecule >> (contribution from each = >> chemical=20 >> bond (bond stretching), angle bending, torsional > terms, >> improper=20 >> torsions, out of plane bending motions and >> non-bonded interactions=20 >> (electrostatic and Van der Waals forces)) we will look >> for energy = >> minimisation=20 >> through the conjugate gradient minimisation >> method.
>>
 
>>
I am looking for a >> similar software to = >> look at or=20 >> any algorithm that could help me. First of all I would >> like to know what = >> is the=20 >> best data structure to use in this kind of software > and >> if there is any = >> similar=20 >> software to look at its code or any algorithm that >> implements the=20 >> UFF.
>>
 
>>
The software imput >> will be atoms and = >> coordinates,=20 >> so it will determine which atoms are bonded. Is there >> any efficient = >> algorithm=20 >> for that?
>>
 
>>
Any >> suggestions?
>>
 
>>
Thanks=20 >> all
>> >> ------=_NextPart_000_0033_01C39ED2.984F9920-- >> >> >> >> --__--__-- >> >> _______________________________________________ >> BiO_Bulletin_Board maillist - >> BiO_Bulletin_Board at bioinformatics.org >> > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >> >> End of BiO_Bulletin_Board Digest > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From val at vtek.com Fri Oct 31 17:25:29 2003 From: val at vtek.com (val) Date: Fri, 31 Oct 2003 17:25:29 -0500 Subject: [BiO BB] Molecular Mechanics (Universal Force Fields models) References: <003601c39eca$36c21fa0$2501a8c0@NORAYBIO.COM> Message-ID: <193701c39ffd$e467dc60$6400a8c0@vt1000> Hi Miguel, Google is your best friend. Try, e.g., google with 'molecule energy software'. But i wouldn't rely much on this type of calculation; it does not help much in answering real questions in (bio)chemistry and bioinformatics. my best, val ----- Original Message ----- From: Miguel Pignatelli To: bio_bulletin_board at bioinformatics.org Sent: Thursday, October 30, 2003 4:43 AM Subject: [BiO BB] Molecular Mechanics (Universal Force Fields models) Hi, I'm trying to make a program in C that calculates the energy of a molecule from the coordinates X,Y,Z of its atoms. We want to apply the Universal Force Fields (UFF) described by Rappe. Once we have the total energy of the molecule (contribution from each chemical bond (bond stretching), angle bending, torsional terms, improper torsions, out of plane bending motions and non-bonded interactions (electrostatic and Van der Waals forces)) we will look for energy minimisation through the conjugate gradient minimisation method. I am looking for a similar software to look at or any algorithm that could help me. First of all I would like to know what is the best data structure to use in this kind of software and if there is any similar software to look at its code or any algorithm that implements the UFF. The software imput will be atoms and coordinates, so it will determine which atoms are bonded. Is there any efficient algorithm for that? Any suggestions? Thanks all From rossini at blindglobe.net Wed Oct 29 19:53:26 2003 From: rossini at blindglobe.net (A.J. Rossini) Date: Wed, 29 Oct 2003 16:53:26 -0800 Subject: [BiO BB] Release of Bioconductor 1.3 Message-ID: <857k2nzgu1.fsf@blindglobe.net> The Bioconductor core group would like to announce the 1.3 release of the Bioconductor software. There are many new packages as well as several major upgrades and fixes in older packages, and users are encouraged to check them out. Release 1.3 is intended to be operated with R version 1.8.X, which can be obtained at CRAN (http://cran.r-project.org/) -- WHAT FEATURES DOES THIS RELEASE PROVIDE? All packages from the 1.2 release are included. All current bug fixes have been applied, and most have upgraded and provide enhanced functionality. -- NEW PACKAGES AND MAJOR UPGRADES FOR RELEASE 1.3 -- The following is an overview of the most important changes, additions, and upgrades: --- affy There have been many improvements to the affy package. There were big speed and memory improvement of ReadAffy, read.affybatch, justRMA. A mas5calls method was added to get Affymetrix's P/M/A calls. Cel and Cdf classes are no longer supported. Function, read.celfile and other Cel related methods and functions removed. Most Cdf related functions have moved to the makecdfenv package. Function read.probematrix added. It reads CEL files and returns a matrix of PM, MM, or both. This function is more memory efficient than read.affybatch. Also, affy no longer depends on the affydata package. For this reason some examples have been moved from affy vignettes to the affydata vignette. The previously deprecated express function has been completely removed. Lastly, most normalization routines for AffyBatches can now be called with the parameter type which specifies whether the normalization should be applied as a PM-only, MM-only, both PM and MM together or PM and MM separately. --- affycomp: New assessment was added: assessSpikeIn2. Examples of new feature: Local slopes are computes and ROC curves divided by overall expression. Also, all functions that work for hgu95a spike in now also work for hgu133a spike in experiment --- annaffy: Functions for handling data from Bioconductor Affymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria. --- Biobase: The generic function as.data.frame() now works on objects of class exprSet. This lets one access the extensive modeling facilities through formula offered by R and packages like 'nlm'. --- factDesign: A package containing functions useful for analyzing data from factorial designed microarray experiments. --- gpls: Classification using partial least squares (PLS), a popular dimension reduction tool in chemometrics, in the context of generalized linear regression based on a previous approach, Iteratively ReWeighted Partial Least Squares (IRWPLS) by Marx (1996). Both two-group and multi-group classifications are incorporated. Firth's bias reduction procedure is also incorporated to ensure more stable and finite regression coefficients. --- graph, Rgraphviz, and RBGL: Graph/Network handling is greatly improved. There is tighter integration between graph, RBGL and Rgraphviz. Colors and SubGraph layouts are now supported in Rgraphviz. RBGL support includes minimal spanning trees, both strong and weakly connected components, and Dijkstra's shortest path algorithm. In graph, enhancements in validity checking and representation have been made. New classes have been established that will allow for general representations of nodes and edges. Capabilities include adding or deleting both nodes and edges, combining sets of nodes into a single node. Unions, intersections and complements of graphs defined on a common set of nodes. Joining of two graphs into a single graph. Functions to compute indegree and outdegree. --- limma: Substantial updates including support for more image analysis programs, new background correction methods, single channel normalization, support for import of exprSet and marrayNorm data objects, improved support for design and contrast matrices, new fitted model object class, within-gene multiple testing, Venn diagrams and generally a move to a simpler command style at the user level. --- matchprobes: A new package providing tools for working with probe sequence information: calculate ATCG content, reverse, complement, mismatch sequences; fast exact sequence matching; combine AffyBatches of different chip types; create probe data packages. --- Measurement.cor: A package to fit a two-level measurement error model for estimation of correlation coefficient between two random variables assuming bivariate normality for both the true value and measurement error. This model allows dependence between measurement errors hence is more flexible. --- ontoTools: Software for working with ontologies (structured vocabularies) and their associations with general data resources. --- Rdbi, RdbiPgSQL: Generic framework for database access in R. Adapted from Rdbi authored by Timothy H. Keitt, with methods for accessing data stored in PostgreSQL tables (Adapted from Rdbi.PgSQL, authored by Timothy H. Keitt) --- SNPtools: Currently an interface to the SNPper data resource maintained at Childrens' Boston, which curates SNP-related data from a variety of sources. --- splicegear: A new package that works with oligonucleotide microarrays designed to monitor or confirm the existence of splice variants. It can extract simple splice-variant information in XML format. This is demonstrated by the connectivity to an existing database of putative splice variants. The package can also integrate easily with the results obtained from the package 'matchprobes'. --- vsn: Two new functions were added 'sagmbSimulateData' and 'sagmbAssess' to quantitatively verify finite sample properties and outlier robustness of the parameter estimation in vsn(). -- TOOLS: The released packages include tools which facilitate: * annotation (AnnBuilder, annotate). * data management and organization through the use of the S4 class structure (Biobase, marrayClasses, limma). * identification of differentially expressed genes and clustering (edd, genefilter, geneplotter, multtest, ROC, limma) * analysis of Affymetrix expression array data (affy, affycomp, gcrma) * diagnostic plots and normalization for cDNA array data (marrayInput, marrayNorm, marrayPlots) * storage and retrieval of large datasets (rhdf5, externalVector, Rdbi, RdbiPgSQL). * facilitate user interaction (tkWidgets, widgetTools) There are currently a total of 48 packages, not including precomputed annotation data packages for Affymetrix GeneChips(tm), KEGG, GO, and LocusLink mappings. -- HELP AND RESOURCES: The packages and more details may be found on the Bioconductor WWW site: http://www.bioconductor.org/ Information on subscribing to the mailing list and viewing its archives can be found at: http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Please use that list to discuss Bioconductor specific issues, bugs, and problems. Note that every package has a vignette (a literate program which provides an annotated example of the package's use) as well as possibly some "HOWTO"s. These document the tool's usage, and are provided in the "doc" subdirectory of each package library. -- WHO: For the Bioconductor development team: Douglas Bates, University of Wisconsin, USA. Ben Bolstad, Division of Biostatistics, UC Berkeley, USA. Vince Carey, Harvard Medical School, USA. Marcel Dettling, Federal Inst. Technology, Switzerland. Sandrine Dudoit, Division of Biostatistics, UC Berkeley, USA. Byron Ellis, Harvard Department of Statistics, USA. Laurent Gautier, Technial University of Denmark, Denmark. Robert Gentleman, Harvard Medical School, USA. Jeff Gentry, Dana-Farber Cancer Institute, USA. Kurt Hornik, Technische Universitat Wien, Austria. Torsten Hothorn, Institut fuer Medizininformatik, Biometrie und Epidemiologie, Germany. Wolfgang Huber, DKFZ Heidelberg, Molecular Genome Analysis, Germany. Stefano Iacus, Italy Rafael Irizarry, Department of Biostatistics (JHU), USA. Friedrich Leisch, Technische Universitat Wien, Austria. Martin Maechler, Federal Inst. Technology, Switzerland. Colin Smith, Scripps Research Institute, USA. Gordon Smyth, Walter and Eliza Hall Institute, Australia. Anthony Rossini, University of Washington and the Fred Hutchinson Cancer Research Center, USA. Gunther Sawitzki, Institute fur Angewandte Mathematik, Germany. Luke Tierney, University of Iowa, USA. Jean Yee Hwa Yang, University of California, San Francisco, USA. Jianhua (John) Zhang, Dana-Farber Cancer Institute, USA. -- rossini at u.washington.edu http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachments may be confidential and privileged. If you received this message in error, please destroy it and notify the sender. Thank you.