From jeff at bioinformatics.org Thu Nov 4 00:23:01 2004 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 04 Nov 2004 00:23:01 -0500 Subject: [BiO BB] RasMol mailing list becomes Molecular Visualization list at Bioinformatics.Org Message-ID: <4189BCB5.4000607@bioinformatics.org> This was posted on BiO News a few days ago: The RasMol mailing list at UMass Amherst is now the Molecular Visualization list at Bioinformatics.Org: ``Molvis-list is for discussion of molecular visualization software, especially free software and its uses in education, such as MDL Chime, Protein Explorer, and RasMol, among many. Technical questions, `How do I ...', comparisons between software packages, or questions about pros and cons, are welcome. Discussions may include molvis packages that have their own dedicated email lists, such as Jmol or DeepView, although technical questions about those packages should be sent to their dedicated lists. Discussions may also include commercial molvis software packages. ``Subscribers with commercial affiliations are welcome. Advertising is prohibited, but occasional, brief, low-key announcements of commercial products of interest to the subscribership are welcome, as are announcements of relevant meetings, positions available or sought. ``Before broadcasting questions to this list, please see Frequently Asked Questions (FAQ). Molvis-list was founded in 1995 (originally as the `RasMol list') by Eric Martz of the University of Massachusetts, Amherst (USA). The list was moved from umass.edu to bioinformatics.org in November, 2004. The number of subscribers has remained steady at around 600 since 2001. Traffic averages 1-2 messages/day.'' FAQ: http://bioinformatics.org/molvis-list/ Mailman page for the list: http://bioinformatics.org/lists/molvis-list New subscriptions are welcome. Please see the above URL to subscribe. Cheers. Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From mourad12345678 at yahoo.com Wed Nov 3 20:48:52 2004 From: mourad12345678 at yahoo.com (Mourad Elloumi) Date: Wed, 3 Nov 2004 17:48:52 -0800 (PST) Subject: [BiO BB] Call for Papers : ALBIO'05 Message-ID: <20041104014852.5932.qmail@web12303.mail.yahoo.com> CALL FOR PAPERS ALBIO'05 Algorithms in Molecular Biology Session of 6th International Symposium on Computational Biology and Genome Informatics Salt Lake City Marriott City Center, Salt Lake City, Utah, USA July 21-26, 2005 http://www.jcis.org/ Computational Molecular Biology, has emerged from the Human Genome Project as an important discipline for academic research and industrial application. The growing size of biological databases, the complexity of biological problems and the necessity to deal with errors in biological sequences all result in large run time and memory requirements. Biological sequence databases are growing at an exponential rate. All of these factors will make the development of fast, low memory requirements and high-performances algorithms increasingly important in Computational Molecular Biology. In our session, we are interested in papers that deal with all aspects of algorithms in Molecular Biology. We are, particularly, interested in algorithms that address fundamental and/or applied problems in Molecular Biology, that are computationally efficient, that have been implemented and experimented on simulated and/or on real biological sequences and that provide interesting new results. The submitted papers should present recent research results and identify and explore directions for future research. Topics include, but not limited to: (i) strings processing, (ii) biological sequences comparison, (iii) structures prediction, (iv) phylogeny reconstruction, (v) DNA sequences assembly, clustering, and mapping, (vi) molecular evolution, (vii) genes prediction/recognition, (viii) genes expression INSTRUCTIONS TO AUTHORS All papers must be in Word or PDF format and may not exceed 4 pages in length, including figures, tables and references. Any papers exceeding 4 pages will be charged a $50 fee per additional page. Papers should be formatted with double columns and should be single-spaced in a 10 point font such as Times Roman. A template will be provided for final paper submission. All papers should be sent to the Session Chair : Dr. Mourad Elloumi : E.Mail: Mourad.Elloumi at fsegt.rnu.tn Important Dates December 1, 2004 : Paper due for authors requiring early notification. January 15, 2005 : Paper due for standard submission. February 1, 2005 : Notification of acceptance - invitation letters sent to authors who require early notification. March 15, 2005 : Notification of acceptance - invitation letters sent to authors for the standard submission. April 30, 2005 : Final camera ready papers due (including invited papers) April 30, 2005 : Deadline for authors with accepted and invited papers to register and submit the minimum $180 publication fee/registration deposit, or early discounted registration fees. __________________________________ Do you Yahoo!? Check out the new Yahoo! Front Page. www.yahoo.com -------------- next part -------------- A non-text attachment was scrubbed... Name: ALBIO'05.doc Type: application/msword Size: 31744 bytes Desc: ALBIO'05.doc URL: From jeff at bioinformatics.org Mon Nov 8 22:16:22 2004 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Mon, 08 Nov 2004 22:16:22 -0500 Subject: [BiO BB] Bioinformatics books via Bioinformatics.Org Message-ID: <41903686.8090304@bioinformatics.org> Purchase books online and help Bioinformatics.Org at the same time! Bioinformatics.Org announces membership in the Barnes & Noble Affiliates Program. We have created one of the largest and best organized book lists for bioinformatics on the Internet: 30 sections, 128 entries and counting! Just click on a cover image and make the purchase via the B&N website. 5.5% of the purchase price goes to Bioinformatics.Org to help us with operations, but you get THE SAME PRICE as if you shopped directly at B&N. Preliminary sections include the following: General, introductory texts * General (introduction to) bioinformatics * General (introduction to) computational biology * General (introduction to) computational bio/chemistry and bio/cheminformatics * General (introduction to) scientific computing Computing for biology * General software development for biology * Artificial intelligence and machine learning for biology * Databases, knowledgebases and data mining for biology * Biomathematics, biostatistics and biological modeling with computers Biology with computers * Evolutionary analysis, phylogenetics and systematics with computers * Genomics, genetics and related sequence analysis with computers * Proteomics and protein science with computers * Structure/function analysis and modeling with computers * Biopathways and biochemical simulation with computers * Biochip and microarray analysis with computers * Drug design and discovery with computers Selected topics in biology * General biology * Biochemistry * Biophysics and physical biochemistry * Biological structure and function * Drug design and discovery Selected topics in computer science * General software development * Artificial intellegence * Databases, knowledgebases, and data mining * Mathematics, statistics and modeling * Performance and cluster computing Additional * New releases * Reference: dictionaries and encyclopedias * Opinion and ideology * Technical writing * Special O'Reilly section URL: http://books.bioinformatics.org/ Note that some sections are incomplete. Suggestions are welcome. All other books purchased with the Bioinformatics.Org source ID will contribute a percentage to our operations too: http://www.barnesandnoble.com/?sourceid=00411364016205342503 Cheers. Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From ahmed at users.sourceforge.net Wed Nov 10 10:30:52 2004 From: ahmed at users.sourceforge.net (Ahmed Moustafa) Date: Wed, 10 Nov 2004 07:30:52 -0800 Subject: [BiO BB] SWDA Message-ID: <4192342C.60402@users.sourceforge.net> Ryan, Regarding your post on 17 September (http://bioinformatics.org/pipermail/bio_bulletin_board/2004-September/002100.html), your implementation was not incorporated into JAligner, I built the source code from scratch from the algorithm in Pavel Pevzner's Computational Molecular Biology (as I mentioned to you before), and it was already up and running before you voluntarily sent me your code and discussed one improvement with me which I acknowledged on the project homepage (http://jaligner.sourceforge.net). So it was wrong to declare that JAligner was a rework of your code. Regards, Ahmed Moustafa From lgoldfinger at ucsd.edu Wed Nov 10 20:27:15 2004 From: lgoldfinger at ucsd.edu (Larry Goldfinger) Date: Wed, 10 Nov 2004 17:27:15 -0800 Subject: [BiO BB] FW: HMMer for Windows Message-ID: <000701c4c78d$93df2f10$13a0ef84@Larry> Does anyone know of a HMMer downloadable for Windows? All I can find are UNIX/Linus platforms. Thanks. Lawrence E. Goldfinger, Ph.D. Division of Rheumatology Department of Medicine University of California, San Diego Leichtag Bldg., Room 181 9500 Gilman Drive, Dept 0726 La Jolla, CA 92073-0726 phone: (858) 822-6506 e-mail: lgoldfinger at ucsd.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgollery at unr.edu Wed Nov 10 20:50:57 2004 From: mgollery at unr.edu (Martin Gollery) Date: Wed, 10 Nov 2004 17:50:57 -0800 Subject: [BiO BB] FW: HMMer for Windows In-Reply-To: <000701c4c78d$93df2f10$13a0ef84@Larry> References: <000701c4c78d$93df2f10$13a0ef84@Larry> Message-ID: <4192C581.2020207@unr.edu> Interesting- there used to be one! I have a copy of HMMer 2.1for windows, so I know it was there. Perhaps someone could port the latest? Larry Goldfinger wrote: Does anyone know of a HMMer downloadable for Windows? All I can find are UNIX/Linus platforms. Thanks. > > > _Lawrence__ E. Goldfinger, Ph.D._ > > Division of Rheumatology > > Department of Medicine > > University of California, San Diego > > Leichtag Bldg., Room 181 > > 9500 Gilman Drive, Dept 0726 > > La Jolla, CA 92073-0726 > > phone: (858) 822-6506 > > e-mail: lgoldfinger at ucsd.edu > > > From yvan.strahm at med.monash.edu.au Wed Nov 10 23:10:58 2004 From: yvan.strahm at med.monash.edu.au (Yvan) Date: Thu, 11 Nov 2004 15:10:58 +1100 Subject: [BiO BB] FW: HMMer for Windows In-Reply-To: <4192C581.2020207@unr.edu> References: <000701c4c78d$93df2f10$13a0ef84@Larry> <4192C581.2020207@unr.edu> Message-ID: <4192E652.3050100@med.monash.edu.au> Hello, Did you have a look at this URL: http://hmmer.wustl.edu/ There is a precompiled version working with Cygwin. good luck yvan Martin Gollery wrote: > > Interesting- there used to be one! I have a copy of HMMer 2.1for > windows, so I know it was there. Perhaps someone could port the latest? > > > > Larry Goldfinger wrote: > > Does anyone know of a HMMer downloadable for Windows? All I can find > are UNIX/Linus platforms. Thanks. > >> >> >> _Lawrence__ E. Goldfinger, Ph.D._ >> >> Division of Rheumatology >> >> Department of Medicine >> >> University of California, San Diego >> >> Leichtag Bldg., Room 181 >> >> 9500 Gilman Drive, Dept 0726 >> >> La Jolla, CA 92073-0726 >> >> phone: (858) 822-6506 >> >> e-mail: lgoldfinger at ucsd.edu >> >> >> > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From enoumen at rsvs.ulaval.ca Fri Nov 12 14:23:54 2004 From: enoumen at rsvs.ulaval.ca (Etienne Noumen) Date: Fri, 12 Nov 2004 14:23:54 -0500 Subject: [BiO BB] convert scanarray and quantarray to mev References: <000701c4c78d$93df2f10$13a0ef84@Larry> <4192C581.2020207@unr.edu> <4192E652.3050100@med.monash.edu.au> Message-ID: <000b01c4c8ed$294e2cd0$5da0cb84@sbf.ulaval.ca> I am trying in vain to convert a scanarray file to Mev file. I am able to convert a quantarray file for the same data to mev using expresconverter from tigr, but i would like to convert it from my scanarray file. Does somebody knows how i can do that, (from scanarray to quantarray or from scanarray to Mev). thank you in advance. -------------------------- Etienne Noumen Forestry Biology Research Center 2251 Pav. Marchand-University of Laval Tel(O): (418) 656 2131 # 6116 Qu?bec, CANADA G1K 7P4 ---------------------------------------------- ----- Original Message ----- From: "Yvan" To: Sent: Wednesday, November 10, 2004 11:10 PM Subject: Re: [BiO BB] FW: HMMer for Windows > Hello, > > Did you have a look at this URL: > > http://hmmer.wustl.edu/ > > There is a precompiled version working with Cygwin. > > good luck > > yvan > > Martin Gollery wrote: > > > > > Interesting- there used to be one! I have a copy of HMMer 2.1for > > windows, so I know it was there. Perhaps someone could port the latest? > > > > > > > > Larry Goldfinger wrote: > > > > Does anyone know of a HMMer downloadable for Windows? All I can find > > are UNIX/Linus platforms. Thanks. > > > >> > >> > >> _Lawrence__ E. Goldfinger, Ph.D._ > >> > >> Division of Rheumatology > >> > >> Department of Medicine > >> > >> University of California, San Diego > >> > >> Leichtag Bldg., Room 181 > >> > >> 9500 Gilman Drive, Dept 0726 > >> > >> La Jolla, CA 92073-0726 > >> > >> phone: (858) 822-6506 > >> > >> e-mail: lgoldfinger at ucsd.edu > >> > >> > >> > > > > _______________________________________________ > > 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 jeff at bioinformatics.org Sun Nov 14 10:52:01 2004 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Sun, 14 Nov 2004 10:52:01 -0500 Subject: [BiO BB] Now accepting nominations for the 2005 Benjamin Franklin Award Message-ID: <41977F21.6050605@bioinformatics.org> It's that time of year again! Benjamin Franklin (1706-1790) was one of the most remarkable men of his time. Scientist, inventor, statesman, Franklin freely and openly shared his ideas and refused to patent his inventions. It is the opinion of the founders of the Bioinformatics Organization, Inc. that he embodied the best traits of a scientist, and we seek to honor those who share these virtues. The ``Benjamin Franklin Award in Bioinformatics'' is a humanitarian award presented annually by this organization to an individual who has, in his or her practice, promoted free and open access to the methods and materials used in the scientific field of bioinformatics. Past laureates include Lincoln Stein (2004), Jim Kent (2003) and Michael Eisen (2002). Nominations may be made online by registered members of Bioinformatics.Org. The deadline is December 1. Please see the BFA website for more information: http://bioinformatics.org/franklin/ Online nomination form (must be logged in): http://bioinformatics.org/franklin/nominate/ Cheers. Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From combiofriends at yahoo.com Fri Nov 12 16:30:03 2004 From: combiofriends at yahoo.com (com bio) Date: Fri, 12 Nov 2004 13:30:03 -0800 (PST) Subject: [BiO BB] gdb-debugging perl codes Message-ID: <20041112213003.21424.qmail@web51009.mail.yahoo.com> hello, i am familiar with the built in perl debugger that comes with the interpreter.but i would like to know if we can debug perl programs with gdb.i had been using gdb to debug c,c++ programs.sorry for my ignorance. thanks and regards deepan charkavarthy n ===== link to deepan's home page: http://www.geocities.com/combiofriends/deepan.html ------------------------------------------- center for biotechnology anna university chennai-25 india __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From ahmed.rebai at cbs.rnrt.tn Thu Nov 11 03:11:17 2004 From: ahmed.rebai at cbs.rnrt.tn (Ahmed Rebai) Date: Thu, 11 Nov 2004 09:11:17 +0100 Subject: [BiO BB] bioinformatics course Message-ID: <200411110700.IAA09154@mail.pubfsi.tn> Dear colleagues, Applications for the Course < Bioinformatics and genome data analysis" which is a CBS/Institut Pasteur/ICGEB/EMBO/ICRO/IUBMB/AUF course are open till December 31, 2004. Accepted applicants will have their full accommodation for free (hotel and meals).; they just have to pay their travelling costs and get some money to buy souvenirs ! The course will take place on March 23 to April 02 2005 in Tunisia. Details are on the URL: http://anibal.webzzanine.net/bioinformatics/ Please forward this email to all interested colleagues of yours; Pr Ahmed Rebai Organizer of the course -------------- next part -------------- An HTML attachment was scrubbed... URL: From hjm at tacgi.com Tue Nov 16 18:56:56 2004 From: hjm at tacgi.com (Harry Mangalam) Date: Tue, 16 Nov 2004 15:56:56 -0800 Subject: [BiO BB] gdb-debugging perl codes In-Reply-To: <20041112213003.21424.qmail@web51009.mail.yahoo.com> References: <20041112213003.21424.qmail@web51009.mail.yahoo.com> Message-ID: <200411161556.56379.hjm@tacgi.com> No, I don't think so, unless with deep magic. You can however, use the ddd debugger front end with gdb, the perl debugger, the python debugger, and others to give you a nice consistent gui interface for all the languages. Altho the features will change, depending on what the underlying debugger symbols emerge. hjm On Friday 12 November 2004 1:30 pm, com bio wrote: > hello, > i am familiar with the built in perl debugger that > comes with the interpreter.but i would like to know if > we can debug perl programs with gdb.i had been using > gdb to debug c,c++ programs.sorry for my ignorance. > thanks and regards > deepan charkavarthy n > > ===== > link to deepan's home page: > http://www.geocities.com/combiofriends/deepan.html > > ------------------------------------------- > center for biotechnology > anna university > chennai-25 > india > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > 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 (vox; email for fax) - hjm at tacgi.com <> From information at virtualgenomics.org Tue Nov 16 20:59:43 2004 From: information at virtualgenomics.org (information at virtualgenomics.org) Date: Tue, 16 Nov 2004 18:59:43 -0700 Subject: [BiO BB] Virtual Genomics: Virtual Seminar Message-ID: <20041117015943.1065.qmail@webmail07.mesa1.secureserver.net> An HTML attachment was scrubbed... URL: From information at virtualgenomics.org Tue Nov 16 20:59:43 2004 From: information at virtualgenomics.org (information at virtualgenomics.org) Date: Tue, 16 Nov 2004 18:59:43 -0700 Subject: [BiO BB] Virtual Genomics: Virtual Seminar Message-ID: <20041117015943.1065.qmail@webmail07.mesa1.secureserver.net> An HTML attachment was scrubbed... URL: From pculpep at hotmail.com Wed Nov 17 13:23:06 2004 From: pculpep at hotmail.com (Pamela Culpepper) Date: Wed, 17 Nov 2004 18:23:06 +0000 Subject: [BiO BB] gdb-debugging perl codes Message-ID: Deepan, Try this. If you have Perl code that calls a C/C++ module that is compiled with debug, have your Perl debugger set a break for that modle. Then use gdb on the Perl PID to access the C module an poke around. Pam >From: Harry Mangalam >Reply-To: bio_bulletin_board at bioinformatics.org >To: bio_bulletin_board at bioinformatics.org >Subject: Re: [BiO BB] gdb-debugging perl codes >Date: Tue, 16 Nov 2004 15:56:56 -0800 > >No, I don't think so, unless with deep magic. You can however, use >the ddd debugger front end with gdb, the perl debugger, the python >debugger, and others to give you a nice consistent gui interface for >all the languages. Altho the features will change, depending on what >the underlying debugger symbols emerge. > >hjm > > >On Friday 12 November 2004 1:30 pm, com bio wrote: > > hello, > > i am familiar with the built in perl debugger that > > comes with the interpreter.but i would like to know if > > we can debug perl programs with gdb.i had been using > > gdb to debug c,c++ programs.sorry for my ignorance. > > thanks and regards > > deepan charkavarthy n > > > > ===== > > link to deepan's home page: > > http://www.geocities.com/combiofriends/deepan.html > > > > ------------------------------------------- > > center for biotechnology > > anna university > > chennai-25 > > india > > > > __________________________________________________ > > Do You Yahoo!? > > Tired of spam? Yahoo! Mail has the best spam protection around > > http://mail.yahoo.com > > _______________________________________________ > > 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 (vox; email for fax) - hjm at tacgi.com > <> >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From applmicro at formatex.org Wed Nov 17 21:30:42 2004 From: applmicro at formatex.org (BioMicroWorld 2005) Date: Thu, 18 Nov 2004 03:30:42 +0100 Subject: [BiO BB] Invitation to submit abstract(s) and Deadline reminder References: Message-ID: <1a6001c4cd16$b080c460$06001aac@PUESTO2> 1st International Conference on Environmental, Industrial and Applied Microbiology (BioMicroWorld-2005) March 15-18th 2005, Badajoz, Spain http://www.formatex.org/biomicroworld2005 Dear Colleague, further to our recent invitation to you to take part of the forthcoming BioMicroWorld-2005 International Conference, we would like to remind that if you intend to take part of it, deadline for submission of abstracts is November 22nd (next Monday). While we will be able to accept some late abstract during the whole next week, this will be possible only for POSTERS presentations. Next monday is the absolute deadline for submission of proposals for oral presentations. Below please find some important informations about the conference. All the information is being continously updated at the website http://www.formatex.org/biomicroworld2005 MAIN TOPICS Main topics of the Conference are - Environmental Microbiology, Marine Microbiology, Water/Aquatic Microbiology, Geomicrobiology - Industrial Microbiology - Future Bioindustries - Food Microbiology - Cell Engineering - Pharmaceutical Microbiology - Agriculture, Soil, Forest Microbiology - Structure and Morphogenesis - Analytical Techniques, Imaging Techniques, Microscopy - Microbial Physiology, Metabolism and Gene Expression - Microbial Biotechnology - Aerospace Microbiology, Astro(micro)biology - Quantitative Models and Bioinformatics in Microbiology - Methods in Basic and Applied Microbiology - Medical Microbiology - Microbiology Education IMPORTANT DEADLINES Submission of abstracts: November 22th, 2004 (abstracts for posters presentations will be accepted until November 27th) Submission of Full Papers for publication: On site CONFERENCE PUBLICATIONS - PROCEEDINGS 1. Book A multi-volume book entitled "Recent Advances in Multidisciplinary Applied Microbiology. Biological, Physical, Chemical and Engineering Aspects" will be published including Full papers of works (oral, posters) presented at the conference. The book will be published by an international publisher (now in negotiations with Elsevier Science), in order to give it a broad international distribution and is intended to serve as a good reference book of the state of the art of Modern Applied Microbiology as of 2005. Submission of Full Papers is optional. 2. Abstracts Book A separate Abstracts Booklet will be published with abstracts of works presented at the Conference. It will be distributed at the beginning of the conference. 3. International Journals special issues Agreements have been arranged with several international journals, in order to produce special issues based on very good papers presented at the Conference. Manuscripts must be delivered during the Conference, according to the instructions we will give in due course for each journal. All papers will be strictly reviewed and treated as regular papers. Our goal is to produce high quality and high impact special issues based on some of the best conference papers. Papers submitted for a journal special issue and rejected (for scientific/editorial/space reasons), can be considered for inclusion in the Book. Please refer to the conference website for details. Journals considering publication of special issues include Antonie van Leeuvenhoek (Springer,confirmed), Enzyme and Microbial Technology (Elsevier,confirmed), International Biodeterioration and Biodegradation (Elsevier), Colloids and Surfaces B: Biointerfaces (Elsevier,confirmed), Geomicrobiology Journal (Elsevier), FEMS Microbiology Ecology (Elsevier), Microscopy and Microanalysis (American Microscopy Society, confirmed), Micron (Elsevier). SPECIAL SESSIONS - WORKSHOPS - Workshop on Modern Microscopy Techniques in Applied Microbiology - MICROFACTORIES - Microbial Production of Chemicals and Pharmaceuticals - Workshop on Biotechnologically Relevant Enzymes and Proteins - Workshop on Studies on Extracellular Matrix: Biology and Physico/chemistry - Workshop on Biosurfactants: Purification, Mass production, Applications - Workshop on Yeast and Bacterial Flocculation: Fundamentals and Industrial interest - Worskhop on Microbial Biosensors - Methods in Cell, Proteins, Enzymes and other Biomolecules Immobilisation - Workshop on Biohydrogen - Hydrogen production by Microorganisms, as a Novel Source of Renewable Energy - Workshop on Bioremediation - Workshop on Microbial Biopolymers: Synthesis, Characterization and Applications - Methods in Cell Adhesion: Classical and Novel Methods, from Macroscopic to Nanometer scale, from Biochemistry to Nano(bio)technology PLENARY LECTURES Plenary talks include: "Biomarkers to Define Interactions in the Environment and Health" David C. White, Director of the Center for Biomarker Analysis, University of Tennessee, USA "Novel Time-resolved Fluoresecence Based Immunoassays and Real-time PCR Assays in Microbiological Applications" Timo Lovgren, Department of Biochemistry and Food Chemistry/Biotechnology, University of Turku, Finland "The Genetics and Biochemistry of Malonate and 2,4-D Biodegradation by Burkholderia cepacia Strain 2a" Ian James Bruce, Nanobiotechnology Research Group, Istituto di Scienze Chimiche, Universita degli Studi di Urbino, ITALY / School of Science, University of Greenwich, UK Alexander Steinbuchel, Institut fur Molekulare Mikrobiologie und Biotechnologie, Munster, GERMANY [titletobeannounced] We hope you find it interesting to present your work(s) at the Conference, and we certainly hope to receive your abstract(s) in due course. Of course every suggestion or collaboration proposals will be appreciated to make the conference reach its goals. Best wishes, Fatima Penya BioMicroWorld-2005 Secretariat Formatex Research Centre C/Zurbaran, 1 2a Planta, Office 1 06001 Badajoz, SPAIN Phone/Fax: +34 924258615 E-mail: applmicro at formatex.org From jstroud at mbi.ucla.edu Thu Nov 18 12:49:31 2004 From: jstroud at mbi.ucla.edu (James Stroud) Date: Thu, 18 Nov 2004 09:49:31 -0800 Subject: [BiO BB] map swissprot to gi num Message-ID: <200411180949.31925.jstroud@mbi.ucla.edu> Hello all, I'm looking for a way to completely (if possible) map swissprot accession ids to gi numbers. Some type of database file would be best. Most anything will do. Any suggestions? Thank you in advance, James -- James Stroud, Ph.D. UCLA-DOE Institute for Genomics and Proteomics 611 Charles E. Young Dr. S. MBI 205, UCLA 951570 Los Angeles CA 90095-1570 http://www.jamesstroud.com/ From sariego9 at yahoo.com Thu Nov 18 14:24:21 2004 From: sariego9 at yahoo.com (Diego Martinez) Date: Thu, 18 Nov 2004 11:24:21 -0800 (PST) Subject: [BiO BB] map swissprot to gi num In-Reply-To: <200411180949.31925.jstroud@mbi.ucla.edu> Message-ID: <20041118192421.39038.qmail@web14309.mail.yahoo.com> Dear James, If I understand your need correctly, I may have an easy solution to the mapping. you can get the entire swissprot db from ncbi in fasta format, with the ncbi id in the standard defline, as follows: >gi|51315800|sp|Q9UPA5|BSN_HUMAN Bassoon protein (Zinc-finger protein 231) you will notice that the gi and the "Q\w+" identifier are in the defline. a simple command line perl or grep to awk will work. if you do not know these, write me back, I will send you the command line for it. the ncbi version of swissprot is available(kinda hard to find) at: ftp://ftp.ncbi.nih.gov/blast/db/FASTA/swissprot.gz goodluck. Diego --- James Stroud wrote: > Hello all, > > I'm looking for a way to completely (if possible) map swissprot accession ids > to gi numbers. Some type of database file would be best. Most anything will > do. > > Any suggestions? > > Thank you in advance, > James > > -- > James Stroud, Ph.D. > UCLA-DOE Institute for Genomics and Proteomics > 611 Charles E. Young Dr. S. > MBI 205, UCLA 951570 > Los Angeles CA 90095-1570 > http://www.jamesstroud.com/ > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > ===== ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .=$=. .=$=. .=$=. .=$=. .=$=. .=$=. @ @ | | | @ | | | @ @ | | | @ | | | @ @ | | | @ | | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | | @ | | | @ @ | | | @ | | | @ @ | | | @ | | | @ @ | ~' `~$~' `~$~' `~$~' `~$~' `~$~' `~ __________________________________ Do you Yahoo!? Meet the all-new My Yahoo! - Try it today! http://my.yahoo.com From dmb at mrc-dunn.cam.ac.uk Thu Nov 18 16:10:33 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 18 Nov 2004 21:10:33 +0000 (GMT) Subject: [BiO BB] map swissprot to gi num In-Reply-To: <200411180949.31925.jstroud@mbi.ucla.edu> Message-ID: On Thu, 18 Nov 2004, James Stroud wrote: >Hello all, > >I'm looking for a way to completely (if possible) map swissprot accession ids >to gi numbers. Some type of database file would be best. Most anything will >do. > >Any suggestions? One way is to query an API 1,000,000 times. It's a real pain, but you can try seqhound or uniparc or srs (perhaps the latter two are the same thing, I am not sure). Please let me know how you get on, Dan. > >Thank you in advance, >James > > From deepan_3356 at yahoo.co.in Sun Nov 21 13:21:19 2004 From: deepan_3356 at yahoo.co.in (deepan chakravarthy n) Date: Sun, 21 Nov 2004 18:21:19 +0000 (GMT) Subject: [BiO BB] gdb-debugging perl codes In-Reply-To: Message-ID: <20041121182119.79035.qmail@web8401.mail.in.yahoo.com> hello Pamela, what u said makes a lot of sense.. thanks for ur suggestion Pamela Culpepper wrote: Deepan, Try this. If you have Perl code that calls a C/C++ module that is compiled with debug, have your Perl debugger set a break for that modle. Then use gdb on the Perl PID to access the C module an poke around. Pam >From: Harry Mangalam >Reply-To: bio_bulletin_board at bioinformatics.org >To: bio_bulletin_board at bioinformatics.org >Subject: Re: [BiO BB] gdb-debugging perl codes >Date: Tue, 16 Nov 2004 15:56:56 -0800 > >No, I don't think so, unless with deep magic. You can however, use >the ddd debugger front end with gdb, the perl debugger, the python >debugger, and others to give you a nice consistent gui interface for >all the languages. Altho the features will change, depending on what >the underlying debugger symbols emerge. > >hjm > > >On Friday 12 November 2004 1:30 pm, com bio wrote: > > hello, > > i am familiar with the built in perl debugger that > > comes with the interpreter.but i would like to know if > > we can debug perl programs with gdb.i had been using > > gdb to debug c,c++ programs.sorry for my ignorance. > > thanks and regards > > deepan charkavarthy n > > > > ===== > > link to deepan's home page: > > http://www.geocities.com/combiofriends/deepan.html > > > > ------------------------------------------- > > center for biotechnology > > anna university > > chennai-25 > > india > > > > __________________________________________________ > > Do You Yahoo!? > > Tired of spam? Yahoo! Mail has the best spam protection around > > http://mail.yahoo.com > > _______________________________________________ > > 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 (vox; email for fax) - hjm at tacgi.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 my home page http://geocities.com/combiofriends/deepan.html --------------------------------------------- deepan chakravarthy n 3rd year,(5th sem), b.tech(biotech), center for biotechnology, anna university , chennai. ph no: hostel:044-22354862,room no108, home:04287-241199,04287-244399, brother no:9840824399, address: ac tech hostel (jh 108), anna university, chennai-25. --------------------------------- Win a castle for NYE with your mates and Yahoo! Messenger -------------- next part -------------- An HTML attachment was scrubbed... URL: From information at virtualgenomics.org Mon Nov 22 22:59:30 2004 From: information at virtualgenomics.org (information at virtualgenomics.org) Date: Mon, 22 Nov 2004 20:59:30 -0700 Subject: [BiO BB] Bioinformatics Education Survey Message-ID: <20041123035930.11208.qmail@webmail03.mesa1.secureserver.net> An HTML attachment was scrubbed... URL: From information at virtualgenomics.org Mon Nov 22 23:01:32 2004 From: information at virtualgenomics.org (information at virtualgenomics.org) Date: Mon, 22 Nov 2004 21:01:32 -0700 Subject: [BiO BB] Bioinformatics Education Biosurvey Message-ID: <20041123040132.28063.qmail@webmail-2-5.mesa1.secureserver.net> An HTML attachment was scrubbed... URL: From vxg189 at bham.ac.uk Tue Nov 23 06:44:29 2004 From: vxg189 at bham.ac.uk (Vibhor Gupta) Date: Tue, 23 Nov 2004 11:44:29 -0000 Subject: [BiO BB] The concept of GAL and GPR files Message-ID: <1B4C5BA3CB5F2849B0C8DB99156046A43AC464@med-ex1.bham.ac.uk> Hi everyone, I am having problems in understanding the concept of GAL and GPR files. So, far I have understood the theoretical definition of both of these. GAL files contain the details about the positions of spots for a microarray slide and the ID and name of the gene being represented by the spot. On the other hand GPR files contain the information that was mentioned in the GAL files and the intensity measurements for these spots (which is what I think we need to analyse). Now, both can be generated by GenePix. This is what I am not able to understand, maybe because I have not worked with GenePix at all. What is the importance of generating both of them? Another question is if I have a GAL file that has some annotations missing, how can I obtain those annotations? From pfern at igc.gulbenkian.pt Tue Nov 23 12:57:44 2004 From: pfern at igc.gulbenkian.pt (Pedro Fernandes) Date: Tue, 23 Nov 2004 17:57:44 -0000 Subject: [BiO BB] Basic Sequence Analysis course in Portugal Message-ID: <0edf01c4d185$ef2e6ff0$962016ac@biocasept> 2004 - The Gulbenkian Training Programme in Bioinformatics Instituto Gulbenkian de Ci?ncia Oeiras PORTUGAL Please be informed that applications for the Bioinformatics Course "Biological Sequence Analysis" (BSA04), that will take place on December 13th - 17th, are open. Deadline for receiving applications, by e-mail or fax, December 2nd. More details on this course: http://central.igc.gulbenkian.pt/bicourses/ and you can find the application forms in MS-Word and RTF formats in: http://central.igc.gulbenkian.pt/bicourses/BSA04/BSA04.html Pedro Fernandes and Isabel Marques Course organizers Unidade de Bioinform?tica Instituto Gulbenkian de Ci?ncia R: Quinta Grande, 6 - Apt. 14 2781-901 OEIRAS Portugal Tel: 351 + 214407914 Fax: 351+ 214407970 Email: bicourses at igc.gulbenkian.pt -------------- next part -------------- An HTML attachment was scrubbed... URL: From MAG at Stowers-Institute.org Tue Nov 30 13:43:17 2004 From: MAG at Stowers-Institute.org (Goel, Manisha) Date: Tue, 30 Nov 2004 12:43:17 -0600 Subject: [BiO BB] Extracting blocks of seq alignment Message-ID: <20041130184327.510BAD1EFC@www.bioinformatics.org> Hi All, I have been looking for an alignment editor/ script that will extract blocks of multiple sequence alignment (when given the residue numbers etc.) from a longer multiple sequence alignment. Any suggetions will be helpful. Thanks, - Manisha Goel -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgollery at unr.edu Tue Nov 30 14:26:14 2004 From: mgollery at unr.edu (Martin Gollery) Date: Tue, 30 Nov 2004 11:26:14 -0800 Subject: [BiO BB] Extracting blocks of seq alignment In-Reply-To: <20041130184327.510BAD1EFC@www.bioinformatics.org> References: <20041130184327.510BAD1EFC@www.bioinformatics.org> Message-ID: <41ACC956.3050404@unr.edu> Hi Manisha, Take a look at BlockMaker at http://blocks.fhcrc.org/blocks/blockmkr/make_blocks.html Marty Goel, Manisha wrote: > Hi All, > > I have been looking for an alignment editor/ script that will extract > blocks of multiple sequence alignment (when given the residue numbers > etc.) from a longer multiple sequence alignment. > > Any suggetions will be helpful. > > Thanks, > - Manisha Goel > > > ------------------------------------------------------------------------ > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ----------- Marty's Law- the number of Bioinformatics acronyms will double every 18 months. From info at mario-albrecht.de Tue Nov 30 14:30:25 2004 From: info at mario-albrecht.de (Mario Albrecht) Date: Tue, 30 Nov 2004 20:30:25 +0100 (MET) Subject: [BiO BB] Re: Extracting blocks of seq alignment Message-ID: You might use ClustalX 1.83: http://www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.html However, be aware of the bug that ClustalX may compute wrong start and end position numbers for the partial block sequences. To my knowledge, this numbering bug has not been fixed yet. But the selected block itself is extracted properly. Mario On Tue, 30 Nov 2004, Goel, Manisha wrote: > Hi All, > > I have been looking for an alignment editor/ script that will extract > blocks of multiple sequence alignment (when given the residue numbers > etc.) from a longer multiple sequence alignment. > Any suggetions will be helpful. > > Thanks, > - Manisha Goel > > From christoph.gille at charite.de Tue Nov 30 16:51:39 2004 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Tue, 30 Nov 2004 22:51:39 +0100 (MET) Subject: [BiO BB] Extracting blocks of seq alignment In-Reply-To: <20041130184327.510BAD1EFC@www.bioinformatics.org> References: <20041130184327.510BAD1EFC@www.bioinformatics.org> Message-ID: <38698.192.168.220.204.1101851499.squirrel@webmail.charite.de> Hi all, STRAP would work as well. 1. import of the Multiple sequ file (MSF or clustalw file). 2. Export and setting the alignment begin and end index. Both is found in the file menu. Warning: requires about 20 min for the intro tutorial. http://www.charite.de/bioinf/strap/ Good look Christoph > Hi All, > > > I have been looking for an alignment editor/ script that will extract > blocks of multiple sequence alignment (when given the residue numbers etc.) > from a longer multiple sequence alignment. Any suggetions will be helpful. > > > Thanks, > - Manisha Goel > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From rich at thevillas.eclipse.co.uk Fri Nov 26 12:40:29 2004 From: rich at thevillas.eclipse.co.uk (rich) Date: Fri, 26 Nov 2004 17:40:29 +0000 Subject: [BiO BB] spatial contact Message-ID: <41A76A8D.2070600@thevillas.eclipse.co.uk> Hi, i'm need to look at specific sites within protein sequence work out they are to sites annotated as BINDING,LIPID,METAL,etc, etc. Any thoughts on what might be a reasonable route to take? thanks From charbit at necker.fr Tue Nov 30 06:06:37 2004 From: charbit at necker.fr (alain charbit) Date: Tue, 30 Nov 2004 12:06:37 +0100 Subject: [BiO BB] strider 1.4 Message-ID: Bonjour, Je souhaiterais obtenir DNA strider version 1.4 pour Mac OSX. COmment dois-je faire, ? qui dois-je le demander ? Merci Alain Charbit From pett at cgl.ucsf.edu Tue Nov 30 14:15:04 2004 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 30 Nov 2004 11:15:04 -0800 Subject: [BiO BB] Re: pdb-l: Extracting blocks of seq alignment In-Reply-To: <200411301843.iAUIhRR23307@postal.sdsc.edu> References: <200411301843.iAUIhRR23307@postal.sdsc.edu> Message-ID: <239BE1EC-4304-11D9-807D-000393CD9B40@cgl.ucsf.edu> Chimera's MultAlignViewer tool allows you to save subsections of an alignment. That feature is described here: http://www.cgl.ucsf.edu/chimera/1.2038/docs/ContributedSoftware/ multalignviewer/multalignviewer.html#editing You can get Chimera itself from: http://www.cgl.ucsf.edu/chimera Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu On Nov 30, 2004, at 10:43 AM, Goel, Manisha wrote: > Hi All, > > I have been looking for an alignment editor/ script that will extract > blocks of multiple sequence alignment (when given the residue numbers > etc.) from a longer multiple sequence alignment. > > Any suggetions will be helpful. > > Thanks, > - Manisha Goel -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1383 bytes Desc: not available URL: From yvan.strahm at med.monash.edu.au Tue Nov 30 17:51:58 2004 From: yvan.strahm at med.monash.edu.au (yvan) Date: Wed, 01 Dec 2004 09:51:58 +1100 Subject: [BiO BB] strider 1.4 In-Reply-To: References: Message-ID: <7110BD55-4322-11D9-976B-000A956ADFE6@med.monash.edu.au> Bonjour, Peut ?tre en suivant cette discussion tu trouveras ton bonheur! http://bioinformatics.org/pipermail/bio_bulletin_board/2004-March/ 001818.html Bonne journ?e! Yvan On 30/11/2004, at 22:06, alain charbit wrote: > Bonjour, > Je souhaiterais obtenir DNA strider version 1.4 pour Mac OSX. COmment > dois-je faire, ? qui dois-je le demander ? > Merci > > Alain Charbit > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From cortig at free.fr Tue Nov 30 20:42:15 2004 From: cortig at free.fr (Corentin =?iso-8859-1?Q?Cras=2DM=E9neur?=) Date: Tue, 30 Nov 2004 19:42:15 -0600 Subject: [BiO BB] strider 1.4 In-Reply-To: References: Message-ID: ? 12:06 +0100 le 11/30/04, alain charbit a ?crit: >Bonjour, >Je souhaiterais obtenir DNA strider version 1.4 >pour Mac OSX. COmment dois-je faire, ? qui >dois-je le demander ? >Merci Il faut faire une demande par courrier: Christian Mark B?t 142 CEA/Saclay 91191 Gif sur Yvette Cedex France La version 1.3 co?tait $200.... N?anmoins, on s'en sort bien mieux (mais au prix d'un peu de travail) en installant EMBOSS. Je viens de compiler la derni?re version sur mon Mac (avec ghoscript, clustalw, primer3 et en chargeant les bases Rebase) et tout tourne parfaitement depuis l'interface utilisateur embossRUNNER 1.2. Il ne me manque pas grand chose de strider. Corentin From boris.steipe at utoronto.ca Tue Nov 30 23:44:55 2004 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Wed, 1 Dec 2004 00:44:55 -0400 Subject: [BiO BB] spatial contact In-Reply-To: <41A76A8D.2070600@thevillas.eclipse.co.uk> Message-ID: On Friday, Nov 26, 2004, at 13:40 Canada/Atlantic, rich wrote: > > Hi, > > i'm need to look at specific sites within protein sequence work out > they are to sites annotated as BINDING,LIPID,METAL,etc, etc. > [...] Look at SMID ( http://smid.blueprint.org/ ) for residue-level annotations of small-molecule binding sites in proteins. Boris