From seabi at indiatimes.com Wed Sep 4 07:00:52 2002 From: seabi at indiatimes.com (seabi) Date: Wed, 04 Sep 2002 16:30:52 +0530 Subject: [BiO BB] Now Accepting Nominations for the 2003 Benjamin Franklin Award Message-ID: <200209041048.QAA24320@WS0005.indiatimes.com> bio_bulletin_board at bioinformatics.org wrote: Greetings. These are the nominations we've received so far: Name No. Nominations ========================================== =============== James Kent, UC Santa Cruz 1 Michael Ashburner, Cambridge University 1 We do need to get **2** nominations per candidate, in order for them to appear on the ballot. You are welcome to second the nomination of any person listed above or to nominate someone else. https://bioinformatics.org/franklin/nominate/ (you must be a member and logged in) We would like to begin voting in a couple weeks. It will be the first membership vote at Bioinformatics.Org, and we will be testing our new voting system, being developed by Dmitry Mozzherin. Cheers. Jeff "J.W. Bizzaro" wrote: > > 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 > Bioinformatics.Org that he embodied the best traits of a scientist, and we seek > to honor those who share these virtues. > > The Benjamin Franklin Award is presented annually by Bioinformatics.Org to an > individual who has in his or her practice promoted freedom and openness in the > field of bioinformatics. > > We are now accepting nominations for the 2003 Benjamin Franklin Award from the > members of Bioinformatics.Org. They may be submitted using this form: > > https://bioinformatics.org/franklin/nominate/ > > NOTE: You must be a member and logged in to submit a nomination. > > Please also note the following criteria for nominees: > > 1. There must ultimately be at least two (2) nominations submitted per nominee. > 2. All nominations must be submitted by current members of Bioinformatics.Org. > 3. The nominee must be living. There will be no posthumous awards. > 4. There must be evidence that the nominee has done something to promote freedom > and openness in bioinformatics. > > The list of nominees will then be presented to the individual members of > Bioinformatics.Org for a vote. > > The ceremony for the presentation of the Award is held at the Annual Meeting of > Bioinformatics.Org. It involves a short introduction, the presentation of the > certificate, and the laureate seminar. > > Award home page: > http://bioinformatics.org/franklin/ -- J.W. Bizzaro jeff at bioinformatics.org Director, 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 -- _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board Get Your Private, Free E-mail from Indiatimes at http://email.indiatimes.com Buy Music, Video, CD-ROM, Audio-Books and Music Accessories from http://www.planetm.co.in Change the way you talk. Indiatimes presents "Valufon", Your PC to Phone service with clear voice at rates far less than the normal ISD rates. Go to http://www.valufon.indiatimes.com. Choose your plan. BUY NOW. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Nadia.Bolshakova at cs.tcd.ie Thu Sep 5 09:40:27 2002 From: Nadia.Bolshakova at cs.tcd.ie (Nadia Bolshakova) Date: Thu, 5 Sep 2002 14:40:27 +0100 Subject: [BiO BB] Bioinformatics Conferences Message-ID: <012001c254e1$cb734860$6e26e286@DBNJK90J> Hi there, Could anybody advice me good websites with information on current and future bioinformatics/computer science conferences? Thanks in advance, Nadia. -------------- next part -------------- An HTML attachment was scrubbed... URL: From letondal at pasteur.fr Thu Sep 5 09:47:36 2002 From: letondal at pasteur.fr (Catherine Letondal) Date: Thu, 05 Sep 2002 15:47:36 +0200 Subject: [BiO BB] Bioinformatics Conferences In-Reply-To: Your message of "Thu, 05 Sep 2002 14:40:27 BST." <012001c254e1$cb734860$6e26e286@DBNJK90J> Message-ID: <200209051347.g85DlauY198078@electre.pasteur.fr> "Nadia Bolshakova" wrote: > > Hi there, > > Could anybody advice me good websites with information on current and = > future bioinformatics/computer science conferences? > > Thanks in advance, > Nadia. > You can try this: http://www.pasteur.fr/cgi-bin/biology/bnb_s.pl?bool=et&english=1&rsc=forums,+meetings&bio=bio-computing -- Catherine Letondal -- Pasteur Institute Computing Center From miller at pharm.sunysb.edu Thu Sep 5 10:19:03 2002 From: miller at pharm.sunysb.edu (Holly Miller) Date: Thu, 05 Sep 2002 10:19:03 -0400 Subject: [BiO BB] Bioinformatics Conferences References: <012001c254e1$cb734860$6e26e286@DBNJK90J> Message-ID: <3D7767D7.D473FA63@pharm.sunysb.edu> Hi Nadia, Bioinformatics.Org keeps a calendar of bioinformatics related events: http://bioinformatics.org/calendar/month.php Cheers, Holly Nadia Bolshakova wrote: > Hi there, Could anybody advice me good websites > with information on current and future > bioinformatics/computer science > conferences? Thanks in advance,Nadia. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mhbadri at yahoo.com Thu Sep 5 11:50:35 2002 From: mhbadri at yahoo.com (Mohammad Badri) Date: Thu, 5 Sep 2002 08:50:35 -0700 (PDT) Subject: [BiO BB] Bioinformatics Conferences In-Reply-To: <012001c254e1$cb734860$6e26e286@DBNJK90J> Message-ID: <20020905155035.92284.qmail@web13708.mail.yahoo.com> Hi Dear Miss Nadia Here is some of these conference and seminar I know: --------------------------------------- Bioinformatics Technology Cenference: O'Reilly Bioinformatics Conference Westin Horton Plaza --------------------------------------- The Seventh Annual International Conference on Research in Computational Molecular Biology RECOMB2003 --------------------------------------- The first Asia-Pacific Bioinformatics Conference http://www.fit.qut.edu.au/~chenp/APBC2003 ---------------------------------------- SAC 2003 18th ACM Symposium on applied Computing Bioinformatics Track ----------------------------------------- regards, --Mohammad Badri Director of Bioinformatics Research Center Advanced Information and Communication Technology Center Sharif University of Technology Tehran, Iran email: Badri at Bio-IT.org Tel : (9821) 6006399 Fax : (9821) 6047662 ====================================================== --- Nadia Bolshakova wrote: > Hi there, > > Could anybody advice me good websites with > information on current and future > bioinformatics/computer science conferences? > > Thanks in advance, > Nadia. > __________________________________________________ Do You Yahoo!? Yahoo! Finance - Get real-time stock quotes http://finance.yahoo.com From mhbadri at yahoo.com Thu Sep 5 11:50:48 2002 From: mhbadri at yahoo.com (Mohammad Badri) Date: Thu, 5 Sep 2002 08:50:48 -0700 (PDT) Subject: [BiO BB] Bioinformatics Conferences In-Reply-To: <012001c254e1$cb734860$6e26e286@DBNJK90J> Message-ID: <20020905155048.2118.qmail@web13702.mail.yahoo.com> Hi Dear Miss Nadia Here is some of these conference and seminar I know: --------------------------------------- Bioinformatics Technology Cenference: O'Reilly Bioinformatics Conference Westin Horton Plaza --------------------------------------- The Seventh Annual International Conference on Research in Computational Molecular Biology RECOMB2003 --------------------------------------- The first Asia-Pacific Bioinformatics Conference http://www.fit.qut.edu.au/~chenp/APBC2003 ---------------------------------------- SAC 2003 18th ACM Symposium on applied Computing Bioinformatics Track ----------------------------------------- regards, --Mohammad Badri Director of Bioinformatics Research Center Advanced Information and Communication Technology Center Sharif University of Technology Tehran, Iran email: Badri at Bio-IT.org Tel : (9821) 6006399 Fax : (9821) 6047662 ====================================================== --- Nadia Bolshakova wrote: > Hi there, > > Could anybody advice me good websites with > information on current and future > bioinformatics/computer science conferences? > > Thanks in advance, > Nadia. > __________________________________________________ Do You Yahoo!? Yahoo! Finance - Get real-time stock quotes http://finance.yahoo.com From satagopa at lionbioscience.com Thu Sep 5 13:03:29 2002 From: satagopa at lionbioscience.com (Venkata Satagopam) Date: Thu, 05 Sep 2002 19:03:29 +0200 Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #317 - 5 msgs References: <20020905160110.AAE1F63A9C@www.bioinformatics.org> Message-ID: <3D778E61.9F76BF06@lionbioscience.com> Hello Nadia Bolshakova, There is one bioinformatics conference in germany ECCB 2002, October 6-9, 2002. you can get more details from the following link http://www.zbi.uni-saarland.de/ECCB2002/index2.html Best Regards, venkata ===== Venkata Pardhasaradhi Satagopam, Scientist, Genomics IT Research, Office Address :LION Bioscience AG, Waldhofer Str.98,69123 Heidelberg,GERMANY. Tel: 0049-(0)6221 4038 414 Home Address :Fritz-Frey-Str.8/112.301.01, 69121 HEIDELBERG, GERMANY. Tel:0049-(0)6221 475635 (Mobile):0049-(0)179 7927494 bio_bulletin_board-request at bioinformatics.org wrote: > Send BiO_Bulletin_Board mailing list submissions to > bio_bulletin_board at bioinformatics.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > or, via email, send a message with subject or body 'help' to > bio_bulletin_board-request at bioinformatics.org > > You can reach the person managing the list at > bio_bulletin_board-admin at bioinformatics.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of BiO_Bulletin_Board digest..." > > Today's Topics: > > 1. Bioinformatics Conferences (Nadia Bolshakova) > 2. Re: Bioinformatics Conferences (Catherine Letondal) > 3. Re: Bioinformatics Conferences (Holly Miller) > 4. Re: Bioinformatics Conferences (Mohammad Badri) > 5. Re: Bioinformatics Conferences (Mohammad Badri) > > --__--__-- > > Message: 1 > From: "Nadia Bolshakova" > To: > Date: Thu, 5 Sep 2002 14:40:27 +0100 > Subject: [BiO BB] Bioinformatics Conferences > Reply-To: bio_bulletin_board at bioinformatics.org > > This is a multi-part message in MIME format. > > ------=_NextPart_000_011D_01C254EA.2D249D90 > Content-Type: text/plain; > charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > Hi there, > > Could anybody advice me good websites with information on current and = > future bioinformatics/computer science conferences? > > Thanks in advance, > Nadia. > > ------=_NextPart_000_011D_01C254EA.2D249D90 > Content-Type: text/html; > charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > > > http-equiv=3DContent-Type> > > > > >
>
Hi there,
>
 
>
Could anybody advice me good websites = > with=20 > information on current and future bioinformatics/computer science=20 > conferences?
>
 
>
Thanks in advance,
>
size=3D2>Nadia.
> > ------=_NextPart_000_011D_01C254EA.2D249D90-- > > --__--__-- > > Message: 2 > From: Catherine Letondal > To: bio_bulletin_board at bioinformatics.org > Subject: Re: [BiO BB] Bioinformatics Conferences > Date: Thu, 05 Sep 2002 15:47:36 +0200 > Reply-To: bio_bulletin_board at bioinformatics.org > > "Nadia Bolshakova" wrote: > > > > Hi there, > > > > Could anybody advice me good websites with information on current and = > > future bioinformatics/computer science conferences? > > > > Thanks in advance, > > Nadia. > > > > You can try this: > http://www.pasteur.fr/cgi-bin/biology/bnb_s.pl?bool=et&english=1&rsc=forums,+meetings&bio=bio-computing > > -- > Catherine Letondal -- Pasteur Institute Computing Center > > --__--__-- > > Message: 3 > Date: Thu, 05 Sep 2002 10:19:03 -0400 > From: Holly Miller > Subject: Re: [BiO BB] Bioinformatics Conferences > To: bio_bulletin_board at bioinformatics.org > Reply-To: bio_bulletin_board at bioinformatics.org > > --Boundary_(ID_UvmUPckGITvgLv92UErdpA) > Content-type: text/plain; charset=us-ascii > Content-transfer-encoding: 7BIT > > Hi Nadia, > > Bioinformatics.Org keeps a calendar of > bioinformatics related events: > > http://bioinformatics.org/calendar/month.php > > Cheers, > Holly > > Nadia Bolshakova wrote: > > > Hi there, Could anybody advice me good websites > > with information on current and future > > bioinformatics/computer science > > conferences? Thanks in advance,Nadia. > > --Boundary_(ID_UvmUPckGITvgLv92UErdpA) > Content-type: text/html; charset=us-ascii > Content-transfer-encoding: 7BIT > > > > > Hi Nadia, >

Bioinformatics.Org keeps a calendar of bioinformatics related events: >

http://bioinformatics.org/calendar/month.php >

Cheers, >
Holly >

Nadia Bolshakova wrote: >

> Hi > there, Could anybody > advice me good websites with information on current and future bioinformatics/computer > science conferences? Thanks > in advance,Nadia.
> >
  > > > > --Boundary_(ID_UvmUPckGITvgLv92UErdpA)-- > > --__--__-- > > Message: 4 > Date: Thu, 5 Sep 2002 08:50:35 -0700 (PDT) > From: Mohammad Badri > Subject: Re: [BiO BB] Bioinformatics Conferences > To: bio_bulletin_board at bioinformatics.org > Reply-To: bio_bulletin_board at bioinformatics.org > > Hi > Dear Miss Nadia > > Here is some of these conference and seminar I know: > > --------------------------------------- > Bioinformatics Technology Cenference: > O'Reilly Bioinformatics Conference > Westin Horton Plaza > --------------------------------------- > The Seventh Annual International Conference on > Research in Computational Molecular Biology > RECOMB2003 > --------------------------------------- > The first Asia-Pacific Bioinformatics Conference > http://www.fit.qut.edu.au/~chenp/APBC2003 > ---------------------------------------- > SAC 2003 > 18th ACM Symposium on applied Computing > Bioinformatics Track > ----------------------------------------- > > regards, > > --Mohammad Badri > > Director of Bioinformatics Research Center > Advanced Information and Communication Technology > Center > Sharif University of Technology > Tehran, Iran > email: Badri at Bio-IT.org > Tel : (9821) 6006399 > Fax : (9821) 6047662 > > ====================================================== > --- Nadia Bolshakova > wrote: > > Hi there, > > > > Could anybody advice me good websites with > > information on current and future > > bioinformatics/computer science conferences? > > > > Thanks in advance, > > Nadia. > > > > __________________________________________________ > Do You Yahoo!? > Yahoo! Finance - Get real-time stock quotes > http://finance.yahoo.com > > --__--__-- > > Message: 5 > Date: Thu, 5 Sep 2002 08:50:48 -0700 (PDT) > From: Mohammad Badri > Subject: Re: [BiO BB] Bioinformatics Conferences > To: bio_bulletin_board at bioinformatics.org > Reply-To: bio_bulletin_board at bioinformatics.org > > Hi > Dear Miss Nadia > > Here is some of these conference and seminar I know: > > --------------------------------------- > Bioinformatics Technology Cenference: > O'Reilly Bioinformatics Conference > Westin Horton Plaza > --------------------------------------- > The Seventh Annual International Conference on > Research in Computational Molecular Biology > RECOMB2003 > --------------------------------------- > The first Asia-Pacific Bioinformatics Conference > http://www.fit.qut.edu.au/~chenp/APBC2003 > ---------------------------------------- > SAC 2003 > 18th ACM Symposium on applied Computing > Bioinformatics Track > ----------------------------------------- > > regards, > > --Mohammad Badri > > Director of Bioinformatics Research Center > Advanced Information and Communication Technology > Center > Sharif University of Technology > Tehran, Iran > email: Badri at Bio-IT.org > Tel : (9821) 6006399 > Fax : (9821) 6047662 > > ====================================================== > --- Nadia Bolshakova > wrote: > > Hi there, > > > > Could anybody advice me good websites with > > information on current and future > > bioinformatics/computer science conferences? > > > > Thanks in advance, > > Nadia. > > > > __________________________________________________ > Do You Yahoo!? > Yahoo! Finance - Get real-time stock quotes > http://finance.yahoo.com > > --__--__-- > > _______________________________________________ > 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 vijayendran_vijay at hotmail.com Fri Sep 6 00:36:18 2002 From: vijayendran_vijay at hotmail.com (vijay endran) Date: Fri, 06 Sep 2002 04:36:18 +0000 Subject: [BiO BB] project work: Message-ID: From, C.Vijayendran, II M.Sc Bioinformatics, Department of Botany, Bioinformatics Division, Bharathiar University, Coimbatore- 46. Tamil Nadu. INDIA. hello to all, I did my B.Sc(under graduate) Biotechnology under the same University at Coimbatore. I did a short-term training in vaccine production for Rabies and DTP at Pasture Institute of India, Coonoor, Nilgiris. At the end of my first year of M.Sc(post graduate), I did my summer training at Central Drug Research Institute, Lucknow for a period of two months, entitled Structure Based Drug Design For Cancer X-ray crystallographic structure determination of 10,13-deacetyl-abeo-baccatum IV and molecular docking using Bioinformatics Tools. For my completion of my MS.c Degree I should do a six months training for the partial fulfillment of my Degree. I have a planned activity in which i have described a novel way to design novel anti-inflammatory drugs(chemokines as target) in which I would be pleased to do my project work. If any scientist who his intrested to work in this area or who is working in this area may provide me a chance to work under them for my six months project. So, later on i may forward my planned activity. Thanking you, Yours sincerely, C.Vijayendran. _________________________________________________________________ Join the world?s largest e-mail service with MSN Hotmail. http://www.hotmail.com From virajj at lycos.com Fri Sep 6 03:44:28 2002 From: virajj at lycos.com (vijaya raj) Date: Fri, 06 Sep 2002 03:44:28 -0400 Subject: [BiO BB] project work: Message-ID: dear vijayendran what happened to your ccmb work. hope u get some help from this bioinfo community wishing u all the best.. vijayaraj -- On Fri, 06 Sep 2002 04:36:18 vijay endran wrote: > > >From, >C.Vijayendran, >II M.Sc Bioinformatics, >Department of Botany, >Bioinformatics Division, >Bharathiar University, >Coimbatore- 46. >Tamil Nadu. >INDIA. > > >hello to all, > > >I did my B.Sc(under graduate) Biotechnology under the same University at >Coimbatore. > >I did a short-term training in vaccine production for Rabies and DTP at >Pasture Institute of India, Coonoor, Nilgiris. > >At the end of my first year of M.Sc(post graduate), I did my summer training >at Central Drug Research Institute, Lucknow for a period of two months, >entitled Structure Based Drug Design For Cancer X-ray crystallographic >structure determination of 10,13-deacetyl-abeo-baccatum IV and molecular >docking using Bioinformatics Tools. > >For my completion of my MS.c Degree I should do a six months training for >the partial fulfillment of my Degree. > >I have a planned activity in which i have described a novel way to design >novel anti-inflammatory drugs(chemokines as target) in which I would be >pleased to do my project work. > >If any scientist who his intrested to work in this area or who is working in >this area may provide me a chance to work under them for my six months >project. So, later on i may forward my planned activity. > >Thanking you, > >Yours sincerely, >C.Vijayendran. > > >_________________________________________________________________ >Join the world?s largest e-mail service with MSN Hotmail. >http://www.hotmail.com > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > ___________________________________________________ Communicate with others using Lycos Mail for FREE! http://mail.lycos.com From mllrdm at mail.rnu.tn Fri Sep 6 18:37:45 2002 From: mllrdm at mail.rnu.tn (mllrdm at mail.rnu.tn) Date: Fri, 6 Sep 2002 18:37:45 -0400 Subject: [BiO BB] Bioinformatics Conferences Message-ID: <198950-22002956223745383@M2W028.mail2web.com> Hi Nadia, There is also : Atlantic Symposium on Computational Biology and Genome Information Systems & Technology (CBGI'03) Cary, North Carolina, U.S.A. September 26-30, 2003 Where I'm organizing a session (see below). Best, Mourad. ___________________________________________________________ CALL FOR PAPERS BIOKDD-CBGI'03 Biological Knowledge Discovery and Data Mining Session of Atlantic Symposium on Computational Biology and Genome Information Systems & Technology (CBGI'03) Cary, North Carolina, U.S.A. September 26-30, 2003 With the development of Molecular Biology during the last decades, we arewitnessing an exponential growth of both the volumeand the complexity ofbiological data. The Human Genome Project is providingthe sequence of the 3 billion DNA bases that constitute the human genome.And, consequently, weare provided too with the sequences of about 100,000 proteins. Therefore,we are entering the post-genomic era : After having focused so much efforts on the accumulation of data, we have now to focus as much efforts, and evenmore, on the analysis of these data. This will enable us to learn more about gene expression, protein interactions and other biological mechanisms. Analyzing this huge volume of data is a challenging task because, not only, of its complexity and its multiple numerous correlated factors, but also, because of the continuous evolution of our understanding of the biological mechanisms. Classical approaches of biological data analysis are no longer efficient and produce only a very limited amount of information, compared to the numerous and complex biological mechanisms under study. Actually, these approaches use only a very limited number of parameters, to represent the so-many correlated factors involved in the biological mechanisms. From here comes the necessity to use computer tools and develop new in silico high performance approaches, to support us in the analysis of biological data. And, hence, to help us in our understanding of the correlations that exist between, on one hand, structures and functional patterns of biological sequences, i.e., DNA, RNA and proteins, and, on the other hand, genetic and biochemical mechanisms. Knowledge Discovery and Data mining (KDD) are a response to these new trends : Knowledge discovery is an emerging field where we combine techniques from Algorithmics, Artificial Intelligence, Mathematics and Statistics to deal with the theoretical and practical issues of extracting knowledge, i.e., new concepts or concept relationships, hidden in volumes of raw data. Knowledge discovery offers the capacity to automate complex search and data analysis tasks. We distinguish two types of knowledge discovery systems : verification systems and discovery ones. Verification systems are limited to verifying the users hypothesis, while, discovery ones autonomously predict and explain new knowledge. Biological knowledge discovery process should provide for the selection of the appropriate data mining approaches by taking into account both the characteristics of the biological data and the general requirements of knowledge discovery process. Data mining is one of the pre-processing steps in the knowledge discovery process. It consists in extracting nuggets of information, i.e., pertinent patterns, pattern correlations, estimations or rules, hidden in bodies of data. The extracted information will be used in the verification of hypothesis or the prediction and explanation of knowledge. Biological data mining aims at extracting motifs, functional sites or clustering/classification rules from biological sequences. Numerous techniques suitable for data mining in Molecular Biology are available, however, the selection of ad hoc ones is non-trivial. In our session, we are interested in papers that deal with issues of biological KDD. INSTRUCTIONS TO AUTHORS You are invited to submit a hardcopy or a pdf version of a draft paper, about 4 to 5 pages including figures and references, before May 1, 2003 to the Session Chair: Dr. Mourad Elloumi, Mailing Address: Cite Intilak bloc 6, app. 7, El Menzah 6, 2091 Tunis, Tunisia. Phone : +216 71 233 253 Fax : +216 71 712 093 E.Mail: Mourad.Elloumi at fsegt.rnu.tn BIG : www.groups.yahoo.com/group/bioinformaticsgroup URL : www.MouradElloumi.homestead.com/home.html IMPORTANT DATES May 1, 2003 : Draft papers (about 4 to 5 pages) due June 1, 2003 : Notification of acceptance July 1, 2003 : Camera-Ready papers & Prereg. due September 26 - 30, 2003: CBGI'03 Conference ___________________________________________________________ -------------------------------------------------------------------- mail2web - Check your email from the web at http://mail2web.com/ . -------------- next part -------------- A non-text attachment was scrubbed... Name: Cbgi03.doc Type: application/octet-stream Size: 30208 bytes Desc: Cbgi03.doc URL: From cysu at nlg.csie.ntu.edu.tw Fri Sep 6 22:15:24 2002 From: cysu at nlg.csie.ntu.edu.tw (Chia-Yu Su) Date: Sat, 7 Sep 2002 10:15:24 +0800 Subject: [BiO BB] Bioinformatics Conferences References: <198950-22002956223745383@M2W028.mail2web.com> Message-ID: <005801c25615$59069220$2600a8c0@emily> Hi Mourad, Thanks for your advice. The information is exact what I've been looking for as a Computer Science graduate. Currently, my research is focus on text mining and BioNLP in the domain of biology. I also participate that KDD Cup 2002 task 1 competition this June. Following up with Nadia's question, where can I get the "Call for Paper" information particular about text mining, BioNLP, and Information Extraction in biological or biomedical domain? Thanks a lot. Best regards, Chia-Yu Su From hz5 at njit.edu Sat Sep 7 18:24:31 2002 From: hz5 at njit.edu (hz5 at njit.edu) Date: Sat, 07 Sep 2002 18:24:31 -0400 (EDT) Subject: [BiO BB] How to get the gene sequence efficiently In-Reply-To: <3D331932.6060600@bigfoot.com> References: <3D331932.6060600@bigfoot.com> Message-ID: <1031437471.3d7a7c9f16013@ldap1.njit.edu> Hi, Wu, Entrez has a batch retrieval tool that can be downloaded and run locally with a net connection. If ou want to retrieve Drosophila or yeast, please go to flybase and SGD accordingly. They allow you to specify coordinate for your sequence. Ensemble does a better job in giving flanking sequence for human genes. but hard to specify coordinates. I have a tool that retrieve any region of a specific human gene sequence. You give gene name, coordinates, it retrieve the sequence for you from NCBI. It allows batch retrieval. Like somebody has just retrieved upstream 20kb for 20 sequences, just paste all the gene names, and give coordinate as from "-20000" to "-1", click and wait. Hope this is helpful. ================================================ Haibo Zhang Computational Biology, NJIT & Rutgers University http://afs13.njit.edu/~hz5 ================================================ Quoting Chunlei Wu : > Hi, group, > I have a problem need the help from the group; it may be > easy for the experienced experts here. > I want to get the gene sequences for a list of genes (with > > gene symbol, refseq accession number, etc). I know how to get the gene > > sequence one-by-one from NCBI's genome viewer interface. But I am > wondering how I could get the gene sequences based on gene symbol more > > efficiently and make it suitable to be commited by a script > automatically. That is a very common task when dealing with the genome > > data. I bet there is a good solution already. I hope to get your > suggestion. > > > Thank you in advance. > > > Chunlei Wu > Cancer Genomic Lab > MD Anderson Cancer Center > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From hz5 at njit.edu Sat Sep 7 18:33:48 2002 From: hz5 at njit.edu (hz5 at njit.edu) Date: Sat, 07 Sep 2002 18:33:48 -0400 (EDT) Subject: [BiO BB] How to get the gene sequence efficiently In-Reply-To: <3D344CED.9070004@bigfoot.com> References: <3D344CED.9070004@bigfoot.com> Message-ID: <1031438028.3d7a7ecc6b751@ldap1.njit.edu> Hi Chunlei, these info are specified in the ASN.1 file for the contig at NCBI. you can very easily write a script to extract these infomation out. I am doing it. ======================== Haibo http://afs13.njit.edu/~hz5 hz5 at njit.edu ======================== Quoting Chunlei Wu : > Hi, > Thank you for your valuable suggestions. To make the things > > easier. I am wondering if there is a table available with those info: > > Contig Gene Position > NT_XXXXX gene1 X-XXXXX > NT_XXXXX gene2 XXXXX-XXXXX > ....... > > Thanks again. > > > Chunlei > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > Haibo Zhang Computational Biology, NJIT & Rutgers University http://afs13.njit.edu/~hz5 From hz5 at njit.edu Sat Sep 7 18:37:43 2002 From: hz5 at njit.edu (hz5 at njit.edu) Date: Sat, 07 Sep 2002 18:37:43 -0400 (EDT) Subject: [BiO BB] gene In-Reply-To: <20020718090815.32115.qmail@web9506.mail.yahoo.com> References: <20020718090815.32115.qmail@web9506.mail.yahoo.com> Message-ID: <1031438263.3d7a7fb79c4a1@ldap1.njit.edu> check microarray database? Quoting nikhil gadewal : > Hi group, > > How one can find a presence of a gene in a > particular tissue and level of expression. > > Thank you in advance. > > with regards, > Nikhil > > ===== > NIKHIL. S. GADEWAL * HOME ADDRESS > * # 22, subhshree apts, > Bioinformatics center, * near vijan hospital, > Cancer Research Institute, * college road, > Parel, Mumbai-12. * nashik-422005 > cri3 at soochak.ncst.ernet.in * Phone no. 0253-580490 > Phone no. 4123803 etx. 242 * > > __________________________________________________ > Do You Yahoo!? > Yahoo! Autos - Get free new car price quotes > http://autos.yahoo.com > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > Haibo Zhang Computational Biology, NJIT & Rutgers University http://afs13.njit.edu/~hz5 From hz5 at njit.edu Sat Sep 7 20:15:21 2002 From: hz5 at njit.edu (hz5 at njit.edu) Date: Sat, 07 Sep 2002 20:15:21 -0400 (EDT) Subject: [BiO BB] database for genome... In-Reply-To: References: Message-ID: <1031444121.3d7a96999c47c@ldap1.njit.edu> My professor tell me suffix tree is really helpful! Quoting Tarak Upadhyaya : > I have the genome on my harddrive, and I'm trying to find ways to put it > in > a data structure/database so I can access it faster, or scan through it > > faster. Currently it takes my cpu 128 seconds to go though chromosome 1. > The > way I coded it, however, seems like there is room for optimization. > While I > do that I also want to think of a way to put it in a database so i can > add > more functionality/speed. Maybe something like a quadratic tree? [binary > > tree, but each node branches out into 4 seperate nodes, representing the > > nucliotide bases]. > > -Tarak Upadhyaya > > > > _________________________________________________________________ > Send and receive Hotmail on your mobile device: http://mobile.msn.com > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > Haibo Zhang Computational Biology, NJIT & Rutgers University http://afs13.njit.edu/~hz5 From hz5 at njit.edu Sat Sep 7 20:25:42 2002 From: hz5 at njit.edu (hz5 at njit.edu) Date: Sat, 07 Sep 2002 20:25:42 -0400 (EDT) Subject: [BiO BB] About additivity, I have a question. In-Reply-To: <200207241004.g6OA4iIO087573@mail25.dreamwiz.com> References: <200207241004.g6OA4iIO087573@mail25.dreamwiz.com> Message-ID: <1031444742.3d7a9906976b5@ldap1.njit.edu> additivity is a must for distance matrix. There are four must properties I guess. Quoting ?????? : > Hi, everybody. > > I am working on making a java class for Phylogenetic tree generation, > using Neighbor-joining method. > > While making the class, I read about additivity properties from the > paper and books. > > My question is that if a given distance matrix doesn't hold that > additivity property, than what shall we do and what can be done to avoid > or alleviate that problem. > > I tried to get idea from other program sources, as far as I have been > searching I could not grep any. > > Please help me. :) > > Thanks in advance > Kim, Bong-Hyun from Korea > > > ------------------------------------------------- > DreamWiz Free Mail @ http://www.dreamwiz.com/ > DreamSearch Click the world!!! http://search.dreamwiz.com/ > > Haibo Zhang Computational Biology, NJIT & Rutgers University http://afs13.njit.edu/~hz5 From s_alamelu at yahoo.com Mon Sep 9 11:43:59 2002 From: s_alamelu at yahoo.com (Alamelu Sethuraman) Date: Mon, 9 Sep 2002 08:43:59 -0700 (PDT) Subject: [BiO BB] How to get the gene sequence efficiently In-Reply-To: <1031437471.3d7a7c9f16013@ldap1.njit.edu> Message-ID: <20020909154359.48687.qmail@web11001.mail.yahoo.com> Hai there, I am a molecular biology student. Intrested in computational Biology. I would like any of you to give me some suggestion to start with this computational part. Hope get help. Thanks in advance. Take care, Aruna. --------------------------------- Do You Yahoo!? Yahoo! Finance - Get real-time stock quotes -------------- next part -------------- An HTML attachment was scrubbed... URL: From mllrdm at mail.rnu.tn Tue Sep 10 08:15:33 2002 From: mllrdm at mail.rnu.tn (mllrdm at mail.rnu.tn) Date: Tue, 10 Sep 2002 08:15:33 -0400 Subject: [BiO BB] Bioinformatics Conferences Message-ID: <157240-220029210121533988@M2W092.mail2web.com> Hi Chia-Yu, Try HUGO (HUman Genome Organization) and NCBI (National Center for Biotechnology Information) web sites. Best, Mourad. __________________________________________________ Mailing Address : Dr. Mourad Elloumi, Cite Intilak bloc 6, app. 7, El Menzah 6, 2091 Tunis, Tunisia. Phone : +216 71 233 253 Fax : +216 71 712 093 E.Mail: Mourad.Elloumi at fsegt.rnu.tn BIG : www.groups.yahoo.com/group/bioinformaticsgroup URL : www.MouradElloumi.homestead.com/home.html __________________________________________________ Original Message: ----------------- From: Chia-Yu Su cysu at nlg.csie.ntu.edu.tw Date: Sat, 7 Sep 2002 10:15:24 +0800 To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] Bioinformatics Conferences Hi Mourad, Thanks for your advice. The information is exact what I've been looking for as a Computer Science graduate. Currently, my research is focus on text mining and BioNLP in the domain of biology. I also participate that KDD Cup 2002 task 1 competition this June. Following up with Nadia's question, where can I get the "Call for Paper" information particular about text mining, BioNLP, and Information Extraction in biological or biomedical domain? Thanks a lot. Best regards, Chia-Yu Su _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------------------------------------------------------------- mail2web - Check your email from the web at http://mail2web.com/ . From LSung at law.umaryland.edu Tue Sep 10 18:31:15 2002 From: LSung at law.umaryland.edu (Sung, Lawrence) Date: Tue, 10 Sep 2002 18:31:15 -0400 Subject: [BiO BB] Bioinformatics Conference Message-ID: Dear bio_bulletin_board members: On October 21, 2002, the University of Maryland School of Law will be hosting a conference entitled "At the Crossroads - Public/Private Priorities Concerning Access to Genetic Information." The conference will be held in Rockville, Maryland, and will feature distinguished scientists, lawyers, bioethicists and business leaders, including a luncheon address by Dr. Francis S. Collins, Director of the National Human Genome Research Institute, speaking on issues surrounding bioinformatics and access to genetic data. We invite you to learn more about the conference program contained at the web address (http://www.law.umaryland.edu/pdf_files/conferences/bioinformatics.pdf) along with registration information and to forward this announcement to any members of your organization that might be interested in attending the conference. Thank you for your consideration. Best regards, Lawrence Lawrence M. Sung, Ph.D. Assistant Professor of Law University of Maryland School of Law 500 West Baltimore Street Baltimore, Maryland USA 21201-1786 410.706.1052 (voice) 410.706.2184 (facsimile) lsung at law.umaryland.edu (Internet e-mail) http://www.law.umaryland.edu/fac_lsung.asp (Internet home page) From dfield at ceh.ac.uk Thu Sep 12 17:09:40 2002 From: dfield at ceh.ac.uk (Dawn Field) Date: Thu, 12 Sep 2002 22:09:40 +0100 Subject: [BiO BB] JOBS: 3 bioinformatics/IT posts in UK Message-ID: Jobs Available at the Environmental Genomics Thematic Programme Data Centre at CEH Oxford Bioinformatics/Computing Positions Open (3): Lead Bioinformatician, Data Manager, Linux Developer/System Administrator Location: Oxford Centre for Ecology and Hydrology, Oxford England, UK Background: The ability to scale up from the study of a few genes to complete genomes using developing genomic technologies provides an unprecedented opportunity to ask questions about the molecular mechanisms organisms use to adapt and survive. The recently established Environmental Genomics programme is funded by the NERC at ?16.5M over c. 5 years. The mission of this thematic programme is to use existing & emerging genomic knowledge & technology to gain a better understanding of ecosystem structure & function. This mission will be implemented through projects that address fundamental ecological and evolutionary questions in environmentally important organisms ranging from microbes to vertebrates. As part of the fulfilment of its mission, the Programme is investing in a proactive Data Management Initiative. This Initiative will include the creation of a small, specialised Data Centre at CEH Oxford. Description of Posts We invite applications for three new bioinformatics/computing posts within the Centre. The Centre must collect all data generated by this Thematic Programme and make it available to the research community in an organised and added-value format. The primary focus of the Centre's support and development activities will be on implementing commercial (Silicon Genetics) and open source software to allow the appropriate annotation, interpretation, archiving and mining of microarray and EST data. The Centre is also committed to developing mechanisms for merging evolutionary and ecological meta-data with genomic data. A key part of this informatic strategy will be the development of a bioinformatics-based Linux Distribution that delivers Centre supported software solutions directly to EG funded research groups. The CEH Oxford Centre team will work actively with UK bioinformatics software developers and with EG researchers to implement, create and integrate bioinformatics solutions that will allow the EG community to collect, mine, and exploit its data holdings. Lead Bioinformatician (Ref: CEHOX64) This individual will have an outstanding background in bioinformatics and will co-ordinate the activities of the Centre team, liase most heavily with EG funded researchers, and provide expert consultation on the bioinformatic analysis of microarray and EST sequence data. This individual must be highly skilled in the generation/analysis of microarray data, and will hopefully have extensive experience with the GeneSpring/GeNet/Script Editor software from Silicon Genetics (although this is not absolutely essential). Experience with the maxD transcriptomics software suite and with advanced EST analysis also highly desirable. Data Manager (Ref: CEHOX65) This individual will be a highly skilled database programmer who will have primary responsibility for managing all data holdings and enforcing the programme's meta-data policies. This individual will also have the responsibility of working towards integration of the Centre's Holdings with other NERC and UK databases. Expert knowledge of SQL and experience with the creation, updating, and customisation of Oracle, MySQL, or Postgres databases essential. Linux Developer and System Administrator (Ref: CEHOX66) This individual will possess expert knowledge of Linux (RedHat) and Linux system administration in a multi-user environment, and will be the primary developer of our Bioinformatics-based Linux distribution. This individual should be familiar with the installation and cloning of Linux machines (using SystemImager) and with the development and management of computing clusters. The successful candidates are expected to interact with a large number of external researchers pursuing a wide variety of genomics projects. This team will provide expert scientific and technical consultation to programme members and produce tangibles including open-source informatic pipelines, a community-building web site, and material for a major documentation project and training initiative. All post-holders must be comfortable in a Linux-based computing environment, should have command of at least one programming language (ideally Perl), and will be expected to participate in the development of the Centre's www, programming, and bioinformatics research environments. The Centre Team will be supported by a full time technical administrator. Formal Qualifications The Lead Bioinformatician should have a Ph.D. and relevant research experience in microarray analysis, ideally with a background in evolution and/or ecology. Candidates for the Data Manager and Linux Developer/System Administrator positions should possess either an advanced degree in bioinformatics, computer science, the biological sciences, statistics and/or 2-5 years relevant work experience either in a research lab or in an IT department. Exceptional candidates with very strong IT backgrounds without previous experience in bioinformatics will be considered for these two posts. All team members must possess excellent communications skills and must be willing to travel within the UK as part of the training initiative. Experience with Beowulf cluster computing or GRID highly desirable. Candidates should be able to demonstrate their ability to think and work both independently and as part of a tightly integrated team. Posts will initially be funded for 2 years with the possibility of extension for up to 5 years. For more information about this Thematic Programme please refer to http://www.nerc.ac.uk/funding/thematics/envgen/. For more information about the Centre or the available posts please contact Dr. Dawn Field, Director of the Data Centre, at dfield at ceh.ac.uk or visit the Centre's web site at http://envgen.nox.ac.uk. For an application form please contact Mrs Heather Morris at CEH Oxford on (44) 01865 281630 or by email at HDM at ceh.ac.uk. With the application form you will also receive a more detailed job description and overview of the Data Centre. Please submit a cv and the names of two references with your application. Closing Date: Applications should be submitted by 28 September, 2002. Review of applications will continue until all positions are filled. From Nadia.Bolshakova at cs.tcd.ie Fri Sep 13 07:09:02 2002 From: Nadia.Bolshakova at cs.tcd.ie (Nadia Bolshakova) Date: Fri, 13 Sep 2002 12:09:02 +0100 Subject: [BiO BB] Artificial gene expression data sets Message-ID: <008901c25b15$f82377b0$6e26e286@DBNJK90J> Hello, I am looking for carefully crafted artificial gene expression data. Would anybody give me Internet links where I could downloaded the desired data sets? Thanks, Nadia. -------------- next part -------------- An HTML attachment was scrubbed... URL: From derek at biotechrecruiter.org Sat Sep 14 11:36:26 2002 From: derek at biotechrecruiter.org (Derek Pyper) Date: Sat, 14 Sep 2002 08:36:26 -0700 Subject: [BiO BB] Jobs Message-ID: I am working on a number of position within bioinformatics sales in the US, please call or e-mail me if interested in learning more. Derek Pyper Biotech Recruiters International 2640 Castro Way Sacramento, Ca 95818 derek at biotechrecruiter.org 916-455-7091 916-455-7082 CONFIDENTIALITY STATEMENT: This electronic message contains privileged and confidential information from Biotech Recruiters International. This information is intended solely for the use of the individual(s) or entity(ies) named above. If you are not the intended recipient, be aware that any disclosure, copying, distribution, or use of the contents of this message is prohibited. If you have received this email in error, please notify us immediately by telephone at 916-455-7091 or by email reply. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mhbadri at yahoo.com Sat Sep 14 22:03:43 2002 From: mhbadri at yahoo.com (Mohammad Badri) Date: Sat, 14 Sep 2002 19:03:43 -0700 (PDT) Subject: [BiO BB] bioChemistry in bioinformatics Message-ID: <20020915020343.17227.qmail@web13703.mail.yahoo.com> Hi dear all, Can anyone help me know what is biochemistry role in bioinformatics? thanks, --Mohammad ------------------------------------------------------------------------------------- Director of Bioinformatics Research Group Advanced Information and Communication Technology Center Sharif University of Technology Tehran, Iran email: Badri at Bio-IT.org Badry at ce.sharif.edu Tel : (9821) 6006399 Fax : (9821) 6047662 --------------------------------- Do you Yahoo!? Yahoo! News - Today's headlines -------------- next part -------------- An HTML attachment was scrubbed... URL: From seabi at indiatimes.com Sun Sep 15 04:02:41 2002 From: seabi at indiatimes.com (seabi) Date: Sun, 15 Sep 2002 13:32:41 +0530 Subject: [BiO BB] Artificial gene expression data sets Message-ID: <200209150808.NAA21733@WS0005.indiatimes.com> pl go to www.genomeweb.com may it help u a little. malik bio_bulletin_board at bioinformatics.org wrote: Hello, I am looking for carefully crafted artificial gene expression data. Would anybody give me Internet links where I could downloaded the desired data sets? Thanks, Nadia. Get Your Private, Free E-mail from Indiatimes at http://email.indiatimes.com Buy Music, Video, CD-ROM, Audio-Books and Music Accessories from http://www.planetm.co.in Change the way you talk. Indiatimes presents "Valufon", Your PC to Phone service with clear voice at rates far less than the normal ISD rates. Go to http://www.valufon.indiatimes.com. Choose your plan. BUY NOW. -------------- next part -------------- An HTML attachment was scrubbed... URL: From seabi at indiatimes.com Sun Sep 15 05:18:46 2002 From: seabi at indiatimes.com (seabi) Date: Sun, 15 Sep 2002 14:48:46 +0530 Subject: [BiO BB] bioChemistry in bioinformatics Message-ID: <200209150924.OAA07020@WS0005.indiatimes.com> Mr. badri, see the links of biochem in bioinfo: the following subjects required to read: carbohydrates,proteins,lipids,nucleic acids, enzymes, aminoacid metabolism, carbohydrate meabolism, lipid metabolism, inborn erors of meabolism. more to know go to www.envgen.nox.ac.uk hope u will be satisfied now. malik bio_bulletin_board at bioinformatics.org wrote: Hi dear all, Can anyone help me know what is biochemistry role in bioinformatics? thanks, --Mohammad ------------------------------------------------------------------------------------- Director of Bioinformatics Research Group Advanced Information and Communication Technology Center Sharif University of Technology Tehran, Iran email: Badri at Bio-IT.org Badry at ce.sharif.edu Tel : (9821) 6006399 Fax : (9821) 6047662 Do you Yahoo!? Yahoo! News - Today's headlines Get Your Private, Free E-mail from Indiatimes at http://email.indiatimes.com Buy Music, Video, CD-ROM, Audio-Books and Music Accessories from http://www.planetm.co.in Change the way you talk. Indiatimes presents "Valufon", Your PC to Phone service with clear voice at rates far less than the normal ISD rates. Go to http://www.valufon.indiatimes.com. Choose your plan. BUY NOW. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lilyth at umich.edu Sun Sep 15 19:34:31 2002 From: lilyth at umich.edu (Deanne) Date: Sun, 15 Sep 2002 19:34:31 -0400 (EDT) Subject: [BiO BB] bioChemistry in bioinformatics In-Reply-To: <200209150924.OAA07020@WS0005.indiatimes.com> Message-ID: Mohammad: Biochemistry is necessary to bioinformatics in many respects. Most obviously it is necessary to understanding the systems one is studying. Biochemistry is necessary to understand the mechanisms of systems biology, everything from the mechanisms of signal transduction to enzymatic catalysis. Biochemistry is also necessary to understand how biologists generated the data that bioinformatics studies. It's no good analysing data unless you know how it was produced and under what conditions -- how accurate it might be and what kinds of tests were made. Otherwise you have no idea as to the relevance of your data analysis to the real system you study. ------------ Deanne Taylor, Ph.D. On Sun, 15 Sep 2002, seabi wrote: > Mr. badri, > > > see the links of biochem in bioinfo: > > > the following subjects required to read: carbohydrates,proteins,lipids,nucleic acids, enzymes, aminoacid metabolism, carbohydrate meabolism, lipid metabolism, inborn erors of meabolism. > > > more to know go to www.envgen.nox.ac.uk > > > hope u will be satisfied now. > > > malik > > bio_bulletin_board at bioinformatics.org wrote: > > > > > Hi dear all, > > > Can anyone help me know what is biochemistry role in bioinformatics? > > > thanks, > > > --Mohammad > > > ------------------------------------------------------------------------------------- > > > Director of Bioinformatics Research Group > Advanced Information and Communication Technology Center > Sharif University of Technology > Tehran, Iran > > > email: Badri at Bio-IT.org > Badry at ce.sharif.edu > Tel : (9821) 6006399 > Fax : (9821) 6047662 > > > > > > Do you Yahoo!? > Yahoo! News - Today's headlines > Get Your Private, Free E-mail from Indiatimes at http://email.indiatimes.com > Buy Music, Video, CD-ROM, Audio-Books and Music Accessories from http://www.planetm.co.in > Change the way you talk. Indiatimes presents "Valufon", Your PC to Phone service with clear voice at rates far less than the normal ISD rates. Go to http://www.valufon.indiatimes.com. Choose your plan. BUY NOW. > From vrmmail at yahoo.com Mon Sep 16 14:12:01 2002 From: vrmmail at yahoo.com (MANOJ) Date: Mon, 16 Sep 2002 11:12:01 -0700 (PDT) Subject: [BiO BB] Bioinformatics and PHP In-Reply-To: <20020916160105.7500463AD7@www.bioinformatics.org> Message-ID: <20020916181201.57044.qmail@web40312.mail.yahoo.com> Hello ! Where can I find the resources for PHP programming with context to Bioinformatics ? If yes , then How important is PHP in light of Perl and Python ? Thanks, V.R.Manoj. __________________________________________________ Do you Yahoo!? Yahoo! News - Today's headlines http://news.yahoo.com From ognen_duzlevski at yahoo.com Mon Sep 16 14:20:31 2002 From: ognen_duzlevski at yahoo.com (Ognen Duzlevski) Date: Mon, 16 Sep 2002 11:20:31 -0700 (PDT) Subject: [BiO BB] Bioinformatics and PHP In-Reply-To: <20020916181201.57044.qmail@web40312.mail.yahoo.com> Message-ID: <20020916182031.81701.qmail@web13004.mail.yahoo.com> You should concentrate on new algorithms or on finding a way to improve old ones. Regards, Ognen --- MANOJ wrote: > Hello ! > Where can I find the resources for PHP programming > with context to Bioinformatics ? If yes , then How > important is PHP in light of Perl and Python ? > Thanks, > V.R.Manoj. __________________________________________________ Do you Yahoo!? Yahoo! News - Today's headlines http://news.yahoo.com From Joel.Dudley at asu.edu Mon Sep 16 17:22:07 2002 From: Joel.Dudley at asu.edu (Joel Dudley) Date: Mon, 16 Sep 2002 14:22:07 -0700 Subject: [BiO BB] Bioinformatics and PHP Message-ID: <7D2FB294FA311F4299D03CC8D39043707166F7@mainex5.asu.edu> Although I don't know of any Bioinformatics centric PHP resources I can tell you that I have successfully used PHP for several Bioinformatics projects. With powerful RegEx and interfaces to popular libraries such as Ming, DOM-XML, and GD2 I have never found PHP to be too inflexible or inadequate in Bioinformatics applications. Joel Dudley Faculty Research Associate Arizona State University Center for Evolutionary and Functional Genomics http://lsweb.la.asu.edu/skumar/ -----Original Message----- From: MANOJ [mailto:vrmmail at yahoo.com] Sent: Monday, September 16, 2002 11:12 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Bioinformatics and PHP Hello ! Where can I find the resources for PHP programming with context to Bioinformatics ? If yes , then How important is PHP in light of Perl and Python ? Thanks, V.R.Manoj. __________________________________________________ Do you Yahoo!? Yahoo! News - Today's headlines http://news.yahoo.com _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- An HTML attachment was scrubbed... URL: From seabi at indiatimes.com Wed Sep 18 03:26:26 2002 From: seabi at indiatimes.com (seabi) Date: Wed, 18 Sep 2002 12:56:26 +0530 Subject: [BiO BB] Bioinformatics and PHP Message-ID: <200209180711.MAA30503@WS0005.indiatimes.com> If you require the contents and course of bioinformatics in india contact malik bio_bulletin_board at bioinformatics.org wrote: Hello ! Where can I find the resources for PHP programming with context to Bioinformatics ? If yes , then How important is PHP in light of Perl and Python ? Thanks, V.R.Manoj. __________________________________________________ Do you Yahoo!? Yahoo! News - Today's headlines http://news.yahoo.com _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board Get Your Private, Free E-mail from Indiatimes at http://email.indiatimes.com Buy Music, Video, CD-ROM, Audio-Books and Music Accessories from http://www.planetm.co.in -------------- next part -------------- An HTML attachment was scrubbed... URL: From sbedberg at ucdavis.edu Wed Sep 18 08:07:09 2002 From: sbedberg at ucdavis.edu (Steve Edberg) Date: Wed, 18 Sep 2002 05:07:09 -0700 Subject: [BiO BB] Bioinformatics and PHP In-Reply-To: <20020916181201.57044.qmail@web40312.mail.yahoo.com> References: <20020916181201.57044.qmail@web40312.mail.yahoo.com> Message-ID: I have seen nothing specifically related to PHP and bioinformatics other than the note in the PHP docs for the levenshtein algorithm - http://php.he.net/manual/en/function.levenshtein.php - saying "nobody serious would be doing genetic analysis with PHP." That's because PHP isn't the most efficient language when dealing with large numbers of iterations over long strings. I'd go with compiled Perl or C++, probably. Zend's commercial PHP Encoder and Optimizer may help, though. That being said, I do use PHP for many bioinformatics tasks, since it has so much functionality built in. The database access, string processing and XML tools are very useful. I've written a number of programs in PHP to parse XML annotation files, and process sequences before loading them into a database (both MySQL and PostGreSQL). In these cases, the bulk of the program's time is spent reading/writing text files & databases rather than in computation. PHP is a very convenient tool in that case. To summarize - I, and others in my group have written various pre- and post-processors and viewers in PHP (also Tcl/Tk, Python and Java, depending on the exact tool). The tools we use for analysis - eg; BLAST, ClustalW, etc. - are as far as I know usually written in some C dialect. - steve edberg At 11:12 AM -0700 9/16/02, MANOJ wrote: >Hello ! >Where can I find the resources for PHP programming >with context to Bioinformatics ? If yes , then How >important is PHP in light of Perl and Python ? >Thanks, >V.R.Manoj. > -- +------------------------------------------------------------------------+ | Steve Edberg sbedberg at ucdavis.edu | | University of California, Davis (530)754-9127 | | Programming/Database/SysAdmin http://pgfsun.ucdavis.edu/ | +------------------------------------------------------------------------+ | The end to politics as usual: | | The Monster Raving Loony Party (http://www.omrlp.com/) | +------------------------------------------------------------------------+ From yadhukumar at hotmail.com Wed Sep 18 11:14:14 2002 From: yadhukumar at hotmail.com (yadhu kumar) Date: Wed, 18 Sep 2002 20:44:14 +0530 Subject: [BiO BB] concatenation of nucleic acid or aminoacid Message-ID: Dear Folks, Is there a tool to concatenate nucleic acid or aminoacid sequences esp. the aligned sequences so that at the end of concatenation, one would get the set of proteins or genes sticked together preserving respective alignments. If you know any such programs doing the same please pass on the links and info. Thanks for your time. with regards yadhu @@@@@@@@ \ ^ ^ / -------------------oooO----0--0----Oooo------------------------------ "The ability to perceive or think differently is more important than the knowledge gained" --------------------------------------------------------------------- Mr.Yadhukumar Bioinformatics Unit Department of Microbiology Technical University of Munich Munich , Germany +49 89 28922370 (O) +49 89 21021897 (R) +49 172 8204198 (M) -------------------ooo0-----------0ooo------------------------------- _________________________________________________________________ Send and receive Hotmail on your mobile device: http://mobile.msn.com From pobrien at orbtech.com Wed Sep 18 11:25:25 2002 From: pobrien at orbtech.com (Patrick K. O'Brien) Date: Wed, 18 Sep 2002 10:25:25 -0500 Subject: [BiO BB] Bioinformatics and PHP In-Reply-To: Message-ID: [Steve Edberg] > > To summarize - I, and others in my group have written various pre- > and post-processors and viewers in PHP (also Tcl/Tk, Python and Java, > depending on the exact tool). The tools we use for analysis - eg; > BLAST, ClustalW, etc. - are as far as I know usually written in some > C dialect. Given your experience with the languages you mentioned, I was wondering if you could talk a little about when and why you would choose PHP over the others. In particular, I'm curious to know when you would prefer PHP to Python. (I promise I'm not trying to start a flame war.) Thanks, Pat -- Patrick K. O'Brien Orbtech ----------------------------------------------- "Your source for Python programming expertise." ----------------------------------------------- Web: http://www.orbtech.com/web/pobrien/ Blog: http://www.orbtech.com/blog/pobrien/ Wiki: http://www.orbtech.com/wiki/PatrickOBrien ----------------------------------------------- From Eric_Cervera at frost.com Mon Sep 23 12:24:51 2002 From: Eric_Cervera at frost.com (Eric Cervera) Date: Mon, 23 Sep 2002 11:24:51 -0500 Subject: [BiO BB] Re: Help with an Executive Summit focused on Message-ID: Eric Cervera Public Relations Specialist Executive Summits Division. . . Where Business Does Business! Frost & Sullivan Office # 210-247-2446 Fax # 210-348-1003 http://www.summits.frost.com As a Growth Consulting organization, we enable our clients to meet their Growth Objectives by maximizing the results from their Growth Portfolio and identifying new Growth Opportunities.. ----- Forwarded by Eric Cervera/Mountain_View_CA/US/Frost & Sullivan on 09/23/02 11:27 AM ----- "J.W. Bizzaro" Sent by: jeff at dexter.geoserve.net 09/23/02 11:26 AM To: Eric Cervera cc: Subject: Re: Help with an Executive Summit focused on Hi Eric. You're welcome to send your message to our Bulletin Board: bbb at bioinformatics.org Cheers. Jeff Eric Cervera wrote: > > My name is Eric Cervera. I am the Public Relation > Specialist with Frost & Sullivan. I understand you are the > Newsletter and Website Content Editor for the > Bioinformatics.org. I was wondering I you could lend me a > hand on project I am working on. I am responsible for > evaluating and recruiting speaker and what we call Thought > Leader for our Executive Summits. I have and Executive > Summit coming up focused on Maximizing Outcomes of > Information Technology in Drug Discovery and Development > for which I am currently seeking nominations for the > position of Thought Leader . > > I was wondering if you would not mind sending the message > to you e-newsletter subscriber database. Below is the copy > for the message I am asking you to send. This is not a > sales call. There are no fees associated with being a > Thought Leader. The Thought Leader position is a > prestigious and important role. We will be recognizing > these Thought Leaders for the knowledge and experience. > > Please see the text below and let me know if this is doable. > ============================================================ > ===================================== > I am currently accepting nominations for the prestigious > role of Thought Leader at our high-caliber Executive Summit > focused on: Maximizing Outcomes of Information Technology > in Drug Discovery and Development. > > There are no presentations or speeches required. All I ask > it the Though Leader share his/her insight and perspective > in one of the topics listed below. > > Concurrent Thinktanks, November 5, 2002 > __Thinktank 1: InSilico Drug Discovery > __Thinktank 2: Genomics > __Thinktank 3: Proteomics > > Concurrent Roundtables, November 6, 2002 > __ Roundtable 1: Managing Focused Libraries > __ Roundtable 2: E-Clinical Integration > __ Roundtable 3: Personalized Medicine > > As a Thought Leader there are a number of exclusive > privileges you will enjoy: > Full Complimentary Thought Leader Pass for the Executive > Forum and General Session (Sunday-Wednesday $2095 value) > Your name, title and company in our program brochure and in > our program materials as a participating Thought Leader > Sunday's Executive Golf Tournament on us - we've got the > green fees! > Complimentary daily continental breakfast, lunch and > scheduled receptions and dinners > and more! > > The following is a list of confirmed Thought Leaders: > Francois Nader, MD, MBA, Senior Vice President Medical > Affairs, North America, Aventis Pharmaceutical > Kris Arora, PhD,Vice President, GRA Information Management, > Pharmacia > Sheryl Torr-Brown, PhD, Worldwide Head of Knowledge > Management and Scientific Development, Pfizer > Sangtae Kim, PhD, Vice President and Information Officer, > Lilly Research Laboratories > Mark Cockett, PhD, Executive Director, Applied Genomics, > Bristol-Myers Squibb Company > Charles Jaffe, MD, Ph.D, Director of Medical Informatics, > AstraZeneca Pharmaceuticals > Abdel Laoui, Head Chemoinformatics, Lead Generation > Informatics, Aventis > Nigel Beeley, PhD, Vice President and Chief Chemical > Officer- Arena Pharmaceuticals > Daniel Marshak, PhD, VP and Chief Technology Officer- > Cambrex > Joe Guiles, PhD, Director of High Throughput Chemistry, > Aventis Pharmaceuticals Inc. > Alan Wilson, PhD, Senior Director and Senior Fellow, > PreClinical Development, Pharmacia > Nathan Siemers, Associate Director of Bioinformatics, > Bristol-Myers Squibb Company > Bob Ladner, Sr. VP & Chief Science Officer, Dyax > Steven Gold, PhD, Director of Bioinformatics, CuraGen > Corporation > Thomas Rea, VP Bio-Pharmaceutical Development, Esperion > Therapeutics > Richard Labaurdiniere, PhD, Senior Vice President Research > and Development, Genome Therapeutics > Robert Davis, Executive VP of Drug Discovery, ACADIA > Pharmaceuticals > Lloyd Segal, President & CEO - Caprion Pharmaceuticals > Jurgen Bajorath Ph.D, Senior Director, Computer Aided Drug > Discovery, Albany Molecular Research > Jim Rizzi, Director of Computational Technology- Array > BioPharma > Bruce Keyt, PhD, Vice President Preclinical Development, > Abgenix Inc. > Robin Jackman, VP of Corporate Development, Sequenom > Terrence Chew, MD, SVP, Clinical and Regulatory, Peregrine > Pharmaceutical > David O'Reilly, VP of Corporate Development, Iconix > Pharmaceuticals > Sheila DeWitt, PhD, Vice President Drug Discovery, ArQule > John Saunders, PhD, Vice President of Chemistry, Neucrine > Biosciences, Inc. > > There are a few ground rules: > 1. You must be a Director or above. > 2. You must be from a Pharmaceutical or Biotechnology or > Biopharma company with sales in excess of $10 million/ > year. > 4. Each nominee must go through a brief screening process. > 5. Rules subject to change > > For more information about this event go to > http://www.summits.frost.com > > Please call me at 210-355-4806 or email me at > ecervera at frost.com to nominate yourself or a colleague. > > Best, > Eric > > Eric Cervera > Public Relations Specialist > Executive Summits Division > Frost & Sullivan > Office # 210-247-2446 > Fax # 210-348-1003 > http://www.summits.frost.com -- J.W. Bizzaro jeff at bioinformatics.org Director, 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 -- =============================================================== Frost & Sullivan http://www.frost.com This email, its content and any files transmitted with it are intended solely for the addressee(s) and may be legally privileged and/or confidential. If you are not the intended recipient please delete and contact the sender by return. Messages sent via this medium may be subject to delays, non-delivery and unauthorized alteration. This email has been prepared using information believed by the author to be reliable and accurate, but Frost & Sullivan makes no warranty as to accuracy or completeness. In particular, Frost & Sullivan does not accept responsibility for changes made to this email after it was sent. Any opinions or recommendations expressed herein are solely those of the author. They may be subject to change without notice. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sarathi6 at indiatimes.com Tue Sep 24 02:18:16 2002 From: sarathi6 at indiatimes.com (sarathi6) Date: Tue, 24 Sep 2002 11:48:16 +0530 Subject: [BiO BB] pls tell me that bioinformatics is suitable for electronic engineering Message-ID: <200209240603.LAA22760@WS0005.indiatimes.com> I completed my engineering in Electronics and instrumentation, Now I?m doing my master degree(M.Tech) in bio informatics in sathyabama institute of science and technology. I'm interested in both electronics (robotic engineering , nanotechnology ,or bio sensors) and computers(software development for biology or for robotics in biology field) Dose this course is useful for my interests ? I want to use my electronic knowledge in bio informatics. Kindly suggest some companies which offering projects in bio informatics for electronic students. what i need to do to go for robotics. Get Your Private, Free E-mail from Indiatimes at http://email.indiatimes.com Buy Music, Video, CD-ROM, Audio-Books and Music Accessories from http://www.planetm.co.in -------------- next part -------------- An HTML attachment was scrubbed... URL: From pkeapen at eth.net Tue Sep 24 08:09:25 2002 From: pkeapen at eth.net (Dr. Bell Raj Eapen) Date: Tue, 24 Sep 2002 17:59:25 +0550 Subject: [BiO BB] seeking information regarding PhD in bioinformatics Message-ID: <3d905aa5.bd9.0@punweb01> Sir I am a dermatologist presently working as an Asst professor in a reputed medical college in India with keen interest in bioinformatics. I am presently doing MSc Bioinformatics (Distant Education programme). I wish to do PhD in bioinformatics. My detailed resume is available online at http://www.derminfo.net/resume.htm Please get in touch if you can help. Regards, Dr. Bell R Eapen From synthespian at uol.com.br Tue Sep 24 20:43:04 2002 From: synthespian at uol.com.br (synthespian) Date: 24 Sep 2002 21:43:04 -0300 Subject: [BiO BB] pls tell me that bioinformatics is suitable for electronic engineering In-Reply-To: <200209240603.LAA22760@WS0005.indiatimes.com> References: <200209240603.LAA22760@WS0005.indiatimes.com> Message-ID: <1032914586.17471.29.camel@samadhi> Em Ter, 2002-09-24 ?s 03:18, sarathi6 escreveu: > > > > > > > I completed my engineering in Electronics and instrumentation, Now I?m doing my master degree(M.Tech) in bio informatics in sathyabama institute of science and technology. > > > I'm interested in both electronics (robotic engineering , nanotechnology ,or bio sensors) and computers(software development for biology or for robotics in biology field) > > > Dose this course is useful for my interests ? > > > I want to use my electronic knowledge in bio informatics. Kindly suggest some companies which offering projects in bio informatics for electronic students. > > > what i need to do to go for robotics. You probably want to take a look into the area of sequencer and robots in optical reading of microarray chips. You want the hardware part, not the software which is what concerns Bioinformatics (although the hardware part, too. But that's the Engineer's job, not the Bioinformaticisist - which is precisely what you want). Regs Henry From Joel.Dudley at asu.edu Wed Sep 25 00:04:55 2002 From: Joel.Dudley at asu.edu (Joel Dudley) Date: Tue, 24 Sep 2002 21:04:55 -0700 Subject: [BiO BB] pls tell me that bioinformatics is suitable for elec tronic engineering Message-ID: <7D2FB294FA311F4299D03CC8D390437002D3AC4C@mainex5.asu.edu> You may want to investigate the field of bioengineering. My employer, Arizona State University, has an excellent bioengineering program. You can find information about the ASU program at the following URL: http://www.eas.asu.edu/~bme/ Joel Dudley Faculty Research Associate Arizona State University Center for Evolutionary and Functional Genomics http://lsweb.la.asu.edu/skumar/ -----Original Message----- From: sarathi6 [mailto:sarathi6 at indiatimes.com] Sent: Monday, September 23, 2002 11:18 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] pls tell me that bioinformatics is suitable for electronic engineering I completed my engineering in Electronics and instrumentation, Now I'm doing my master degree(M.Tech) in bio informatics in sathyabama institute of science and technology. I'm interested in both electronics (robotic engineering , nanotechnology ,or bio sensors) and computers(software development for biology or for robotics in biology field) Dose this course is useful for my interests ? I want to use my electronic knowledge in bio informatics. Kindly suggest some companies which offering projects in bio informatics for electronic students. what i need to do to go for robotics. _____ Get Your Private, Free E-mail from Indiatimes at http://email.indiatimes.com Buy Music, Video, CD-ROM, Audio-Books and Music Accessories from http://www.planetm.co.in -------------- next part -------------- An HTML attachment was scrubbed... URL: From seabi at indiatimes.com Wed Sep 25 06:44:49 2002 From: seabi at indiatimes.com (seabi) Date: Wed, 25 Sep 2002 16:14:49 +0530 Subject: [BiO BB] seeking information regarding PhD in bioinformatics Message-ID: <200209251030.QAA09771@WS0005.indiatimes.com> sir, you must have acquire minimum java programming for the course interested in. malik bio_bulletin_board at bioinformatics.org wrote: Sir I am a dermatologist presently working as an Asst professor in a reputed medical college in India with keen interest in bioinformatics. I am presently doing MSc Bioinformatics (Distant Education programme). I wish to do PhD in bioinformatics. My detailed resume is available online at http://www.derminfo.net/resume.htm Please get in touch if you can help. Regards, Dr. Bell R Eapen _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board Get Your Private, Free E-mail from Indiatimes at http://email.indiatimes.com Buy Music, Video, CD-ROM, Audio-Books and Music Accessories from http://www.planetm.co.in -------------- next part -------------- An HTML attachment was scrubbed... URL: From seabi at indiatimes.com Wed Sep 25 06:57:39 2002 From: seabi at indiatimes.com (seabi) Date: Wed, 25 Sep 2002 16:27:39 +0530 Subject: [BiO BB] Bioinformatics and PHP Message-ID: <200209251043.QAA12950@WS0005.indiatimes.com> viewers, kindly help me in finding links offering FREE download of softwares required by our students studying bioinformatics courses. bio_bulletin_board at bioinformatics.org wrote: Hello ! Where can I find the resources for PHP programming with context to Bioinformatics ? If yes , then How important is PHP in light of Perl and Python ? Thanks, V.R.Manoj. __________________________________________________ Do you Yahoo!? Yahoo! News - Today's headlines http://news.yahoo.com _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board Get Your Private, Free E-mail from Indiatimes at http://email.indiatimes.com Buy Music, Video, CD-ROM, Audio-Books and Music Accessories from http://www.planetm.co.in -------------- next part -------------- An HTML attachment was scrubbed... URL: From pfern at igc.gulbenkian.pt Wed Sep 25 14:26:05 2002 From: pfern at igc.gulbenkian.pt (Pedro Fernandes) Date: Wed, 25 Sep 2002 18:26:05 +0000 (GMT) Subject: [BiO BB] Post Graduate course, Portugal Deadline 30 Sept Message-ID: Applications still open, intl students accepted! http://bioinformatics.fc.ul.pt Anyone complying with the requirements can still apply P. Fernandes ----------------------------------------------------------------------------- Pedro Fernandes E-mail: pfern at igc.gulbenkian.pt Instituto Gulbenkian de Ciencia pen - No Portugues da Rede EMBnet Unidade de Bioinformatica URL: http://www.igc.gulbenkian.pt Apartado 14 Telephone (switchboard): +351 21 4407900 2781-901 OEIRAS Telephone (direct) : +351 21 4407912 PORTUGAL Fax : +351 21 4407970 From concini at brenta.dit.unitn.it Thu Sep 26 02:30:02 2002 From: concini at brenta.dit.unitn.it (Michela de Concini) Date: Thu, 26 Sep 2002 08:30:02 +0200 Subject: [BiO BB] call for papers Message-ID: Computational Methods in Systems Biology University of Trento 24-26 February, 2003 Rovereto, Italy www.science.unitn.it/~priami/cmsb.html Molecular biology has until now mainly focussed on individual molecules, on their properties as isolated entities or as complexes in very simple model systems. However, biological molecules in living systems participate in very complex networks, including regulatory networks for gene expression, intracellular metabolic networks and both intra- and intercellular communication networks. Such networks are involved in the maintenance (homeostasis) as well as the differentiation of cellular systems of which we have a very incomplete understanding. Nevertheless, the progress of molecular biology has made possible the detailed description of the components that constitute living systems, notably genes and proteins. Large scale genome sequencing means that we can (at least in principle) delimneate all macromolecular components of a given cellular system, and microarray experiments as well as large scale proteomics will soon give us large amounts of experimental data on gene regulation, molecular interactions and cellular networks. The challenge of the 21st century will be to understand how these individual components integrate to complex systems and the function and evolution of these systems, thus scaling up from molecular biology to systems biology. By combining experimental data with advanced formal theories from computer science, "the formal language for biological systems" to specify dynamic models of interacting molecular entities would be essential for 1. understanding normal behaviour of cellular processes, and how changes may affect the processes and cause disease. It may be possible to correlate genetic properties and symptoms in new and more efficient ways, based on an actual understanding of how various processes interact. 2. Providing predictability and flexibility to academic, pharmaceutical, biotechnology and medical researchers studying gene or protein functions. In particular, it may save time by reducing the number of experiments needed, if inadequate hypotheses could be excluded by computer simulation. Topics of interest include, but are not limited to: Modelling languages for Systems Biology Concurrency theory in Systems Biology Constraint programming in Systems Biology Logical methods in Systems Biology Formal methods to analyse biomolecular systems Quantitative analysis of biomolecular systems Simulation techniques for Systems Biology Case studies IMPORTANT DATES Nov 9, 2002 Submission deadline for papers and demos Nov 30, 2002 Notification of acceptance Dec 16, 2002 Camera-ready version due PROCEEDINGS The proceedings will be published in the Springer LNCS series and will be available at the workshop. SUBMISSION Authors are invited to submit .ps or .pdf original research papers as well as survey or tutorial papers of no more than 12 pages in LNCS format (see http://www.springer.de/comp/lncs/authors.html for instructions) at the address concini at dit.unitn.it For further information please contact us at the addresses [concini,priami]@dit.unitn.it. The papers will pass a peer review process and the accepted ones will appear in the proceedings. INVITED SPEAKERS Ehud Shapiro, Weizmann Institute of Science, Israel To be announced PROGRAMME COMMITTEE Charles Auffray, CNRS, Villejuif (F) Cosima Baldari, Universit? di Siena (I) Alexander Bockmayr, Universit? Henri Poincar?, Nancy (F) Luca Cardelli, Microsoft Research Cambridge (UK) Vincent Danos, Universit? Paris VII (F) Pierpaolo Degano, Universit? di Pisa (I) Fran?ois Fages, INRIA Rocquencourt (F) Drabl?s Finn, , Norwegian University of Science and Technology, Trondheim (N) Monika Heiner, Brandenburg University of Technology at Cottbus - (D) Ina Koch, University of Applied Sciences Berlin, (D). John E. Ladbury, University College London (UK) Patrick Lincoln, SRI (USA) Satoru Miyano, University of Tokyo (JP) Gordon Plotkin, University of Edinburgh (UK) Simon Plyte, Pharmacia Corporation (I) Corrado Priami (CHAIR), Universit? di Trento (I) Aviv Regev, Weizmann Institute of Science (IL) Magali Roux-Rouqui?, BSMI Pasteur Institute (F) Vincent Schachter, Hybrigenics Paris (F) Masaru Tomita, Keio University (JP) Adelinde Uhrmacher, University of Rostock (D) Alfonso Valencia, CNB-CSIC Centro Nacional de Biotecnologia, Cantoblanco Madrid, (E) Olaf Wolkenhauer, UMIST, Manchester (UK) ORGANIZING COMMITTEE Linda Brodo, Michela de Concini, Corrado Priami, Debora Schuch da Rosa Machado -- -------------- next part -------------- An HTML attachment was scrubbed... URL: From potinisamba at yahoo.com Fri Sep 27 11:15:06 2002 From: potinisamba at yahoo.com (SAMBA SIVAPRASAD) Date: Fri, 27 Sep 2002 08:15:06 -0700 (PDT) Subject: [BiO BB] suggestion for duchhen muscular dystrophy Message-ID: <20020927151506.69946.qmail@web21503.mail.yahoo.com> dear sir, > > my son is suffering with duchhen muscular dystrophy desease. > it was identified one year back > his age is 10 years. > CPK count: 5500 > presently, he is able to walk and sit and stand with a > little bit difficulty. he also climbing steps slowly with side railing support. > > sir, shall we get suggestions to get recent > developments/medicines to cure this desease. > > he is regularly doing physio theraphy as directed by doctors > > Thanking you and looking forward for your humble help in > this regard > > P.SAMBA SIVA PRASAD > MIG - 56 > MVP COLONY > VISAKHAPATNAM > ANDRAPRADESH > INDIA > > Phone: 0891 500461 --------------------------------- Do you Yahoo!? New DSL Internet Access from SBC & Yahoo! -------------- next part -------------- An HTML attachment was scrubbed... URL: From drjohn08318 at yahoo.com Fri Sep 27 19:21:34 2002 From: drjohn08318 at yahoo.com (John Hoey) Date: Fri, 27 Sep 2002 16:21:34 -0700 (PDT) Subject: [BiO BB] suggestion for duchhen muscular dystrophy In-Reply-To: <20020927151506.69946.qmail@web21503.mail.yahoo.com> Message-ID: <20020927232134.80150.qmail@web14410.mail.yahoo.com> My Dear Friend: I will pray to my Lord and savior Jesus Christ for his intervention. I strongly suggest you do the same. May Christ bless you, JGH SAMBA SIVAPRASAD wrote: dear sir, > > my son is suffering with duchhen muscular dystrophy desease. > it was identified one year back > his age is 10 years. > CPK count: 5500 > presently, he is able to walk and sit and stand with a > little bit difficulty. he also climbing steps slowly with side railing support. > > sir, shall we get suggestions to get recent > developments/medicines to cure this desease. > > he is regularly doing physio theraphy as directed by doctors > > Thanking you and looking forward for your humble help in > this regard > > P.SAMBA SIVA PRASAD > MIG - 56 > MVP COLONY > VISAKHAPATNAM > ANDRAPRADESH > INDIA > > Phone: 0891 500461 --------------------------------- Do you Yahoo!? New DSL Internet Access from SBC & Yahoo! --------------------------------- Do you Yahoo!? New DSL Internet Access from SBC & Yahoo! -------------- next part -------------- An HTML attachment was scrubbed... URL: From drjohn08318 at yahoo.com Fri Sep 27 19:21:34 2002 From: drjohn08318 at yahoo.com (John Hoey) Date: Fri, 27 Sep 2002 16:21:34 -0700 (PDT) Subject: [BiO BB] suggestion for duchhen muscular dystrophy In-Reply-To: <20020927151506.69946.qmail@web21503.mail.yahoo.com> Message-ID: <20020927232134.80150.qmail@web14410.mail.yahoo.com> My Dear Friend: I will pray to my Lord and savior Jesus Christ for his intervention. I strongly suggest you do the same. May Christ bless you, JGH SAMBA SIVAPRASAD wrote: dear sir, > > my son is suffering with duchhen muscular dystrophy desease. > it was identified one year back > his age is 10 years. > CPK count: 5500 > presently, he is able to walk and sit and stand with a > little bit difficulty. he also climbing steps slowly with side railing support. > > sir, shall we get suggestions to get recent > developments/medicines to cure this desease. > > he is regularly doing physio theraphy as directed by doctors > > Thanking you and looking forward for your humble help in > this regard > > P.SAMBA SIVA PRASAD > MIG - 56 > MVP COLONY > VISAKHAPATNAM > ANDRAPRADESH > INDIA > > Phone: 0891 500461 --------------------------------- Do you Yahoo!? New DSL Internet Access from SBC & Yahoo! --------------------------------- Do you Yahoo!? New DSL Internet Access from SBC & Yahoo! -------------- next part -------------- An HTML attachment was scrubbed... URL: From hyndu007 at hotmail.com Sun Sep 29 17:38:08 2002 From: hyndu007 at hotmail.com (Tarak Upadhyaya) Date: Sun, 29 Sep 2002 17:38:08 -0400 Subject: [BiO BB] Amino Acid Sequence Data Message-ID: Does anybody know where I can get amino acid sequence data with secondary structure predictions and/or known structures that use the 8 DSSP codes? I can't find a database to download data from. I need this information as test sets and training sets for a neural network that I am coding. Thanks in advance! -Tarak Upadhyaya -------------- next part -------------- An HTML attachment was scrubbed... URL: From prasadp77ie at yahoo.ie Mon Sep 30 02:45:22 2002 From: prasadp77ie at yahoo.ie (=?iso-8859-1?q?Prasad=20Phirke?=) Date: Mon, 30 Sep 2002 07:45:22 +0100 (BST) Subject: [BiO BB] pls tell me that bioinformatics is suitable for electronic engineering In-Reply-To: <200209240603.LAA22760@WS0005.indiatimes.com> Message-ID: <20020930064522.65491.qmail@web21003.mail.yahoo.com> Do not go for bioinformatics, instead go for microarray technology. Good Luck Prasad --- sarathi6 wrote: > > > > > > > I completed my engineering in Electronics and > instrumentation, Now I?m doing my master > degree(M.Tech) in bio informatics in sathyabama > institute of science and technology. > > > I'm interested in both electronics (robotic > engineering , nanotechnology ,or bio sensors) and > computers(software development for biology or for > robotics in biology field) > > > Dose this course is useful for my interests ? > > > I want to use my electronic knowledge in bio > informatics. Kindly suggest some companies which > offering projects in bio informatics for > electronic students. > > > what i need to do to go for robotics. > Get Your Private, Free E-mail from Indiatimes at > http://email.indiatimes.com > Buy Music, Video, CD-ROM, Audio-Books and Music > Accessories from http://www.planetm.co.in > ===== Prasad H. PhirkePost - Grad Student,Dublin City University,X1 78, School Of Biotechnology,Glasnevin, Dublin - 9,IRELAND.Mobile - +353 (0)85 721 5335Lab- +353 1 700 5908* __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com From sookjc at yahoo.com Mon Sep 30 16:47:56 2002 From: sookjc at yahoo.com (Sook Jung) Date: Mon, 30 Sep 2002 13:47:56 -0700 (PDT) Subject: [BiO BB] mapmaker data Message-ID: <20020930204756.42824.qmail@web20902.mail.yahoo.com> Hi all, Is there any program/script availble to extract data (loci, linkage group, distance from the end of the linkage group) from a mapmaker output file to load into databases such as oracle? Thanks in advance. ===== Sook Jung, Ph.D. Dept. of Genetics and Biochemistry & CUGI (Clemson University Genomics Institute) Clemson University __________________________________________________ Do you Yahoo!? New DSL Internet Access from SBC & Yahoo! http://sbc.yahoo.com From sbedberg at ucdavis.edu Mon Sep 30 19:50:54 2002 From: sbedberg at ucdavis.edu (Steve Edberg) Date: Mon, 30 Sep 2002 16:50:54 -0700 Subject: [BiO BB] Comments on Apple Xserve? Message-ID: <4.2.2.20020930163028.03075cf0@magenta.ucdavis.edu> Hi - I've been looking at getting one or more external servers to offload heavy duty analyses - mainly BLAST - from my main Sun servers. The Apple XServe looks very attractive (1 RU, 1 or 2 1GHz G4 CPUs, 4 front-loading hotswap drive bays), particularly with the Apple/Genentech optimized NCBI BLAST: http://developer.apple.com/hardware/ve/acgresearch.html There's some info there that says a dualG4 Xserve is ~5x the speed of a 2GHz Pentium4 system, but - considering the source - that might be somewhat biased. Otherwise, I'd go with something like a dual-Athlon 1RU rackmount box running Linux from a vendor like SAG Electronics (www.sagelectronics.com) So, I'm soliciting comments for/against the Apple solution from those who have tried it. Thanks in advance, steve edberg +------------------------------------------------------------------------+ | Steve Edberg sbedberg at ucdavis.edu | | Database/Programming/SysAdmin (530)754-9127 | | University of California, Davis http://pgfsun.ucdavis.edu/ | +---------------------- Gort, Klaatu barada nikto! ----------------------+