From jaam at qu.edu.qa Mon Feb 3 00:12:54 2003 From: jaam at qu.edu.qa (Dr. Jihad Mohamad Jaam) Date: Mon, 3 Feb 2003 08:12:54 +0300 Subject: [BiO BB] AITOCP'03 References: <20030202214954.98317.qmail@web12304.mail.yahoo.com> Message-ID: <002001c2cb42$ece66f40$8f02a8c0@jaam> ----------------------------------------------------------- ------------------ Please apologize for multiple submission ----------------------------------------------------------- ------------------ CALL FOR PAPERS on "Artificial Intelligence Techniques for Optimization and Constrained Problems" THE 7th WORLD MULTI CONFERENCE ON SYSTEMICS, CYBERNETICS AND INFORMATICS SCI 2003 July 27 - 30, 2003 Orlando, Florida, USA Sheraton World http://www.iiisci.org/sci2003/ You are cordially invited to participate in the "Artificial Intelligence Techniques for Optimization and Constrained Problems" within the area of Artificial intelligence and Constraint Programming in the Seventh World Multi-Conference on Systemics, Cybernetics and Informatics. We would like your invitation to either organize and chair one (or more) session(s) or, present an individual paper on the theory and applications of AI to any topics of your interest. This session aims to present original and previously unpublished research in all fields of Artificial Intelligence, including, but not limited to : - Artificial Intelligence Algorithms - Genetic Algorithms - Neural Networks in AI - Search and Meta-Heuristics for AI - Planning and Scheduling - Constraint-Based Reasoning and Constraint Programming - Distributed AI and Multi-agent Systems All accepted papers will be published in the respective conference proceedings. The best papers will be published in an International Journal. PARTICIPANTS -------------------- Participation of both, researchers and practitioners is strongly encouraged. Papers may be submitted on: research in science and engineering, case studies drawn on professional practice and consulting, and position papers based on large and rich experience gained through executive/managerial practices and decision-making. EXTENDED ABSTRACTS AND PAPER DRAFTS SUBMISSION FORM ---------------------------------------------------------------------------- ------- Extended abstracts or paper drafts should be sent taking into account the following: 1. Major theme of the paper, related to the major themes given above. 2. Paper title. 3. Extended abstract of 500 to 1500 words and/or paper drafts of 2000 to 5000 words, in English. 4. Authors and/or co-authors with names, addresses, telephone and fax numbers, and e-mail addresses. 5. All papers must be written in English, starting with a succinct statement of the problem and the application area, the results achieved, their significance and a comparison with previous work (if any). 6. Extended abstracts or paper drafts should be submitted ONLY on-line to: tounsi at emn.fr and jaam at qu.edu.qa 7. For Further details please contact the organizers or Prof. N CALLAOS (ncallaos at telcel.net.ve) 8. Also, more detailed instructions and On-Line Submission Form can be found on the http://www.iiisci.org/sci2003/ DEADLINES ----------------- February 20, 2003: Submission of extended abstracts (500-1500 words) or paper drafts (2000-5000 words). March 20, 2003: Acceptance notifications. April 20, 2003: Submission of camera-ready papers: hard copies and electronic versions. PAPERS REVIEWING AND PUBLICATION ------------------------------------------------------------- Submitted papers will be reviewed and evaluated for originality, significance, clarity, & soundness. Each paper will be refereed by two researchers in the topical area. Accepted papers, which should not exceed six single-spaced typed pages, will be published by means of paper and electronic proceedings. Best papers will be selected for awards and might be recommended for journal publications. Multiple author books will be published by IIIS based on, the best-invited sessions, the best focus symposia or the best mini-conferences and the topic of the papers. CONFERENCE SESSION FORMAT: -------------------------------------------- There will be three types of presentations: * Invited talks, given by internationally renowned scientists * Regular paper presentations * Poster session ORGANISERS: ------------------- Dr. Jihad M. Jaam Computer Science Department, University of Qatar P.O.Box 2713 Doha, Qatar E-mail: jaam at qu.edu.qa Dr. Mohamed Tounsi Computer Science Departmenet SILR, Ecole Polytechnique de Nantes Rue Christian Pauc, Nantes, 44306, FRANCE E-mail: tounsi at emn.fr or mohamed.tounsi at polytech.univ-nantes.fr From okrslar at molgen.mpg.de Mon Feb 3 11:22:38 2003 From: okrslar at molgen.mpg.de (Martin Okrslar) Date: Mon, 03 Feb 2003 17:22:38 +0100 Subject: [BiO BB] annotation format for protein function Message-ID: <3E3E974E.3070401@molgen.mpg.de> Hi all, does anybody know about formats for annotating the function of a protein? Thanks in advance, Martin From yyjia at pmail.ntu.edu.sg Sun Feb 9 09:00:36 2003 From: yyjia at pmail.ntu.edu.sg (#JIA YIYU#) Date: Sun, 9 Feb 2003 22:00:36 +0800 Subject: [BiO BB] How many peptide residues can form a meaningful/functional protein sequence? Message-ID: <295CB338B611594582D82D9F26AEF7060DC6A5@mail02.student.main.ntu.edu.sg> Hi all, Can anybody here tell me how many peptide residues can form a meaningful/functional protein sequence? Or in other words, what is the shortest protein sequence? Or normally, how many peptide residues form one functional sub unit in a protein molecule? Any helpful reference links and papers will be appreciated very much too! Thanks in advance! Jia Yiyu From jmfreeman at attbi.com Sun Feb 9 12:27:49 2003 From: jmfreeman at attbi.com (James Freeman) Date: Sun, 9 Feb 2003 12:27:49 -0500 Subject: [BiO BB] How many peptide residues can form a meaningful/functional protein sequence? In-Reply-To: <295CB338B611594582D82D9F26AEF7060DC6A5@mail02.student.main.ntu.edu.sg> Message-ID: Hi Jia, If you your definition is broad enough that you can use the very small peptide chain held in the MHC complex's "Jaws of Life" as a possible lower bound of a "meaningful functional protein sequence". Take a look at: http://perso.wanadoo.fr/richard.casimir/autoimmunediseases.htm as a basic reference. James Freeman Bioinformatics Consultant On Sunday, February 9, 2003, at 09:00 AM, #JIA YIYU# wrote: > > Hi all, > > Can anybody here tell me how many peptide residues can form a > meaningful/functional protein sequence? Or in other words, what is the > shortest protein sequence? Or normally, how many peptide residues form > one functional sub unit in a protein molecule? > > Any helpful reference links and papers will be appreciated very much > too! Thanks in advance! > > Jia Yiyu > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From jyu at hsc.wvu.edu Fri Feb 7 15:23:11 2003 From: jyu at hsc.wvu.edu (Jing Yu) Date: Fri, 07 Feb 2003 15:23:11 -0500 Subject: [BiO BB] (no subject) Message-ID: Would you advice me the program in which I can search/obtain the CpG Island Prediction. Thank you, Jing Jie Yu, M.D. From yyjia at pmail.ntu.edu.sg Tue Feb 11 04:04:35 2003 From: yyjia at pmail.ntu.edu.sg (#JIA YIYU#) Date: Tue, 11 Feb 2003 17:04:35 +0800 Subject: [BiO BB] How many peptide residues can form a meaningful/functional protein sequence? Message-ID: <295CB338B611594582D82D9F26AEF7060DC6A7@mail02.student.main.ntu.edu.sg> Hi all, Thanks James for his helps. Now I know at least one decapeptide sequence can affect the function of one particular protein. My motivation to ask my last question is about protein sequence homologous alignment because I doubt whether it is meanful action to align two protein sequence under a very low identity threshhold value for investigating the homologue between them. Clearly, if we have two protein sequences, both of which contain ten amino acid residues. But if the shortest length of one functionable peptide sequence was 4, then it is meanless to investigate the 30% homologue alignment between this two ten length peptide sequences. Maybe my question is naive. But further teaching is appreciated very much! Jia Yiyu From mventura at nutecnet.com.br Tue Feb 11 05:46:35 2003 From: mventura at nutecnet.com.br (Manuel Mateus Ventura) Date: Tue, 11 Feb 2003 07:46:35 -0300 Subject: [BiO BB] (no subject) Message-ID: <3E48D48B.384543AF@nutecnet.com.br> mventura at nutecnet.com.br From Guido.Dieterich at gbf.de Tue Feb 11 06:11:15 2003 From: Guido.Dieterich at gbf.de (Guido Dieterich) Date: 11 Feb 2003 12:11:15 +0100 Subject: [BiO BB] XML Message-ID: <1044961875.8745.22.camel@SB289.gbf-braunschweig.de> Hi, can somebody help me with pdb and xml? Greetings Guido -- Dr. Guido Dieterich Dipl.-Biologe BioComputing SB - Strukturbiologie \==-| GBF - Gesellschaft fuer Biotechnologische Forschung \=/ 0010010010100101110010 German Research Centre for Biotechnology /-\ /-==| 0010100100111101010010 WWW: http://www.gbf.de _/_/_/ _/_/_/ _/_/_/ |==-/ EMAIL: gdi at gbf.de _/ _/ _/ _/ _/ \=/ 0100100100010010010101 _/ _/ _/ _/ /\ Mascheroder Weg 1 _/ _/ _/_/_/ _/_/_/ /=-\ 1101001010100101010101 D-38124 Braunschweig _/ _/ _/ _/ _/ Tel: +(49) 531 6181 745 _/ _/ _/ _/ _/ FAX: +(49) 531 2612 388 _/_/_/ _/_/_/ _/ http://struktur.gbf.de/ Es ist nicht genug, zu wissen, man muss auch anwenden, es ist nicht genug, zu wollen, man muss auch tun. JOHANN WOLFGANG VON GOETHE Deutscher Dichter (1749 - 1832) From landman at scalableinformatics.com Tue Feb 11 09:40:12 2003 From: landman at scalableinformatics.com (Joseph Landman) Date: Tue, 11 Feb 2003 09:40:12 -0500 Subject: [BiO BB] XML In-Reply-To: <1044961875.8745.22.camel@SB289.gbf-braunschweig.de> References: <1044961875.8745.22.camel@SB289.gbf-braunschweig.de> Message-ID: <3E490B4C.1030602@scalableinformatics.com> Hi Guido: Try joining the biodevelopers list at bioinformatics.org if this is a development question. If it is a general use question, please post it here. Joe Guido Dieterich wrote: >Hi, > >can somebody help me with pdb and xml? > >Greetings > >Guido > > -- Joseph Landman, Ph.D Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://scalableinformatics.com phone: +1 734 612 4615 From idoerg at burnham.org Tue Feb 11 21:49:58 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Tue, 11 Feb 2003 18:49:58 -0800 Subject: [BiO BB] How many peptide residues can form a meaningful/functional protein sequence? References: <295CB338B611594582D82D9F26AEF7060DC6A7@mail02.student.main.ntu.edu.sg> Message-ID: <3E49B656.2090609@burnham.org> Hi Jia, It is actually almost meaningless to infer homology by sequence identity. You may quite safely infer homology for proteins longer than 80 aa with a >30% pairwise identity, but there are quite a few homologs with a seqid below that threshold, and for proteins shorter than 80, the %ID is a bad estimator to homology, even as a rough yardstick. More sophisticated statistics should be used, like Monte-Carlo simulations of your alignment procedure. I.e., how good does your alignment score when compared to the mean of a collection of random alignnment scores for proteins of the same length and composition? My favorite is to use blast2 (on NCBI's site) for two peptides. They work out the statistics quite well. For further reading look to: Rost-B, Twilight zone of protein sequence alignments. Protein Eng. 1999 Feb;12(2):85-94. and references therein. Best, Iddo -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://bioinformatics.ljcrf.edu/~iddo #JIA YIYU# wrote: > Hi all, > > Thanks James for his helps. Now I know at least one decapeptide sequence can affect the function of one particular protein. > > My motivation to ask my last question is about protein sequence homologous alignment because I doubt > whether it is meanful action to align two protein sequence under a very low identity threshhold value for investigating the > homologue between them. Clearly, if we have two protein sequences, both of which contain ten amino acid residues. > But if the shortest length of one functionable peptide sequence was 4, then it is meanless > to investigate the 30% homologue alignment between this two ten length peptide sequences. > > Maybe my question is naive. But further teaching is appreciated very much! > > Jia Yiyu > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From mkaut at bu.edu Fri Feb 14 17:16:22 2003 From: mkaut at bu.edu (Maurya Kaut) Date: Fri, 14 Feb 2003 17:16:22 -0500 Subject: [BiO BB] DNAPLOT for linux Message-ID: <3E4D6AB6.3040606@bu.edu> Hello, Does anyone possess a copy of M?ller and Althaus's DNAPLOT alignment software? The ftp directories on dnaplot.de appear to no longer be accessible, and the CGI versions (IMGT, VBASE) are not quite convenient for me. Thanks. Maurya -- <><><><><><><><><><><><><><><><><><> Maurya G. Kaut Gerry Amyloid Research Laboratory Boston University School of Medicine 715 Albany St. K-508 Boston, MA 02118 (617) 638-5389 - Voice <><><><><><><><><><><><><><><><><><> From c.johnston at mail.cryst.bbk.ac.uk Sat Feb 15 18:17:41 2003 From: c.johnston at mail.cryst.bbk.ac.uk (Caroline Johnston) Date: Sat, 15 Feb 2003 23:17:41 +0000 Subject: [BiO BB] (no subject) Message-ID: <1045351061.3e4eca95bc65e@webmail.cryst.bbk.ac.uk> Hi, Does anyone know where I could find out about the Ed Southern vs Affymetrix thing over the GeneChip patents? I've tried a google search and I've looked at the Affy website, but I can't find out how the case concluded. Is it ongoing? If someone could point me in the right direction, I would really appreciate it. Many thanks, Cxx. ------------------------------------------------------------------------------- "Anything that is in the world when you're born is normal and ordinary and just a natural part of the way the world works. Anything that's invented between when you're 15 and 35 is new and exciting and revolutionary and you can probably get a career in it. Anything that's invented after you're 35 is against the natural order of things" Douglas Adams ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/ From sdarfoor at attbi.com Sat Feb 15 20:56:24 2003 From: sdarfoor at attbi.com (Sam Darfoor) Date: Sat, 15 Feb 2003 20:56:24 -0500 Subject: [BiO BB] (no subject) In-Reply-To: <1045351061.3e4eca95bc65e@webmail.cryst.bbk.ac.uk> Message-ID: Caroline This may help. Otherwise you can narrow your search with Google to 'Affymtrix court case' or something similar. Since Affymtrix won on appeal I imagine that would be it, unless they went to the House of Lords. Search the Times' (www.thetimes.co.uk) law case repository too. Hope this helps Sam Affymetrix Wins Crucial Patent Case A British court ruled in April that Oxford Gene Technology controlled a patent central to Affymetrix's main revenue-producing genomic tool products. Now Affymetrix has won the appeal. Adding this win to Affymetrix's first-time profitability, the company is in better shape to deal with growing competition. Email this page Format for printing Become a Fool! Receive via Handheld Reuse/Reprint Related Links Biotechnology Sector Page Biotech reports from Soapbox.com Affymetrix Targets Genomics Biochips Ahoy! Corning Muscles in on DNA Chips Discussion Boards Discussion board Biotechnology By Tom Jacobs (TMF Tom9) November 2, 2000 Shares of genetic tool company Affymetrix (Nasdaq: AFFX) jumped as much as 33% on near-record volume this morning after a major legal victory. A British appeals court decided for Affymetrix in a dispute over key patent licensing covering the company's products. The triumph and a profitable third quarter have bumped the stock more than 50% from an October 20 low of $50.38 (though it's still down from a 52-week high of $163.50). Oxford Versus "Affy" Affymetrix sells GeneChip technology and products -- DNA-testing biochip arrays and the reagents, scanners, and software to process and analyze the genetic information. The patent fight concerned rights to this core technology, providing Affymetrix with a projected $200 million in revenue for calendar year 2000. But in 1999, Edwin Southern, an Oxford professor who founded Oxford Gene Technologies (OGT) and transferred his patents to it, sued Affymetrix for infringement. Affymetrix didn't have a Southern license, but competitors such as Incyte Genomics (Nasdaq: INCY) and Agilent Technologies (NYSE: A) did, conceding the Southern patents' importance. Affy end-runs Oxford Wired Magazine has reported that Affy was about to pay OGT $20 million in June 1998 in a cross-licensing agreement, but backed off. Instead, Affy joined a consortium's deal with OGT licensee Beckman Coulter (NYSE: BEC), a laboratory equipment maker of clinical diagnostics and drug-discovery systems. If OGT refused to give the consortium a Southern patent license, Affy would pay Beckman Coulter $10.9 million for its DNA array business and research -- snaring Beckman's license on sale for 50% off the $20 million prior offer to OGT. Affy ultimately made the purchase. A U.K. trial court ruled in April 2000 that the Beckman Coulter deal was a sham, putting Affy in a jam. Under patent law, the patent holder receives a right to exclude anyone from using her invention without a license -- there is no requirement that she use the patented invention or license anyone. So OGT could have put Affymetrix out of business, though a license was more likely. Now, the U.K. Appeals Court has ruled that Affymetrix owns a license as a result of the Beckman Coulter buy. Who's in the chips? Affymetrix's riding high for now, but others smack their lips at a market estimated to be anywhere from $1 billion in five years to $10 billion in 10 years. Big names such as Motorola (NYSE: MOT), Agilent, Corning (NYSE: GLW), 3M (NYSE: MMM), and Hitachi (NYSE: HIT) are moving in on the genetic testing market with their own biochip array systems, hardware, and software -- apparently unconcerned about Affy's own patents. These companies help commercialize technologies in partnership with smaller innovative biotechs such as Rosetta Inpharmatics (Nasdaq: RSTA), Caliper Technologies (Nasdaq: CALP), Lynx Therapeutics (Nasdaq: LYNX), Hyseq (Nasdaq: HYSQ), and Nanogen (Nasdaq: NGEN). Affy is vigorously defending its patents in U.S. lawsuits with Applied Biosystems (NYSE: PEB), Hyseq, and Incyte, but the Southern patent victory may be bigger than any of these. And Affymetrix isn't sitting on its hands, but deploying its cash to move further into functional genomics. Still, with so many companies grappling for the profit prize for adding value to raw human genetic information, it's a tough call to pick the winners in the volatile genomics tool sector. Your Turn: With the Southern patents out of the way, Affymetrix's stock has gone north. Is there clear sailing ahead? Chime in on the Affymetrix discussion board or the Biotechnology discussion board! > From: Caroline Johnston > Reply-To: bio_bulletin_board at bioinformatics.org > Date: Sat, 15 Feb 2003 23:17:41 +0000 > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] (no subject) > > Ed Southern vs Affymetrix -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeff at bioinformatics.org Tue Feb 18 17:31:43 2003 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Tue, 18 Feb 2003 17:31:43 -0500 Subject: [BiO BB] Bioinformatics.Org at Bio-ITWorld Boston Message-ID: <3E52B44F.4080305@bioinformatics.org> We (Bioinformatics.Org) will have a booth at the Bio-ITWorld Conference & Expo, March 25-27, at the Hynes Convention Center, Boston. It was great being at Bio-ITWorld in Boston last year, as we got to meet literally hundreds of people stopping by our booth to find out about Bioinformatics.Org. This year, members of our Organization can receive either 25% off all conference packages there or a free Bio-ITWorld Discovery Pass, but you must register online using priority code "BNF". Here's the website: http://www.bioitworldexpo.com/ We also have a website where we will post some photos from the show: http://bioinformatics.org/events/2003/bioitworld-boston/ If you're going, don't forget to stop by our booth: #1322! Cheers. Jeff -- J.W. Bizzaro jeff at bioinformatics.org President, Bioinformatics.Org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From sasa at muh.biglobe.ne.jp Sun Feb 23 10:58:57 2003 From: sasa at muh.biglobe.ne.jp (Takeshi Sasayama) Date: Mon, 24 Feb 2003 00:58:57 +0900 Subject: [BiO BB] Database schema Message-ID: Hi All, I want to know about database schema of currently famous databases. Does anyone have information on it? Takeshi Sasayama From daniel.ducat at metalife.de Mon Feb 24 01:46:17 2003 From: daniel.ducat at metalife.de (Daniel Ducat) Date: Mon, 24 Feb 2003 08:46:17 +0200 Subject: [BiO BB] Database schema In-Reply-To: Message-ID: <01b001c2dbd0$6f1c6e90$3c01a8c0@metalife.bg> Hello Takeshi Which databases exactly are of your interest? Daniel Ducat Database Developer Metalife AG e-mail: daniel.ducat at metalife.de Phone: +359 (02) 950-18-04 URL: http://www.metalife.de -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Takeshi Sasayama Sent: Sunday, February 23, 2003 5:59 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Database schema Hi All, I want to know about database schema of currently famous databases. Does anyone have information on it? Takeshi Sasayama _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From lhaifeng at dso.org.sg Mon Feb 24 02:02:48 2003 From: lhaifeng at dso.org.sg (Liu Haifeng) Date: Mon, 24 Feb 2003 15:02:48 +0800 Subject: [BiO BB] Database schema References: <01b001c2dbd0$6f1c6e90$3c01a8c0@metalife.bg> Message-ID: <005501c2dbd2$bdc27c90$706712ac@GENETHON> Hi Takeshi, You may be interested to know the schema of dbSNP in the following url: http://www.ncbi.nlm.nih.gov/SNP/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Haifeng Liu Ph.D., Member of Technical Staff IFL/DS DSO National Laboratories 20 Science Park Drive Singapore 118230 Email: lhaifeng at dso.org.sg Tel: (65) 67728220 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ----- Original Message ----- From: "Daniel Ducat" To: Sent: Monday, February 24, 2003 2:46 PM Subject: RE: [BiO BB] Database schema > Hello Takeshi > > Which databases exactly are of your interest? > > > Daniel Ducat > Database Developer Metalife AG > e-mail: daniel.ducat at metalife.de > Phone: +359 (02) 950-18-04 > URL: http://www.metalife.de > > > -----Original Message----- > From: bio_bulletin_board-admin at bioinformatics.org > [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Takeshi > Sasayama > Sent: Sunday, February 23, 2003 5:59 PM > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] Database schema > > > Hi All, > > I want to know about database schema of currently famous databases. Does > anyone have information on it? > > Takeshi Sasayama > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From sasa at muh.biglobe.ne.jp Mon Feb 24 08:36:53 2003 From: sasa at muh.biglobe.ne.jp (Takeshi Sasayama) Date: Mon, 24 Feb 2003 22:36:53 +0900 Subject: [BiO BB] Database schema In-Reply-To: <005501c2dbd2$bdc27c90$706712ac@GENETHON> Message-ID: Hi Daniel and Haifeng, Thanks for your reply. Hopefully I would like to see kind of an overview which compares schemas of major genome databases. I mean general databases which have for example ID, Name, Description, various Features and Sequence, rather than specific databases. I could download mysql schema from Ensembl site but there is little explanation. There may be little common structure among those major databases, but I would like know outlines, without looking for documents in every site. Thanks Takeshi Sasayama From daniel.ducat at metalife.de Mon Feb 24 09:04:33 2003 From: daniel.ducat at metalife.de (Daniel Ducat) Date: Mon, 24 Feb 2003 16:04:33 +0200 Subject: [BiO BB] Database schema In-Reply-To: Message-ID: <01bd01c2dc0d$aa282b40$3c01a8c0@metalife.bg> Hello Takeshi As far as I know, not all he databases have such kind of overviews. Here I am sending you a list of databases and links, which I think can be helpful for you CluSTr: http://www.ebi.ac.uk/clustr/documentation.html GDB: http://gdb.jst.go.jp/gdb/gdbDataModel.html Interpro: http://www.ebi.ac.uk/interpro/interpro_schema_diagram.pdf http://www.ebi.ac.uk/interpro/dataflow_scheme.html Hope it will help you Regards Daniel Ducat Database Developer Metalife AG e-mail: daniel.ducat at metalife.de Phone: +359 (02) 950-18-04 URL: http://www.metalife.de -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Takeshi Sasayama Sent: Monday, February 24, 2003 3:37 PM To: bio_bulletin_board at bioinformatics.org Subject: RE: [BiO BB] Database schema Hi Daniel and Haifeng, Thanks for your reply. Hopefully I would like to see kind of an overview which compares schemas of major genome databases. I mean general databases which have for example ID, Name, Description, various Features and Sequence, rather than specific databases. I could download mysql schema from Ensembl site but there is little explanation. There may be little common structure among those major databases, but I would like know outlines, without looking for documents in every site. Thanks Takeshi Sasayama _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From junding at yahoo.com Mon Feb 24 13:32:24 2003 From: junding at yahoo.com (Jun Ding) Date: Mon, 24 Feb 2003 10:32:24 -0800 (PST) Subject: [BiO BB] Database schema In-Reply-To: Message-ID: <20030224183224.46521.qmail@web11603.mail.yahoo.com> I'm a database expert, but I'm confused by the term "schema". The schema in database usually mean general database struction. Like in Oracle, schema is like: Tablespace->User->Table->Column. This term also used to refer the relational database design structure of an application database in IT area(Which is tables and the relationships between them). Like the Oracle's HR application database example, you may have at least two tables: employee and department, with the following relationship: one employee must work in one and only one department, one department may have one or more employees. And each table have some attributes(columns), like in employee table, there are employee number, employee name, job title, salary, manager, hiring date, department number ... In department table, there are: department number, department name, location. You can see here, database store two things: entity(database table) and their relationship. There are some IT methods or rules can help you how to translate your requriment into a RDBMS(relational database management system) design. Like E-R modeling. Anyway, if your database schema is refer to the 2nd case, I think you need a database design expert to help you on it. Please feel free to tell me if I missunderstand your question or you have more questions about my email. Regards, Jun --- Takeshi Sasayama wrote: > Hi Daniel and Haifeng, > > Thanks for your reply. > Hopefully I would like to see kind of an overview > which compares schemas of > major genome databases. I mean general databases > which have for example ID, > Name, Description, various Features and Sequence, > rather than specific > databases. I could download mysql schema from > Ensembl site but there is > little explanation. There may be little common > structure among those major > databases, but I would like know outlines, without > looking for documents in > every site. > > Thanks > > Takeshi Sasayama > > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From c.johnston at mail.cryst.bbk.ac.uk Mon Feb 24 19:29:33 2003 From: c.johnston at mail.cryst.bbk.ac.uk (Caroline Johnston) Date: Tue, 25 Feb 2003 00:29:33 +0000 Subject: [BiO BB] Re: Database Schema Message-ID: <1046132973.3e5ab8ed3fca9@webmail.cryst.bbk.ac.uk> Hi, Don't know much about databases, so not sure if this is any help, but try: www.dcs.bbk.ac.uk/research/techreps/ 2002/bbkcs-02-01.pdf which details the development of the PFDB database (contains protein family related data). Includes the UML model and details of its implementation. Cxx ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/ From Suman.Rawat at Dartmouth.EDU Tue Feb 25 12:35:52 2003 From: Suman.Rawat at Dartmouth.EDU (Suman Rawat) Date: 25 Feb 2003 12:35:52 EST Subject: [BiO BB] Re: help on biostat courseware Message-ID: <9697742@newblitzen.Dartmouth.EDU> where can I get the books and tutorial on the USE OF STATISTICAL METHODOLOGY IN BIOINFORMATICS? Thanks Suman From idoerg at burnham.org Tue Feb 25 12:44:21 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Tue, 25 Feb 2003 09:44:21 -0800 Subject: [BiO BB] Re: help on biostat courseware References: <9697742@newblitzen.Dartmouth.EDU> Message-ID: <3E5BAB75.90708@burnham.org> As usual, depends on what exactly you have in mind... A good, basic statistics book I like is "Biostatistical Analysis" /Jerrold Zar. Although nothing to do with bioinformatics, it is a good introductory statistics text. A book which I like specifically for bioinformatics: Statisticsal methods in Bioinformatics: An Introduction/ Warren J. Ewens, Gregory R. Grant. Springer publishing. I. Suman Rawat wrote: > where can I get the books and tutorial on the USE OF STATISTICAL METHODOLOGY IN BIOINFORMATICS? > Thanks > > Suman > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://bioinformatics.ljcrf.edu/~iddo From junding at yahoo.com Tue Feb 25 16:44:22 2003 From: junding at yahoo.com (Jun Ding) Date: Tue, 25 Feb 2003 13:44:22 -0800 (PST) Subject: [BiO BB] Database schema In-Reply-To: Message-ID: <20030225214422.12799.qmail@web11607.mail.yahoo.com> Here's the other annotation database schema that implemented in MySQL. For how to set up it a database in MySQL: 1. In your computer, under [Where_MySQL_installed]\data folder, create a subfolder as your database name, like "Ensembl". 2. Copy all the text files your downloaded(which is database tables) into this folder. 3. Go to [Where_MySQL_installed]\bin folder, type "mysql", like: shell>mysql -u root 4. A MySQL prompt will pop up, type "use your_database_name" in this prompt, like: C:\mysql\bin>mysql -u root Welcome to the MySQL monitor. Commands end with ; or \g. Your MySQL connection id is 1 to server version: 3.23.53-max-nt Type 'help;' or '\h' for help. Type '\c' to clear the buffer. mysql>use Ensembl Database changed mysql> 4. Type "GRANT ALL PRIVILEGES ON *.* TO monty at localhost IDENTIFIED BY 'some_pass' WITH GRANT OPTION;" in mysql>. This will create a user monty with password some_pass in your database and have the full privileges on your database. Like: mysql> GRANT ALL PRIVILEGES ON *.* TO Takeshi at localhost IDENTIFIED BY 'Sasayama' WITH GRANT OPTION; 5. mysql>quit Bye 6. shell>mysql -D your_database_name -u user_name Like: C:\mysql\bin>mysql -D Ensembl -u Takeshi Password: Sasayama Welcome to the MySQL monitor. Commands end with ; or \g. Your MySQL connection id is 3 to server version: 3.23.53-max-nt Type 'help;' or '\h' for help. Type '\c' to clear the buffer. mysql> 7. Then your Ensembl database is set up in your MySQL. use: SHOW DATABASES [LIKE wild] or SHOW [OPEN] TABLES [FROM db_name] [LIKE wild] or SHOW [FULL] COLUMNS FROM tbl_name [FROM db_name] [LIKE wild] commands in mysql> to view database structure and use SELECT command to view data. --- Takeshi Sasayama wrote: > Hi Daniel and Haifeng, > > Thanks for your reply. > Hopefully I would like to see kind of an overview > which compares schemas of > major genome databases. I mean general databases > which have for example ID, > Name, Description, various Features and Sequence, > rather than specific > databases. I could download mysql schema from > Ensembl site but there is > little explanation. There may be little common > structure among those major > databases, but I would like know outlines, without > looking for documents in > every site. > > Thanks > > Takeshi Sasayama > > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From junding at yahoo.com Tue Feb 25 16:51:29 2003 From: junding at yahoo.com (Jun Ding) Date: Tue, 25 Feb 2003 13:51:29 -0800 (PST) Subject: [BiO BB] Database schema In-Reply-To: Message-ID: <20030225215129.63260.qmail@web11603.mail.yahoo.com> An annotation database implenmented in MySQL: http://genome.ucsc.edu/goldenPath/14nov2002/database/ --- Takeshi Sasayama wrote: > Hi Daniel and Haifeng, > > Thanks for your reply. > Hopefully I would like to see kind of an overview > which compares schemas of > major genome databases. I mean general databases > which have for example ID, > Name, Description, various Features and Sequence, > rather than specific > databases. I could download mysql schema from > Ensembl site but there is > little explanation. There may be little common > structure among those major > databases, but I would like know outlines, without > looking for documents in > every site. > > Thanks > > Takeshi Sasayama > > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From feagrawa at wicc.weizmann.ac.il Wed Feb 26 11:46:06 2003 From: feagrawa at wicc.weizmann.ac.il (Himanshu Agrawal) Date: Wed, 26 Feb 2003 18:46:06 +0200 Subject: [BiO BB] PHYSICS BASED TECHNIQUES IN BIOINFORMATICS IN METMBS-03 Message-ID: <200302261646.SAA04749@charm.weizmann.ac.il > SUBJECT: PHYSICS BASED TECHNIQUES IN BIOINFORMATICS IN METMBS'03 Dear Colleagues, The 2003 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS '03) is going to be held Monte Carlo Resort, Las Vegas, Nevada, USA during June 23 - 26, 2003 [see http://metmbs.sdsu.edu/]. The conference covers nearly all engineering and mathematical aspects of biological and medical sciences including the rapidly upcoming area of BIOINFORMATICS. In recent years BIOINFORMATICS has attracted attention of physicists and, in return, been enriched through a number of physics based techniques for addressing various problems related to informatics of various types of biological data. In fact, some abstract and unsolved problems of physics find impressive applications in bioinformatics. The developments, however, are by no means complete and there is enormous scope for development of new and more advanced techniques. The most important advantage of these techniques is that they have a very sound physical footing. More recently, techniques for processing data obtained from various biological chips [gene chips (oligonucleotide arrays/microarrays, cDNA microarrays), protein chips, etc.] have become the focus of attention, e.g., for clustering the data, for extracting gene networks from the data, etc. In this exercise also, the physics based techniques seem to be taking lead very rapidly. These techniques seem to be benefiting from the enormous archive of knowledge of physics accumulated over more than a century. Presently it is necessary and also timely to discuss various aspects of the various physics based bioinformatics techniques in a common forum. Such a discussion is likely to generate new ideas, lead to comparison of different techniques, open up new vistas of development, and lead to improvement in existing techniques. To this end Prof. Valafar (Chair, METBMS'03) has agreed to include a session on "Physics based techniques in Bioinformatics" in METMBS'03. In case you are interested in participating and benefiting from this activity and would like to contribute, send A SHORT ONE PAGE ABSTRACT to feagrawa at wicc.weizmann.ac.il (by March 3, 2003). Email submissions are encouraged (there is no time for any other form of submission). In the subject of the email write: METMBS-03 . The deadline for abstract submission for this session has been extended till Monday March 3, 2003. We may be able to accept some very deserving abstracts till Thursday March 6, 2003 but not after that. Acceptance of late abstracts is not guaranteed and late submissions are strongly discouraged. Other details are as given on the conference web page http://metmbs.sdsu.edu/. For this session we are specifically looking for (but not restricted to) papers related to various aspects of physics based bioinformatics techniques (including methods, results, algorithms, etc). Comparison of physics based techniques to others and physical justifications of techniques that not specifically grounded on physics are also welcome. Young bioinformaticians are especially encouraged to participate. Author of accepted papers will be notified by March 21, 2003. The full version of accepted papers can be up to 7 pages and should be submitted by April 22, 2003. Hoping to see you soon, Best Regards, -Himanshu Agrawal Dept. of Physics of Complex Systems Phone: +972-8-9342475/3960 (Office) Weizmann Institute of Science FAX: +972-8-9344109 (Office) Rehovot 76100, Israel Email: feagrawa at wicc.weizmann.ac.il URL: www.weizmann.ac.il/~feagrawa