From sravan_111 at rediffmail.com Tue Jul 2 09:52:32 2002 From: sravan_111 at rediffmail.com (sravan sravan) Date: 2 Jul 2002 13:52:32 -0000 Subject: [BiO BB] (no subject) Message-ID: <20020702135232.11810.qmail@webmail6.rediffmail.com> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From HurtDP at appliedbiosystems.com Wed Jul 3 04:00:43 2002 From: HurtDP at appliedbiosystems.com (HurtDP at appliedbiosystems.com) Date: Wed, 3 Jul 2002 01:00:43 -0700 Subject: [BiO BB] David P Hurt is out of the office. Message-ID: I will be out of the office starting 06/28/2002 and will not return until 07/15/2002. From ngadewal at yahoo.com Wed Jul 3 06:14:06 2002 From: ngadewal at yahoo.com (nikhil gadewal) Date: Wed, 3 Jul 2002 03:14:06 -0700 (PDT) Subject: [BiO BB] immunogenecity Message-ID: <20020703101406.57656.qmail@web9503.mail.yahoo.com> Hi all members, I want to know some free program available on the internet to find out the immunogenecity of a peptide. Thankyou in advance. 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!? Sign up for SBC Yahoo! Dial - First Month Free http://sbc.yahoo.com From idoerg at cc.huji.ac.il Wed Jul 3 07:59:23 2002 From: idoerg at cc.huji.ac.il (Iddo Friedberg) Date: Wed, 03 Jul 2002 14:59:23 +0300 Subject: [BiO BB] immunogenecity References: <20020703101406.57656.qmail@web9503.mail.yahoo.com> Message-ID: <3D22E71B.6060900@cc.huji.ac.il> Try PreDep: http://bioinfo.md.huji.ac.il/marg/Teppred/mhc-bind/index.html Iddo nikhil gadewal wrote: > Hi all members, > I want to know some free program available on the > internet to find out the immunogenecity of a peptide. > > Thankyou in advance. > > 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!? > Sign up for SBC Yahoo! Dial - First Month Free > http://sbc.yahoo.com > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- Iddo Friedberg | Tel: +972-2-6757374 Dept. of Molecular Genetics and Biotechnology | Fax: +972-2-6784010 The Hebrew University - Hadassah Medical School | idoerg at cc.huji.ac.il POB 12272, Jerusalem 91120 | Israel | http://bioinfo.md.huji.ac.il/marg/people-home/iddo/ From mllrdm at mail.rnu.tn Wed Jul 3 09:15:13 2002 From: mllrdm at mail.rnu.tn (mllrdm at mail.rnu.tn) Date: Wed, 3 Jul 2002 09:15:13 -0400 Subject: [BiO BB] Call for Papers/BIOKDD-CBGI'03 Message-ID: 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 are witnessing an exponential growth of both the volume and the complexity of biological data. The Human Genome Project is providing the sequence of the 3 billion DNA bases that constitute the human genome. And, consequently, we are 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 even more, 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 August 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 August 1, 2003 : Draft papers (about 4 to 5 pages) due September 1, 2003 : Notification of acceptance September 10, 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 paolo at ist.unige.it Thu Jul 4 12:11:05 2002 From: paolo at ist.unige.it (Paolo Romano) Date: Thu, 4 Jul 2002 18:11:05 +0200 (DFT) Subject: [BiO BB] NETTAB 2002 Final Remind Message-ID: <200207041611.SAA22404@ist.unige.it> Dear colleagues, this is the final remind for your participation in the NETTAB 2002 Workshop on "Agents in Bioinformatics" that will be held in Bologna, Italy, from July 12 to 14, 2002. The Workshop site is http://www.nettab.org/2002/ . The Scientific Programme, including a list of invited lectures, oral communications, posters and tutorial, is available at http://www.nettab.org/2002/progr.html . On line registration is still possible at http://www.cs.unibo.it/cgi-bin/nettab2002/ . I hope to see many of you in Bologna. Best regards. Paolo Romano -- Paolo Romano (paolo.romano at istge.it) National Cancer Research Institute Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 Fax: +39-010-5737-295 From raju2002 at lycos.com Fri Jul 5 02:23:44 2002 From: raju2002 at lycos.com (Raju S) Date: Thu, 04 Jul 2002 23:23:44 -0700 Subject: [BiO BB] Gene Expression Tools Message-ID: Hi all members, I want to know some free tools available on the internet to find out the gene expression. Thanks. Regards, Raju ---------------------------- S. Raju India Email : raju2002 at lycos.com ---------------------------- _____________________________________________________ Supercharge your e-mail with a 25MB Inbox, POP3 Access, No Ads and NoTaglines --> LYCOS MAIL PLUS. http://www.mail.lycos.com/brandPage.shtml?pageId=plus From jacobsen at contentsoft.de Fri Jul 5 04:12:32 2002 From: jacobsen at contentsoft.de (jacobsen) Date: Fri, 5 Jul 2002 10:12:32 +0200 Subject: [BiO BB] Gene Expression Tools References: Message-ID: <001f01c223fb$b6e91fd0$6508a8c0@winyobbo> Raju, > I want to know some free tools available on the > internet to find out the gene expression. Have a look here: http://ihome.cuhk.edu.hk/~b400559/arraysoft.html http://faculty.ucr.edu/~tgirke/Links.htm Gerry Jacobsen http://www.contentsoft.de GeneViz v1.1 - free for non-profit academic use From JATP at Lundbeck.com Fri Jul 5 08:47:28 2002 From: JATP at Lundbeck.com (Jan Torleif Pedersen) Date: Fri, 5 Jul 2002 14:47:28 +0200 Subject: [BiO BB] BioPerl : How to configure proxy ebhind firewall Message-ID: <87F9FCA5347BD61198520002A513B4A809C03F@ludk0009.lundbeck.com> Greetings, I am attempting to set up BioPerl and I am wondering how one can set up a general default firewall configuration for all the perl modules. I dont know if this is possible or if this has to be done in all calling scripts independently. If anyone has experience - please let me have a solution.... Regards -- Jan Dr. Jan T. Pedersen Dep. of Molecular Genetics H. Lundbeck A/S Ottiliavej 9, 2500 Valby Denmark email: jatp at lundbeck.com phone: +45 36 30 13 11 FAX : +45 36 30 13 85 From landman at scientificappliance.com Fri Jul 5 09:31:39 2002 From: landman at scientificappliance.com (Joe Landman) Date: 05 Jul 2002 09:31:39 -0400 Subject: [BiO BB] Re: How to configure proxy ebhind firewall Message-ID: <1025875900.17549.21.camel@protein.dtw.macsch.com> I believe that the Bioperl objects all rest on the LWP module, so you should be able to use the proxy configs as indicated on the LWP manpage. That is, if you (under tcsh, others will need transliteration): setenv http_proxy "http://poxy.machine.tld:port/" you might have a working system. It is generally recommended that you read the LWP::UserAgent manpage. Joe -----Forwarded Message----- From: Jan Torleif Pedersen To: 'bio_bulletin_board at bioinformatics.org' Subject: [BiO BB] BioPerl : How to configure proxy ebhind firewall Date: 05 Jul 2002 14:47:28 +0200 Greetings, I am attempting to set up BioPerl and I am wondering how one can set up a general default firewall configuration for all the perl modules. I dont know if this is possible or if this has to be done in all calling scripts independently. If anyone has experience - please let me have a solution.... Regards -- Jan Dr. Jan T. Pedersen Dep. of Molecular Genetics H. Lundbeck A/S Ottiliavej 9, 2500 Valby Denmark email: jatp at lundbeck.com phone: +45 36 30 13 11 FAX : +45 36 30 13 85 _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Joe Landman, email: landman at scientificappliance.com web : http://scientificappliance.com From drjohn08318 at yahoo.com Fri Jul 5 09:58:38 2002 From: drjohn08318 at yahoo.com (John Hoey) Date: Fri, 5 Jul 2002 06:58:38 -0700 (PDT) Subject: [BiO BB] (no subject) Message-ID: <20020705135838.35948.qmail@web14408.mail.yahoo.com> Hello Fellow Members: Please take a look at the following job opportunity. A major California-based pharmaceutical company is recruiting for the following position. Senior Scientist (Ph.D./equivalent) with expertise in molecular & cellular biology techniques to join a group developing the use of antisense technology for functional genomics and therapeutic applications in the fields of inflammation. Qualified applicants will have experience with contemporary methods of both mRNA & protein statement analysis as well as the development of in vitro bio-assays. Candidate will work closely with a multi-disciplinary team responsible for defining the function of novel gene products and validating novel genes as potential drug targets; have experience, and an interest, in signal transduction. If you or one of your colleagues (with a desire and authorization to work in the United States) might be interested in this opportunity, please let me know at your earliest convenience. Any help you can provide would be very much appreciated. Sincerely, John G. Hoey, Ph.D. drjohn08318 at yahoo.com --------------------------------- Do You Yahoo!? New! SBC Yahoo! Dial - 1st Month Free & unlimited access -------------- next part -------------- An HTML attachment was scrubbed... URL: From hz5 at njit.edu Fri Jul 5 12:06:26 2002 From: hz5 at njit.edu (hz5 at njit.edu) Date: Fri, 05 Jul 2002 12:06:26 -0400 (EDT) Subject: [BiO BB] perl script In-Reply-To: <20020609183351.76842.qmail@web8005.mail.in.yahoo.com> References: <20020609183351.76842.qmail@web8005.mail.in.yahoo.com> Message-ID: <1025885186.3d25c402b79da@mailhost.njit.edu> Hi, I have a tool that retrieve genomice context sequence of a gene by giving coordinate. So if you list of genes are for the purpose of retrieving DNA sequences, you can try my tool at http://cag.tolias.phri.org/EZRetrieve use the multiple retrieval tool, just paste all the Ids there. The result also give you information about the ATGC content and chromosome , contig informations and link out to genbank searches. Hope help! Haibo Quoting kiran challapalli : > Hi everyone, > I have text file with list of accession Ids for NcBI > entries. I want to know wether any script available on > the net to retieve the entries and store on my > computer in text format. I want to do the same job > with other databases like swissprot and embl. > I know that atleast NCBI has the facility to upload > the text file. But i want to make the job simpler. > Any suggestions or ideas? > Thanks in advance, > Kiran > > ________________________________________________________________________ > Everything you always wanted to know about cars and bikes,now > at: http://in.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 s_mohta at yahoo.com Mon Jul 8 08:54:15 2002 From: s_mohta at yahoo.com (SAMEER MOHTA) Date: Mon, 8 Jul 2002 05:54:15 -0700 (PDT) Subject: [BiO BB] integration of Bioinformatics program Message-ID: <20020708125415.9311.qmail@web14702.mail.yahoo.com> Hi, I am developing a software solution for integration of Bioinformatics Tools/Components/Analysis Programs like Alignment programs, Gene Finders, Protein Analysis programs etc. I want to know is there any Commercial need for this kind of solution ? If so, what kind of companies/institutions are looking for such solutions or in other terms what is the target segment ? Other question is that, has anybody come across need for such kind of solution, if so then kindly let me know that need. Cheers, Sunny __________________________________________________ Do You Yahoo!? Sign up for SBC Yahoo! Dial - First Month Free http://sbc.yahoo.com From rossini at blindglobe.net Mon Jul 8 10:51:32 2002 From: rossini at blindglobe.net (A.J. Rossini) Date: 08 Jul 2002 07:51:32 -0700 Subject: [BiO BB] integration of Bioinformatics program In-Reply-To: <20020708125415.9311.qmail@web14702.mail.yahoo.com> References: <20020708125415.9311.qmail@web14702.mail.yahoo.com> Message-ID: <87wus6xogb.fsf@jeeves.blindglobe.net> >>>>> "sameer" == SAMEER MOHTA writes: sameer> Hi, sameer> I am developing a software solution for integration of sameer> Bioinformatics Tools/Components/Analysis Programs like sameer> Alignment programs, Gene Finders, Protein Analysis sameer> programs etc. sameer> I want to know is there any Commercial need for this sameer> kind of solution ? If so, what kind of sameer> companies/institutions are looking for such solutions sameer> or in other terms what is the target segment ? sameer> Other question is that, has anybody come across need sameer> for such kind of solution, if so then kindly let me sameer> know that need. Obviously people have. That's why you will be reinventing the wheel again... (there are good number of www-based collections of tools, as well as open-source and commericial "collections). best, -tony -- A.J. Rossini Rsrch. Asst. Prof. of Biostatistics U. of Washington Biostatistics rossini at u.washington.edu FHCRC/SCHARP/HIV Vaccine Trials Net rossini at scharp.org -------------- http://software.biostat.washington.edu/ ---------------- FHCRC: M: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email UW: Th: 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX (my tuesday/wednesday/friday locations are completely unpredictable.) From Joel.Dudley at asu.edu Mon Jul 8 11:41:24 2002 From: Joel.Dudley at asu.edu (Joel Dudley) Date: Mon, 08 Jul 2002 08:41:24 -0700 Subject: [BiO BB] integration of Bioinformatics program Message-ID: <7D2FB294FA311F4299D03CC8D39043707165D6@mainex5.asu.edu> Integration solutions have been addressed and an abundance of papers have been published on the subject. There are many commercial and open-source solutions that address the integration problem. Instead of duplicating efforts why don't you join an open-source tool integration initiative? Joel Dudley Faculty Research Associate Arizona State University Kumar Laboratory of Evolutionary Functional Genomics http://lsweb.la.asu.edu/skumar/ -----Original Message----- From: SAMEER MOHTA [mailto:s_mohta at yahoo.com] Sent: Monday, July 08, 2002 5:54 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] integration of Bioinformatics program Hi, I am developing a software solution for integration of Bioinformatics Tools/Components/Analysis Programs like Alignment programs, Gene Finders, Protein Analysis programs etc. I want to know is there any Commercial need for this kind of solution ? If so, what kind of companies/institutions are looking for such solutions or in other terms what is the target segment ? Other question is that, has anybody come across need for such kind of solution, if so then kindly let me know that need. Cheers, Sunny __________________________________________________ Do You Yahoo!? Sign up for SBC Yahoo! Dial - First Month Free http://sbc.yahoo.com _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- An HTML attachment was scrubbed... URL: From zola at k2.pcz.czest.pl Mon Jul 8 12:32:10 2002 From: zola at k2.pcz.czest.pl (Zola Jaroslaw) Date: Mon, 8 Jul 2002 18:32:10 +0200 (METDST) Subject: [BiO BB] nexus format Message-ID: Hi, I am looking for a complete description of NEXUS file format. I am interested also in C++ or C API for this format. Thanks in advance, jz From Joel.Dudley at asu.edu Mon Jul 8 12:38:33 2002 From: Joel.Dudley at asu.edu (Joel Dudley) Date: Mon, 08 Jul 2002 09:38:33 -0700 Subject: [BiO BB] nexus format Message-ID: <7D2FB294FA311F4299D03CC8D39043707165DB@mainex5.asu.edu> Download the source code for Tree View (http://taxonomy.zoology.gla.ac.uk/rod/treeview.html). Tree view is written in VC++ I believe and provides an algorithm for parsing the Nexus tree file format. Joel Dudley Faculty Research Associate Arizona State University Kumar Laboratory of Evolutionary Functional Genomics http://lsweb.la.asu.edu/skumar/ -----Original Message----- From: Zola Jaroslaw [mailto:zola at k2.pcz.czest.pl] Sent: Monday, July 08, 2002 9:32 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] nexus format Hi, I am looking for a complete description of NEXUS file format. I am interested also in C++ or C API for this format. Thanks in advance, jz _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas at cbs.dtu.dk Mon Jul 8 11:47:10 2002 From: thomas at cbs.dtu.dk (Thomas Sicheritz-Ponten) Date: 08 Jul 2002 17:47:10 +0200 Subject: [BiO BB] nexus format In-Reply-To: References: Message-ID: Zola Jaroslaw writes: > I am looking for a complete description of NEXUS file format. I am > interested also in C++ or C API for this format. I have not found any complete description, but the paup documentation http://paup.csit.fsu.edu/Cmd_ref_v2.pdf together with our local paup guru from sytematic botanics usually covers all my needs for nexus processing in python ... You may or may not find this interresting: Maddison, D. R., Swofford, D. L., Maddison, W. P. 1997. NEXUS: An extensible file format for systematic information. Syst. Biol. 46(4):590-621 http://newfish.mbl.edu/Course/References/PDF/maddisonetal.pdf good luck -thomas (if you really find a complete description of NEXUS, please inform me :-) -- Sicheritz-Ponten Thomas, Ph.D, thomas at biopython.org ( Center for Biological Sequence Analysis \ BioCentrum-DTU, Technical University of Denmark ) CBS: +45 45 252485 Building 208, DK-2800 Lyngby ##-----> Fax: +45 45 931585 http://www.cbs.dtu.dk/thomas ) / ... damn arrow eating trees ... ( From zola at imi.pcz.czest.pl Tue Jul 9 08:14:14 2002 From: zola at imi.pcz.czest.pl (Jaroslaw Zola) Date: Tue, 9 Jul 2002 14:14:14 +0200 (CEST) Subject: [BiO BB] nexus format In-Reply-To: Message-ID: : You may or may not find this interresting: : Maddison, D. R., Swofford, D. L., Maddison, W. P. 1997. : NEXUS: An extensible file format for systematic information. : Syst. Biol. 46(4):590-621 : http://newfish.mbl.edu/Course/References/PDF/maddisonetal.pdf Thank for your help. This paper + extensive source codes analysis should be enough. BTW it is surprising that nexus which is quite popular format is still undocumented. Best regards, jz From newgene at bigfoot.com Mon Jul 15 14:49:22 2002 From: newgene at bigfoot.com (Chunlei Wu) Date: Mon, 15 Jul 2002 13:49:22 -0500 Subject: [BiO BB] How to get the gene sequence efficiently Message-ID: <3D331932.6060600@bigfoot.com> 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 From bio100 at rediffmail.com Tue Jul 16 00:04:04 2002 From: bio100 at rediffmail.com (rajeshwar gongalla) Date: 16 Jul 2002 04:04:04 -0000 Subject: [BiO BB] How to get the gene sequence efficiently Message-ID: <20020716040404.23772.qmail@webmail30.rediffmail.com> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From rbrinkman at xenongenetics.com Tue Jul 16 12:19:59 2002 From: rbrinkman at xenongenetics.com (Ryan Brinkman) Date: Tue, 16 Jul 2002 09:19:59 -0700 Subject: [BiO BB] How to get the gene sequence efficiently Message-ID: This is something that Ensembl is quite good at, and they have already written the scripts (well the Perl API) for you. www.ensembl.org Have a browse through their tutorial, which I believe shows examples of what you need. http://www.ensembl.org/Docs/wiki/html/EnsemblDocs/CodeTutorial.html Message: 1 Date: Mon, 15 Jul 2002 13:49:22 -0500 From: Chunlei Wu To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] How to get the gene sequence efficiently Reply-To: bio_bulletin_board at bioinformatics.org 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 --__--__-- Message: 2 Date: 16 Jul 2002 04:04:04 -0000 From: "rajeshwar gongalla" To: bio_bulletin_board at bioinformatics.org Cc: "Chunlei Wu" Subject: Re: [BiO BB] How to get the gene sequence efficiently Reply-To: bio_bulletin_board at bioinformatics.org Hai, What I understand from your query is to batch entries. which is option avaliable in entrez. what all u need to do is make text file of list of entries and submit as batch. If your question is different, please let me know. or else if you want to retrieve from a genome with different key words try to write a perl program with patteren matching it will do the rest of work. with regards, G.RAJESHWAR SCIENTIST-C FRONTIER LIFE SCIENCE LTD. On Tue, 16 Jul 2002 Chunlei Wu wrote : >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 _________________________________________________________ There is always a better job for you at Monsterindia.com. Go now http://monsterindia.rediff.com/jobs --__--__-- _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board End of BiO_Bulletin_Board Digest ************************************************************************* This email message is confidential and may contain privileged information. Any unauthorized dissemination or copying is strictly prohibited. If you have received this message in error, please delete it and notify us immediately. < XGI > From newgene at bigfoot.com Tue Jul 16 12:42:21 2002 From: newgene at bigfoot.com (Chunlei Wu) Date: Tue, 16 Jul 2002 11:42:21 -0500 Subject: [BiO BB] How to get the gene sequence efficiently Message-ID: <3D344CED.9070004@bigfoot.com> 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 From maureen at mri-fresno.com Tue Jul 16 18:36:05 2002 From: maureen at mri-fresno.com (Maureen McCarthy) Date: Tue, 16 Jul 2002 15:36:05 -0700 Subject: [BiO BB] Oracle DBA with MDL experience needed In-Reply-To: <200207161601.g6GG1h308297@www.bioinformatics.org> Message-ID: Oracle Database Administrator with MDL experience needed immediately for a San Diego biotechnology professional resource company that services bio-tech companies nationally for the design, deployment, management, customization and integration of chemical and biological informatics systems. They specialize in the design and implementation of mission critical software and datebases for biotechnology and pharmaceutical research. If you know an Orcale DBS with MDL experience interested in an excellent career enhancing opportunity in San Diego (must already be eligible to work in the USA without sponsorship)... please contact Maureen McCarthy at maureen at mri-fresno.com. -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of bio_bulletin_board-request at bioinformatics.org Sent: Tuesday, July 16, 2002 9:02 AM To: bio_bulletin_board at bioinformatics.org Subject: BiO_Bulletin_Board digest, Vol 1 #290 - 2 msgs Send BiO_Bulletin_Board mailing list submissions to bio_bulletin_board at bioinformatics.org To subscribe or unsubscribe via the World Wide Web, visit http://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. How to get the gene sequence efficiently (Chunlei Wu) 2. Re: How to get the gene sequence efficiently (rajeshwar gongalla) --__--__-- Message: 1 Date: Mon, 15 Jul 2002 13:49:22 -0500 From: Chunlei Wu To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] How to get the gene sequence efficiently Reply-To: bio_bulletin_board at bioinformatics.org 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 --__--__-- Message: 2 Date: 16 Jul 2002 04:04:04 -0000 From: "rajeshwar gongalla" To: bio_bulletin_board at bioinformatics.org Cc: "Chunlei Wu" Subject: Re: [BiO BB] How to get the gene sequence efficiently Reply-To: bio_bulletin_board at bioinformatics.org Hai, What I understand from your query is to batch entries. which is option avaliable in entrez. what all u need to do is make text file of list of entries and submit as batch. If your question is different, please let me know. or else if you want to retrieve from a genome with different key words try to write a perl program with patteren matching it will do the rest of work. with regards, G.RAJESHWAR SCIENTIST-C FRONTIER LIFE SCIENCE LTD. On Tue, 16 Jul 2002 Chunlei Wu wrote : >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 _________________________________________________________ There is always a better job for you at Monsterindia.com. Go now http://monsterindia.rediff.com/jobs --__--__-- _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board End of BiO_Bulletin_Board Digest From ngadewal at yahoo.com Thu Jul 18 05:08:15 2002 From: ngadewal at yahoo.com (nikhil gadewal) Date: Thu, 18 Jul 2002 02:08:15 -0700 (PDT) Subject: [BiO BB] gene Message-ID: <20020718090815.32115.qmail@web9506.mail.yahoo.com> 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 From pajailwala at yahoo.com Thu Jul 18 09:22:56 2002 From: pajailwala at yahoo.com (Parthav Jailwala) Date: Thu, 18 Jul 2002 06:22:56 -0700 (PDT) Subject: [BiO BB] gene In-Reply-To: <20020718090815.32115.qmail@web9506.mail.yahoo.com> Message-ID: <20020718132256.87881.qmail@web12304.mail.yahoo.com> Hi Nikhil, I guess you question has its answer in 'microarray analysis' of gene expression profiles. You can find several intro on this if you type the keyword 'microarray' in any search engine. After all my interaction with gene expression profiles, i have come to a conclusion that these expression ratios are only a 'snapshot' or a 'freeze' of the expression of sequences at a point in time......actual biological significance can only be derived if you do a temporal analysis of a group of related genes....let me know what you read. Parthav Jailwala Research Assistant Marquette University Milwaukee, WI, USA --- nikhil gadewal wrote: > 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 ===== ---------------------------------------------------------- The less time I have to work with, the more things I get done. ---------------------------------------------------------- Parthav Jailwala Ph : Home : (414) 283 0403 Mobile : (414) 305 9633 __________________________________________________ Do You Yahoo!? Yahoo! Autos - Get free new car price quotes http://autos.yahoo.com From kucej at fns.uniba.sk Thu Jul 18 09:27:55 2002 From: kucej at fns.uniba.sk (Martin Kucej) Date: Thu, 18 Jul 2002 15:27:55 +0200 Subject: [BiO BB] large file uploads Message-ID: <3D36DE7B.24298.6245FD5@localhost> Hi, I made a simple php program, that manages upload of PDF files via http form (http://bioinformatics.org/librarian). It works with Apache, PHP and MySQL. Now, the problem is, that the upload is very buggy with files larger than 1Mb (or even smaller) on Windows machines. And I have no idea why. I setup upload limit in php.ini to 4M, but it makes no difference. When you try to upload large PDF, you immediately obtain error, so it looks like Apache or Windows bug. Or something with network connection. Does anyone have any experience with large file uploads? Thanks a lot, martin Martin Kucej Department of Biochemistry Comenius University Mlynska dolina CH-1 Bratislava 84215 Slovak Republic From tdhoufek at unity.ncsu.edu Thu Jul 18 15:19:01 2002 From: tdhoufek at unity.ncsu.edu (T.D. Houfek) Date: Thu, 18 Jul 2002 15:19:01 -0400 (EDT) Subject: [BiO BB] large file uploads In-Reply-To: <3D36DE7B.24298.6245FD5@localhost> Message-ID: I believe there are two separate variables you need to adjust to allow the upload of large files. One is the upload_max_filesize you've already discovered. The other is called post_max_size. It specifies an upper limit on the amount of data allowed in any POST operation -- including file uploads. So if upload_max_filesize=2G and post_max_size=8M, you will still only be able to upload file of size <=8M. At least, that's what I read the other day. I've never actually tried it. So let me know if it works, eh? T.D. T.D. Houfek system administrator / bioinformatics developer Fungal Genomics Laboratory Center for Integrated Fungal Research (CIFR) North Carolina State University ph: (919)513-0025 e: tdhoufek at unity.ncsu.edu On Thu, 18 Jul 2002, Martin Kucej wrote: > Hi, > > I made a simple php program, that manages upload of PDF files via http form (http://bioinformatics.org/librarian). It works with Apache, PHP > and MySQL. > > Now, the problem is, that the upload is very buggy with files larger than 1Mb (or even smaller) on Windows machines. And I have no idea why. > > I setup upload limit in php.ini to 4M, but it makes no difference. When you try to upload large PDF, you immediately obtain error, so it > looks like Apache or Windows bug. Or something with network connection. > > Does anyone have any experience with large file uploads? > > Thanks a lot, > martin > > Martin Kucej > Department of Biochemistry > Comenius University > Ml~ynska dolina CH-1 > Bratislava 84215 > Slovak Republic > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From jay at ccmb.res.in Sat Jul 20 04:38:17 2002 From: jay at ccmb.res.in (jayanti) Date: Sat, 20 Jul 2002 15:08:17 +0630 Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #293 - 1 msg In-Reply-To: <200207191601.g6JG15n27298@www.bioinformatics.org> Message-ID: Hi all, am jai, a newcomer to the group ......I find the group very active & its great to b part of the group.....I just wanted to know if there is a monitor kind of person for the group...to whom V can write some suggestions....... Hoping to hear soon, Bye, Jai. From goswami at archeanit.com Sat Jul 20 05:44:33 2002 From: goswami at archeanit.com (Satyakam Goswami) Date: Sat, 20 Jul 2002 15:14:33 +0530 (IST) Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #293 - 1 msg In-Reply-To: References: <200207191601.g6JG15n27298@www.bioinformatics.org> Message-ID: <1847.203.115.124.59.1027158273.squirrel@mail.archeanit.com> jayanti said: > Hi all, > am jai, a newcomer to the group ......I find the group very you are most welcome > active & its great to b part of the group.....I just wanted to know if >there is a monitor kind of person for the group...to whom V can write some > suggestions....... you can post all u r suggestions directly to the list it will be taken care of ,hope your stay here will be a memorable one. cheers S.Goswami -- Archean Infotech Victory Vihar,Himayatnagar,Hyderabad 500029 India,www.archeanit.com Ph:3228666,6570704,3228674 Mobile:091-40-6550145 ----------------------------------------- This email was sent using SquirrelMail. "Webmail for nuts!" http://squirrelmail.org/ From hyndu007 at hotmail.com Sun Jul 21 14:25:29 2002 From: hyndu007 at hotmail.com (Tarak Upadhyaya) Date: Sun, 21 Jul 2002 14:25:29 -0400 Subject: [BiO BB] database for genome... Message-ID: 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 From landman at scientificappliance.com Sun Jul 21 20:59:26 2002 From: landman at scientificappliance.com (Joe Landman) Date: 21 Jul 2002 20:59:26 -0400 Subject: [BiO BB] database for genome... In-Reply-To: References: Message-ID: <1027299566.11347.40.camel@protein.dtw.macsch.com> Hi Tarak: A few points. First, we have a nice biodevelopers group that has many people who might be able to help with this. Second, from a program performance point of view, what is your code doing? Are you simply looking at how long it takes to read in the chromosome, or are you doing processing in the loop as well? Is the data in a flat file (somewhat implied)? A database will not speed up read access unless you need to look at small specific subsets of the data. Before building other data structures, a better understanding of what the code is doing, how it is doing it, and so forth are in order. Please describe it in greater detail, and post it to biodevelopers. Joe On Sun, 2002-07-21 at 14:25, Tarak Upadhyaya wrote: > 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 -- Joe Landman, email: landman at scientificappliance.com web : http://scientificappliance.com From pjminicuci at yahoo.com Mon Jul 22 17:29:04 2002 From: pjminicuci at yahoo.com (phyllis minicuci) Date: Mon, 22 Jul 2002 14:29:04 -0700 (PDT) Subject: [BiO BB] Paracel Message-ID: <20020722212904.2374.qmail@web9908.mail.yahoo.com> Does anyone have experience with the Paracel line of products? If so what has been your experience with the products and company (ease of use, support...ie- Genematcher, BlastMachine etc.). Thanks Phil pjminicuci at yahoo.com __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com From raju2002 at lycos.com Tue Jul 23 10:08:28 2002 From: raju2002 at lycos.com (Raju S) Date: Tue, 23 Jul 2002 07:08:28 -0700 Subject: [BiO BB] Paracel Message-ID: Hi all, If anybody knows about gene expression tools (free download) then please let me know. Thanks & regards, S. Raju Chennai, India Email : raju2002 at lycos.com _____________________________________________________ Supercharge your e-mail with a 25MB Inbox, POP3 Access, No Ads and NoTaglines --> LYCOS MAIL PLUS. http://www.mail.lycos.com/brandPage.shtml?pageId=plus From jacobsen at contentsoft.de Tue Jul 23 10:45:33 2002 From: jacobsen at contentsoft.de (jacobsen) Date: Tue, 23 Jul 2002 16:45:33 +0200 Subject: [BiO BB] Paracel References: Message-ID: <13a801c23257$997b8db0$6508a8c0@winyobbo> > If anybody knows about gene expression tools (free download) then please let me know. Some quite comprehensive overview: http://ihome.cuhk.edu.hk/~b400559/arraysoft.html Gerry Jacobsen Contentsoft AG http://www.contentsoft.de GeneViz - Free for academic non-profit research > > Thanks & regards, > > S. Raju > Chennai, India > Email : raju2002 at lycos.com > > > _____________________________________________________ > Supercharge your e-mail with a 25MB Inbox, POP3 Access, No Ads > and NoTaglines --> LYCOS MAIL PLUS. > http://www.mail.lycos.com/brandPage.shtml?pageId=plus > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From joshuabhkim at dreamwiz.com Wed Jul 24 06:04:44 2002 From: joshuabhkim at dreamwiz.com (=?EUC-KR?B?sei6wMf2?=) Date: Wed, 24 Jul 2002 19:04:44 +0900 (KST) Subject: [BiO BB] About additivity, I have a question. Message-ID: <200207241004.g6OA4iIO087573@mail25.dreamwiz.com> 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/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From bioinfo at biosystemsconsulting.com Wed Jul 24 22:14:22 2002 From: bioinfo at biosystemsconsulting.com (bioinfo) Date: Wed, 24 Jul 2002 22:14:22 -0400 Subject: [BiO BB] TimeLogic Message-ID: <000001c23380$ff0f2bd0$befea8c0@raptor> Hello, Does anyone have any experience with TimeLogic's Decypher nodes? What kind of performance do the get and how do they compare in a real deployment to a cpu farm? 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URL: From Hao.Zhou at celera.com Thu Jul 25 12:11:18 2002 From: Hao.Zhou at celera.com (Zhou, Hao) Date: Thu, 25 Jul 2002 12:11:18 -0400 Subject: [BiO BB] RE: BiO_Bulletin_Board digest, Vol 1 #298 - 1 msg Message-ID: test -----Original Message----- From: bio_bulletin_board-request at bioinformatics.org [mailto:bio_bulletin_board-request at bioinformatics.org] Sent: Thursday, July 25, 2002 12:01 PM To: bio_bulletin_board at bioinformatics.org Subject: BiO_Bulletin_Board digest, Vol 1 #298 - 1 msg Send BiO_Bulletin_Board mailing list submissions to bio_bulletin_board at bioinformatics.org To subscribe or unsubscribe via the World Wide Web, visit http://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. TimeLogic (bioinfo) --__--__-- Message: 1 From: "bioinfo" To: Date: Wed, 24 Jul 2002 22:14:22 -0400 Subject: [BiO BB] TimeLogic Reply-To: bio_bulletin_board at bioinformatics.org This is a multi-part message in MIME format. ------=_NextPart_000_0001_01C2335F.77FFD5C0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hello, Does anyone have any experience with TimeLogic's Decypher nodes? What kind of performance do the get and how do they compare in a real deployment to a cpu farm? Thanks for any input ------=_NextPart_000_0001_01C2335F.77FFD5C0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Message
Hello,
    Does anyone have any experience with TimeLogic's Decypher = nodes? =20 What kind of performance do the get and how do they compare in a real = deployment=20 to a cpu farm?

Thanks for any=20 input
 
------=_NextPart_000_0001_01C2335F.77FFD5C0-- --__--__-- _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board End of BiO_Bulletin_Board Digest From lilc79 at yahoo.com Mon Jul 29 18:36:02 2002 From: lilc79 at yahoo.com (Longcheng Li) Date: Mon, 29 Jul 2002 15:36:02 -0700 (PDT) Subject: [BiO BB] about Factual Data Message-ID: <20020729223602.93395.qmail@web9503.mail.yahoo.com> Hello, I would like to know what extactly is Factual Data and Factual Database? Thank you. Long \\|// (o o) -oOOo~(_)~oOOo- --------------------------------- Do You Yahoo!? Yahoo! Health - Feel better, live better -------------- next part -------------- An HTML attachment was scrubbed... URL: From brian at justmgt.com Tue Jul 30 08:29:32 2002 From: brian at justmgt.com (Brian Seitzman) Date: Tue, 30 Jul 2002 08:29:32 -0400 Subject: [BiO BB] about Factual Data In-Reply-To: <20020729223602.93395.qmail@web9503.mail.yahoo.com> Message-ID: <000301c237c4$c4067370$7900a8c0@dsl.gtei.net> I'm sorry, but I think you've sent this email to the wrong person. I'm not sure why you'd be asking me this question. Brian -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Longcheng Li Sent: Monday, July 29, 2002 6:36 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] about Factual Data Hello, I would like to know what extactly is Factual Data and Factual Database? Thank you. Long \\|// (o o) -oOOo~(_)~oOOo- ---------------------------------------------------------------------------- -- Do You Yahoo!? Yahoo! Health - Feel better, live better -------------- next part -------------- An HTML attachment was scrubbed... URL: From jay at ccmb.res.in Tue Jul 30 08:54:24 2002 From: jay at ccmb.res.in (jayanti) Date: Tue, 30 Jul 2002 19:24:24 +0630 Subject: [BiO BB] No mails received since 27th july In-Reply-To: <200207261601.g6QG14c08814@www.bioinformatics.org> Message-ID: Dear all, I didn't receive any messages from our group from 27th july......I would like to verify whether am still a subscriber...... Awaiting an early reply, Sincerely yours, Jai. Following is the last mail received from the group..... On Fri, 26 Jul 2002 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 > http://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. RE: BiO_Bulletin_Board digest, Vol 1 #298 - 1 msg (Zhou, Hao) > > --__--__-- > > Message: 1 > Date: Thu, 25 Jul 2002 12:11:18 -0400 > From: "Zhou, Hao" > To: > Subject: [BiO BB] RE: BiO_Bulletin_Board digest, Vol 1 #298 - 1 msg > Reply-To: bio_bulletin_board at bioinformatics.org > > test > > -----Original Message----- > From: bio_bulletin_board-request at bioinformatics.org > [mailto:bio_bulletin_board-request at bioinformatics.org] > Sent: Thursday, July 25, 2002 12:01 PM > To: bio_bulletin_board at bioinformatics.org > Subject: BiO_Bulletin_Board digest, Vol 1 #298 - 1 msg > > > Send BiO_Bulletin_Board mailing list submissions to > bio_bulletin_board at bioinformatics.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://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. TimeLogic (bioinfo) > > -- __--__-- > > Message: 1 > From: "bioinfo" > To: > Date: Wed, 24 Jul 2002 22:14:22 -0400 > Subject: [BiO BB] TimeLogic > Reply-To: bio_bulletin_board at bioinformatics.org > > This is a multi-part message in MIME format. > > ------=_NextPart_000_0001_01C2335F.77FFD5C0 > Content-Type: text/plain; > charset="us-ascii" > Content-Transfer-Encoding: 7bit > > Hello, > Does anyone have any experience with TimeLogic's Decypher nodes? > What kind of performance do the get and how do they compare in a real > deployment to a cpu farm? > > Thanks for any input > > > ------=_NextPart_000_0001_01C2335F.77FFD5C0 > Content-Type: text/html; > charset="us-ascii" > Content-Transfer-Encoding: quoted-printable > > > > charset=3Dus-ascii"> > Message > > > >
size=3D2>Hello,
>
    face=3DArial=20 > size=3D2>Does anyone have any experience with TimeLogic's Decypher = > nodes? =20 > What kind of performance do the get and how do they compare in a real = > deployment=20 > to a cpu farm?
>
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Thanks for any=20 > input
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> > ------=_NextPart_000_0001_01C2335F.77FFD5C0-- > > > > -- __--__-- > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > End of BiO_Bulletin_Board Digest > > > --__--__-- > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > End of BiO_Bulletin_Board Digest > From Bill_A_Nussbaumer at bd.com Tue Jul 30 11:15:09 2002 From: Bill_A_Nussbaumer at bd.com (Bill_A_Nussbaumer at bd.com) Date: Tue, 30 Jul 2002 11:15:09 -0400 Subject: [BiO BB] No mails received since 27th july Message-ID: Did you get your own message? jayanti @bioinformatics.org on 07/30/2002 08:54:24 AM Please respond to bio_bulletin_board at bioinformatics.org Sent by: bio_bulletin_board-admin at bioinformatics.org To: bio_bulletin_board at bioinformatics.org cc: Subject: [BiO BB] No mails received since 27th july Dear all, I didn't receive any messages from our group from 27th july......I would like to verify whether am still a subscriber...... Awaiting an early reply, Sincerely yours, Jai. Following is the last mail received from the group..... On Fri, 26 Jul 2002 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 > http://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. RE: BiO_Bulletin_Board digest, Vol 1 #298 - 1 msg (Zhou, Hao) > > --__--__-- > > Message: 1 > Date: Thu, 25 Jul 2002 12:11:18 -0400 > From: "Zhou, Hao" > To: > Subject: [BiO BB] RE: BiO_Bulletin_Board digest, Vol 1 #298 - 1 msg > Reply-To: bio_bulletin_board at bioinformatics.org > > test > > -----Original Message----- > From: bio_bulletin_board-request at bioinformatics.org > [mailto:bio_bulletin_board-request at bioinformatics.org] > Sent: Thursday, July 25, 2002 12:01 PM > To: bio_bulletin_board at bioinformatics.org > Subject: BiO_Bulletin_Board digest, Vol 1 #298 - 1 msg > > > Send BiO_Bulletin_Board mailing list submissions to > bio_bulletin_board at bioinformatics.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://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. TimeLogic (bioinfo) > > -- __--__-- > > Message: 1 > From: "bioinfo" > To: > Date: Wed, 24 Jul 2002 22:14:22 -0400 > Subject: [BiO BB] TimeLogic > Reply-To: bio_bulletin_board at bioinformatics.org > > This is a multi-part message in MIME format. > > ------=_NextPart_000_0001_01C2335F.77FFD5C0 > Content-Type: text/plain; > charset="us-ascii" > Content-Transfer-Encoding: 7bit > > Hello, > Does anyone have any experience with TimeLogic's Decypher nodes? > What kind of performance do the get and how do they compare in a real > deployment to a cpu farm? > > Thanks for any input > > > ------=_NextPart_000_0001_01C2335F.77FFD5C0 > Content-Type: text/html; > charset="us-ascii" > Content-Transfer-Encoding: quoted-printable > > > > charset=3Dus-ascii"> > Message > > > >
size=3D2>Hello,
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    face=3DArial=20 > size=3D2>Does anyone have any experience with TimeLogic's Decypher = > nodes? =20 > What kind of performance do the get and how do they compare in a real = > deployment=20 > to a cpu farm?
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Thanks for any=20 > input
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> > ------=_NextPart_000_0001_01C2335F.77FFD5C0-- > > > > -- __--__-- > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > End of BiO_Bulletin_Board Digest > > > --__--__-- > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > End of BiO_Bulletin_Board Digest > _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From cdwan at mail.ahc.umn.edu Tue Jul 30 14:35:01 2002 From: cdwan at mail.ahc.umn.edu (Chris Dwan (CCGB)) Date: Tue, 30 Jul 2002 13:35:01 -0500 (CDT) Subject: [BiO BB] TimeLogic In-Reply-To: <000001c23380$ff0f2bd0$befea8c0@raptor> References: <000001c23380$ff0f2bd0$befea8c0@raptor> Message-ID: <15686.56405.338063.817542@branch.ahc.umn.edu> > Does anyone have any experience with TimeLogic's Decypher nodes? > What kind of performance do the get and how do they compare in a real > deployment to a cpu farm? We (The University of Minnesota Center for Computational Genomics and Bioinformatics) have two 'G' series DeCypher boards from TimeLogic. We also have a total of 15 nodes of compute farm (various shapes and sizes of Linux) scheduled using PBSPro and a bunch of home-brew scripts. The TimeLogic machine is wicked fast, but it can be a little cranky to work with. There are lots of gotchas on query size (below 100,000bp is best) and other things in the interface that just require learning. Given that the user is willing to take the time to learn how to drive it, people like it a lot. For the folks who have 80,000 to 100,000bp of sequence at a time that they need to TblastX vs. NCBI's NT, dbEST, whole chromosomes, or whatever, it's a great machine. For those folks who want optimal results (Smith & Waterman and others...) the TimeLogic machine can't be beat. The cluster, on the other hand, is most useful for 1st pass annotation and analysis on massive sets of data: millions of BLASTNs to find the really close relations farm out very cleanly. The cluster also has superior automation tools in place, but that's mostly because we've been working on it longer. I have no experience with ParaCell's products. -Chris Dwan University of Minnesota Center for Computational Genomics and Bioinformatics