From dmb at mrc-dunn.cam.ac.uk Wed Nov 2 04:23:31 2005 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Wed, 02 Nov 2005 09:23:31 +0000 Subject: [BiO BB] PUBMED --> Genes ?? Message-ID: <43688593.8060003@mrc-dunn.cam.ac.uk> Hello, After playing with some stuff on the NCBI / PubMed site, I wonder if there is a list mapping PUBMED ID to Gene ID (of some kind, like refseq for example)? For a given gene I would like to look up all the associated literature. Any recomendations on how to do that? Is there a tab delimited pubmed database that links pubmed id to keywords for example? Cheers, Dan. From basu at pharm.sunysb.edu Wed Nov 2 08:09:29 2005 From: basu at pharm.sunysb.edu (Siddhartha Basu) Date: Wed, 02 Nov 2005 08:09:29 -0500 Subject: [BiO BB] PUBMED --> Genes ?? In-Reply-To: <43688593.8060003@mrc-dunn.cam.ac.uk> References: <43688593.8060003@mrc-dunn.cam.ac.uk> Message-ID: <4368BA89.3010804@pharm.sunysb.edu> Hi, Try this one. ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2pubmed.gz -siddhartha Dan Bolser wrote: > Hello, > > After playing with some stuff on the NCBI / PubMed site, I wonder if > there is a list mapping PUBMED ID to Gene ID (of some kind, like refseq > for example)? > > For a given gene I would like to look up all the associated literature. > Any recomendations on how to do that? > > Is there a tab delimited pubmed database that links pubmed id to > keywords for example? > > Cheers, > Dan. > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From judyyuyu at hotmail.com Wed Nov 2 08:39:13 2005 From: judyyuyu at hotmail.com (Judy Li) Date: Wed, 02 Nov 2005 08:39:13 -0500 Subject: [BiO BB] please help Message-ID: An HTML attachment was scrubbed... URL: From dmb at mrc-dunn.cam.ac.uk Wed Nov 2 09:32:04 2005 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Wed, 02 Nov 2005 14:32:04 +0000 Subject: [BiO BB] PUBMED --> Genes ?? In-Reply-To: <4368BA89.3010804@pharm.sunysb.edu> References: <43688593.8060003@mrc-dunn.cam.ac.uk> <4368BA89.3010804@pharm.sunysb.edu> Message-ID: <4368CDE4.5050904@mrc-dunn.cam.ac.uk> Siddhartha Basu wrote: > Hi, > Try this one. > ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2pubmed.gz Brilliant! Now I am just missing a pubmed database, so I can link keywords to PMID's and then to genes... I heard about a 'pubmed database' for downloading, but I can't find it... > -siddhartha > > Dan Bolser wrote: > >> Hello, >> >> After playing with some stuff on the NCBI / PubMed site, I wonder if >> there is a list mapping PUBMED ID to Gene ID (of some kind, like >> refseq for example)? >> >> For a given gene I would like to look up all the associated >> literature. Any recomendations on how to do that? >> >> Is there a tab delimited pubmed database that links pubmed id to >> keywords for example? >> >> Cheers, >> Dan. >> >> _______________________________________________ >> Bioinformatics.Org general forum - >> BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From jgentry at jimmy.harvard.edu Wed Nov 2 10:18:51 2005 From: jgentry at jimmy.harvard.edu (Jeff Gentry) Date: Wed, 2 Nov 2005 10:18:51 -0500 (EST) Subject: [BiO BB] PUBMED --> Genes ?? In-Reply-To: <4368CDE4.5050904@mrc-dunn.cam.ac.uk> Message-ID: > After playing with some stuff on the NCBI / PubMed site, I wonder if > there is a list mapping PUBMED ID to Gene ID (of some kind, like > refseq for example)? This sort of functionality and quite a bit more exists within the Bioconductor project (www.bioconductor.org) From P.Curley at westminster.ac.uk Wed Nov 2 20:01:20 2005 From: P.Curley at westminster.ac.uk (paul) Date: Wed, 2 Nov 2005 17:01:20 -0800 Subject: [BiO BB] PDB codes? Message-ID: Hi Folks, Anyone know where I get get a list of the codes (i.e. H = helix, E = beta sheet, etc.) used by PDB to describe secondary structure elements in PDB structures? I have trawled the PDB site to no avail... Thanks again and best regards, Paul From molvisions at mac.com Wed Nov 2 13:10:24 2005 From: molvisions at mac.com (Timothy Driscoll) Date: Wed, 2 Nov 2005 13:10:24 -0500 Subject: [BiO BB] PDB codes? In-Reply-To: References: Message-ID: <3B6C0E99-EA33-4447-977F-492188E605BD@mac.com> On Nov 2, 2005, at 8:01 p, paul wrote: > Hi Folks, > > Anyone know where I get get a list of the codes (i.e. H = helix, E > = beta > sheet, etc.) used by PDB to describe secondary structure elements > in PDB > structures? I have trawled the PDB site to no avail... > > specifically section 5. hth, tim -- Timothy Driscoll em: molvisions at mac.com molvisions - see. grasp. learn. ph: 919-368-2667 im: molvisions usa:virginia:blacksburg tx: molvisions at vtext.com From christoph.gille at charite.de Wed Nov 2 16:44:17 2005 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Wed, 2 Nov 2005 22:44:17 +0100 (CET) Subject: [BiO BB] evaluating alignment algothythms Message-ID: <64008.84.190.38.162.1130967857.squirrel@webmail.charite.de> To compare different algorhythms for multiple sequence alignments I need to compare the alignment outputs to a benchmark alignment. Do programs exist that can take a computed alignment and compare it to the "optimal" alignment and produce a score ? Many thanks Christoph From boris.steipe at utoronto.ca Wed Nov 2 17:59:57 2005 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Wed, 2 Nov 2005 17:59:57 -0500 Subject: [BiO BB] evaluating alignment algothythms In-Reply-To: <64008.84.190.38.162.1130967857.squirrel@webmail.charite.de> References: <64008.84.190.38.162.1130967857.squirrel@webmail.charite.de> Message-ID: Yes, The reference database is BAliBASE and on the site you will find C source to compute the score. http://bips.u-strasbg.fr/fr/Products/Databases/BAliBASE2/ regards, Boris On 2 Nov 2005, at 16:44, Dr. Christoph Gille wrote: > To compare different algorhythms for multiple sequence alignments > I need to compare the alignment outputs to a benchmark alignment. > > Do programs exist that can take a computed alignment and compare it > to the "optimal" alignment and produce a score ? > > Many thanks > Christoph > > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From stefanielager at gmail.com Thu Nov 3 02:30:03 2005 From: stefanielager at gmail.com (Stefanie Lager) Date: Thu, 3 Nov 2005 08:30:03 +0100 Subject: [BiO BB] PUBMED --> Genes ?? In-Reply-To: <43688593.8060003@mrc-dunn.cam.ac.uk> References: <43688593.8060003@mrc-dunn.cam.ac.uk> Message-ID: <88a1d5c50511022330u5f352a42m35242d0c8ab4dd8@mail.gmail.com> You can also try the iHOP service http://www.ihop-net.org/UniPub/iHOP/ On 11/2/05, Dan Bolser wrote: > > Hello, > > After playing with some stuff on the NCBI / PubMed site, I wonder if > there is a list mapping PUBMED ID to Gene ID (of some kind, like refseq > for example)? > > For a given gene I would like to look up all the associated literature. > Any recomendations on how to do that? > > Is there a tab delimited pubmed database that links pubmed id to > keywords for example? > > Cheers, > Dan. > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanielager at gmail.com Thu Nov 3 02:32:49 2005 From: stefanielager at gmail.com (Stefanie Lager) Date: Thu, 3 Nov 2005 08:32:49 +0100 Subject: [BiO BB] evaluating alignment algothythms In-Reply-To: <64008.84.190.38.162.1130967857.squirrel@webmail.charite.de> References: <64008.84.190.38.162.1130967857.squirrel@webmail.charite.de> Message-ID: <88a1d5c50511022332r2d7ea86aud08972e272f7a308@mail.gmail.com> A graphical comparison of two multiple alignments can be done using the AltAVisT tool http://bibiserv.techfak.uni-bielefeld.de/altavist/ Stefanie On 11/2/05, Dr. Christoph Gille wrote: > To compare different algorhythms for multiple sequence alignments > I need to compare the alignment outputs to a benchmark alignment. > > Do programs exist that can take a computed alignment and compare it > to the "optimal" alignment and produce a score ? > > Many thanks > Christoph > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -------------- next part -------------- An HTML attachment was scrubbed... URL: From aloraine at gmail.com Thu Nov 3 09:42:26 2005 From: aloraine at gmail.com (Ann Loraine) Date: Thu, 3 Nov 2005 08:42:26 -0600 Subject: [BiO BB] PUBMED --> Genes ?? In-Reply-To: <88a1d5c50511022330u5f352a42m35242d0c8ab4dd8@mail.gmail.com> References: <43688593.8060003@mrc-dunn.cam.ac.uk> <88a1d5c50511022330u5f352a42m35242d0c8ab4dd8@mail.gmail.com> Message-ID: <83722dde0511030642q3d67a0e9s5c8232980d3f92f5@mail.gmail.com> Is there anything that is scriptable? E.g., I make a URL like: http://someservice.org?gene=TP53 and read it like this: import urllib data = urllib.urlopen(url) while 1: nicelyformattedline = fh.readline() ... and so on Also, I think you can get Pubmed ids from Entrez Gene records, which are downloadable from NCBI ftp site. -Ann On 11/3/05, Stefanie Lager wrote: > You can also try the iHOP service > http://www.ihop-net.org/UniPub/iHOP/ > > > On 11/2/05, Dan Bolser wrote: > > Hello, > > > > After playing with some stuff on the NCBI / PubMed site, I wonder if > > there is a list mapping PUBMED ID to Gene ID (of some kind, like refseq > > for example)? > > > > For a given gene I would like to look up all the associated literature. > > Any recomendations on how to do that? > > > > Is there a tab delimited pubmed database that links pubmed id to > > keywords for example? > > > > Cheers, > > Dan. > > > > _______________________________________________ > > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > -- Ann Loraine Assistant Professor Section on Statistical Genetics University of Alabama at Birmingham http://www.ssg.uab.edu From dmb at mrc-dunn.cam.ac.uk Thu Nov 3 10:04:35 2005 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 03 Nov 2005 15:04:35 +0000 Subject: [BiO BB] PUBMED --> Genes ?? In-Reply-To: <83722dde0511030642q3d67a0e9s5c8232980d3f92f5@mail.gmail.com> References: <43688593.8060003@mrc-dunn.cam.ac.uk> <88a1d5c50511022330u5f352a42m35242d0c8ab4dd8@mail.gmail.com> <83722dde0511030642q3d67a0e9s5c8232980d3f92f5@mail.gmail.com> Message-ID: <436A2703.6060809@mrc-dunn.cam.ac.uk> Ann Loraine wrote: > Also, I think you can get Pubmed ids from Entrez Gene records, which > are downloadable from NCBI ftp site. Yes. I think ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gives me everything I need for a large set of "gene to PMID" mappings. I can get an equivelent set from UNIPROT, making for a very large set. Now what I am looking for is a PUBMED data set, linking PMID to keywords. Cheers, Dan. > > -Ann > >> >>On 11/2/05, Dan Bolser wrote: >> >>>Hello, >>> >>>After playing with some stuff on the NCBI / PubMed site, I wonder if >>>there is a list mapping PUBMED ID to Gene ID (of some kind, like refseq >>>for example)? >>> >>>For a given gene I would like to look up all the associated literature. >>>Any recomendations on how to do that? >>> >>>Is there a tab delimited pubmed database that links pubmed id to >>>keywords for example? >>> >>>Cheers, >>>Dan. >>> >>>_______________________________________________ >>>Bioinformatics.Org general forum - >> >>BiO_Bulletin_Board at bioinformatics.org >> >>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >> >>_______________________________________________ >>Bioinformatics.Org general forum - >>BiO_Bulletin_Board at bioinformatics.org >>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >> >> > > > > -- > > Ann Loraine > Assistant Professor > Section on Statistical Genetics > University of Alabama at Birmingham > http://www.ssg.uab.edu > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From MEC at Stowers-Institute.org Thu Nov 3 13:03:30 2005 From: MEC at Stowers-Institute.org (Cook, Malcolm) Date: Thu, 3 Nov 2005 12:03:30 -0600 Subject: [BiO BB] promoter sequence analysis for TFBS .. using phylogeny Message-ID: http://nar.oxfordjournals.org/cgi/content/full/33/10/3154 ?? -------------- next part -------------- An HTML attachment was scrubbed... URL: From ccottap at lcc.uma.es Fri Nov 4 03:41:51 2005 From: ccottap at lcc.uma.es (Carlos Cotta) Date: Fri, 04 Nov 2005 09:41:51 +0100 Subject: [BiO BB] CFP: EvoBIO 2006 - deadline extension Message-ID: <5.1.0.14.2.20051104094044.044d3810@sol10.lcc.uma.es> Dear Colleague, the submission deadline for EvoBIO 2006 (the Fourth European Workshop on Evolutionary Computation and Machine Learning in Bioinformatics) to be held in Budapest, Hungary has been extended to *** November 11, 2005 ***. More information and submission guidelines are available at: http://evonet.lri.fr/eurogp2006/?page=evobio http://www.cs.vu.nl/~evobio/evobio06.html ****** Important Dates ****** *Extended* submission deadline: 11 November 2005 Notification of acceptance: 12 December 2005 Camera ready papers due: 9 January 2006 EvoBIO and Evo-events: 10-12 April 2006 Best regards, EvoBIO Team From vnadeem at gmail.com Tue Nov 8 05:14:04 2005 From: vnadeem at gmail.com (V.Nadeem Ahmad) Date: Tue, 8 Nov 2005 15:44:04 +0530 Subject: [BiO BB] Re: Linear Bioinformatics workflow? In-Reply-To: <339D68B133EAD311971E009027DC47970391A3DD@montecarlo.cgr.harvard.edu> References: <339D68B133EAD311971E009027DC47970391A3DD@montecarlo.cgr.harvard.edu> Message-ID: Hi All, I have a small question. I have two protein sequences . I want to know whether they interact or not. I dont have the structures of both. will be glad to have your opinion kind regards Nadeem Ahmad -------------- next part -------------- An HTML attachment was scrubbed... URL: From boris.steipe at utoronto.ca Tue Nov 8 09:24:05 2005 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Tue, 8 Nov 2005 09:24:05 -0500 Subject: [BiO BB] Interaction prediction Was: Re. Linear Bioinformatics workflow? In-Reply-To: References: <339D68B133EAD311971E009027DC47970391A3DD@montecarlo.cgr.harvard.edu> Message-ID: <93AD65D2-842E-4003-9777-5FC2644FB649@utoronto.ca> The BIND database has a tool called BIND-BLAST ( http://bind.ca/ BINDBlast ) that allows you to search interaction partners by sequence similarity. Of course, these so-called "interologs" are only a hypothesis. On the other hand, in case an interaction between the two proteins has been experimentally determined, BIND will tell you that as well. HTH Boris On 8 Nov 2005, at 05:14, V.Nadeem Ahmad wrote: > Hi All, > I have a small question. I have two protein sequences . I want to > know whether they interact or not. I dont have the structures of > both. will be glad to have your opinion > > kind regards > Nadeem Ahmad > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From ahiresunita at yahoo.com Tue Nov 8 15:27:44 2005 From: ahiresunita at yahoo.com (sunita ahire) Date: Tue, 8 Nov 2005 12:27:44 -0800 (PST) Subject: [BiO BB] Molecular Genomics Message-ID: <20051108202744.10838.qmail@web61017.mail.yahoo.com> Hi everyone, I am new to bioinformatics. Can somebody tell me what topics are covered under the subject of "molecular" genomics. Thank u in advance __________________________________ Yahoo! FareChase: Search multiple travel sites in one click. http://farechase.yahoo.com From martin_jambon at emailuser.net Tue Nov 8 15:57:24 2005 From: martin_jambon at emailuser.net (Martin Jambon) Date: Tue, 8 Nov 2005 12:57:24 -0800 (PST) Subject: [BiO BB] Molecular Genomics In-Reply-To: <20051108202744.10838.qmail@web61017.mail.yahoo.com> References: <20051108202744.10838.qmail@web61017.mail.yahoo.com> Message-ID: On Tue, 8 Nov 2005, sunita ahire wrote: > Hi everyone, > > I am new to bioinformatics. > Can somebody tell me what topics are covered under the > subject of "molecular" genomics. Molecular biology refers to biological macromolecules such as DNA or proteins and their manipulation, often using other macromolecules, and does not mean "chemistry applied to biology". So I guess that "molecular genomics" means that it consists in using the techniques of "molecular biology" for "genomics". It would be a buzzword which replaces "molecular genetics", but I have to say that I never understood the nuance between "molecular biology" and "molecular genetics" anyway. Martin -- Martin Jambon, PhD http://martin.jambon.free.fr From mkgovindis at yahoo.com Tue Nov 8 22:44:51 2005 From: mkgovindis at yahoo.com (govind mk) Date: Tue, 8 Nov 2005 19:44:51 -0800 (PST) Subject: [BiO BB] Interaction prediction Was: Re. Linear Bioinformatics workflow? In-Reply-To: <93AD65D2-842E-4003-9777-5FC2644FB649@utoronto.ca> Message-ID: <20051109034451.62447.qmail@web34715.mail.mud.yahoo.com> Hi Nadeem You could use the STRING website which also uses genomic context based algorithms. http://string.embl.de/ It has data of interacting proteins derived from curation effort as well ... Data from Reactome and HPRD have also been incorporated in it -Govind --- Boris Steipe wrote: > The BIND database has a tool called BIND-BLAST ( > http://bind.ca/ > BINDBlast ) that allows you to search interaction > partners by > sequence similarity. Of course, these so-called > "interologs" are only > a hypothesis. On the other hand, in case an > interaction between the > two proteins has been experimentally determined, > BIND will tell you > that as well. > > HTH > > Boris > > On 8 Nov 2005, at 05:14, V.Nadeem Ahmad wrote: > > > Hi All, > > I have a small question. I have two protein > sequences . I want to > > know whether they interact or not. I dont have the > structures of > > both. will be glad to have your opinion > > > > kind regards > > Nadeem Ahmad > > _______________________________________________ > > Bioinformatics.Org general forum - > > BiO_Bulletin_Board at bioinformatics.org > > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > __________________________________ Yahoo! FareChase: Search multiple travel sites in one click. http://farechase.yahoo.com From svozil at uochb.cas.cz Wed Nov 9 11:06:58 2005 From: svozil at uochb.cas.cz (Daniel Svozil) Date: Wed, 09 Nov 2005 17:06:58 +0100 Subject: [BiO BB] Postdocs in Structural Bioinformatics @ Prague Message-ID: <43721EA2.2090302@uochb.cas.cz> The Group of Structural Bioinformatics, Institute of Organic Chemistry and Biochemistry (IOCB), Prague, Czech Republic, has openings for postdoctoral researchers. Appointments are available for one year, with a possible extension up to two years. The focus of the group is structure and dynamics of nucleic acids. A successful candidate should have research experience in some of the following fields: nucleic acids structure, structural bioinformatics and databases, molecular modeling, ab initio quantum chemistry calculations. Programming skills are significant advantage and strong interest in academic research is highly desired. Prospective applicants should forward their resume (CV) to: Dr. Bohdan Schneider bohdan.schneider at uochb.cas.cz Institute of Organic Chemistry and Biochemistry Fleming Square 2 Prague 6 CZ-166 10 Czech Republic -- Daniel Svozil, PhD Institute of Organic Chemistry and Biochemistry Center for Biomolecules and Complex Molecular Systems http://www.molecular.cz/~svozil Czech Republic phone: +420-220 410 312 From logan at cacs.louisiana.edu Fri Nov 11 10:51:48 2005 From: logan at cacs.louisiana.edu (Raja Loganantharaj) Date: Fri, 11 Nov 2005 09:51:48 -0600 Subject: [BiO BB] CFP:Special Session on Bioinformatics (June 27-30) Message-ID: <4374BE14.3010201@cacs.louisiana.edu> You are invited to submit a paper to the BioInformatics track of the IEA/AIE 2006 conference in Annecy FRANCE June 27-30. The goal of the special track is to facilitate collaboration between AI researchers and biologists by presenting cutting edge algorithms, ideas and the applications of AI technology to solve interesting problems in computational biology. We plan to accept up to 10 papers for presentation (after a formal peer review process) and these will be included in the IEA/AIE 2006 conference proceedings, which is published in a bound volume by Springer-Verlag in their 'Lecture Notes in Artificial Intelligence' series. All the accepted papers will be considered for a special issue of the Journal of Applied Intelligence. The topics of interests include, but not limited to: * Sequence Alignment * Gene Discovery * Protein /RNA structure Prediction and Modeling * Comparative Genomics * Regulatory modules and Pathway analysis * Evolution and Phylogenetics * Molecular Structures * Interactions between protein to protein, and protein to dna. * MicroArray data analysis and high dimensional reductions * Application of machine learning to molecular biology View the details at http://esia2.univ-savoie.fr/conf-iea-aie/index.php?id=18 The important dates are *December 9, 2005* /Electronic Paper Submission Deadline/ *January 23, 2006* /Author(s) Notification/ *February 24, 2006* /Camera-Ready Copy Deadline/ *June 27-30, 2006* /IEA/AIE-06 Special session on Bioinformatics/ Thank you -- Dr. Raja Loganantharaj Director of Bioinformatics Research Lab Center for Advanced Computer Studies University of Louisiana PO Box 44330 Lafayette, LA 70504-4330 ------------------------------- Voice: 337-482-5345 http://www.cacs.louisiana.edu/~logan/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From srdshigella2001 at yahoo.co.in Mon Nov 14 01:59:53 2005 From: srdshigella2001 at yahoo.co.in (Sangeetha Subramaniam) Date: Mon, 14 Nov 2005 12:29:53 +0530 Subject: [BiO BB] Metabolic pathway -profile generation. Message-ID: <293eae50511132259p3bee17d5i399d43136cf90526@mail.gmail.com> Hi, Could anyone let me know if you are working with profile generation of metabolic pathway. Thanks sangeetha -- S.Sangeetha Centre for Computational Biology and Bioinformatics School of Information Technology Jawaharlal Nehru Univeristy, NewDelhi-110067 -------------- next part -------------- An HTML attachment was scrubbed... URL: From info at wikiomics.org Mon Nov 14 17:55:01 2005 From: info at wikiomics.org (Martin Jambon) Date: Mon, 14 Nov 2005 14:55:01 -0800 (PST) Subject: [BiO BB] Announcement: Wikiomics - http://wikiomics.org Message-ID: Wikiomics is an open documentation initiative in the field of bioinformatics and systems biology. Wikiomics consists in a free space for storing and sharing information that joins together practical and theoretical aspects of bioinformatics. Anyone can initiate or modify an article at Wikiomics and use it as a collection of notes, links and papers on a specific problem. Page history and email notification make it easy to track changes made by other users of this wiki. Each article of Wikiomics is a dynamic, easy-to-maintain review which would eventually provide: - brief explanations of strategies and methods, possibly with figures and math formulas - links to relevant bioinformatics services and software distributors - links to PubMed abstracts, thanks to a built-in citation manager So make yourself at home at http://wikiomics.org And have fun! Martin Jambon, for the Wikiomics technical staff. -- Martin Jambon, PhD Keep up with Bioinformatics at http://wikiomics.org From elavv2003 at gmail.com Tue Nov 15 04:03:53 2005 From: elavv2003 at gmail.com (Elavazhagan) Date: Tue, 15 Nov 2005 14:33:53 +0530 Subject: [BiO BB] how to localize a database manually. Message-ID: Hi, I would like to know how to localize a small biological database. Means that need to localize the EST database of NCBI. Where can I get the raw information regarding that work. Ur guidences will be mostly appreciated. Thanking You. -- The eternal mystery of the world is its comprehensibility. E.Elavazhagan +91 9444332083 From pfern at igc.gulbenkian.pt Tue Nov 15 05:56:11 2005 From: pfern at igc.gulbenkian.pt (Pedro Fernandes) Date: Tue, 15 Nov 2005 10:56:11 -0000 (WET) Subject: [BiO BB] how to localize a database manually. In-Reply-To: References: Message-ID: <35283.192.168.50.3.1132052171.squirrel@webmail.igc.gulbenkian.pt> Hi just follow http://www.expasy.org/ Under Links to lists of molecular biology resources Go to ExPASy's Life Sciences Directory - http://www.expasy.org/links.html Search for the string "EST", you will hit dbEST, what you are looking for. P. Fernandes Elavazhagan said: > Hi, > I would like to know how to localize a small biological database. > Means that need to localize the EST database of NCBI. Where can I get > the raw information regarding that work. Ur guidences will be mostly > appreciated. > Thanking You. > > -- > The eternal mystery of the world is its comprehensibility. > > E.Elavazhagan > +91 9444332083 > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From nicefrd_iet at yahoo.com Sat Nov 12 03:33:46 2005 From: nicefrd_iet at yahoo.com (anamika awasthi) Date: Sat, 12 Nov 2005 00:33:46 -0800 (PST) Subject: [BiO BB] regarding molecular modeling Message-ID: <20051112083346.50861.qmail@web60625.mail.yahoo.com> Hello, I've done my thesis in applied chemistry, i wants to expertise in molecular modeling, can anyone guide me regarding this. can anyone tell me who is doing work in molecular modeling in biological systems. ThanK You Anamika --------------------------------- Yahoo! FareChase - Search multiple travel sites in one click. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bortier at gmail.com Tue Nov 15 12:20:10 2005 From: bortier at gmail.com (Burak Kutlu) Date: Tue, 15 Nov 2005 09:20:10 -0800 Subject: [BiO BB] how to localize a database manually. In-Reply-To: References: Message-ID: have a look here: http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+databanks best -burak On 11/15/05, Elavazhagan wrote: > > Hi, > I would like to know how to localize a small biological database. > Means that need to localize the EST database of NCBI. Where can I get > the raw information regarding that work. Ur guidences will be mostly > appreciated. > Thanking You. > > -- > The eternal mystery of the world is its comprehensibility. > > E.Elavazhagan > +91 9444332083 > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeff at bioinformatics.org Tue Nov 15 15:18:45 2005 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Tue, 15 Nov 2005 15:18:45 -0500 Subject: [BiO BB] Re: regarding molecular modeling In-Reply-To: <20051112083346.50861.qmail@web60625.mail.yahoo.com> References: <20051112083346.50861.qmail@web60625.mail.yahoo.com> Message-ID: <437A42A5.3020202@bioinformatics.org> Anamika, "Molecular modeling" is a very broad topic, so your question is a bit vague. I'd recommend some background reading if you're unfamiliar with the topic(s). For structural modeling with computers: http://books.bioinformatics.org/compstruct.php For pathway modeling with computers: http://books.bioinformatics.org/compbiopath.php For developing mathematical models: http://books.bioinformatics.org/biomath.php The next step would be to look at some of the research articles in your area of interest and identify research groups you'd like to work with. Cheers, Jeff anamika awasthi wrote: > Hello, > I've done my thesis in applied chemistry, i wants to expertise in > molecular modeling, can anyone guide me regarding this. can anyone tell > me who is doing work in molecular modeling in biological systems. > ThanK You > Anamika > -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From boris.steipe at utoronto.ca Tue Nov 15 15:37:05 2005 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Tue, 15 Nov 2005 15:37:05 -0500 Subject: [BiO BB] Re: regarding molecular modeling In-Reply-To: <437A42A5.3020202@bioinformatics.org> References: <20051112083346.50861.qmail@web60625.mail.yahoo.com> <437A42A5.3020202@bioinformatics.org> Message-ID: <7BE85C26-9684-45EC-B410-16D34B9A52AB@utoronto.ca> Also this - Wikipedia is currently doing a remarkable job on survey-level information on bioinformatics topics. See the links from http://en.wikipedia.org/wiki/Molecular_modeling HTH, Boris On 15 Nov 2005, at 15:18, J.W. Bizzaro wrote: > Anamika, > > "Molecular modeling" is a very broad topic, so your question is a > bit vague. I'd recommend some background reading if you're > unfamiliar with the topic(s). > > For structural modeling with computers: > > http://books.bioinformatics.org/compstruct.php > > For pathway modeling with computers: > > http://books.bioinformatics.org/compbiopath.php > > For developing mathematical models: > > http://books.bioinformatics.org/biomath.php > > The next step would be to look at some of the research articles in > your area of interest and identify research groups you'd like to > work with. > > Cheers, > Jeff > > > anamika awasthi wrote: >> Hello, >> I've done my thesis in applied chemistry, i wants to expertise >> in molecular modeling, can anyone guide me regarding this. can >> anyone tell me who is doing work in molecular modeling in >> biological systems. >> ThanK You >> Anamika > > -- > J.W. Bizzaro > Bioinformatics Organization, Inc. (Bioinformatics.Org) > E-mail: jeff at bioinformatics.org > Phone: +1 508 890 8600 > -- > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From landman at scalableinformatics.com Wed Nov 16 11:21:00 2005 From: landman at scalableinformatics.com (Joe Landman) Date: Wed, 16 Nov 2005 11:21:00 -0500 Subject: [BiO BB] Fast HMMer and BLASTN code Message-ID: <437B5C6C.9000104@scalableinformatics.com> Hi folks: I want to announce that we appear to have the fastest HMMer and BLASTN builds and benchmarks for AMD Opteron architecture machines. Our HMMer benchmarking gives us a 2x advantage over the commonly downloaded binaries, and 2.5x on some customer tests. The blastn binaries give us about 22-24% advantage over the code downloadable from NCBI. These builds are immediately available from Scalable Informatics and our partners. Please contact us offline for more information. Some benchmark snapshots may be seen at http://www.scalableinformatics.com . Joe ps: while we are at SC'05, you can see our blog/comments at http://scalability.org and our photos at http://photos.scalability.org . -- Joseph Landman, Ph.D Founder and CEO Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://www.scalableinformatics.com phone: +1 734 786 8423 fax : +1 734 786 8452 cell : +1 734 612 4615 From marty.gollery at gmail.com Wed Nov 16 12:53:11 2005 From: marty.gollery at gmail.com (Martin Gollery) Date: Wed, 16 Nov 2005 09:53:11 -0800 Subject: [BiO BB] Fast HMMer and BLASTN code In-Reply-To: <437B5C6C.9000104@scalableinformatics.com> References: <437B5C6C.9000104@scalableinformatics.com> Message-ID: It might be interesting to compare all the optimized HMMer codes. A couple of years I wanted to compare SPSpfam to LDhmmer, but the folks at Logical Depth wouldn't give me a demo of their code. Logical Depth claims a 10x speedup for their code over the standard HMMer. I did test SPSpfam and saw speedups of around 20X although other people have seen speedups of 60x. None of these can touch an accelerator, but then, they are much cheaper! Marty On 11/16/05, Joe Landman wrote: > > Hi folks: > > I want to announce that we appear to have the fastest HMMer and > BLASTN builds and benchmarks for AMD Opteron architecture machines. Our > HMMer benchmarking gives us a 2x advantage over the commonly downloaded > binaries, and 2.5x on some customer tests. The blastn binaries give us > about 22-24% advantage over the code downloadable from NCBI. > > These builds are immediately available from Scalable Informatics and > our partners. Please contact us offline for more information. Some > benchmark snapshots may be seen at http://www.scalableinformatics.com . > > Joe > > ps: while we are at SC'05, you can see our blog/comments at > http://scalability.org and our photos at http://photos.scalability.org . > > -- > Joseph Landman, Ph.D > Founder and CEO > Scalable Informatics LLC, > email: landman at scalableinformatics.com > web : http://www.scalableinformatics.com > phone: +1 734 786 8423 > fax : +1 734 786 8452 > cell : +1 734 612 4615 > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- -- Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ----------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From landman at scalableinformatics.com Wed Nov 16 14:17:52 2005 From: landman at scalableinformatics.com (Joe Landman) Date: Wed, 16 Nov 2005 14:17:52 -0500 Subject: [BiO BB] Fast HMMer and BLASTN code In-Reply-To: References: <437B5C6C.9000104@scalableinformatics.com> Message-ID: <437B85E0.2020406@scalableinformatics.com> We would be willing to do this, or ask someone else to do this if they are willing. Martin Gollery wrote: > It might be interesting to compare all the optimized HMMer codes. A > couple of years I wanted to compare SPSpfam to LDhmmer, but the folks at > Logical Depth wouldn't give me a demo of their code. Logical Depth > claims a 10x speedup for their code over the standard HMMer. I did test > SPSpfam and saw speedups of around 20X although other people have seen > speedups of 60x. > > None of these can touch an accelerator, but then, they are much cheaper! > > Marty > > On 11/16/05, *Joe Landman* < landman at scalableinformatics.com > > wrote: > > Hi folks: > > I want to announce that we appear to have the fastest HMMer and > BLASTN builds and benchmarks for AMD Opteron architecture machines. Our > HMMer benchmarking gives us a 2x advantage over the commonly downloaded > binaries, and 2.5x on some customer tests. The blastn binaries give us > about 22-24% advantage over the code downloadable from NCBI. > > These builds are immediately available from Scalable Informatics and > our partners. Please contact us offline for more information. Some > benchmark snapshots may be seen at http://www.scalableinformatics.com . > > Joe > > ps: while we are at SC'05, you can see our blog/comments at > http://scalability.org and our photos at > http://photos.scalability.org . > > -- > Joseph Landman, Ph.D > Founder and CEO > Scalable Informatics LLC, > email: landman at scalableinformatics.com > > web : http://www.scalableinformatics.com > phone: +1 734 786 8423 > fax : +1 734 786 8452 > cell : +1 734 612 4615 > > _______________________________________________ > Bioinformatics.Org general > forum - BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > -- > -- > Martin Gollery > Associate Director > Center For Bioinformatics > University of Nevada at Reno > Dept. of Biochemistry / MS330 > 775-784-7042 > ----------- > > > ------------------------------------------------------------------------ > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Joseph Landman, Ph.D Founder and CEO Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://www.scalableinformatics.com phone: +1 734 786 8423 fax : +1 734 786 8452 cell : +1 734 612 4615 From narcis at fiserlab.org Thu Nov 17 17:04:34 2005 From: narcis at fiserlab.org (Narcis Fernandez-Fuentes) Date: Thu, 17 Nov 2005 17:04:34 -0500 Subject: [BiO BB] clustering short sequences Message-ID: <437CFE72.8030702@fiserlab.org> Hi all, Does anybody knows a program to sequentially cluster short protein fragments, between 8 to 14 residues long? I tried cd-hit, it works find in the range of 12 to 14 but below it crash. Any suggestion? Thanks! Narcis From cher at biorainbow.com Thu Nov 17 23:09:28 2005 From: cher at biorainbow.com (Evgeny Cheremushkin) Date: Fri, 18 Nov 2005 10:09:28 +0600 Subject: [BiO BB] How to align whole query sequence with blast Message-ID: <486065889.20051118100928@biorainbow.com> Hello bio_bb, I want to align whole query sequence onto genome with blast (not only a part of query sequence). Is there any option for that? -- Best regards, Evgeny Cheremushkin, BioRainbow Group, phone: +7 (383) 3306470 mobile: +7 (913) 8916858 e-mail: cher at biorainbow.com web: http://www.biorainbow.com From Bin_Feng at dfci.harvard.edu Thu Nov 17 22:54:03 2005 From: Bin_Feng at dfci.harvard.edu (Feng, Bin) Date: Thu, 17 Nov 2005 22:54:03 -0500 Subject: [BiO BB] what's the limit of number of sequence for blastn's input? Message-ID: <3DE7903CEEF960499FED6CC53FED102D01A72B4C@PHSXMB1.partners.org> I'm using multiple fasta file as input. Each query is 60 nt. What's the max number of sequence for the input file? From stefanielager at gmail.com Fri Nov 18 03:30:41 2005 From: stefanielager at gmail.com (Stefanie Lager) Date: Fri, 18 Nov 2005 09:30:41 +0100 Subject: [BiO BB] How to align whole query sequence with blast In-Reply-To: <486065889.20051118100928@biorainbow.com> References: <486065889.20051118100928@biorainbow.com> Message-ID: <88a1d5c50511180030i3fb5614di3cbbc09d2cbedcb7@mail.gmail.com> If you want to align cDNA or proten sequences to genomic DNA it's better to use the algorithms GMAP http://www.gene.com/share/gmap or Exonerate http://www.ebi.ac.uk/~guy/exonerate/ instead of BLAST . These two algorithms are faster then blast, and they are made to handle introns. Wu TD, Watanabe CK. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics. 2005 May 1;21(9):1859-75. Epub 2005 Feb 22. PMID: 15728110 Slater GS, Birney E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics. 2005 Feb 15;6(1):31. PMID: 15713233 Stefanie On 11/18/05, Evgeny Cheremushkin wrote: > > Hello bio_bb, > > I want to align whole query sequence onto genome with blast > (not only a part of query sequence). Is there any option for > that? > > -- > Best regards, > Evgeny Cheremushkin, > BioRainbow Group, > phone: +7 (383) 3306470 > mobile: +7 (913) 8916858 > e-mail: cher at biorainbow.com > web: http://www.biorainbow.com > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.d.vanschaik at amc.uva.nl Fri Nov 18 10:04:43 2005 From: b.d.vanschaik at amc.uva.nl (Barbera van Schaik) Date: Fri, 18 Nov 2005 16:04:43 +0100 Subject: [BiO BB] First Announcement: ISNB 2006 3rd INTERNATIONAL SYMPOSIUM ON NETWORKS IN BIOINFORMATICS Message-ID: <437DED8B.60701@amc.uva.nl> First Announcement: ISNB 2006 3rd INTERNATIONAL SYMPOSIUM ON NETWORKS IN BIOINFORMATICS May 29 - 31, 2006 in Amsterdam Science Park Amsterdam University of Amsterdam, the Netherlands The understanding of biological networks such as metabolic and signal transduction pathways is crucial for understanding molecular and cellular processes in the organism or system under study. This field is subject of lively research and both experimental and computational approaches are used to elucidate the biological networks. The bioinformatics of biological networks involves a broad range of research and approaches. Research includes the identification of regulatory elements in DNA, genome context analysis, modeling and simulation of pathways, reconstruction of pathways from experimental data, visualization of pathways, and the representation of pathways in database, graphs and markup languages. To accelerate our understanding of the (dynamics) of biological networks it is seems imperative that these efforts are combined and subsequently have to be applied to real biological problems. It is clear that this field of research can only advance when bioinformaticians and experimental biologists (for example working on model organisms such as Drosophila and organisms with a relatively simple and basal body plan such as sponges and scleractinian corals) work closely together. During this three day symposium we will bring together researchers from different disciplines (biology, mathematics and computational sciences) working on different aspects of networks to exchange ideas and approaches. During the first day of the symposium we have scheduled six introductory lectures, which aim at introducing specific subjects to the audience. The lectures are open for all participants and will provide background knowledge for the scientific presentations. For more program and registration details http://isnb.amc.uva.nl/ This symposium is supported by the Netherlands Bioinformatics Centre (NBIC;www.nbic.nl), The Academic Medical Center (AMC; www.amc.nl), The Netherlands Organisation for Scientific Reseach (NWO; www.nwo.nl), IOP Genomics (www.senternovem.nl/iopgenomics/) -- ._._._._._._._._._._._._._._._._._._._._._._. Barbera D.C. van Schaik Bioinformatics Laboratory (J1B.205) Academic Medical Center University of Amsterdam PO Box 22700 1100 DE Amsterdam The Netherlands Bioinformatics Laboratory / Human Genetics Room: J1B.205 / M1.131 Phone: (+31) 20 - 566 47 11 (+31) 20 - 566 65 92 Email: B.D.vanSchaik at amc.uva.nl _._._._._._._._._._._._._._._._._._._._._._._ From golharam at umdnj.edu Fri Nov 18 10:08:46 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 18 Nov 2005 10:08:46 -0500 Subject: [BiO BB] How to align whole query sequence with blast In-Reply-To: <88a1d5c50511180030i3fb5614di3cbbc09d2cbedcb7@mail.gmail.com> Message-ID: <01d301c5ec51$f8f30770$5022db82@GOLHARMOBILE1> Alternatively, you can use Splign or Spidey from NCBI... -----Original Message----- From: bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org [mailto:bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org ] On Behalf Of Stefanie Lager Sent: Friday, November 18, 2005 3:31 AM To: Evgeny Cheremushkin; The general forum at Bioinformatics.Org Subject: Re: [BiO BB] How to align whole query sequence with blast If you want to align cDNA or proten sequences to genomic DNA it's better to use the algorithms GMAP http://www.gene.com/share/gmap or Exonerate http://www.ebi.ac.uk/~guy/exonerate/ instead of BLAST . These two algorithms are faster then blast, and they are made to handle introns. Wu TD, Watanabe CK. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics. 2005 May 1;21(9):1859-75. Epub 2005 Feb 22. PMID: 15728110 Slater GS, Birney E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics. 2005 Feb 15;6(1):31. PMID: 15713233 Stefanie On 11/18/05, Evgeny Cheremushkin wrote: Hello bio_bb, I want to align whole query sequence onto genome with blast (not only a part of query sequence). Is there any option for that? -- Best regards, Evgeny Cheremushkin, BioRainbow Group, phone: +7 (383) 3306470 mobile: +7 (913) 8916858 e-mail: cher at biorainbow.com web: http://www.biorainbow.com _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- An HTML attachment was scrubbed... URL: From idoerg at burnham.org Mon Nov 21 13:55:28 2005 From: idoerg at burnham.org (Iddo Friedberg) Date: Mon, 21 Nov 2005 10:55:28 -0800 Subject: [BiO BB] all-vs-all bl2seq Message-ID: <43821820.8030202@burnham.org> Does anybody have a script which receives as input a FASTA file and outputs results for an all-vs-all bl2seq? Thanks, Iddo -- Iddo Friedberg, Ph.D. Burnham Institute for Medical Research 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 713 9949 http://ffas.ljcrf.edu/~iddo From landman at scalableinformatics.com Mon Nov 21 22:52:19 2005 From: landman at scalableinformatics.com (Joe Landman) Date: Mon, 21 Nov 2005 22:52:19 -0500 Subject: [BiO BB] CfP: Second IEEE Workshop on High Performance Computing in Medicine and Biology Message-ID: <438295F3.5020606@scalableinformatics.com> http://pdcl.wayne.edu/HiPCoMB-2006/ -- Joseph Landman, Ph.D Founder and CEO Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://www.scalableinformatics.com phone: +1 734 786 8423 fax : +1 734 786 8452 cell : +1 734 612 4615 From vanloenen at xtra.co.nz Tue Nov 22 14:13:29 2005 From: vanloenen at xtra.co.nz (Aledni) Date: Wed, 23 Nov 2005 08:13:29 +1300 Subject: [BiO BB] CfP: Second IEEE Workshop on High Performance Computing in Medicine and Biology In-Reply-To: <438295F3.5020606@scalableinformatics.com> Message-ID: <5.1.0.14.1.20051123081324.00bb82a0@pop3.xtra.co.nz> At 22:52 21/11/2005 -0500, you wrote: >http://pdcl.wayne.edu/HiPCoMB-2006/ > >-- >Joseph Landman, Ph.D >Founder and CEO >Scalable Informatics LLC, >email: landman at scalableinformatics.com >web : http://www.scalableinformatics.com >phone: +1 734 786 8423 >fax : +1 734 786 8452 >cell : +1 734 612 4615 > >_______________________________________________ >Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From dsterry at iupui.edu Tue Nov 22 18:43:02 2005 From: dsterry at iupui.edu (Daniel Terry) Date: Tue, 22 Nov 2005 18:43:02 -0500 Subject: [BiO BB] PhD Programs: CS vs bioinformatics Message-ID: <4383AD06.4020003@iupui.edu> I am finishing my applications for doctoral study for next fall, but I had a question before I send all this off. I am a computer science undergrad wanting to work in bioinformatics (with CS focus), but don't have a whole lot of biology and chemistry background. I will get most of what most programs want by the time I graduate, but most of this won't show up on transcripts (I just started these classes this semester). I'm sure I want to work in bioinformatics, so the ability to switch focus areas in CS wouldn't be much of an advantage. Many of the schools I am applying to have a computational biology or bioinformatics PhD-offering programs and a computer science department that also does lots of research in this area. Which would make the most sense for me to apply to? Would the specialty programs be more likely to accept me because I am specifically interested in their area, or should I apply to CS since I have a stronger background in that? Thanks for any suggestions. -- Daniel Terry Senior Undergraduate in Computer Science Purdue University - Indianapolis (IUPUI) http://www.cs.iupui.edu/~dsterry/ From jeff at bioinformatics.org Tue Nov 22 23:52:28 2005 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Tue, 22 Nov 2005 23:52:28 -0500 Subject: [BiO BB] Re: PhD Programs: CS vs bioinformatics In-Reply-To: <4383AD06.4020003@iupui.edu> References: <4383AD06.4020003@iupui.edu> Message-ID: <4383F58C.4000508@bioinformatics.org> Hi Daniel, Some of the "cross-over" questions are addressed in our FAQ: http://bioinformatics.org/faq/ Cheers, Jeff Daniel Terry wrote: > I am finishing my applications for doctoral study for next fall, but I > had a question before I send all this off. I am a computer science > undergrad wanting to work in bioinformatics (with CS focus), but don't > have a whole lot of biology and chemistry background. I will get most > of what most programs want by the time I graduate, but most of this > won't show up on transcripts (I just started these classes this > semester). I'm sure I want to work in bioinformatics, so the ability to > switch focus areas in CS wouldn't be much of an advantage. > > Many of the schools I am applying to have a computational biology or > bioinformatics PhD-offering programs and a computer science department > that also does lots of research in this area. Which would make the most > sense for me to apply to? Would the specialty programs be more likely > to accept me because I am specifically interested in their area, or > should I apply to CS since I have a stronger background in that? > > Thanks for any suggestions. > -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From golharam at umdnj.edu Wed Nov 23 00:19:55 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Wed, 23 Nov 2005 00:19:55 -0500 Subject: [BiO BB] PhD Programs: CS vs bioinformatics In-Reply-To: <4383AD06.4020003@iupui.edu> Message-ID: <045101c5efed$8a8c1110$5022db82@GOLHARMOBILE1> Hi Daniel, I can offer a little information as I went through this already. I have a B.S. in Computer Science and am about to finish my PhD in a bioinformatics program. Both sides have their advantages and disadvantages. One of my co-chairs is a geneticist, another is a molecular biophysicist. They can provide me with information on the molecular biology side of bioinformatics, but can't help much on the computer science. For that, I have another advisor on my committee who is a computer scientist. I work with the geneticist and computer scientist primarily. The bioinformatics focus offered by most CS depts are focused applying CS algorithms, statistics, combinatorial math, and CS techniques to solving problems in bioinformatics. They maintain a strong CS focus. You will pick up the necessary molecular biology along the way, and more so if you work with people outside of the the CS dept. You will probably struggle a little bit catching up on the biology/chemistry part, but it should be muc of a problem as long as you are aware of it. If you go to a computational biology or bioinformatics programs, your education will be more rounded and not just about computer science. Make sure you thoroughly research your advisors backgrounds and interests. Find out what they know and are capable of helping you on. If they don't have a CS background, then they won't be able to help you with the CS side of things, especially if that is where you want to keep your focus. If you aren't as intersted in the CS side, then this might be the better way to go. I recommend you obtain someone within the field you are focusing on outside of CS to be on your committee. I see some of the graduate students in the CS dept focusing on bioinformatics (and sometimes the advisors as well), but they usually seem a little lost at first. Some of the presentations I went to, you could tell they didn't totally grasp the molecular biology part of the problems they are focusing on. Make sure you have advisors from the different fields regardless of which path you take. Good luck! Ryan -----Original Message----- From: bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org [mailto:bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org ] On Behalf Of Daniel Terry Sent: Tuesday, November 22, 2005 6:43 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] PhD Programs: CS vs bioinformatics I am finishing my applications for doctoral study for next fall, but I had a question before I send all this off. I am a computer science undergrad wanting to work in bioinformatics (with CS focus), but don't have a whole lot of biology and chemistry background. I will get most of what most programs want by the time I graduate, but most of this won't show up on transcripts (I just started these classes this semester). I'm sure I want to work in bioinformatics, so the ability to switch focus areas in CS wouldn't be much of an advantage. Many of the schools I am applying to have a computational biology or bioinformatics PhD-offering programs and a computer science department that also does lots of research in this area. Which would make the most sense for me to apply to? Would the specialty programs be more likely to accept me because I am specifically interested in their area, or should I apply to CS since I have a stronger background in that? Thanks for any suggestions. -- Daniel Terry Senior Undergraduate in Computer Science Purdue University - Indianapolis (IUPUI) http://www.cs.iupui.edu/~dsterry/ _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From blanchem at mcb.mcgill.ca Thu Nov 24 21:55:54 2005 From: blanchem at mcb.mcgill.ca (Mathieu Blanchette) Date: Thu, 24 Nov 2005 21:55:54 -0500 Subject: [BiO BB] Announcement: Phylogenomics conference Message-ID: ********* Conference announcement ****************** First International Conference on Phylogenomics Dates: March 16-19 2006 Location: Sainte-Ad?le (near Montreal), Qu?bec, Canada Web site: http://www.bioinfo.umontreal.ca/evenements/phylogenomics.html Organizers: Herv? Philippe and Mathieu Blanchette Scope: This conference aims to reunite experts focusing on two distinct aspects of phylogenomics: the use of genome data inferring species phylogeny and the use of phylogenetic approaches to gain insights into gene functions. The methods developed for phylogenetic inference (especially the models of sequence evolution) are quite advanced and could benefit to function prediction. Similarly, the knowledge of the accurate species phylogeny increases the quantity of functional information that can be extracted. Conversely, knowledge of gene function and the other selective constraints is primordial to improve tree reconstruction methods. This conference will create synergy between these two phylogenomic communities, bridging the gap between there respective scientific endeavors. A special issue of BMC Evolutionary Biology will be dedicated to the conference, allowing contributors of the conference to submit their manuscripts. Invited speakers: * Ford Doolittle Dalhousie University, Canada * Jonathan Eisen, The Institute for Genomic Research, USA * Brian Golding, McMaster University, Canada * Nick Goldman, EMBL-EBI Cambridge, UK * Richard Goldstein, National Institute for Medical Research, USA * Jotun Hein, University of Oxford, UK * Mark Pagel, University of Reading, UK * Eduardo Rocha, Universit? Paris 6, France * Andrew Roger, Dalhousie University, Canada * Michael Sanderson, University of California, USA * Adam Siepel, Cornell University, USA * Yves van de Peer, Ghent University, Belgium Important dates: Deadline for early registration: January 15th 2006. Deadline for abstract submission for presentation: January 15th 2006 Deadline for manuscript submission (accepted abstracts only): March 1st 2006 -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 2233 bytes Desc: not available URL: From dmb at mrc-dunn.cam.ac.uk Mon Nov 28 08:26:27 2005 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Mon, 28 Nov 2005 13:26:27 +0000 Subject: [BiO BB] mounting london on linux... Message-ID: <438B0583.1030004@mrc-dunn.cam.ac.uk> Add the following lines to your /etc/fstab... //london.mrc-dunn.cam.ac.uk/Homes$ /mnt/London/Homes smbfs credentials=/etc/smb.cred,uid=2052,gid=10101 //london/Group\040Data /mnt/London/GroupData/ smbfs credentials=/etc/smb.cred,uid=2052,gid=10101 and configure the mount with using the smb.cred... username=dmb password=xxxxxx From dmb at mrc-dunn.cam.ac.uk Mon Nov 28 08:33:07 2005 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Mon, 28 Nov 2005 13:33:07 +0000 Subject: Oops... PLEASE IGNORE! Re: [BiO BB] mounting london on linux... In-Reply-To: <438B0583.1030004@mrc-dunn.cam.ac.uk> References: <438B0583.1030004@mrc-dunn.cam.ac.uk> Message-ID: <438B0713.4080209@mrc-dunn.cam.ac.uk> This new emailer is kinda fiddly... Needless to say this email was not intended for the list! Dan Bolser wrote: > Add the following lines to your /etc/fstab... > > //london.mrc-dunn.cam.ac.uk/Homes$ /mnt/London/Homes smbfs > credentials=/etc/smb.cred,uid=2052,gid=10101 > //london/Group\040Data /mnt/London/GroupData/ > smbfs credentials=/etc/smb.cred,uid=2052,gid=10101 > > and configure the mount with using the smb.cred... > > username=dmb > password=xxxxxx > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From rwang at bccrc.ca Mon Nov 28 14:25:43 2005 From: rwang at bccrc.ca (Renxue Wang) Date: Mon, 28 Nov 2005 11:25:43 -0800 Subject: [BiO BB] bioperl-ext installation Message-ID: <0BE438149FF2254DB4199E2682C8DFEB7028F6@crcmail1.BCCRC.CA> Hi, There, I am trying to install bioperl-ext package on my Redhat 9.0, but the hit a lot of problems. I followed the instructions of README and some points in some web postings, but it did not go through. I thought someone might have some better ideas on what is going on there and what I should do. Would you let me know if you do? I attach the error messages below. Thanks a lot, Renxue _______________________________________________________________ Here is what I got, > perl Makefile.PL Writing Makefile for Bio::Ext::Align Found Staden io_lib "libread" in /usr/local/lib ... Automatically using the Read.h found in /usr/local/include/io_lib ... Writing Makefile for Bio::SeqIO::staden::read Writing Makefile for Bio One or more DATA sections were not processed by Inline. [root at VLING010 bioperl-ext]# also, in "make", I got this in the end, read.xs:145: request for member `info' in something not a structure or union make[2]: *** [read.o] Error 1 make[2]: Leaving directory `/home/hok/bioperl-ext/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/r ead' A problem was encountered while attempting to compile and install your Inline C code. The command that failed was: make The build directory was: /home/hok/bioperl-ext/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/re ad To debug the problem, cd to the build directory, and inspect the output files. at -e line 0 INIT failed--call queue aborted. make[1]: *** [read.inl] Error 2 make[1]: Leaving directory `/home/hok/bioperl-ext/Bio/SeqIO/staden' make: *** [subdirs] Error 2 in "make test", this came up, [root at VLING010 Align]# make test PERL_DL_NONLAZY=1 /usr/bin/perl "-Iblib/lib" "-Iblib/arch" test.pl 1..9 # Running under perl version 5.008 for linux # Current time local: Thu Nov 17 13:21:45 2005 # Current time GMT: Thu Nov 17 21:21:45 2005 # Using Test.pm version 1.23 Can't locate Bio/Ext/Align.pm in @INC (@INC contains: blib/lib blib/arch /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 .) at test.pl line 14. BEGIN failed--compilation aborted at test.pl line 14. make: *** [test_dynamic] Error 2 [root at VLING010 Align]# I ignored these and went ahead with make install. The program did not work with my alignment script using Bio::Tools::pSW. Seems some components (here "blosum62.bla") was not installed properly. [root at VLING010 melan_simu4th]# ./align.pl test.ORTH test Warning Error Could not open blosum62.bla as a filename for read Blast matrix ------------- EXCEPTION ------------- MSG: blosum62.bla cannot be read as a BLAST comparison matrix file STACK Bio::Tools::pSW::matrix /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/pSW.pm:360 STACK Bio::Tools::pSW::new /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/pSW.pm:155 STACK toplevel ./align.pl:11 -------------------------------------- [root at VLING010 melan_simu4th]# From logan at cacs.louisiana.edu Wed Nov 30 15:02:07 2005 From: logan at cacs.louisiana.edu (Raja Loganantharaj) Date: Wed, 30 Nov 2005 14:02:07 -0600 Subject: [BiO BB] 2nd CFP:Special Session on Bioinformatics (June 27-30) In-Reply-To: <4374BE14.3010201@cacs.louisiana.edu> References: <4374BE14.3010201@cacs.louisiana.edu> Message-ID: <438E053F.2010405@cacs.louisiana.edu> You are invited to submit a paper to the BioInformatics track of the IEA/AIE 2006 conference in Annecy FRANCE June 27-30. The goal of the special track is to facilitate collaboration between AI researchers and biologists by presenting cutting edge algorithms, ideas and the applications of AI technology to solve interesting problems in computational biology. We plan to accept up to 10 papers for presentation (after a formal peer review process) and these will be included in the IEA/AIE 2006 conference proceedings, which is published in a bound volume by Springer-Verlag in their 'Lecture Notes in Artificial Intelligence' series. All the accepted papers will be considered for a special issue of the Journal of Applied Intelligence. The topics of interests include, but not limited to: * Sequence Alignment * Gene Discovery * Protein /RNA structure Prediction and Modeling * Comparative Genomics * Regulatory modules and Pathway analysis * Evolution and Phylogenetics * Molecular Structures * Interactions between protein to protein, and protein to dna. * MicroArray data analysis and high dimensional reductions * Application of machine learning to molecular biology View the details at http://esia2.univ-savoie.fr/conf-iea-aie/index.php?id=18 The important dates are *December 9, 2005* /Electronic Paper Submission Deadline/ *January 23, 2006* /Author(s) Notification/ *February 24, 2006* /Camera-Ready Copy Deadline/ *June 27-30, 2006* /IEA/AIE-06 Special session on Bioinformatics/ Thank you Raja Loganantharaj A pdf version of the CFP is attached -------------- next part -------------- A non-text attachment was scrubbed... Name: cfp.pdf Type: application/pdf Size: 32492 bytes Desc: not available URL: