From jeff at bioinformatics.org Fri Jun 2 11:05:14 2006 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri, 02 Jun 2006 11:05:14 -0400 Subject: [BiO BB] ANNOUNCE: New On-Site and On-Line Courses Message-ID: <448053AA.4050000@bioinformatics.org> (Apologies for multiple copies) The non-profit Bioinformatics Organization (Bioinformatics.Org) is pleased to announce the expansion of its educational services with the introduction of on-site and on-line training courses in bioinformatics. Since 1998, Bioinformatics.Org has been providing free hosting services for bioinformaticists. They've been focused largely on software development projects, but we're now expanding both research and educational services. Training courses and static tutorials will employ the open-source Moodle course management system to manage student registration and course materials. It's located here: http://edu.bioinformatics.org/ (Note: Account registration will be separate for this system until it can be integrated with the rest of the Bioinformatics.Org website. If you are member of Bioinformatics.Org, you'll need to re-register for this site in order to use it.) While the on-line course materials will remain gratis, courses lead by an instructor will often require a fee -- tiered for academics and economies -- to compensate the instructor and to help the Organization. Our very first course is on-site and targeted toward laboratory researchers who wish to learn how two open-source scripting languages can become powerful tools for data analysis. Please pass the following announcement on to any researcher who would be interested in this course. OPEN SOURCE BIOINFORMATICS FOR RESEARCHERS CAMBRIDGE, MA SEPT. 19 & 20, 2006 DESCRIPTION: This is a course on the fundamentals of open-source programming, to help biologists understand how and when to use the right computer tools for solving computational biology problems, whether sequence analysis, gene expression, mass spectrometry, or systems biology. This course is modularized so that researchers can understand two distinct tools: a programming and scripting language such as Perl, and a data analysis and visualization language such as R. Armed with knowledge and some hands-on experience with these tools (including add-on modules like BioPerl and Bioconductor), scientists will be able to appreciate and use software better in their organization, and also be able to put research questions in the context of these tools. They will be able to do basic computational tasks themselves and better communicate with their IT group. PREREQUISITES: There are no prerequisites for this course other than having a need to learn some of the fundamentals of programming, in case the scientist has any bioinformatic tasks in their day-to-day work. COURSE OUTLINE: Day 1: 09:00 - 12:00 pm: Basics of Perl 12:00 - 01:00 pm: LUNCH 01:00 - 04:30 pm: Data manipulation using Perl/BioPerl Day 2: 09:00 - 12:00 pm: Basics of R 12:00 - 01:00 pm: LUNCH 01:00 - 04:30 pm: Bioconductor for microarray analysis Breakfast and afternoon tea is provided, but lunch is not. LOGISTICS: When: September 19th & 20th, 2006 Where: The Radisson, Cambridge, Massachusetts COURSE FEES: Commercial: $600/person Academic: $300/person All attendees are encouraged to bring their own notebook computers, since this will be a hands-on workshop. CDs will be provided to install the necessary software, and lecture notes and exercises will be provided. Register today (account required): http://edu.bioinformatics.org/course/view.php?id=2 Additionally, please let us know if you'd like the Bioinformatics Organization to come to your institution and provide training in the following areas: Scripting Languages for Biology: - Perl/BioPerl Statistical Tools for Biology: - R/Bioconductor - Matlab and Octave Data Management Tools for Biology: - MySQL Also let us know if you're interested in creating and running your own course. Cheers, Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From skhadar at gmail.com Sat Jun 3 04:53:21 2006 From: skhadar at gmail.com (Shameer Khadar) Date: Sat, 3 Jun 2006 14:23:21 +0530 Subject: [BiO BB] CGI to pass a single PDB file to multiple server Message-ID: Hi All, We have three web servers (say a,b,c) that take a similar file (pdb) and gives the results. Now, we want to make a meta-server with three check-boxes and only one input form. The purpose is to accept a single file and run the 'checked' server and provide the results as separate links in next page. > Is it possible to pass files to different CGI/perl program using one single form ? (I know this is possible and people are implimenting this as a part of Meta-Server. )How ? Any sample codes / applications around ? Happy Bioinformtics, Shameer Khadar -------------- next part -------------- An HTML attachment was scrubbed... URL: From skhadar at gmail.com Sat Jun 3 04:57:47 2006 From: skhadar at gmail.com (Shameer Khadar) Date: Sat, 3 Jun 2006 14:27:47 +0530 Subject: [BiO BB] How to deploy a Bioinformatics Web Service ? Message-ID: Hi all, I have a Web Server/Database and I want to deploy a web service based on that. It will be really helpful, If I could get some of my basic doubts cleared. 1) How to write a WSDL for my server. (I checked several bioinformatics WSDL, but none of them are pointing towards the web server as such - my basic doubt is how the WSDL will interact with my Server ) 2) How should I write a server side program ? Where should I keep this program in the Server ? (Is there any standard code available) Happy Bioinformatics, Shameer -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamid at ibb.ut.ac.ir Sat Jun 3 06:25:47 2006 From: hamid at ibb.ut.ac.ir (hamid) Date: Sat, 03 Jun 2006 14:55:47 +0430 Subject: [BiO BB] A series of Pairwise alignments In-Reply-To: References: Message-ID: Hi buddy, Does anybody know how can I perform a series of pairwise alignments among all members of a set of proteins (almost 150 proteins) those I have their FastA sequences and sort mostly matched couples? I do not want to use ClustalW multiple alignment. Yours, Hamid /* Hamid Nikbakht, M.Sc of Cell and Molecular Biology, Laboratory of Biophysics and Molecular Biology, Bioinformatics Center, Institute of Biochemistry and Biophysics(IBB), University of Tehran, Tehran,Iran. Tel: +98-21-6111-3322 Fax: +98-21-6640-4680 Alt. E-mail: nikbakht at ibb.ut.ac.ir */ From aloraine at gmail.com Sat Jun 3 10:00:23 2006 From: aloraine at gmail.com (Ann Loraine) Date: Sat, 3 Jun 2006 09:00:23 -0500 Subject: [BiO BB] A series of Pairwise alignments In-Reply-To: References: Message-ID: <83722dde0606030700x563b6197v139c0fdc0b3bf3be@mail.gmail.com> Howdy, Probably you would want to run a pairwise alignment program over each pair of seqs and then write some wrapper code around that to process the data as you like. The alignment program you select should be something that fits your goal - do you want global or local alignment? What kind of scoring system do you need? And so on. For fun, take a look at: http://helix.biology.mcmaster.ca/721/outline2/node42.html -Ann On 6/3/06, hamid wrote: > Hi buddy, > Does anybody know how can I perform a series of pairwise alignments among > all members of a set of proteins (almost 150 proteins) those I have their > FastA sequences and sort mostly matched couples? I do not want to use > ClustalW multiple alignment. > Yours, > Hamid > > /* > Hamid Nikbakht, > M.Sc of Cell and Molecular Biology, > Laboratory of Biophysics and Molecular Biology, > Bioinformatics Center, > Institute of Biochemistry and Biophysics(IBB), > University of Tehran, > Tehran,Iran. > Tel: +98-21-6111-3322 > Fax: +98-21-6640-4680 > Alt. E-mail: nikbakht at ibb.ut.ac.ir > */ > > > _______________________________________________ > 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 http://www.transvar.org From mmarchywka at eyewonder.com Sat Jun 3 10:23:53 2006 From: mmarchywka at eyewonder.com (Mike Marchywka) Date: Sat, 3 Jun 2006 10:23:53 -0400 Subject: [BiO BB] A series of Pairwise alignments Message-ID: <73CA026E5E77C74398C69F3338C5967C07553E3F@atlexc01.atlanta.eyewonder.com> Yeah, it occured to me the objective would drive the definitions. I've been thinking about stuff like this from the immune's system point of view. Consider something like clustering software since with that many sequences they probably can be lumped into clusters. It occured to me you could take each sequence, break it up (generate "words" (peptides) using your favorite epitope prediction code ), and cluster the sequences based on "vocabulary". This may tell you which groups of proteins look similar to the immune system. btw, has anyone used tools or features like the "signatures" mentioned here? http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/printscontents.html#Receptors ************************************************************************* -----Original Message----- From: bio_bulletin_board-bounces+mmarchywka=eyewonder.com at bioinformatics.org [mailto:bio_bulletin_board-bounces+mmarchywka=eyewonder.com at bioinformati cs.org]On Behalf Of Ann Loraine Sent: SaturdayJune-03-2006 10:00 AM To: The general forum at Bioinformatics.Org Subject: Re: [BiO BB] A series of Pairwise alignments Howdy, Probably you would want to run a pairwise alignment program over each pair of seqs and then write some wrapper code around that to process the data as you like. The alignment program you select should be something that fits your goal - do you want global or local alignment? What kind of scoring system do you need? And so on. For fun, take a look at: http://helix.biology.mcmaster.ca/721/outline2/node42.html -Ann \ From skhadar at gmail.com Sat Jun 3 10:59:48 2006 From: skhadar at gmail.com (Shameer Khadar) Date: Sat, 3 Jun 2006 07:59:48 -0700 Subject: [BiO BB] How to deploy a Bioinformatics Web Service ? In-Reply-To: References: Message-ID: Hi all, We have a Web Server/Database which perform some analysis on protein structure and I want to deploy a web service based on that. It will be really helpful, If I could get some of my basic doubts cleared. 1) How to write a WSDL for my server. (I checked several bioinformatics WSDL, but none of them are pointing towards the web server as such - my basic doubt is how the WSDL will interact with my Server ) 2) How should I write a server side program ? Where should I keep this program in the Server ? (Is there any standard code available) Happy Bioinformatics, Shameer -------------- next part -------------- An HTML attachment was scrubbed... URL: From skhadar at gmail.com Sat Jun 3 11:00:16 2006 From: skhadar at gmail.com (Shameer Khadar) Date: Sat, 3 Jun 2006 08:00:16 -0700 Subject: [BiO BB] CGI to pass a single PDB file to multiple server In-Reply-To: References: Message-ID: Hi All, We have three web servers (say a,b,c) that take a similar file (pdb) and gives the results. Now, we want to make a meta-server with three check-boxes and only one input form. The purpose is to accept a single file and run the 'checked' server and provide the results as separate links in next page. > Is it possible to pass files to different CGI/perl program using one single form ? (I know this is possible and people are implimenting this as a part of Meta-Server. )How ? Any sample codes / applications around ? Happy Bioinformtics, Shameer Khadar -------------- next part -------------- An HTML attachment was scrubbed... URL: From clement at cs.byu.edu Sat Jun 3 16:55:10 2006 From: clement at cs.byu.edu (Mark Clement) Date: Sat, 3 Jun 2006 14:55:10 -0600 Subject: [BiO BB] Biotechnology and Bioinformatics Symposium (Submission Deadine Extended to June 12) Message-ID: Many authors asked for an extension of the submission deadline. The deadline will now be June 12, 2006, but there will be no further extensions. ======================== Call for Papers (BIOT-2006) Provo, Utah October 20-21, 2006 http://www.biotconf.org/ ========================= Research and development in biotechnology requires the collaboration of scientists and engineers in fields such as biology, chemistry, computer science, chemical engineering, and electrical engineering. This symposium will bring together scientists, engineers and scholars from relevant fields with practitioners from industry in order to help each group to understand progress made in the area as a whole. The Biotechnology and Bioinformatics Symposium 2006 will be held in Provo , Utah on October 20-21, 2006, hosted by Brigham Young University. Topics of interest include: Bio-molecular and Phylogenetic Databases Molecular Evolution and Phylogenetic analysis Drug Delivery Systems Bio-Ontology and Data Mining Sequence Search and Alignment Microarray Analysis System Biology Pathway analysis Identification and Classification of Genes Protein Structure Prediction and Molecular Simulation Functional Genomics Proteomics Tertiary structure prediction Drug Docking Gene Expression Analysis Biomedical Imaging Submissions An extended abstract or a paper must report significant research results, findings or advances within its own field. However, since the symposium is geared toward a diverse audience of biologists, computer scientists, chemists, engineers, technology transfer individuals, graduate students, professors, industry individuals, etc., the papers or extended abstracts must be presented in a lucid manner accessible to such individuals. A pdf version of your paper can be submitted at http://www.biotconf.org/papersubmission/openconf.php ---------------- Dr. Mark Clement Department of Computer Science Brigham Young University 3370 TMCB Provo, Utah 84602 (801) 422-7608 clement at cs.byu.edu From skhadar at gmail.com Sat Jun 3 10:51:24 2006 From: skhadar at gmail.com (Shameer Khadar) Date: Sat, 3 Jun 2006 07:51:24 -0700 Subject: [BiO BB] A series of Pairwise alignments In-Reply-To: <73CA026E5E77C74398C69F3338C5967C07553E3F@atlexc01.atlanta.eyewonder.com> References: <73CA026E5E77C74398C69F3338C5967C07553E3F@atlexc01.atlanta.eyewonder.com> Message-ID: * Please try FMALIGN @ NCBS * This server aligns two or more sequences by fixing sequentially conserved region or motifs within the aligned sequences. By fixing conserved regions this method allows flexibility and accuracy to the alignment. It also provides conserved regions for a set of sequences which can be used for FMALIGN. FMALIGN SERVER URL : http://www.ncbs.res.in/~faculty/mini/FMALIGN/home.html Cheers, Shameer Khadar Prof. R. Sowdhamini's Lab NCBS - TIFR On 6/3/06, Mike Marchywka wrote: > > > Yeah, it occured to me the objective would drive the definitions. > I've been thinking about stuff like this from the immune's system point of > view. > Consider something like clustering software since with that many > sequences they probably can be lumped into clusters. It occured to me you > could > take each sequence, break it up (generate "words" (peptides) using your > favorite epitope > prediction code ), and cluster the sequences based on "vocabulary". > This may tell you which groups of proteins look similar to the immune > system. > > btw, has anyone used tools or features like the "signatures" mentioned > here? > http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/printscontents.html#Receptors > > ************************************************************************* > > > -----Original Message----- > From: > bio_bulletin_board-bounces+mmarchywka=eyewonder.com at bioinformatics.org > [mailto:bio_bulletin_board-bounces+mmarchywka=eyewonder.com at bioinformati > cs.org]On Behalf Of Ann Loraine > Sent: SaturdayJune-03-2006 10:00 AM > To: The general forum at Bioinformatics.Org > Subject: Re: [BiO BB] A series of Pairwise alignments > > > Howdy, > > Probably you would want to run a pairwise alignment program over each > pair of seqs and then write some wrapper code around that to process > the data as you like. > > The alignment program you select should be something that fits your > goal - do you want global or local alignment? What kind of scoring > system do you need? And so on. > > For fun, take a look at: > > http://helix.biology.mcmaster.ca/721/outline2/node42.html > > -Ann > \ > _______________________________________________ > 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 maximilianh at gmail.com Mon Jun 5 02:16:32 2006 From: maximilianh at gmail.com (Maximilian Haeussler) Date: Sun, 4 Jun 2006 22:16:32 -0800 Subject: [BiO BB] Extracting upstream sequence of a gene In-Reply-To: <1147195811.4460d1a332659@netmail.bsd.uchicago.edu> References: <1147124919.445fbcb75d225@netmail.bsd.uchicago.edu> <445FBE9C.3070407@terra.com.br> <1147195811.4460d1a332659@netmail.bsd.uchicago.edu> Message-ID: <76f031ae0606042316kf80a88asf23f54c9a308a76@mail.gmail.com> (Kind of late reply.) There are various methods. Biomart is one of them. But you can do the same thing with the UCSC browser. You have two options here: a) download directly from their website (they have upstreamxxxx.zip-files prepared for you!) e.g. for mouse: http://hgdownload.cse.ucsc.edu/goldenPath/mm7/bigZips/ b) with the table browser (I quote an old mail from Jen from UCSC): Using the Table browser form ("Tables" in blue navigation bar): 1. Select genome/release = mm7, group/track = RefSeq, region=genome 2. Output = sequence, type in a file name, select .gzip compression 3. On next page sequence type = genomic 4. And on final page specify the amount of upstream sequence good luck, Max > Here is the link to Biomart: > http://www.ensembl.org/Multi/martview > > Steps: > 1) Under Dataset: > -Selected (ensembl 38, homo sapiens genes ) > 2) Filters: > -GENE > - ID LIST LIMIT - "HGNC Symbols", Enter symbols or upload a list. > 3) OUTPUT > - ATTRIBUTE - (Select Sequences) > - SEQUENCES - (Select Flank(Gene)) > - Check box "Upstream Flank" > Choose as many other attributes as you need in your output file. > > > -Kiran > Quoting Paulo Nuin : > > > Hi > > > > If you have the IDs of these genes you can do that on the UCSC genome > > browser. You can set a region to download automatically from a multiple > > search. > > > > Regards > > > > Paulo > > > > > > kannaiah at bsd.uchicago.edu wrote: > > > Hello, > > > > > > I have seen a few posts asking similar questions. I am looking to do > > something > > > similar too. > > > > > > I want to extract the upstream sequence of genes (upto 3000bp upstream) > > in > > > Human. But going thru the ensembl website is ok, if one has few genes. > > > > > > But i have a few hundred genes. I was wondering what would be the best way > > to > > > automate this. > > > Should i try blasting the gene sequences to the Human Chromosome files, and > > then > > > parse the blast output to get the position of the genes, and go back and > > read > > > the chromosome sequence where it was found and get the upstream sequence. > > > > > > That would be a long way, hopefully there is someother shorter way to do > > this, > > > which i am not aware of. > > > Any suggestions would be welcome:) > > > > > > Thank you > > > > > > -hak > > > > > > > > > > > > > > > ------------------------------------------------- > > > This email is intended only for the use of the individual or entity to > > which > > > it is addressed and may contain information that is privileged and > > > confidential. If the reader of this email message is not the intended > > > recipient, you are hereby notified that any dissemination, distribution, > > or > > > copying of this communication is prohibited. If you have received this > > email > > > in error, please notify the sender and destroy/delete all copies of the > > > transmittal. Thank you. > > > ------------------------------------------------- > > > _______________________________________________ > > > Bioinformatics.Org general forum - > > BiO_Bulletin_Board at bioinformatics.org > > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > E-mail classificado pelo Identificador de Spam Inteligente Terra. > > > Para alterar a categoria classificada, visite > > > > > > http://mail.terra.com.br/protected_email/imail/imail.cgi?+_u=pnuin&_l=1,1147124935.329176.19195.ambrose.hst.terra.com.br,5320,Des15,Des15 > > > > > > Esta mensagem foi verificada pelo E-mail Protegido Terra. > > > Scan engine: McAfee VirusScan / Atualizado em 08/05/2006 / Vers?o: > > 4.4.00/4757 > > > Proteja o seu e-mail Terra: http://mail.terra.com.br/ > > > > > > > > > > > > > _______________________________________________ > > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > > > > > > > ------------------------------------------------- > This email is intended only for the use of the individual or entity to which > it is addressed and may contain information that is privileged and > confidential. If the reader of this email message is not the intended > recipient, you are hereby notified that any dissemination, distribution, or > copying of this communication is prohibited. If you have received this email > in error, please notify the sender and destroy/delete all copies of the > transmittal. Thank you. > ------------------------------------------------- > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Maximilian Haeussler, CNRS Gif-sur-Yvette, Paris tel: +33 6 12 82 76 16 icq: 3825815 -- msn: maximilian.haeussler at hpi.uni-potsdam.de skype: maximilianhaeussler From hararid at bgu.ac.il Mon Jun 5 03:36:37 2006 From: hararid at bgu.ac.il (Daniel Harari) Date: Mon, 05 Jun 2006 09:36:37 +0200 Subject: [BiO BB] Quantifying protein Domains En Mass Message-ID: <4483DF05.6000304@bgu.ac.il> Hi, I am after a way in which I can analyze large data sets of protein sequences, where the readout is a quantification of different protein domains that are found within a given list of sequences (e.g. a list of 500 protein sequences in FASTA format). Preferably the output would be at the systems level (e.g. 230 Tyrosine Kinase domains) rather than that describing domains only at a protein-by protein level. Thanks, Daniel -- Daniel Harari, Ph.D. Rubin Lab. National Institute for Biotechnology in the Negev Building 39, room -113 Ben-Gurion University of the Negev Beer-Sheva 84105, Israel Email: hararid at bgu.ac.il Tel: 08-6477180 Fax: 08-6472983 From marty.gollery at gmail.com Sun Jun 4 11:57:26 2006 From: marty.gollery at gmail.com (Martin Gollery) Date: Sun, 4 Jun 2006 08:57:26 -0700 Subject: [BiO BB] A series of Pairwise alignments In-Reply-To: <73CA026E5E77C74398C69F3338C5967C07553E3F@atlexc01.atlanta.eyewonder.com> References: <73CA026E5E77C74398C69F3338C5967C07553E3F@atlexc01.atlanta.eyewonder.com> Message-ID: Hi Mike, Yes, I have used the PRINTS tools- they are a very useful part of Interpro, and can be used with InterProScan or stand-alone. Marty On 6/3/06, Mike Marchywka wrote: > > > Yeah, it occured to me the objective would drive the definitions. > I've been thinking about stuff like this from the immune's system point of > view. > Consider something like clustering software since with that many > sequences they probably can be lumped into clusters. It occured to me you > could > take each sequence, break it up (generate "words" (peptides) using your > favorite epitope > prediction code ), and cluster the sequences based on "vocabulary". > This may tell you which groups of proteins look similar to the immune > system. > > btw, has anyone used tools or features like the "signatures" mentioned > here? > http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/printscontents.html#Receptors > > ************************************************************************* > > > -----Original Message----- > From: > bio_bulletin_board-bounces+mmarchywka=eyewonder.com at bioinformatics.org > [mailto:bio_bulletin_board-bounces+mmarchywka=eyewonder.com at bioinformati > cs.org]On Behalf Of Ann Loraine > Sent: SaturdayJune-03-2006 10:00 AM > To: The general forum at Bioinformatics.Org > Subject: Re: [BiO BB] A series of Pairwise alignments > > > Howdy, > > Probably you would want to run a pairwise alignment program over each > pair of seqs and then write some wrapper code around that to process > the data as you like. > > The alignment program you select should be something that fits your > goal - do you want global or local alignment? What kind of scoring > system do you need? And so on. > > For fun, take a look at: > > http://helix.biology.mcmaster.ca/721/outline2/node42.html > > -Ann > \ > _______________________________________________ > 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 christoph.gille at charite.de Mon Jun 5 10:19:51 2006 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Mon, 5 Jun 2006 16:19:51 +0200 (CEST) Subject: [BiO BB] A series of Pairwise alignments In-Reply-To: References: Message-ID: <61040.84.190.38.195.1149517191.squirrel@webmail.charite.de> http://3d-alignment.eu/ can compute all pairwise alignments of a set of protein sequences. It writes a table of values of sequence similarities or alignment scores. The user can chose the prefered alignment method. It is found in menu "analyze" / "compare some proteins". The software is relatively complex and not easy to use for novices. Christoph From carlosjmviana at gmail.com Mon Jun 5 20:23:58 2006 From: carlosjmviana at gmail.com (Carlos Viana) Date: Mon, 5 Jun 2006 20:23:58 -0400 Subject: [BiO BB] note or error in formatdb ? Message-ID: Hi members, Today, I performed formatdb tool with the following line command: >>>> formatdb -i file.fasta -o T -p T But I had this message in formatdb.log: "NOTE: ncbiapi [000.000] SeqIdParse Failure at >gi|200001" So, anyone know what kind of message is this? Is this an error or just a warning? I performed with versions 2.2.12 and 2.2.14. Thanks, cviana -------------- next part -------------- An HTML attachment was scrubbed... URL: From landman at scalableinformatics.com Mon Jun 5 20:28:00 2006 From: landman at scalableinformatics.com (Joe Landman) Date: Mon, 05 Jun 2006 20:28:00 -0400 Subject: [BiO BB] note or error in formatdb ? In-Reply-To: References: Message-ID: <4484CC10.7060906@scalableinformatics.com> Carlos Viana wrote: > Hi members, > > Today, I performed formatdb tool with the following line command: > > >>>> formatdb -i file.fasta -o T -p T > > But I had this message in formatdb.log: > > "NOTE: ncbiapi [000.000] SeqIdParse Failure at >gi|200001" Is this a duplicate? Try using the -V option with 2.2.14 > > So, anyone know what kind of message is this? > Is this an error or just a warning? > I performed with versions 2.2.12 and 2.2.14. > > Thanks, > cviana > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 or +1 866 888 3112 cell : +1 734 612 4615 From pj.siivola at luukku.com Tue Jun 6 04:18:51 2006 From: pj.siivola at luukku.com (=?ISO-8859-1?Q?p=E4ivi_siivola?=) Date: Tue, 6 Jun 2006 11:18:51 +0300 (EEST) Subject: [BiO BB] note or error in formatdb ? Message-ID: <1149581931440.pj.siivola.19617.RQYmc3Hp5b1fBQ5aMFsWAA@luukku.com> Hi! I ran to same kind of problem. Formatdb is sensitive about the title line of the fasta formatted sequence. (Title line= line starting with >). If I remember correct, I got the same kind error when my title line was not "FASTA Defline Format". Read from the page http://bioinformatics.ubc.ca/resources/tools/?name=formatdb the section "FASTA Defline Format". Hope it helps ! T: P?ivi Carlos Viana kirjoitti 06.06.2006 kello 03:23: > Hi members, > > Today, I performed formatdb tool with the following line command: > > >>>> formatdb -i file.fasta -o T -p T > > But I had this message in formatdb.log: > > "NOTE: ncbiapi [000.000] SeqIdParse Failure at >gi|200001" > > So, anyone know what kind of message is this? > Is this an error or just a warning? > I performed with versions 2.2.12 and 2.2.14. > > Thanks, > cviana ................................................................... Luukku Plus paketilla p??set eroon tila- ja turvallisuusongelmista. Hanki Luukku Plus ja helpotat el?m??si. http://www.mtv3.fi/luukku From deletto at unisa.it Tue Jun 6 11:27:31 2006 From: deletto at unisa.it (deletto at unisa.it) Date: Tue, 6 Jun 2006 17:27:31 +0200 Subject: [BiO BB] bac database, mouse genome(different strains) In-Reply-To: References: Message-ID: <1149607651.44859ee3796b0@webmail.unisa.it> Hello everyone, I am wondering if someone of you could help me. I am looking for a comprensive database of Bac clones for MOuse Genome from different strain. For istance, I would like to find a specific sequence within the genome of SV129 (or 129 Sv) Strain. I will appreciate any help. Thanks in advance. Davide \ Scrive Carlos Viana : > Hi members, > > Today, I performed formatdb tool with the following line command: > > >>>> formatdb -i file.fasta -o T -p T > > But I had this message in formatdb.log: > > "NOTE: ncbiapi [000.000] SeqIdParse Failure at >gi|200001" > > So, anyone know what kind of message is this? > Is this an error or just a warning? > I performed with versions 2.2.12 and 2.2.14. > > Thanks, > cviana > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From Michael.Muratet at operon.com Tue Jun 6 11:53:25 2006 From: Michael.Muratet at operon.com (Michael Muratet US-Huntsville) Date: Tue, 6 Jun 2006 10:53:25 -0500 Subject: [BiO BB] Withdrawl of Refseq accessions Message-ID: <2000234931344D4BA434A0C235D1956B0C4850@hsv-exmail02.operonads.local> Greetings I recently discovered that about 3000 Refseq accessions that were present in the 4/2005 release have been withdrawn. The ones I've looked at appear to be NCBI predictions using their gnomon tool and had 'XM_*' accessions. I'm concerned that a database that is supposed to be stable is so dynamic. I asked NCBI about it, but didn't get an explanation. Does anybody have any experience with such large scale withdrawls? Does anybody know why? Thanks Mike -------------- next part -------------- An HTML attachment was scrubbed... URL: From aloraine at gmail.com Tue Jun 6 12:22:57 2006 From: aloraine at gmail.com (Ann Loraine) Date: Tue, 6 Jun 2006 11:22:57 -0500 Subject: [BiO BB] Withdrawl of Refseq accessions In-Reply-To: <2000234931344D4BA434A0C235D1956B0C4850@hsv-exmail02.operonads.local> References: <2000234931344D4BA434A0C235D1956B0C4850@hsv-exmail02.operonads.local> Message-ID: <83722dde0606060922v456cbb54l93da7e5b6ab1189f@mail.gmail.com> What genome was it? Yours, Ann L. On 6/6/06, Michael Muratet US-Huntsville wrote: > > Greetings > > I recently discovered that about 3000 Refseq accessions that were present in > the 4/2005 release have been withdrawn. The ones I've looked at appear to be > NCBI predictions using their gnomon tool and had 'XM_*' accessions. I'm > concerned that a database that is supposed to be stable is so dynamic. I > asked NCBI about it, but didn't get an explanation. Does anybody have any > experience with such large scale withdrawls? Does anybody know why? > > Thanks > > Mike > _______________________________________________ > 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 http://www.transvar.org From Michael.Muratet at operon.com Tue Jun 6 12:24:38 2006 From: Michael.Muratet at operon.com (Michael Muratet US-Huntsville) Date: Tue, 6 Jun 2006 11:24:38 -0500 Subject: [BiO BB] Withdrawl of Refseq accessions Message-ID: <2000234931344D4BA434A0C235D1956B0C4851@hsv-exmail02.operonads.local> Human. Thanks Mike -----Original Message----- From: bio_bulletin_board-bounces+michael.muratet=operon.com at bioinformatics.org [mailto:bio_bulletin_board-bounces+michael.muratet=operon.com at bioinforma tics.org]On Behalf Of Ann Loraine Sent: Tuesday, June 06, 2006 11:23 AM To: The general forum at Bioinformatics.Org Subject: Re: [BiO BB] Withdrawl of Refseq accessions What genome was it? Yours, Ann L. On 6/6/06, Michael Muratet US-Huntsville wrote: > > Greetings > > I recently discovered that about 3000 Refseq accessions that were present in > the 4/2005 release have been withdrawn. The ones I've looked at appear to be > NCBI predictions using their gnomon tool and had 'XM_*' accessions. I'm > concerned that a database that is supposed to be stable is so dynamic. I > asked NCBI about it, but didn't get an explanation. Does anybody have any > experience with such large scale withdrawls? Does anybody know why? > > Thanks > > Mike > _______________________________________________ > 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 http://www.transvar.org _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From ethan.strauss at promega.com Tue Jun 6 12:25:52 2006 From: ethan.strauss at promega.com (Ethan Strauss) Date: Tue, 6 Jun 2006 11:25:52 -0500 Subject: [BiO BB] Withdrawl of Refseq accessions Message-ID: I've noticed this in human. Not sure about others... Ethan -----Original Message----- From: bio_bulletin_board-bounces+ethan.strauss=promega.com at bioinformatics.org [mailto:bio_bulletin_board-bounces+ethan.strauss=promega.com at bioinformat ics.org] On Behalf Of Ann Loraine Sent: Tuesday, June 06, 2006 11:23 AM To: The general forum at Bioinformatics.Org Subject: Re: [BiO BB] Withdrawl of Refseq accessions What genome was it? Yours, Ann L. On 6/6/06, Michael Muratet US-Huntsville wrote: > > Greetings > > I recently discovered that about 3000 Refseq accessions that were > present in the 4/2005 release have been withdrawn. The ones I've > looked at appear to be NCBI predictions using their gnomon tool and > had 'XM_*' accessions. I'm concerned that a database that is supposed > to be stable is so dynamic. I asked NCBI about it, but didn't get an > explanation. Does anybody have any experience with such large scale withdrawls? Does anybody know why? > > Thanks > > Mike > _______________________________________________ > 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 http://www.transvar.org _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From hlapp at gmx.net Tue Jun 6 12:08:23 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 6 Jun 2006 12:08:23 -0400 Subject: [BiO BB] Withdrawl of Refseq accessions In-Reply-To: <2000234931344D4BA434A0C235D1956B0C4850@hsv-exmail02.operonads.local> References: <2000234931344D4BA434A0C235D1956B0C4850@hsv-exmail02.operonads.local> Message-ID: RefSeq predictions get withdrawn, modified, and promoted to reviewed transcripts all the time in the course of curation and manual review, more than in the thousands ... In fact, the NM_ section (reviewed and better) is equally dynamic, only withdrawals are rare and most changes concern annotation ... Which reminds me: how many times has the 'final' human genome been published now? On Jun 6, 2006, at 11:53 AM, Michael Muratet US-Huntsville wrote: > Greetings > > I recently discovered that about 3000 Refseq accessions that were > present in the 4/2005 release have been withdrawn. The ones I've > looked at appear to be NCBI predictions using their gnomon tool and > had 'XM_*' accessions. I'm concerned that a database that is > supposed to be stable is so dynamic. I asked NCBI about it, but > didn't get an explanation. Does anybody have any experience with > such large scale withdrawls? Does anybody know why? > > Thanks > > Mike > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: From Yannick.Wurm at unil.ch Mon Jun 5 19:28:32 2006 From: Yannick.Wurm at unil.ch (Yannick Wurm) Date: Mon, 5 Jun 2006 19:28:32 -0400 Subject: [BiO BB] Re: BiO_Bulletin_Board Digest, Vol 20, Issue 5 In-Reply-To: <20060605160034.286EF36857A@primary.bioinformatics.org> References: <20060605160034.286EF36857A@primary.bioinformatics.org> Message-ID: <7515C868-0EAB-447A-95A6-A24B454C7D52@unil.ch> Hi Daniel, have a look at iprscan, which is a very complete tool: http://www.ebi.ac.uk/InterProScan/ For command-line access, see: http://www.ebi.ac.uk/Tools/webservices/WSInterProScan.html You can also set it up locally. For each protein, the output is one line per domain found on that protein. I concatenate the output files into one big file, and then count the different domains I have. Best, yannick ___________________________________ yannick.wurm at unil.ch - Doctoral student Department of Ecology and Evolution http://www.unil.ch/dee/page28685.html #3106, Biophore, Universite de Lausanne 1015 Lausanne, Switzerland land: +41.21.692.4182 fax: +41.21.692.4165 cell: +41.78.87.87.001 On 5 juin 06, at 12:00, bio_bulletin_board-request at bioinformatics.org wrote: > > > I am after a way in which I can analyze large data sets of protein > sequences, where the readout is a quantification of different protein > domains that are found within a given list of sequences (e.g. a > list of > 500 protein sequences in FASTA format). Preferably the output > would be > at the systems level (e.g. 230 Tyrosine Kinase domains) rather than > that > describing domains only at a protein-by protein level. > > Thanks, > > Daniel -------------- next part -------------- An HTML attachment was scrubbed... URL: From golharam at umdnj.edu Tue Jun 6 17:02:18 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Tue, 06 Jun 2006 17:02:18 -0400 Subject: [BiO BB] Withdrawl of Refseq accessions In-Reply-To: <2000234931344D4BA434A0C235D1956B0C4850@hsv-exmail02.operonads.local> Message-ID: <029c01c689ac$7f9fff10$e6028a0a@GOLHARMOBILE1> XM_ sequences are predicted sequences. I would not rely on them as they have not been verified. NM_ sequences are RefSeq sequences, and are much more stable - They are the NCBI curated sequences and have evidence supporting them. In some cases, you can do from the XM_ sequences to the GeneID to the new NM_ sequence that represents that Gene. I think the XM_ GenBank entry also documents the new NM_ entry. 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 Michael Muratet US-Huntsville Sent: Tuesday, June 06, 2006 11:53 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Withdrawl of Refseq accessions Greetings I recently discovered that about 3000 Refseq accessions that were present in the 4/2005 release have been withdrawn. The ones I've looked at appear to be NCBI predictions using their gnomon tool and had 'XM_*' accessions. I'm concerned that a database that is supposed to be stable is so dynamic. I asked NCBI about it, but didn't get an explanation. Does anybody have any experience with such large scale withdrawls? Does anybody know why? Thanks Mike -------------- next part -------------- An HTML attachment was scrubbed... URL: From Michael.Muratet at operon.com Tue Jun 6 17:18:39 2006 From: Michael.Muratet at operon.com (Michael Muratet US-Huntsville) Date: Tue, 6 Jun 2006 16:18:39 -0500 Subject: [BiO BB] Withdrawl of Refseq accessions Message-ID: <2000234931344D4BA434A0C235D1956B0C4857@hsv-exmail02.operonads.local> Ryan & Hilmar Thanks for the help. I checked the transcript stable ID tables over past releases of Ensembl to see how may IDs were created/terminated and it looked to be in the hundreds (but not thousands). I thought it might be a one-time transient at Refseq. It still seems like a lot to me given that we're now on the third or fourth 'final' release of the human genome as you noted, and I'll start processing each new release to see what's changed. Thanks, Mike -------------- next part -------------- An HTML attachment was scrubbed... URL: From aloraine at gmail.com Tue Jun 6 22:58:05 2006 From: aloraine at gmail.com (Ann Loraine) Date: Tue, 6 Jun 2006 21:58:05 -0500 Subject: [BiO BB] Withdrawl of Refseq accessions In-Reply-To: <2000234931344D4BA434A0C235D1956B0C4857@hsv-exmail02.operonads.local> References: <2000234931344D4BA434A0C235D1956B0C4857@hsv-exmail02.operonads.local> Message-ID: <83722dde0606061958k2b853590xfba398d901078c3@mail.gmail.com> Howdy again, Regarding multiple releases of the human genome: In some ways this is a good thing, because, in theory, newer releases improve upon the previous. And...well...they create greater need for bioinformatics professionals such as ourselves. Also, think about how the human genome is assembled. At every stage, decisions must be made. Are they the best? And for what purpose? And remember .... someday soon the $1,000 genome sequence will be upon us. How will we handle *that* ? How we will we handle the inevitable deletions, duplications, and (easy!) single-base pair changes these data will introduce into our vision of the genome? -Ann On 6/6/06, Michael Muratet US-Huntsville wrote: > > > Ryan & Hilmar > > Thanks for the help. I checked the transcript stable ID tables over past > releases of Ensembl to see how may IDs were created/terminated and it looked > to be in the hundreds (but not thousands). I thought it might be a one-time > transient at Refseq. It still seems like a lot to me given that we're now on > the third or fourth 'final' release of the human genome as you noted, and > I'll start processing each new release to see what's changed. > > Thanks, > > Mike > _______________________________________________ > 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 http://www.transvar.org From golharam at umdnj.edu Tue Jun 6 23:21:39 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Tue, 06 Jun 2006 23:21:39 -0400 Subject: [BiO BB] Withdrawl of Refseq accessions In-Reply-To: <83722dde0606061958k2b853590xfba398d901078c3@mail.gmail.com> Message-ID: <02c501c689e1$7f4a4ae0$e6028a0a@GOLHARMOBILE1> >>And...well...they create greater need for bioinformatics >>professionals such as ourselves. Good, cause I'm starting to look for a job. -----Original Message----- From: Ann Loraine [mailto:aloraine at gmail.com] Sent: Tuesday, June 06, 2006 10:58 PM To: The general forum at Bioinformatics.Org Cc: golharam at umdnj.edu; Hilmar Lapp Subject: Re: [BiO BB] Withdrawl of Refseq accessions Howdy again, Regarding multiple releases of the human genome: In some ways this is a good thing, because, in theory, newer releases improve upon the previous. And...well...they create greater need for bioinformatics professionals such as ourselves. Also, think about how the human genome is assembled. At every stage, decisions must be made. Are they the best? And for what purpose? And remember .... someday soon the $1,000 genome sequence will be upon us. How will we handle *that* ? How we will we handle the inevitable deletions, duplications, and (easy!) single-base pair changes these data will introduce into our vision of the genome? -Ann On 6/6/06, Michael Muratet US-Huntsville wrote: > > > Ryan & Hilmar > > Thanks for the help. I checked the transcript stable ID tables over > past releases of Ensembl to see how may IDs were created/terminated > and it looked to be in the hundreds (but not thousands). I thought it > might be a one-time transient at Refseq. It still seems like a lot to > me given that we're now on the third or fourth 'final' release of the > human genome as you noted, and I'll start processing each new release > to see what's changed. > > Thanks, > > Mike > _______________________________________________ > 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 http://www.transvar.org From raghu at ncbs.res.in Wed Jun 7 00:36:48 2006 From: raghu at ncbs.res.in (Raghu Prasad Rao, Metpally) Date: Wed, 7 Jun 2006 10:06:48 +0530 (IST) Subject: [BiO BB] Re: note or error in formatdb ? In-Reply-To: <20060606160050.C56AD36865C@primary.bioinformatics.org> References: <20060606160050.C56AD36865C@primary.bioinformatics.org> Message-ID: <33267.192.168.1.186.1149655008.squirrel@192.168.1.186> hi, Check out formatdb.log file, it looks like header line(s) of fasta sequence has some errors cheers Raghu From letondal at pasteur.fr Wed Jun 7 04:29:41 2006 From: letondal at pasteur.fr (Catherine Letondal) Date: Wed, 7 Jun 2006 10:29:41 +0200 Subject: [BiO BB] How to deploy a Bioinformatics Web Service ? In-Reply-To: References: Message-ID: On Jun 3, 2006, at 10:57 AM, Shameer Khadar wrote: > Hi all, > > > I have a Web Server/Database and I want to deploy a web service based > on that. > It will be really helpful, If I could get some of my basic doubts > cleared. > > > > 1) How to write a WSDL for my server. (I checked several > bioinformatics > WSDL, but none of them are pointing towards the web server as such - > my > > basic doubt is how the WSDL will interact with my Server ) > > 2) How should I write a server side program ? Where should I keep > this program in the > > Server ? (Is there any standard code available) > See www.biomoby.org > Happy Bioinformatics, > Shameer > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From carlosjmviana at gmail.com Wed Jun 7 09:26:15 2006 From: carlosjmviana at gmail.com (Carlos Viana) Date: Wed, 7 Jun 2006 10:26:15 -0300 Subject: [BiO BB] Re: note or error in formatdb ? In-Reply-To: <33267.192.168.1.186.1149655008.squirrel@192.168.1.186> References: <20060606160050.C56AD36865C@primary.bioinformatics.org> <33267.192.168.1.186.1149655008.squirrel@192.168.1.186> Message-ID: Hi members, The error was at header line of fasta sequence in the middle of my multi-fasta file. Thanks for advices. On 6/7/06, Raghu Prasad Rao, Metpally wrote: > > hi, > > Check out formatdb.log file, it looks like header line(s) of fasta > sequence has some errors > > cheers > Raghu > > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- ********************************************** * Carlos Juliano ********************************************** * msn: carlos_jmv2004 at hotmail.com ********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From aloraine at gmail.com Wed Jun 7 11:33:11 2006 From: aloraine at gmail.com (Ann Loraine) Date: Wed, 7 Jun 2006 10:33:11 -0500 Subject: [BiO BB] TM-HMM Web service for class? Message-ID: <83722dde0606070833l6bf3f80fv5b2af7e8c41cdd07@mail.gmail.com> Hi, I'm looking for a Web service that will let me upload a protein sequence (can't use ids, sorry...these are gene predictions) and then retrieve results from TM-HMM or a similar program that predicts membrane-spanning regions and topology. This is for a class demo and also for students doing term projects. Any advice would be much appreciated! Yours, Ann -- Ann Loraine Assistant Professor Section on Statistical Genetics University of Alabama at Birmingham http://www.ssg.uab.edu http://www.transvar.org From yqzhou at buffalo.edu Wed Jun 7 11:40:50 2006 From: yqzhou at buffalo.edu (Yaoqi Zhou) Date: Wed, 7 Jun 2006 11:40:50 -0400 Subject: [BiO BB] TM-HMM Web service for class? In-Reply-To: <83722dde0606070833l6bf3f80fv5b2af7e8c41cdd07@mail.gmail.com> References: <83722dde0606070833l6bf3f80fv5b2af7e8c41cdd07@mail.gmail.com> Message-ID: Try THUMBUP at http://theory.med.buffalo.edu Yaoqi Zhou, Associate Professor **CHECK out Newly UPDATED webpage** on http://theory.med.buffalo.edu Department of Physiology and Biophysics University at Buffalo, State University of New York 124 Sherman Hall, Buffalo, NY 14214 (716) 829-2985 Fax (716) 829-2344 Email: yqzhou at buffalo.edu NEW Office/Lab Address: 306/308 Cary Hall On Jun 7, 2006, at 11:33 AM, Ann Loraine wrote: > Hi, > > I'm looking for a Web service that will let me upload a protein > sequence (can't use ids, sorry...these are gene predictions) and then > retrieve results from TM-HMM or a similar program that predicts > membrane-spanning regions and topology. > > This is for a class demo and also for students doing term projects. > > Any advice would be much appreciated! > > Yours, > > Ann > > -- > Ann Loraine > Assistant Professor > Section on Statistical Genetics > University of Alabama at Birmingham > http://www.ssg.uab.edu > http://www.transvar.org > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From aloraine at gmail.com Wed Jun 7 11:50:49 2006 From: aloraine at gmail.com (Ann Loraine) Date: Wed, 7 Jun 2006 10:50:49 -0500 Subject: [BiO BB] TM-HMM Web service for class? In-Reply-To: References: <83722dde0606070833l6bf3f80fv5b2af7e8c41cdd07@mail.gmail.com> Message-ID: <83722dde0606070850l5d4aab2te768aa4bf6c1cc37@mail.gmail.com> Thank you very much. Would it be possible to access the algorithm using a non-Web page interface? Students will be accessing the data programmatically, from inside an interpreter (python or R) and not a Web browser. (The Web page interface would be used mainly to check code and understanding.) Cheers, Ann On 6/7/06, Yaoqi Zhou wrote: > Try THUMBUP at http://theory.med.buffalo.edu > > > Yaoqi Zhou, Associate Professor > **CHECK out Newly UPDATED webpage** on > http://theory.med.buffalo.edu > Department of Physiology and Biophysics > University at Buffalo, State University of New York > 124 Sherman Hall, Buffalo, NY 14214 > (716) 829-2985 Fax (716) 829-2344 > Email: yqzhou at buffalo.edu > NEW Office/Lab Address: 306/308 Cary Hall > > On Jun 7, 2006, at 11:33 AM, Ann Loraine wrote: > > > Hi, > > > > I'm looking for a Web service that will let me upload a protein > > sequence (can't use ids, sorry...these are gene predictions) and then > > retrieve results from TM-HMM or a similar program that predicts > > membrane-spanning regions and topology. > > > > This is for a class demo and also for students doing term projects. > > > > Any advice would be much appreciated! > > > > Yours, > > > > Ann > > > > -- > > Ann Loraine > > Assistant Professor > > Section on Statistical Genetics > > University of Alabama at Birmingham > > http://www.ssg.uab.edu > > http://www.transvar.org > > _______________________________________________ > > 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 http://www.transvar.org From skhadar at gmail.com Thu Jun 8 01:45:38 2006 From: skhadar at gmail.com (Shameer Khadar) Date: Thu, 8 Jun 2006 11:15:38 +0530 Subject: [BiO BB] TM-HMM Web service for class? In-Reply-To: References: <83722dde0606070833l6bf3f80fv5b2af7e8c41cdd07@mail.gmail.com> Message-ID: Hi, I couldnt find any WebServices here - I found only web servers !!!!! -- S K On 6/7/06, Yaoqi Zhou wrote: > > Try THUMBUP at http://theory.med.buffalo.edu > > > Yaoqi Zhou, Associate Professor > **CHECK out Newly UPDATED webpage** on > http://theory.med.buffalo.edu > Department of Physiology and Biophysics > University at Buffalo, State University of New York > 124 Sherman Hall, Buffalo, NY 14214 > (716) 829-2985 Fax (716) 829-2344 > Email: yqzhou at buffalo.edu > NEW Office/Lab Address: 306/308 Cary Hall > > On Jun 7, 2006, at 11:33 AM, Ann Loraine wrote: > > > Hi, > > > > I'm looking for a Web service that will let me upload a protein > > sequence (can't use ids, sorry...these are gene predictions) and then > > retrieve results from TM-HMM or a similar program that predicts > > membrane-spanning regions and topology. > > > > This is for a class demo and also for students doing term projects. > > > > Any advice would be much appreciated! > > > > Yours, > > > > Ann > > > > -- > > Ann Loraine > > Assistant Professor > > Section on Statistical Genetics > > University of Alabama at Birmingham > > http://www.ssg.uab.edu > > http://www.transvar.org > > _______________________________________________ > > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexbutar at gmail.com Wed Jun 7 19:20:37 2006 From: alexbutar at gmail.com (Alex butarbutar) Date: Wed, 7 Jun 2006 16:20:37 -0700 Subject: [BiO BB] Clustring Large Datasets Message-ID: Hello, I am having a difficult time of finding a program / statistical package that will allow clustring of large data sets. By large data sets, I mean 100,000 x 500,000 matrix data from a microarray experiment. I know this will probably an excess of computational time / memory I've tried using R only to find out that i does not allow matrix of that size. any suggestion ? alex b From hlapp at gmx.net Thu Jun 8 09:17:02 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 8 Jun 2006 09:17:02 -0400 Subject: [BiO BB] Clustring Large Datasets In-Reply-To: References: Message-ID: Using a simple back of the envelope calculation you would see that the size of your matrix would be at least 46GB if every matrix element would occupy only a single byte. Do you have a machine with this much memory? R uses doubles, hence the size would be 8x as much. If the matrix is sparse you may be able to use a sparse matrix representation - but I doubt this will be applicable to clustering. If not, you'll have to write some code to farm it out in chunks over hundreds of nodes of a compute farm. Note that another back of the envelope calculation tells you that computing the pairwise distances will take 57 days if a single pairwise distance takes 1ms. If I were you I would rethink what you're trying to do and reduce the dimensionality upfront. -hilmar On Jun 7, 2006, at 7:20 PM, Alex butarbutar wrote: > Hello, > I am having a difficult time of finding a program / statistical > package that will allow clustring of large data sets. By large data > sets, I mean 100,000 x 500,000 matrix data from a microarray > experiment. I know this will probably an excess of computational time > / memory > I've tried using R only to find out that i does not allow matrix of > that size. > any suggestion ? > > alex b > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From yqzhou at buffalo.edu Thu Jun 8 12:36:54 2006 From: yqzhou at buffalo.edu (Yaoqi Zhou) Date: Thu, 8 Jun 2006 12:36:54 -0400 Subject: [BiO BB] TM-HMM Web service for class? In-Reply-To: References: <83722dde0606070833l6bf3f80fv5b2af7e8c41cdd07@mail.gmail.com> Message-ID: <6e54dc8383a47f46ad3ee23db53eea68@buffalo.edu> You have to input your sequences. Yaoqi Zhou, Associate Professor **CHECK out Newly UPDATED webpage** on http://theory.med.buffalo.edu Department of Physiology and Biophysics University at Buffalo, State University of New York 124 Sherman Hall, Buffalo, NY 14214 (716) 829-2985 Fax (716) 829-2344 Email: yqzhou at buffalo.edu NEW Office/Lab Address: 306/308 Cary Hall On Jun 8, 2006, at 1:45 AM, Shameer Khadar wrote: > Hi, > > I couldnt find any WebServices here - > I found only web servers !!!!! > -- > S K > > On 6/7/06, Yaoqi Zhou > wrote:http://theory.med.buffalo.edu >> >> >> Yaoqi Zhou, Associate Professor >> **CHECK out Newly UPDATED webpage** on >> http://theory.med.buffalo.edu >> Department of Physiology and Biophysics >> University at Buffalo, State University of New York >> 124 Sherman Hall,??Buffalo, NY 14214 >> (716) 829-2985 Fax (716) 829-2344 >> Email: yqzhou at buffalo.edu >> NEW Office/Lab Address: 306/308 Cary Hall >> >> On Jun 7, 2006, at 11:33 AM, Ann Loraine wrote: >> >> > Hi, >> > >> > I'm looking for a Web service that will let me upload a protein >> > sequence (can't use ids, sorry...these are gene predictions) and >> then >> > retrieve results from TM-HMM or a similar program that predicts >> > membrane-spanning regions and topology. >> > >> > This is for a class demo and also for students doing term projects. >> > >> > Any advice would be much appreciated! >> > >> > Yours, >> > >> > Ann >> > >> > -- >> > Ann Loraine >> > Assistant Professor >> > Section on Statistical Genetics >> > University of Alabama at Birmingham >> > http://www.ssg.uab.edu >> > http://www.transvar.org >> > _______________________________________________ >> > 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 > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From sariego9 at yahoo.com Thu Jun 8 14:31:45 2006 From: sariego9 at yahoo.com (Diego Martinez) Date: Thu, 8 Jun 2006 11:31:45 -0700 (PDT) Subject: [BiO BB] TM-HMM Web service for class? In-Reply-To: <6e54dc8383a47f46ad3ee23db53eea68@buffalo.edu> Message-ID: <20060608183145.79396.qmail@web32515.mail.mud.yahoo.com> you might want to try Phobius, there is an academic license at the bottom of this page. Diego http://phobius.cgb.ki.se/instructions.html --- Yaoqi Zhou wrote: > You have to input your sequences. > > Yaoqi Zhou, Associate Professor > **CHECK out Newly UPDATED webpage** on > http://theory.med.buffalo.edu > Department of Physiology and Biophysics > University at Buffalo, State University of New York > 124 Sherman Hall, Buffalo, NY 14214 > (716) 829-2985 Fax (716) 829-2344 > Email: yqzhou at buffalo.edu > NEW Office/Lab Address: 306/308 Cary Hall > > On Jun 8, 2006, at 1:45 AM, Shameer Khadar wrote: > > > Hi, > > > > I couldnt find any WebServices here - > > I found only web servers !!!!! > > -- > > S K > > > > On 6/7/06, Yaoqi Zhou > > wrote:http://theory.med.buffalo.edu > >> > >> > >> Yaoqi Zhou, Associate Professor > >> **CHECK out Newly UPDATED webpage** on > >> http://theory.med.buffalo.edu > >> Department of Physiology and Biophysics > >> University at Buffalo, State University of New York > >> 124 Sherman Hall, Buffalo, NY 14214 > >> (716) 829-2985 Fax (716) 829-2344 > >> Email: yqzhou at buffalo.edu > >> NEW Office/Lab Address: 306/308 Cary Hall > >> > >> On Jun 7, 2006, at 11:33 AM, Ann Loraine wrote: > >> > >> > Hi, > >> > > >> > I'm looking for a Web service that will let me upload a protein > >> > sequence (can't use ids, sorry...these are gene predictions) and > >> then > >> > retrieve results from TM-HMM or a similar program that predicts > >> > membrane-spanning regions and topology. > >> > > >> > This is for a class demo and also for students doing term projects. > >> > > >> > Any advice would be much appreciated! > >> > > >> > Yours, > >> > > >> > Ann > >> > > >> > -- > >> > Ann Loraine > >> > Assistant Professor > >> > Section on Statistical Genetics > >> > University of Alabama at Birmingham > >> > http://www.ssg.uab.edu > >> > http://www.transvar.org > >> > _______________________________________________ > >> > 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 > > _______________________________________________ > > 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 > http://phobius.cgb.ki.se/instructions.html ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .=$=. .=$=. .=$=. .=$=. .=$=. .=$=. @ @ | | | @ | | | @ @ | | | @ | | | @ @ | | | @ | | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | | @ | | | @ @ | | | @ | | | @ @ | | | @ | | | @ @ | ~' `~$~' `~$~' `~$~' `~$~' `~$~' `~ __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From letondal at pasteur.fr Fri Jun 9 04:28:20 2006 From: letondal at pasteur.fr (Catherine Letondal) Date: Fri, 9 Jun 2006 10:28:20 +0200 Subject: [BiO BB] TM-HMM Web service for class? In-Reply-To: <20060608183145.79396.qmail@web32515.mail.mud.yahoo.com> References: <20060608183145.79396.qmail@web32515.mail.mud.yahoo.com> Message-ID: <2f3d3c972447021436cb203e0c0b6330@pasteur.fr> Hi, You can try: http://bioweb.pasteur.fr/seqanal/interfaces/toppred.html It's also a Web server, but you can script it through a bioperl module: http://www.pasteur.fr/recherche/unites/sis/Pise/#pisebioperl (there is even an example for toppred : http://www.pasteur.fr/recherche/unites/sis/Pise/bioperl-examples/ toppred.pl) You can also download it: ftp://ftp.pasteur.fr/pub/GenSoft/unix/protein/toppred HTH C. Letondal On Jun 8, 2006, at 8:31 PM, Diego Martinez wrote: >>>> l >>>> >>>> On Jun 7, 2006, at 11:33 AM, Ann Loraine wrote: >>>> >>>>> Hi, >>>>> >>>>> I'm looking for a Web service that will let me upload a protein >>>>> sequence (can't use ids, sorry...these are gene predictions) and >>>> then >>>>> retrieve results from TM-HMM or a similar program that predicts >>>>> membrane-spanning regions and topology. >>>>> >>>>> This is for a class demo and also for students doing term projects. >>>>> >>>>> Any advice would be much appreciated! >>>>> >>>>> Yours, >>>>> >>>>> Ann >>>>> >>>>> -- >>>>> Ann Loraine >>>>> Assistant Professor >>>>> Section on Statistical Genetics >>>>> University of Alabama at Birmingham >>>>> http://www.ssg.uab.edu >>>>> http://www.transvar.org >>>>> _______________________________________________ >>>>> Bioinformatics.Org general forum - >>>>> BiO_Bulletin_Board at bioinformatics.org >>>>> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >>>>> >>>>> From skhadar at gmail.com Thu Jun 8 13:44:31 2006 From: skhadar at gmail.com (Shameer Khadar) Date: Thu, 8 Jun 2006 23:14:31 +0530 Subject: [BiO BB] TM-HMM Web service for class? In-Reply-To: <6e54dc8383a47f46ad3ee23db53eea68@buffalo.edu> References: <83722dde0606070833l6bf3f80fv5b2af7e8c41cdd07@mail.gmail.com> <6e54dc8383a47f46ad3ee23db53eea68@buffalo.edu> Message-ID: Hi, I found the web server, but not a Web Service. I am afraid that, I couldnt fine any API/WSDL or client program samples related to the server you have mentioned etc. Thanks, Shameer Khadar Prof. R. Sowdhamini's Lab NCBS - TIFR On 6/8/06, Yaoqi Zhou wrote: > > You have to input your sequences. > > Yaoqi Zhou, Associate Professor > **CHECK out Newly UPDATED webpage** on > http://theory.med.buffalo.edu > Department of Physiology and Biophysics > University at Buffalo, State University of New York > 124 Sherman Hall, Buffalo, NY 14214 > (716) 829-2985 Fax (716) 829-2344 > Email: yqzhou at buffalo.edu > NEW Office/Lab Address: 306/308 Cary Hall > > On Jun 8, 2006, at 1:45 AM, Shameer Khadar wrote: > > > Hi, > > > > I couldnt find any WebServices here - > > I found only web servers !!!!! > > -- > > S K > > > > On 6/7/06, Yaoqi Zhou > > wrote:http://theory.med.buffalo.edu > >> > >> > >> Yaoqi Zhou, Associate Professor > >> **CHECK out Newly UPDATED webpage** on > >> http://theory.med.buffalo.edu > >> Department of Physiology and Biophysics > >> University at Buffalo, State University of New York > >> 124 Sherman Hall,Buffalo, NY 14214 > >> (716) 829-2985 Fax (716) 829-2344 > >> Email: yqzhou at buffalo.edu > >> NEW Office/Lab Address: 306/308 Cary Hall > >> > >> On Jun 7, 2006, at 11:33 AM, Ann Loraine wrote: > >> > >> > Hi, > >> > > >> > I'm looking for a Web service that will let me upload a protein > >> > sequence (can't use ids, sorry...these are gene predictions) and > >> then > >> > retrieve results from TM-HMM or a similar program that predicts > >> > membrane-spanning regions and topology. > >> > > >> > This is for a class demo and also for students doing term projects. > >> > > >> > Any advice would be much appreciated! > >> > > >> > Yours, > >> > > >> > Ann > >> > > >> > -- > >> > Ann Loraine > >> > Assistant Professor > >> > Section on Statistical Genetics > >> > University of Alabama at Birmingham > >> > http://www.ssg.uab.edu > >> > http://www.transvar.org > >> > _______________________________________________ > >> > 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 > > _______________________________________________ > > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From min.song at njit.edu Fri Jun 9 11:07:35 2006 From: min.song at njit.edu (min.song at njit.edu) Date: Fri, 09 Jun 2006 11:07:35 -0400 (EDT) Subject: [BiO BB] Call for Papers: TMBIO 2006 Message-ID: <1149865654.44898eb704edc@webmail.njit.edu> *******Apologies for multiple copies********** Call for Papers ACM First International Workshop on Text Mining in Bioinformatics (TMBIO) 2006 November 10, 2006. In conjunction with ACM Fifteenth Conference on Information and Knowledge Management (CIKM), November 6-11, 2006, Sheraton Crystal City Hotel, Arlington, VA 22202 USA A fundamental issue that biological researchers encounter today is how to make effective use of the enormous amount of biomedical data to improve their understanding of complex biological systems. The biomedical data repositories are formed from various ways such as bibliographic information from electronic medical journals, gene expression data from Microarray experiments, protein identification and quantification data from proteomics experiments, and genomic sequences gathered by the Human Genome Project. The ability to automatically and effectively extract, integrate, understand and make use of information embedded in such heterogeneous unstructured data remains a challenging task. Topic of Interests The relevant topics include the following (but not limited to): * Application and assessment of Text Mining (TM) algorithms, * Information extraction from biomedical literatures, * TM dealing with large and distributed biomedical data sets, * Entities extraction from unstructured biomedical data sets, * Improving and assessing data quality in TM, * Application of ontologies to biomedical domains, * Integration of Information Retrieval to TM in biomedical domains, * Case studies, * Evaluation methods for TM, * Information integration for TM, * Mining multi-relational data. Goals and Intended Audience In order to build Text Mining systems that contribute to our understanding of biological systems, solutions to the above problems have to be assembled into efficient and scalable systems. The workshop aims at facilitating this process, and at enhancing the exchange of knowledge between computational biologists and knowledge discovery researchers. Accordingly, our intended audiences are both computational biologists and Text Mining researchers. A Special Journal Issue Expanded versions of the best accepted papers will be invited to appear in a special issue of International Journal of Data Mining and Bioinformatics. Submission Guidelines Authors are invited to submit original, unpublished research papers that are not being considered for publication in any other forum. Manuscripts should be submitted electronically, in PDF format and formatted using the ACM camera-ready templates available at http://www.acm.org/sigs/pubs/proceed/template.html. A website with camera-ready instructions is available at http://www.sheridanprinting.com/typedept/cikm.htm. Please send your submission electronically to min.song at njit.edu by the deadline listed below. Important Dates Paper Submission Due: July 21, 2006 Notification of Acceptance: August 15, 2006 Camera-ready Paper Due: August 31, 2006 Workshop: November 10, 2006 Program Chair Min Song, New Jersey Institute of Technology, U.S.A. Zoran Obradovic, Temple University, U.S.A. Program Committee Robert B. Allen, Drexel University, U.S.A. Steffen Bickel, Humboldt University, Germany Christian Blaschke, Bioalma, Spain Aaron M. Cohen, Oregon Health & Science University, U.S.A. Milton Corn, NIH, U.S.A. David J. Foran, The Cancer Institute of New Jersey - UMDNJ, U.S.A. Xiaohua Tony Hu, Drexel University, U.S.A. Tapas Kanungo, IBM Almaden Research Center, U.S.A. Hongfang Liu, Georgetown University, U.S.A. Martin Middendorf, University of Leipzig, Germany Haesun Park, Georgia Tech, U.S.A. Predrag Radivojac, Indiana University, U.S.A. Melissa Rogers, UMDNJ - NJ Medical School, U.S.A. Hagit Shatkay, Queen?s University, Canada Padmini Srinivasan, University of Iowa, U.S.A. Alfonso Valencia, Spanish National Cancer Research Centre, Spain Slobodan Vucetic, Temple University, U.S.A. Jason T. L. Wang, New Jersey Institute of Technology, U.S.A. Brook Wu, New Jersey Institute of Technology, U.S.A. From pwill68 at yahoo.com Sun Jun 11 16:20:13 2006 From: pwill68 at yahoo.com (Weiqun Peng) Date: Sun, 11 Jun 2006 13:20:13 -0700 (PDT) Subject: [BiO BB] looking for a tool for producing intron/exon structures Message-ID: <20060611202013.68810.qmail@web32612.mail.mud.yahoo.com> Hi, I am looking for a software that can produce a graphic visualization of the gene model (intron/exon structure) if I tell it the genomic sequence of the gene and the CDNA. I need the software to be able to produce a figure that can be used for publications. Any pointers are appreciated. I searched through the archive and could not find any hits. Thanks in advance. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From lichunjiang at sibs.ac.cn Sun Jun 11 21:03:10 2006 From: lichunjiang at sibs.ac.cn (lichunjiang) Date: Mon, 12 Jun 2006 09:03:10 +0800 (CST) Subject: [BiO BB] looking for a tool for producing intron/exon structures In-Reply-To: <20060611202013.68810.qmail@web32612.mail.mud.yahoo.com> References: <20060611202013.68810.qmail@web32612.mail.mud.yahoo.com> Message-ID: <3114.10.10.224.88.1150074190.squirrel@webmail.sibs.ac.cn> hi,does www.ensembl.org meet your need?-if genome of the orgnism is included in ensembl. WTH! Lichun Jiang > Hi, > > I am looking for a software that can produce a graphic > visualization of the gene model (intron/exon > structure) if I tell it the genomic sequence of the > gene and the CDNA. I need the software to be able to > produce a figure that can be used for publications. > Any pointers are appreciated. I searched through the > archive and could not find any hits. Thanks in > advance. > > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- lichunjiang at sibs.ac.cn Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: From golharam at umdnj.edu Sun Jun 11 23:15:26 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Sun, 11 Jun 2006 23:15:26 -0400 Subject: [BiO BB] looking for a tool for producing intron/exon structures In-Reply-To: <20060611202013.68810.qmail@web32612.mail.mud.yahoo.com> Message-ID: <049d01c68dce$746037c0$e6028a0a@GOLHARMOBILE1> I have a bit of code using BioPerl to do this. It generates a .png file. I use it on a web page. I've attached an example png image to this message. Let me know if its what you are looking for... 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 Weiqun Peng Sent: Sunday, June 11, 2006 4:20 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] looking for a tool for producing intron/exon structures Hi, I am looking for a software that can produce a graphic visualization of the gene model (intron/exon structure) if I tell it the genomic sequence of the gene and the CDNA. I need the software to be able to produce a figure that can be used for publications. Any pointers are appreciated. I searched through the archive and could not find any hits. Thanks in advance. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- A non-text attachment was scrubbed... Name: exonintron.png Type: image/png Size: 1841 bytes Desc: not available URL: From idoerg at burnham.org Mon Jun 12 02:58:54 2006 From: idoerg at burnham.org (Iddo Friedberg) Date: Sun, 11 Jun 2006 23:58:54 -0700 Subject: [BiO BB] AFP 2006: last call for poster abstracts Message-ID: <448D10AE.4050303@burnham.org> An HTML attachment was scrubbed... URL: From jordi.puiggene at gmail.com Mon Jun 12 11:19:26 2006 From: jordi.puiggene at gmail.com (=?ISO-8859-1?Q?Jordi_Puiggen=E9?=) Date: Mon, 12 Jun 2006 17:19:26 +0200 Subject: [BiO BB] looking for a tool for producing intron/exon structures In-Reply-To: <20060611202013.68810.qmail@web32612.mail.mud.yahoo.com> References: <20060611202013.68810.qmail@web32612.mail.mud.yahoo.com> Message-ID: <96b731c50606120819x27797c4dr@mail.gmail.com> As Ryan, I used in my own app the module Bio::Graphics(by Lincoln Stein) written in perl. It allows you to create several images from the 'features' keys defined in an EMBL sequence file format, so if you have an EMBL file format with 'exon/intron' features, you can generate a graphic as Ryan has shown. There are some examples on Bio::Graphics website. Greets, Jordi 2006/6/11, Weiqun Peng : > > Hi, > > I am looking for a software that can produce a graphic > visualization of the gene model (intron/exon > structure) if I tell it the genomic sequence of the > gene and the CDNA. I need the software to be able to > produce a figure that can be used for publications. > Any pointers are appreciated. I searched through the > archive and could not find any hits. Thanks in > advance. > > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.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 gauravsohoni at gmail.com Thu Jun 15 02:55:08 2006 From: gauravsohoni at gmail.com (Gaurav) Date: Wed, 14 Jun 2006 23:55:08 -0700 Subject: [BiO BB] Query Message-ID: <9319253b0606142355n7a9b5343yc3a86668cb19a8cd@mail.gmail.com> I read about a job opening on ur site. It says one has to contact tribiosys at mail.com. I want to ask wher can I send my resume. Please guide me. -- Experience is what you get when you don't get what you want. -------------- next part -------------- An HTML attachment was scrubbed... URL: From golharam at umdnj.edu Thu Jun 15 10:44:43 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 15 Jun 2006 10:44:43 -0400 Subject: [BiO BB] Query In-Reply-To: <9319253b0606142355n7a9b5343yc3a86668cb19a8cd@mail.gmail.com> Message-ID: <004501c6908a$3d263ac0$e6028a0a@GOLHARMOBILE1> If you are sending an email to this mailling list asking about this, I don't think you should bother send your resume. -----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 Gaurav Sent: Thursday, June 15, 2006 2:55 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Query I read about a job opening on ur site. It says one has to contact tribiosys at mail.com. I want to ask wher can I send my resume. Please guide me. -- Experience is what you get when you don't get what you want. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeff at bioinformatics.org Thu Jun 15 11:01:23 2006 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 15 Jun 2006 11:01:23 -0400 Subject: [BiO BB] Query In-Reply-To: <9319253b0606142355n7a9b5343yc3a86668cb19a8cd@mail.gmail.com> References: <9319253b0606142355n7a9b5343yc3a86668cb19a8cd@mail.gmail.com> Message-ID: <44917643.6090702@bioinformatics.org> Gaurav, tribiosys at mail.com == tribiosys at mail.com But the message you're referring to is 5 years old. Your sig in this case seems very appropriate :-) Jeff Gaurav wrote: > I read about a job opening on ur site. It says one has to contact > tribiosys at mail.com . I want to ask wher can I send > my resume. Please guide me. > > -- > Experience is what you get when you don't get what you want. -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From delete at elfdata.com Thu Jun 15 19:01:29 2006 From: delete at elfdata.com (Theodore H. Smith) Date: Fri, 16 Jun 2006 00:01:29 +0100 Subject: [BiO BB] Papers/techniques on early culling of Smith-Waterman operation? Message-ID: <4EE2A2F7-75BD-48C5-BC58-119FE8A04926@elfdata.com> Hi people, Do you know of any technique to end a Smith-Waterman operation early, by saying that if the operation cannot find a match of a certain desired minimum strength, then we won't do anymore? We'll end the operation early? We would at every row, check the "Best score we can possibly get based upon the current best score". If the "Best score we could possibly get" is below our desired score, we end the SW operation. Or do you know of any papers on this subject? Or even can you think of good keywords for me to search with? Perhaps the way I'm describing it isn't the best way. So, let's say you have a standard SW operation. You have a square Matrix, and you run from left to right across the matrix, line by line down the matrix. Let's say, the matrix has 90 rows, as we are trying to match a protein sequence of 90 letters. Now, is there anyway, some way, by logical analysis or guesswork, to tell perhaps by the time we get to row 70, we know that we'll not be able to get any better score matches than the one we got, and thus cull the SW operation? So that we don't search through rows 71 to 90? The numbers 70 or 90 don't matter, as long as we can check at every row, whether the "best match score" gets better or not. I have something like this for a global alignment producer, and it slices the time down to a small fraction!! Even though it only kills the last third or so, of the alignment, it still cuts down the time required down to less than 66%, perhaps even down to 20%. Basically, I've spent a few months, as a hobby, putting my inventive capacity into making a SmithWaterman-based, BLAST-like searcher. I do things like this because I can, although I think this is probably the most complex thing I'll ever work on in my entire life. My BLAST-like searcher, stores all of it's data in a tree (a "trie" actually). Protein sequences that are shared across many proteins, are stored in the root or earlier branches of the tree. So any work done on the early parts of the tree is reused across many many proteins. This is good, it saves CPU-time. Most of the work then, is done processing the leaves of the tree. This is why the last few rows of the SW Matrix are so important, because most of the work is done there to process them! This is why I want to shave the last few rows off, when possible. But of course, the idea is to process the entire leaf, if the "best score match" is going to get better. For that reason some kind of quick hueristic predictive trick would be desired, so that we don't cull good leaves. Any ideas anyone? This would mean so much to me if I can find a paper, or if anyone even knows what I am talking about and can give me some help. If anyone doesn't know what I am talking about but feels like helping should you understand me, please let me know that I need to explain this in a different better way? I've spent many months on this algorithm. I have a nearly identical algorithm that already works to do global alignmnents, it just doesn't do local alignments, and the global aligner is pretty quick actually. It's just the CPU-saving tricks I've done with global alignment, don't seem to cross over to local alignment, and I'm scratching my brain wondering if these past few months were a waste or not. Because of this "loss of tricks" (that worked with global alignment) situation, I am asking for new tricks, here! Thankfully, I was smart enough to do this work part-time, as a hobby :) I also have a proper normal job that doesn't rely on the success of proposed inventions to make me money. I decided it wasn't a good idea to starve myself just for an idea that might never produce anything worthwhile. Help anyone! Thanks a lot :) -- http://elfdata.com/plugin/ From gauravsohoni at gmail.com Fri Jun 16 01:46:29 2006 From: gauravsohoni at gmail.com (Gaurav) Date: Thu, 15 Jun 2006 22:46:29 -0700 Subject: [BiO BB] Query In-Reply-To: <44917643.6090702@bioinformatics.org> References: <9319253b0606142355n7a9b5343yc3a86668cb19a8cd@mail.gmail.com> <44917643.6090702@bioinformatics.org> Message-ID: <9319253b0606152246n7e16ce16ofea1368207deb14e@mail.gmail.com> Thanks for the reply. I had tried this before asking for the help. But it bounced back. Thanks. On 6/15/06, J.W. Bizzaro wrote: > > Gaurav, > > tribiosys at mail.com == tribiosys at mail.com > > But the message you're referring to is 5 years old. > > Your sig in this case seems very appropriate :-) > > Jeff > > Gaurav wrote: > > I read about a job opening on ur site. It says one has to contact > > tribiosys at mail.com . I want to ask wher can I send > > my resume. Please guide me. > > > > -- > > Experience is what you get when you don't get what you want. > > -- > 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 > -- Experience is what you get when you don't get what you want. -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamid at ibb.ut.ac.ir Fri Jun 16 07:15:44 2006 From: hamid at ibb.ut.ac.ir (hamid) Date: Fri, 16 Jun 2006 15:45:44 +0430 Subject: [BiO BB] RefSeq Accession Numbers Message-ID: Hi buddy, Does any body know, how can I retrieve SwissProt Accession number using the protein RefSeq accession number? It seems there is not any cross reference between thses two databases! Yours, Behnam /* Hamid Nikbakht, M.Sc of Cell and Molecular Biology, Laboratory of Biophysics and Molecular Biology, Bioinformatics Center, Institute of Biochemistry and Biophysics(IBB), University of Tehran, Tehran,Iran. Tel: +98-21-6111-3322 Fax: +98-21-6640-4680 Alt. E-mail: nikbakht at ibb.ut.ac.ir */ From hlapp at gmx.net Fri Jun 16 08:55:43 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 16 Jun 2006 08:55:43 -0400 Subject: [BiO BB] RefSeq Accession Numbers In-Reply-To: References: Message-ID: Ensembl cross-references them. I'm not sure whether you have access to that through Biomart, but probably you do. On Jun 16, 2006, at 7:15 AM, hamid wrote: > Hi buddy, > Does any body know, how can I retrieve SwissProt Accession number > using the > protein RefSeq accession number? It seems there is not any cross > reference > between thses two databases! > Yours, > Behnam > > /* > Hamid Nikbakht, > M.Sc of Cell and Molecular Biology, > Laboratory of Biophysics and Molecular Biology, > Bioinformatics Center, > Institute of Biochemistry and Biophysics(IBB), > University of Tehran, > Tehran,Iran. > Tel: +98-21-6111-3322 > Fax: +98-21-6640-4680 > Alt. E-mail: nikbakht at ibb.ut.ac.ir > */ > > > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From marty.gollery at gmail.com Thu Jun 15 19:32:16 2006 From: marty.gollery at gmail.com (Martin Gollery) Date: Thu, 15 Jun 2006 16:32:16 -0700 Subject: [BiO BB] Papers/techniques on early culling of Smith-Waterman operation? In-Reply-To: <4EE2A2F7-75BD-48C5-BC58-119FE8A04926@elfdata.com> References: <4EE2A2F7-75BD-48C5-BC58-119FE8A04926@elfdata.com> Message-ID: This sounds quite similar to a banded Smith-Waterman, which cuts off the corners of the matrix using the assumption that the most significant score will likely be close to the main diagonal. A banded alignment is used in things like crossmatch, SSAHA, and some other programs. Marty On 6/15/06, Theodore H. Smith wrote: > > > Hi people, > > Do you know of any technique to end a Smith-Waterman operation early, > by saying that if the operation cannot find a match of a certain > desired minimum strength, then we won't do anymore? We'll end the > operation early? We would at every row, check the "Best score we can > possibly get based upon the current best score". If the "Best score > we could possibly get" is below our desired score, we end the SW > operation. > > Or do you know of any papers on this subject? Or even can you think > of good keywords for me to search with? Perhaps the way I'm > describing it isn't the best way. > > So, let's say you have a standard SW operation. You have a square > Matrix, and you run from left to right across the matrix, line by > line down the matrix. Let's say, the matrix has 90 rows, as we are > trying to match a protein sequence of 90 letters. > > Now, is there anyway, some way, by logical analysis or guesswork, to > tell perhaps by the time we get to row 70, we know that we'll not be > able to get any better score matches than the one we got, and thus > cull the SW operation? So that we don't search through rows 71 to 90? > The numbers 70 or 90 don't matter, as long as we can check at every > row, whether the "best match score" gets better or not. > > I have something like this for a global alignment producer, and it > slices the time down to a small fraction!! Even though it only kills > the last third or so, of the alignment, it still cuts down the time > required down to less than 66%, perhaps even down to 20%. > > Basically, I've spent a few months, as a hobby, putting my inventive > capacity into making a SmithWaterman-based, BLAST-like searcher. I do > things like this because I can, although I think this is probably the > most complex thing I'll ever work on in my entire life. > > My BLAST-like searcher, stores all of it's data in a tree (a "trie" > actually). Protein sequences that are shared across many proteins, > are stored in the root or earlier branches of the tree. So any work > done on the early parts of the tree is reused across many many > proteins. This is good, it saves CPU-time. Most of the work then, is > done processing the leaves of the tree. > > This is why the last few rows of the SW Matrix are so important, > because most of the work is done there to process them! This is why I > want to shave the last few rows off, when possible. But of course, > the idea is to process the entire leaf, if the "best score match" is > going to get better. For that reason some kind of quick hueristic > predictive trick would be desired, so that we don't cull good leaves. > > Any ideas anyone? This would mean so much to me if I can find a > paper, or if anyone even knows what I am talking about and can give > me some help. > > If anyone doesn't know what I am talking about but feels like helping > should you understand me, please let me know that I need to explain > this in a different better way? > > I've spent many months on this algorithm. I have a nearly identical > algorithm that already works to do global alignmnents, it just > doesn't do local alignments, and the global aligner is pretty quick > actually. It's just the CPU-saving tricks I've done with global > alignment, don't seem to cross over to local alignment, and I'm > scratching my brain wondering if these past few months were a waste > or not. > > Because of this "loss of tricks" (that worked with global alignment) > situation, I am asking for new tricks, here! > > Thankfully, I was smart enough to do this work part-time, as a > hobby :) I also have a proper normal job that doesn't rely on the > success of proposed inventions to make me money. I decided it wasn't > a good idea to starve myself just for an idea that might never > produce anything worthwhile. > > Help anyone! Thanks a lot :) > > -- > http://elfdata.com/plugin/ > > > > _______________________________________________ > 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 delete at elfdata.com Fri Jun 16 09:57:08 2006 From: delete at elfdata.com (Theodore H. Smith) Date: Fri, 16 Jun 2006 14:57:08 +0100 Subject: [BiO BB] Papers/techniques on early culling of Smith-Waterman operation? In-Reply-To: References: <4EE2A2F7-75BD-48C5-BC58-119FE8A04926@elfdata.com> Message-ID: Hi Martin, Yes, this is exactly the kind of trick that I am looking for. Interestingly enough, I did this "banding" already, with my global alignment algorithm, because I know for certain that I cannot miss any matches, due to the fact that a global alignment must align the entire string. I actually was unaware of the term "banding". Instead I made up my own name :), I called it a "Diamond cut", because we'd "cut" away part of the matrix, to leave a diamond-like shape to process. It looked like this: ......... xxxxx.... .xxxxx... ..xxxxx.. ...xxxxx. ....xxxxx Well, slightly diamond-like. I believed that I could not do this banding with Smith-Waterman, because I could miss some good matches. Now it turns out that some people are still doing this banding with Smith-Waterman? I will look into crossmatch, and SSAHA right away :) Thanks very much for the tip! On 16 Jun 2006, at 00:32, Martin Gollery wrote: > This sounds quite similar to a banded Smith-Waterman, which cuts > off the corners of the matrix using the assumption that the most > significant score will likely be close to the main diagonal. A > banded alignment is used in things like crossmatch, SSAHA, and some > other programs. > > Marty > > On 6/15/06, Theodore H. Smith wrote: > Hi people, > > Do you know of any technique to end a Smith-Waterman operation early, > by saying that if the operation cannot find a match of a certain > desired minimum strength, then we won't do anymore? We'll end the > operation early? We would at every row, check the "Best score we can > possibly get based upon the current best score". If the "Best score > we could possibly get" is below our desired score, we end the SW > operation. > > Or do you know of any papers on this subject? Or even can you think > of good keywords for me to search with? Perhaps the way I'm > describing it isn't the best way. > > So, let's say you have a standard SW operation. You have a square > Matrix, and you run from left to right across the matrix, line by > line down the matrix. Let's say, the matrix has 90 rows, as we are > trying to match a protein sequence of 90 letters. > > Now, is there anyway, some way, by logical analysis or guesswork, to > tell perhaps by the time we get to row 70, we know that we'll not be > able to get any better score matches than the one we got, and thus > cull the SW operation? So that we don't search through rows 71 to 90? > The numbers 70 or 90 don't matter, as long as we can check at every > row, whether the "best match score" gets better or not. > > I have something like this for a global alignment producer, and it > slices the time down to a small fraction!! Even though it only kills > the last third or so, of the alignment, it still cuts down the time > required down to less than 66%, perhaps even down to 20%. > > Basically, I've spent a few months, as a hobby, putting my inventive > capacity into making a SmithWaterman-based, BLAST-like searcher. I do > things like this because I can, although I think this is probably the > most complex thing I'll ever work on in my entire life. > > My BLAST-like searcher, stores all of it's data in a tree (a "trie" > actually). Protein sequences that are shared across many proteins, > are stored in the root or earlier branches of the tree. So any work > done on the early parts of the tree is reused across many many > proteins. This is good, it saves CPU-time. Most of the work then, is > done processing the leaves of the tree. > > This is why the last few rows of the SW Matrix are so important, > because most of the work is done there to process them! This is why I > want to shave the last few rows off, when possible. But of course, > the idea is to process the entire leaf, if the "best score match" is > going to get better. For that reason some kind of quick hueristic > predictive trick would be desired, so that we don't cull good leaves. > > Any ideas anyone? This would mean so much to me if I can find a > paper, or if anyone even knows what I am talking about and can give > me some help. > > If anyone doesn't know what I am talking about but feels like helping > should you understand me, please let me know that I need to explain > this in a different better way? > > I've spent many months on this algorithm. I have a nearly identical > algorithm that already works to do global alignmnents, it just > doesn't do local alignments, and the global aligner is pretty quick > actually. It's just the CPU-saving tricks I've done with global > alignment, don't seem to cross over to local alignment, and I'm > scratching my brain wondering if these past few months were a waste > or not. > > Because of this "loss of tricks" (that worked with global alignment) > situation, I am asking for new tricks, here! > > Thankfully, I was smart enough to do this work part-time, as a > hobby :) I also have a proper normal job that doesn't rely on the > success of proposed inventions to make me money. I decided it wasn't > a good idea to starve myself just for an idea that might never > produce anything worthwhile. > > Help anyone! Thanks a lot :) > > -- > http://elfdata.com/plugin/ > > > > _______________________________________________ > 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 -- http://elfdata.com/plugin/ From pmr at ebi.ac.uk Fri Jun 16 11:38:22 2006 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Fri, 16 Jun 2006 16:38:22 +0100 (BST) Subject: [BiO BB] RefSeq Accession Numbers In-Reply-To: References: Message-ID: <1571.192.130.162.193.1150472302.squirrel@webmail.ebi.ac.uk> Hi Hamid, > Does any body know, how can I retrieve SwissProt Accession number using > the > protein RefSeq accession number? It seems there is not any cross reference > between thses two databases! No explicit cross reference, but enough information to find the link. The EBI's SRS server will link from a UniProt entry to RefSeqP. I believe the link goes through UniParc (the UniProt archive). As a shortcut, you can insert the SwissProt accession of your choice into this URL: http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[uniprot-acc:P13569]>refseqp (add +-ascii to the end to get the original entry) Hope that helps Peter From hamid at ibb.ut.ac.ir Fri Jun 16 10:37:15 2006 From: hamid at ibb.ut.ac.ir (hamid) Date: Fri, 16 Jun 2006 19:07:15 +0430 Subject: [BiO BB] RefSeq Accession Numbers In-Reply-To: References: Message-ID: Dear Hilmar Lapp, These proteins belong to bacteria, so ensemble does ont fit in this case. Yours, Hamid /* Hamid Nikbakht, M.Sc of Cell and Molecular Biology, Laboratory of Biophysics and Molecular Biology, Bioinformatics Center, Institute of Biochemistry and Biophysics(IBB), University of Tehran, Tehran,Iran. Tel: +98-21-6111-3322 Fax: +98-21-6640-4680 Alt. E-mail: nikbakht at ibb.ut.ac.ir */ -----Original Message----- From: Hilmar Lapp To: "The general forum at Bioinformatics.Org" Date: Fri, 16 Jun 2006 08:55:43 -0400 Subject: Re: [BiO BB] RefSeq Accession Numbers > Ensembl cross-references them. I'm not sure whether you have access > to that through Biomart, but probably you do. > > On Jun 16, 2006, at 7:15 AM, hamid wrote: > > > Hi buddy, > > Does any body know, how can I retrieve SwissProt Accession number > > using the > > protein RefSeq accession number? It seems there is not any cross > > reference > > between thses two databases! > > Yours, > > Behnam > > > > /* > > Hamid Nikbakht, > > M.Sc of Cell and Molecular Biology, > > Laboratory of Biophysics and Molecular Biology, > > Bioinformatics Center, > > Institute of Biochemistry and Biophysics(IBB), > > University of Tehran, > > Tehran,Iran. > > Tel: +98-21-6111-3322 > > Fax: +98-21-6640-4680 > > Alt. E-mail: nikbakht at ibb.ut.ac.ir > > */ > > > > > > _______________________________________________ > > Bioinformatics.Org general forum - > > BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > > > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From hamid at ibb.ut.ac.ir Fri Jun 16 11:33:46 2006 From: hamid at ibb.ut.ac.ir (hamid) Date: Fri, 16 Jun 2006 20:03:46 +0430 Subject: [BiO BB] RefSeq Accession Numbers In-Reply-To: <1571.192.130.162.193.1150472302.squirrel@webmail.ebi.ac.uk> References: <1571.192.130.162.193.1150472302.squirrel@webmail.ebi.ac.uk> Message-ID: Hi Peter, I tried this : http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[refseqp-acc:AP_000714]>uniprot+-ascii but this error has been shown: Error:No Entries found when I remove the last part (>uniprot) http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[refseqp-acc:AP_000714]+-ascii it retrieves the result for AP_000714. but for your accession number:uniprot-acc:P13569 the reverse retrieves NP_000483 and when I try: http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[refseqp-acc:AP_000483]>uniprot+-ascii I get the result ... It is strange! /* Hamid Nikbakht, M.Sc of Cell and Molecular Biology, Laboratory of Biophysics and Molecular Biology, Bioinformatics Center, Institute of Biochemistry and Biophysics(IBB), University of Tehran, Tehran,Iran. Tel: +98-21-6111-3322 Fax: +98-21-6640-4680 Alt. E-mail: nikbakht at ibb.ut.ac.ir */ -----Original Message----- From: pmr at ebi.ac.uk To: "The general forum at Bioinformatics.Org" Date: Fri, 16 Jun 2006 16:38:22 +0100 (BST) Subject: Re: [BiO BB] RefSeq Accession Numbers > Hi Hamid, > > > Does any body know, how can I retrieve SwissProt Accession number > using > > the > > protein RefSeq accession number? It seems there is not any cross > reference > > between thses two databases! > > No explicit cross reference, but enough information to find the link. > > The EBI's SRS server will link from a UniProt entry to RefSeqP. I > believe > the link goes through UniParc (the UniProt archive). > > As a shortcut, you can insert the SwissProt accession of your choice > into > this URL: > > http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[uniprot-acc:P13569]>refse > qp > > (add +-ascii to the end to get the original entry) > > Hope that helps > > Peter > > > _______________________________________________ > 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 pmr at ebi.ac.uk Fri Jun 16 16:55:53 2006 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Fri, 16 Jun 2006 21:55:53 +0100 (BST) Subject: [BiO BB] RefSeq Accession Numbers In-Reply-To: References: <1571.192.130.162.193.1150472302.squirrel@webmail.ebi.ac.uk> Message-ID: <2767.192.130.162.193.1150491353.squirrel@webmail.ebi.ac.uk> Hi Hamid, > I tried this : > http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[refseqp-acc:AP_000714]>uniprot+-ascii > but this error has been shown: > Error:No Entries found > when I remove the last part (>uniprot) > http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[refseqp-acc:AP_000714]+-ascii > it retrieves the result for AP_000714. > but for your accession number:uniprot-acc:P13569 the reverse retrieves > NP_000483 and when I try: > http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[refseqp-acc:AP_000483]>uniprot+-ascii > I get the result ... It is strange! Interesting ... it depends on how the links are built. One weakness in SRS is that there is only one default path for links, but you can also make them explicit. I may have been wrong in assuming links will go through UniParc. We had an example last year where we found links - not at EBI but at another SRS server - between Genbank and RefSeq defaulted to going through the taxonomy database (start with one human gene, find them all!!!) I suspect in this case the route is not through UniParc. It could be entrezgene or IPI, both of which fail for your entry. We can check and maybe find a better preferred link that will include bacterial proteins. You can force the route through UniParc with an extra redirect: http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[refseqp-acc:AP_000714]>uniparc>uniprot+-ascii (If email mangles that, I added ">uniparc" before ">uniprot" in your refseq to uniprot link). You can also just link to UniParc and choose your own links. Hope that helps, Peter Rice From nikbakht at ibb.ut.ac.ir Fri Jun 16 16:38:00 2006 From: nikbakht at ibb.ut.ac.ir (Hamid Nikbakht) Date: Sat, 17 Jun 2006 01:08:00 +0430 Subject: [BiO BB] RefSeq Accession Numbers In-Reply-To: <2767.192.130.162.193.1150491353.squirrel@webmail.ebi.ac.uk> References: <1571.192.130.162.193.1150472302.squirrel@webmail.ebi.ac.uk> <2767.192.130.162.193.1150491353.squirrel@webmail.ebi.ac.uk> Message-ID: Dear Peter, It seems it works but I should check it along my accession numbers. Thak you for your care, Yours, Hamid /* Hamid( Behnam )Nikbakht, M.Sc of Cell and Molecular Sciences Bioinformatics Center Laboratory of Biophysics and Molecular Biology Institute of Biochemistry and Biophysics University of Tehran P.O.Box 13145-1384 Tehran, Iran. Tel: (+98 21) 664-98672 Fax: (+98 21) 669-56985 Alt. E-Mail : hamid at ibb.ut.ac.ir */ -----Original Message----- From: pmr at ebi.ac.uk To: "The general forum at Bioinformatics.Org" Cc: ebisrs at ebi.ac.uk Date: Fri, 16 Jun 2006 21:55:53 +0100 (BST) Subject: Re: [BiO BB] RefSeq Accession Numbers > Hi Hamid, > > > I tried this : > > > http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[refseqp-acc:AP_000714]>un > iprot+-ascii > > but this error has been shown: > > Error:No Entries found > > when I remove the last part (>uniprot) > > > http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[refseqp-acc:AP_000714]+-a > scii > > it retrieves the result for AP_000714. > > but for your accession number:uniprot-acc:P13569 the reverse > retrieves > > NP_000483 and when I try: > > > http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[refseqp-acc:AP_000483]>un > iprot+-ascii > > I get the result ... It is strange! > > Interesting ... it depends on how the links are built. One weakness in > SRS > is that there is only one default path for links, but you can also make > them explicit. > > I may have been wrong in assuming links will go through UniParc. We had > an > example last year where we found links - not at EBI but at another SRS > server - between Genbank and RefSeq defaulted to going through the > taxonomy database (start with one human gene, find them all!!!) > > I suspect in this case the route is not through UniParc. It could be > entrezgene or IPI, both of which fail for your entry. We can check and > maybe find a better preferred link that will include bacterial > proteins. > > You can force the route through UniParc with an extra redirect: > > http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[refseqp-acc:AP_000714]>un > iparc>uniprot+-ascii > > (If email mangles that, I added ">uniparc" before ">uniprot" in your > refseq to uniprot link). > > You can also just link to UniParc and choose your own links. > > Hope that helps, > > Peter Rice > > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From kannaiah at bsd.uchicago.edu Sat Jun 17 12:11:39 2006 From: kannaiah at bsd.uchicago.edu (kannaiah at bsd.uchicago.edu) Date: Sat, 17 Jun 2006 11:11:39 -0500 Subject: [BiO BB] SNP position matching... Message-ID: <1150560699.449429bb5713d@netmail.bsd.uchicago.edu> Hello, We have a large number of SNPs with rs#'s and and their physical positions according to build 35. We are trying to match them to a list of physical position windows based on build 34. Is there a way to batch query rs#s at ncbi or ucsc to get the positions in a previous build (e.g. 34)? Thanks for any help -K ------------------------------------------------- This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you. ------------------------------------------------- From lichunjiang at sibs.ac.cn Sun Jun 18 21:52:22 2006 From: lichunjiang at sibs.ac.cn (lichunjiang) Date: Mon, 19 Jun 2006 09:52:22 +0800 (CST) Subject: [BiO BB] poly(A) signal Message-ID: <1243.10.10.224.88.1150681942.squirrel@webmail.sibs.ac.cn> hi, I wonder how can I figure out whether poly(A) signal is included in a genome DNA sequence which is not well denoted. Any advice? Thanks! Lichun Jiang -- lichunjiang at sibs.ac.cn Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: From albin.p at ocimumbio.com Mon Jun 19 08:14:36 2006 From: albin.p at ocimumbio.com (Albin Paul) Date: Mon, 19 Jun 2006 17:44:36 +0530 Subject: [BiO BB] Microarray probe design References: <20060602160138.0E379368A41@primary.bioinformatics.org> Message-ID: <00b101c69399$f37fdbc0$b601a8c0@ocimumbio.net> Hi Ocimum Biosolutions has a software called Oligostar which is can be used for Oligodesigning Ocimum also offers Genowiz a microarray data analysis software that gives GO and Pathway analysis features and many more thourgh this user friendly and cost effective software Thanks Alvin Xavier From kannaiah at bsd.uchicago.edu Mon Jun 19 08:57:28 2006 From: kannaiah at bsd.uchicago.edu (kannaiah at bsd.uchicago.edu) Date: Mon, 19 Jun 2006 07:57:28 -0500 Subject: [BiO BB] SNP position matching... Message-ID: <1150721848.44969f386017b@netmail.bsd.uchicago.edu> Hello, We have a large number of SNPs with rs#'s and and their physical positions according to build 35. We are trying to match them to a list of physical position windows based on build 34. Is there a way to batch query rs#s at ncbi or ucsc to get the positions in a previous build (e.g. 34)? Thanks for any help -K ------------------------------------------------- This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you. ------------------------------------------------- From safee.ullah at gmail.com Mon Jun 19 09:11:12 2006 From: safee.ullah at gmail.com (Safee) Date: Mon, 19 Jun 2006 22:11:12 +0900 Subject: [BiO BB] Ideal course work for a Masters/PhD in Computational and Systems Biology? Message-ID: <624273170606190611h16b6093r845be8eb1320eddf@mail.gmail.com> Hello everyone, I wanted to share your insight into an ideal combination of course work for an MS/Phd in computational and systems biology for a person having a background in computer science? I shall be highly grateful for your help. Kind Regards -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeff at bioinformatics.org Mon Jun 19 10:00:18 2006 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Mon, 19 Jun 2006 10:00:18 -0400 Subject: [BiO BB] Ideal course work for a Masters/PhD in Computational and Systems Biology? In-Reply-To: <624273170606190611h16b6093r845be8eb1320eddf@mail.gmail.com> References: <624273170606190611h16b6093r845be8eb1320eddf@mail.gmail.com> Message-ID: <4496ADF2.90608@bioinformatics.org> Safee, you might want to check our FAQ, which addresses cross-training and lists a number of degree programs in bioinformatics (from which you could gather what is being taught in places): http://bioinformatics.org/faq/ Cheers, Jeff Safee wrote: > Hello everyone, > > I wanted to share your insight into an ideal combination of course work > for an MS/Phd in computational and systems biology for a person having a > background in computer science? > > I shall be highly grateful for your help. > > Kind Regards -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From kannaiah at bsd.uchicago.edu Mon Jun 19 11:19:23 2006 From: kannaiah at bsd.uchicago.edu (kannaiah at bsd.uchicago.edu) Date: Mon, 19 Jun 2006 10:19:23 -0500 Subject: [BiO BB] SNP position matching... In-Reply-To: <1150721848.44969f386017b@netmail.bsd.uchicago.edu> References: <1150721848.44969f386017b@netmail.bsd.uchicago.edu> Message-ID: <1150730363.4496c07b5d3ce@netmail.bsd.uchicago.edu> SO, i was looking at the NCBI site...and it seems like they dont allow any search on the old builds of dbSNP Human. Anybody know if it can be done using UCSC genome browser of ENSEMBL or anyother way? The current release is build 35 and we want to search build 34. Thanks Quoting kannaiah at bsd.uchicago.edu: > Hello, > > We have a large number of SNPs with rs#'s and and their physical > positions according to build 35. We are trying to match them to a list of > physical position windows based on build 34. Is there a way to batch query > rs#s at ncbi or ucsc to get the positions in a previous build (e.g. 34)? > > Thanks for any help > -K > > > > > > > ------------------------------------------------- > This email is intended only for the use of the individual or entity to > which > it is addressed and may contain information that is privileged and > confidential. If the reader of this email message is not the intended > recipient, you are hereby notified that any dissemination, distribution, or > copying of this communication is prohibited. If you have received this > email > in error, please notify the sender and destroy/delete all copies of the > transmittal. Thank you. > ------------------------------------------------- > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > ------------------------------------------------- This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you. ------------------------------------------------- From roex0050 at umn.edu Tue Jun 20 12:28:30 2006 From: roex0050 at umn.edu (Dave Roe) Date: Tue, 20 Jun 2006 11:28:30 -0500 Subject: [BiO BB] predicting functional genomic neighborboods Message-ID: <20060620162830.GA25748@droe-rt-dsl.real-time.com> I have a contig containing several genes from an otherwise unsequenced bacteria. I want to do comparative genomic analysis to check for evidence that the genes in this contig are functionally related (i.e., in the same pathway). If the coexistance of these genes is conserved (especially in a module/neighborhood/operon/etc.), it lends evidence for functional linkages between them. I have found several tools/databases that support this this type of investigation: STRING[1], Prolinks[2], MaGe[3], IMG[4], MetaCyc[5], KEGG[6], and others. However, all these resources are made from fully sequenced genomes and do not seem to allow direct analysis of user-inputted sequences. Does anybody know of other resources I should look into, especially ones that do allow analysis of user-provided sequences? If not, I can think of two general approaches to take: 1. Using the above tools, find the closest homolog/family/COG/etc. that they have for each of my genes, and assume their analysis of them would apply to my genes as well. 2. Write my own code to do profiling by using BLAST, etc. to find homologs for each of my genes and "union" them per genome (preferably taking chromosomal proximity into account if possible). Any criticisms and or advice on these approaches or about any others I should consider? 1. http://string.embl.de/ 2. http://128.97.39.94/cgi-bin/functionator/pronav 3. http://www.genoscope.cns.fr/agc/mage 4. http://img.jgi.doe.gov 5. http://metacyc.org 6. http://www.genome.jp/kegg/ -- Dave Roe roex0050 at umn.edu From idoerg at burnham.org Tue Jun 20 17:00:01 2006 From: idoerg at burnham.org (Iddo Friedberg) Date: Tue, 20 Jun 2006 14:00:01 -0700 Subject: [BiO BB] AFP 2006 program now online Message-ID: <449861D1.5040707@burnham.org> (Please forward as appropriate, thanks). Dear all, The program for the Automated Function Prediction 2006 meeting is now available online. We have a very exciting program this year, and we encourage you to look at the extended abstracts of the keynote and contributed talks. http://biofunctionprediction.org/AFP/afp06/program/ The meeting will begin on August 30, 9:00 am, and will end 1:00 pm on September 1. Please plan your travel accordingly. Note that Friday September 1 is the beginning of the US Labor Day weekend, and heavier than normal traffic is expected from the early afternoon hours. Take care to add extra time to your airport commute (or stay in San Diego for a Labor Day vacation). We will place travel instructions, as well as an accommodation guide shortly. Due to the proximity to Labor Day, we urge you to book your flights and accommodations well in advance. For those wishing to stay in San Diego for the weekend and are staying at the UCSD campus accommodations, there are provisions for additional nights. Please check with UCSD conference services with respect to pricing and availability (contact information on the registration form). Best, Iddo -- Iddo Friedberg, Ph.D. Burnham Institute for Medical Research 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: In the making. Fax: +1 (858) 713 9949 http://iddo-friedberg.org http://BioFunctionPrediction.org From harry.mangalam at uci.edu Wed Jun 21 01:12:32 2006 From: harry.mangalam at uci.edu (Harry Mangalam) Date: Tue, 20 Jun 2006 22:12:32 -0700 Subject: [BiO BB] MacOSX Strider version In-Reply-To: <9319253b0606152246n7e16ce16ofea1368207deb14e@mail.gmail.com> References: <9319253b0606142355n7a9b5343yc3a86668cb19a8cd@mail.gmail.com> <44917643.6090702@bioinformatics.org> <9319253b0606152246n7e16ce16ofea1368207deb14e@mail.gmail.com> Message-ID: <200606202212.32701.harry.mangalam@uci.edu> Hi - I've heard from pretty reliable sources that Christian has released the MacOSX-native version of DNA Strider. Does anyone have a recent email for him? I tried emailing him at all the saclay.cea.fr addresses I have without reply. Any other hints? -- Harry Mangalam - Research Computing at NACS, E2148, Engineering Gateway, UC Irvine 92697 949 824 0084(o), 949 285 4487(c) harry.mangalam at uci.edu From schuerer at genomining.com Wed Jun 21 05:47:59 2006 From: schuerer at genomining.com (Katja Schuerer) Date: Wed, 21 Jun 2006 11:47:59 +0200 Subject: [BiO BB] Course in informatics for biology 2007 at Institut Pasteur Message-ID: <449915CF.4080405@genomining.com> Hi, ************************************************************************* Course in informatics for biology 2007 at Institut Pasteur http://www.pasteur.fr/formation/infobio-en.html ************************************************************************* In the series of courses offered at the Pasteur Institute, a course will be offered in informatics in biology. The next session will take place from January to end of April 2007. The main goal of this course is to provide researchers in biology an initial exposure to informatics. Admitance in the course is reserved for those with a degree in biology or a related discipline. With more and more bioinformatics tools available, it becomes increasingly important for researchers in biology to be able both to manage their data, implement their ideas, and judge for themselves the usefulness of new algorithms and software. This course will emphasize fundamental aspects of computer science and apply them to biological examples. Theoretical aspects (algorithm development, logic, problem modeling and design methods), and technical applications (databases and web technologies) that are relevant for biologists will be thoroughly discussed. Programming is presented through the object-oriented paradigm, using a modern high-level language, Python, provided with tools for biology and enabling both prototyping or scripting and the building of important software systems. Learning of an additional language (C) will be available for interested students. Learning during the course will be reinforced with computing exercises, and effective training will be provided by a 2 month research project. The working language of the course is French. For further information, please consult: http://www.pasteur.fr/formation/infobio-en.html *** Registration will be closed on October 15 2006. *** Sincerely, -- Catherine Letondal, Institut Pasteur & Katja Schuerer, Genomining Course informatics for biology From pankaj at nii.res.in Thu Jun 22 05:22:39 2006 From: pankaj at nii.res.in (Pankaj) Date: Thu, 22 Jun 2006 14:52:39 +0530 Subject: [BiO BB] SCOp ids from PDB id Message-ID: <20060622092239.M52175@nii.res.in> Hi all, I have a few PDB ids. I want to know whether these structures are related or not. One way was to do it by calculating RMSD among all of them and seeing if they r related or not. Other way was to get their SCOP id's and comapre if they belong to same SCOP family. My question is given a PDB id, how do I get its SCOP id? Thanking all in advance, Pankaj Khurana Research Scholar National Institute of Immunology New Delhi India -- Open WebMail Project (http://openwebmail.org) From pankaj at nii.res.in Thu Jun 22 06:55:50 2006 From: pankaj at nii.res.in (Pankaj) Date: Thu, 22 Jun 2006 16:25:50 +0530 Subject: [BiO BB] SCOP ids from PDB id Message-ID: <20060622105550.M35346@nii.res.in> Hi all, I have a few PDB ids. I want to know whether these structures are related or not. One way was to do it by calculating RMSD among all of them and seeing if they r related or not. Other way was to get their SCOP id's and comapre if they belong to same SCOP family. My question is given a PDB id, how do I get its SCOP id? Thanking all in advance, Pankaj Khurana Research Scholar National Institute of Immunology New Delhi India -- Open WebMail Project (http://openwebmail.org) From narcis at fiserlab.org Thu Jun 22 10:09:05 2006 From: narcis at fiserlab.org (Narcis Fernandez-Fuentes) Date: Thu, 22 Jun 2006 10:09:05 -0400 Subject: [BiO BB] SCOp ids from PDB id In-Reply-To: <20060622092239.M52175@nii.res.in> References: <20060622092239.M52175@nii.res.in> Message-ID: <449AA481.1030508@fiserlab.org> just use search engine at SCOP website ... Pankaj wrote: > Hi all, > I have a few PDB ids. > I want to know whether these structures are related or not. > One way was to do it by calculating RMSD among all of them and seeing if they > r related or not. > Other way was to get their SCOP id's and comapre if they belong to same SCOP > family. > My question is given a PDB id, how do I get its SCOP id? > Thanking all in advance, > > Pankaj Khurana > Research Scholar > National Institute of Immunology > New Delhi > India > -- > Open WebMail Project (http://openwebmail.org) > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From MAG at Stowers-Institute.org Thu Jun 22 10:19:15 2006 From: MAG at Stowers-Institute.org (Goel, Manisha) Date: Thu, 22 Jun 2006 09:19:15 -0500 Subject: [BiO BB] SCOP ids from PDB id Message-ID: Hi Pankaj, If you really have only a few PDB ids.. you could go to SCOP site and put them in the "Keyword search for SCOP entries" .. it will take you to the scop entry for the respective PDB files. The RCSB (PDB) site also gives you an option making the tabulated report.. you could choose the options of "SCOP domain" for all the PDB files of your interest and then look at the report. Also, not a very elegant option but something that I tried for a larger number of PDBids is to download the SCOP parseable file and write a small script to "grep" for each pdb-id in this file.. It will come up with the scop_id for each file.. Hopefully somebody else on the list will have a better method for generating this result. I could try to help if you wnat to try any of the above three options. All the best ! -Manisha PostDoctoral Associate Stowers Institute for Medical Research Kansas city, MO -64110 -----Original Message----- From: bio_bulletin_board-bounces+mag=stowers-institute.org at bioinformatics.org [mailto:bio_bulletin_board-bounces+mag=stowers-institute.org at bioinformat ics.org] On Behalf Of Pankaj Sent: Thursday, June 22, 2006 5:56 AM To: bio; bioperl Subject: [BiO BB] SCOP ids from PDB id Hi all, I have a few PDB ids. I want to know whether these structures are related or not. One way was to do it by calculating RMSD among all of them and seeing if they r related or not. Other way was to get their SCOP id's and comapre if they belong to same SCOP family. My question is given a PDB id, how do I get its SCOP id? Thanking all in advance, Pankaj Khurana Research Scholar National Institute of Immunology New Delhi India -- Open WebMail Project (http://openwebmail.org) _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From tcan at ceng.metu.edu.tr Thu Jun 22 10:59:46 2006 From: tcan at ceng.metu.edu.tr (Tolga Can) Date: Thu, 22 Jun 2006 17:59:46 +0300 Subject: [BiO BB] SCOp ids from PDB id In-Reply-To: <20060622092239.M52175@nii.res.in> Message-ID: <20060622145829.37F79360A7@newton.ceng.metu.edu.tr> You can try the following address: http://scop.berkeley.edu/search.cgi? or, download the following parseable SCOP file and locate your PDB ids in that file: http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.cla.scop.txt_1.69 Tolga Can tcan at ceng.metu.edu.tr -----Original Message----- From: bio_bulletin_board-bounces+tcan=ceng.metu.edu.tr at bioinformatics.org [mailto:bio_bulletin_board-bounces+tcan=ceng.metu.edu.tr at bioinformatics.org] On Behalf Of Pankaj Sent: 22 Haziran 2006 Per?embe 12:23 To: bio; bioperl Subject: [BiO BB] SCOp ids from PDB id Hi all, I have a few PDB ids. I want to know whether these structures are related or not. One way was to do it by calculating RMSD among all of them and seeing if they r related or not. Other way was to get their SCOP id's and comapre if they belong to same SCOP family. My question is given a PDB id, how do I get its SCOP id? Thanking all in advance, Pankaj Khurana Research Scholar National Institute of Immunology New Delhi India _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From sankar.achuth at gmail.com Thu Jun 22 11:21:05 2006 From: sankar.achuth at gmail.com (Dr. Achuthsankar S. Nair) Date: Thu, 22 Jun 2006 20:51:05 +0530 Subject: [BiO BB] MPhil Bioinformatics, Kerala University Message-ID: <2b168b460606220821v66418d1escfdc8c70b4974d25@mail.gmail.com> Please encourage good PG holders (MTech/MCA/MSc(CS)/MSc(Life Science) etc apply *Kerala University invites applications for 3rd batch of MPhil Bioinformatics* (To start in January 2007) The *one-year MPhil (Bioinformatics) programme* of the University of Kerala is a novel inter-disciplinary programme in the frontier area of application of computing and information technologies to cutting-edge problems in life sciences. This is the only MPhil programme in the area offered by Indian Universities. Application forms and bochures are available from * www.cbi.keralauniversity.edu* and the *last date for application is 30 Sept 2006.* The programme *admits postgraduate students from engineering, computing and life sciences or allied streams. *Those who hold a recognized post-graduate degree in any one of the following disciplines with a minimum of 55% marks in aggregate, may apply: Engineering & Technology ? Any branch (MTech), Computer Sciences (MSc, MCA), Electronics (MSc), Life Sciences (Zoology, Botany, Bio-chemistry, Bio-technology, Environmental Sciences, Aquatic Biology, Molecular Biology) (MSc), Agriculture (MSc), Pharmacy (MPharm), Medicine (MD), Science (Chemistry, Maths, Operations Research, Statistics, Geology etc) (MSc), Bioinformatics (MSc). There shall be 15 seats for the programme, of which 3 seats shall be for sponsored candidates. 6 seats shall be reserved for life-science stream and 6 for non-life science stream. Reservations for SC/ST, SEBC etc shall be as per University rules. Admissions for applicants except foreign students shall be based on (i) an entrance test to be conducted at Thiruvananthapuram (which will be based on logical reasoning, numerical ability, and life sciences and computing) and (ii) aggregate marks scored in the qualifying postgraduate examinations, with 50 : 50 weightage. The tuition fees are as follows: Non-sponsored : Rs 10,000 / semester, Sponsored : Rs 25,000 / semester. Two batches have been admitted so far. The first batch which came out in early 2006 have announced the formation of the first Bioinformatics company in Kerala: *Soorya Kiran Bioinformatics Pvt Ltd.* Bioinformatics is a nascent field which is predicted to generate a large number of job opportunities in the coming decade. One of the key areas of growth is computer aided drug design which is expected to revitalize the pharma sector. This is especially so after the patent amendment in India which has forced pharmaceutical companies to focus on R&D, as drug molecules can no longer be copied. A study conducted by the Department of Information Technology (DIT), Govt of India, in collaboration with the Confederation of Indian Industries(CII) has predicted that the demand for Indian professionals from the rest of the world is expected to rise from less than500 in 2004 to over 8000 by 2012. Indian bioinformatics market is currently 2.5% of the global market. The M.Phil (Bioinformatics) programme aims to prepare the students for understanding biological data at molecular level from both informational and biological perspective and impart conceptual, computational and practical skills to acquire, analyze, process or use the data to address significant problems in the field of Bioinformatics, of both pure and applied nature. The programme incorporates advanced level education in basic biological (DNA, RNA, Protein) sequence analysis, sequence alignments, sequence data base handling, RNA and protein structure prediction, molecular phylogenetics, molecular visualisation, drug discovery, gene expression studies using micro arrays and data mining. The programme also gives training in relevant mathematical principles, programming tools etc and also research methodology. Considering heterogeneous student group, primer on information technology and life sciences shall be offered as electives for the life science and computer streams respectively. University is offering the programme as an interdisciplinary programme involving Life Sciences and Computer Science. The programme is run under the choice-based credit and semester scheme. -- Dr Achuthsankar S Nair Hon. Director Centre for Bioinformatics University of Kerala, Trivandrum 695581, INDIA Tel (O) 471-2412759 (R) 471-2542220 www.cbi.keralauniversity.edu www.achu.keralauniversity.edu =================================================================== Admissions to MPhil Bioinformatics for Jan 2007 Open - Brochure and Application forms can be downloaded from www.cbi.keralauniversity.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From pfern at igc.gulbenkian.pt Thu Jun 22 13:40:23 2006 From: pfern at igc.gulbenkian.pt (Pedro Fernandes) Date: Thu, 22 Jun 2006 18:40:23 +0100 Subject: [BiO BB] International Training Programme in Oeiras, Portugal Message-ID: <1150998023.449ad607d0584@webmail.igc.gulbenkian.pt> Hello Since 1999 the Inst. Gulbenkian de Ci?ncia in Oeiras, Portugal, runs a yearly trainig programme in Bioinformatics. Many international students come to our courses. Please refer to the website http://gtpb.igc.gulbenkian.pt under gtpb where information on the Programme is continuously updated. -- Pedro Fernandes Inst.Gulbenkian de Ci?ncia OEIRAS PORTUGAL From codeshepherd at gmail.com Thu Jun 22 13:48:26 2006 From: codeshepherd at gmail.com (codeshepherd) Date: Thu, 22 Jun 2006 23:18:26 +0530 Subject: [BiO BB] bionix yum repository Message-ID: <449AD7EA.8090205@gmail.com> Hello Everyone, I had made a simple yum repository that will support popular biotechnology related packages. As of now it supports gromacs, emboss, bioperl. To get the yum repository working in your machine install the rpm http://bioinformatics.org/BIO-NIX/yum/bionix-1.0-1.noarch.rpm . After this you should be able to install gromacs, emboss, bioperl as follows $yum install gromacs $yum install EMBOSS-devel $yum install EMBOSS-libs $yum install perl-bioperl and so on.. I am planning to add more packages. If any of the package developer is interested in adding his or her package please send me a mail. I am prepared to write spec file for their package and add it to my repository. (no fees :)). Please do help in making this project a success. Deepan www.codeshepherd.com Project home page: www.bioinformatics.org/BIO-NIX/ From jeff at bioinformatics.org Thu Jun 22 14:18:56 2006 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 22 Jun 2006 14:18:56 -0400 Subject: [BiO BB] bionix yum repository In-Reply-To: <449AD7EA.8090205@gmail.com> References: <449AD7EA.8090205@gmail.com> Message-ID: <449ADF10.4060608@bioinformatics.org> Note that the BIO-NIX RPMs are currently for Fedora Core 5. I'll also add that Bioinformatics.Org is trying to consolidate various repositories and include yum support. Hopefully BIO-NIX will be part of that. Cheers, Jeff codeshepherd wrote: > Hello Everyone, > I had made a simple yum repository that will support popular > biotechnology related packages. As of now it supports gromacs, emboss, > bioperl. To get the yum repository working in your machine install the > rpm http://bioinformatics.org/BIO-NIX/yum/bionix-1.0-1.noarch.rpm . > > After this you should be able to install gromacs, emboss, bioperl as > follows > > $yum install gromacs > $yum install EMBOSS-devel > $yum install EMBOSS-libs > $yum install perl-bioperl > > and so on.. > I am planning to add more packages. If any of the package developer is > interested in adding his or her package please send me a mail. I am > prepared to write spec file for their package and add it to my > repository. (no fees :)). Please do help in making this project a success. > > Deepan > www.codeshepherd.com > > Project home page: www.bioinformatics.org/BIO-NIX/ -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From jeremymann at gmail.com Thu Jun 22 14:31:29 2006 From: jeremymann at gmail.com (Jeremy Mann) Date: Thu, 22 Jun 2006 13:31:29 -0500 Subject: [BiO BB] bionix yum repository In-Reply-To: <449AD7EA.8090205@gmail.com> References: <449AD7EA.8090205@gmail.com> Message-ID: <79ec289f0606221131l16e7908br3c0104b423318085@mail.gmail.com> In your Emboss package, do you include EMNU, TOPO and MSE? If not, I can send you SPEC files for each. On 6/22/06, codeshepherd wrote: > Hello Everyone, > I had made a simple yum repository that will support popular > biotechnology related packages. As of now it supports gromacs, emboss, > bioperl. To get the yum repository working in your machine install the > rpm http://bioinformatics.org/BIO-NIX/yum/bionix-1.0-1.noarch.rpm . > > After this you should be able to install gromacs, emboss, bioperl as follows > > $yum install gromacs > $yum install EMBOSS-devel > $yum install EMBOSS-libs > $yum install perl-bioperl > > and so on.. > I am planning to add more packages. If any of the package developer is > interested in adding his or her package please send me a mail. I am > prepared to write spec file for their package and add it to my > repository. (no fees :)). Please do help in making this project a success. > > Deepan > www.codeshepherd.com > > Project home page: www.bioinformatics.org/BIO-NIX/ > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Jeremy From golharam at umdnj.edu Thu Jun 22 16:19:08 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 22 Jun 2006 16:19:08 -0400 Subject: [BiO BB] PAML (baseml) Message-ID: <006b01c69639$1df29fe0$2f01a8c0@GOLHARMOBILE1> Has anyone every used PAML for measuring substitution rates? I'm using baseml to do this, however the documentation mentions NOTHING about how to interpret the output files. If anyone has used this I could sure you your help... From marcel at bioinformatics.org Fri Jun 23 04:59:25 2006 From: marcel at bioinformatics.org (Marcel van den Bosch) Date: Fri, 23 Jun 2006 04:59:25 -0400 (EDT) Subject: [BiO BB] BioInformatics Workbench project Message-ID: Hi All, I am looking for people that want to help me create a set of functional requirements and technical specifications (for example: flowcharts, classdiagrams, etc) for the development of a complete workbench solution created in C# and .NET. This workbench should be an "easy to use" application which researchers, students and others that are interested can use. The workbench would be an open-source suite that contains all useful tools that are around. The first step in this project would be to define a list of functional requirements, so that we can get an overview what features our new solution should be able to do. So my question is: If you would like to usage a all-in-one bioinformatics application, what do you want to do with it? Any help is welcome. Thanks, Marcel van den Bosch From golharam at umdnj.edu Fri Jun 23 10:52:03 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 23 Jun 2006 10:52:03 -0400 Subject: [BiO BB] PAML (baseml) In-Reply-To: <449BE973.3020909@biologie.uni-freiburg.de> Message-ID: <008701c696d4$96fb1bb0$2f01a8c0@GOLHARMOBILE1> Thanks Stefan. My output actually looks like this. This is from an intron, and I'm trying to measure the substitution rate (Ki). I'm looking at this and not quite sure how to interpet these numbers. What is Ki? I thought it would be 1.3471, but then what is 2.1629 (and lnL?). 1.3471 seems a little high. BASEML (in paml 3.14beta, July 2003) /tmp/ZBQQHmB5FA/FzTq4tS9qr HKY85 ns = 2 ls = 645 # site patterns = 16 39 32 96 100 20 34 60 16 17 37 28 32 39 39 26 30 chick GTATATTCGA CGACCG human AC..CGAGCT ..GTAT Frequencies.. T C A G chick 0.3504 0.1690 0.2977 0.1829 human 0.3194 0.1504 0.3426 0.1876 Average 0.3349 0.1597 0.3202 0.1853 # constant sites: 256 (39.69%) ln Lmax (unconstrained) = -1691.878455 Distances:HKY85 (kappa) (alpha set at 0.00) This matrix is not used in later m.l. analysis. chick human 1.3471( 2.1629) stage 0: (1, 2); lnL(ntime: 2 np: 3): -1696.679873 3..1 3..2 0.99850 0.37679 2.25465 best tree: (1, 2); lnL: -1696.679873 (chick: 0.998497, human: 0.376793); -----Original Message----- From: Stefan Rensing [mailto:stefan.rensing at biologie.uni-freiburg.de] Sent: Friday, June 23, 2006 9:16 AM To: golharam at umdnj.edu; The general forum at Bioinformatics.Org Subject: Re: [BiO BB] PAML (baseml) Ryan, the main_result.txt contains at its end some lines like this: Substitution rate is per time unit Gene 1: 0.023706 +- 0.002073 Gene 2: 0.061812 +- 0.005858 Nodes and Times (JeffNode is for Thorne's multidivtime. ML analysis uses ingroup data only.) Node 7 (Jeffnode 10) Time 10.15223 +- 0.94581 Node 8 (Jeffnode 9) Time 6.74960 +- 0.58392 Node 9 (Jeffnode 8) Time 4.17529 +- 0.27483 Node 10 (Jeffnode 7) Time 3.20000 Node 11 (Jeffnode 6) Time 2.34832 +- 0.20325 rates for 2 genes: 1 0.06181 Dunno if this helps; I have used PAML for calculation of divergence times. Have you tried r8s? http://ginger.ucdavis.edu/r8s/ It offers a lot more options. Best regards, Stefan Ryan Golhar wrote: > Has anyone every used PAML for measuring substitution rates? I'm > using baseml to do this, however the documentation mentions NOTHING > about how to interpret the output files. > > If anyone has used this I could sure you your help... > > > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Dr. Stefan Rensing, Group Leader Computational Biology Plant Biotechnology, Faculty of Biology, University of Freiburg Schaenzlestr. 1, D-79104 Freiburg, Fon: +49 761 203-6974, Fax: -6945 http://www.plant-biotech.net/ http://www.cosmoss.org/ stefan.rensing at biologie.uni-freiburg.de "Mr. Musgrave, please don't interrupt me when I'm asking rhetorical questions." From omoya at uib.es Fri Jun 23 09:57:23 2006 From: omoya at uib.es (Oscar Moya) Date: Fri, 23 Jun 2006 15:57:23 +0200 Subject: [BiO BB] BioInformatics Workbench project In-Reply-To: Message-ID: <01M3YXJB8BT8AZXUAV@uib.es> Hi Marcel, Your project looks quite interesting but it sounds too broad to me. Could you give some examples of the kind of tools you would like to include in your package? Which are the problems you want to solve with your program? I mean, bioinformatics is too broad to speak about a "complete solution". I am working in the field of phylogenetics and phylogeography and the set of programs, analysis and approaches available for that kind of studies is really huge. I cannot imagine how many are included under the concept of bioinformatics. As example, there is attached a flowchart showing programs and web resources I used (and their complementarity) during a single phylogeographic study. They are only a small representation of the alternative analytical approaches and programs that can be used. There is a project in evolutionary biology called Mesquite that could give you some ideas: http://mesquiteproject.org/mesquite/mesquite.html Take a look to Bioknoppix as well: http://bioknoppix.hpcf.upr.edu/ Good luck with your project! ?scar -----Mensaje original----- De: bio_bulletin_board-bounces+omoya=uib.es at bioinformatics.org [mailto:bio_bulletin_board-bounces+omoya=uib.es at bioinformatics.org] En nombre de Marcel van den Bosch Enviado el: viernes, 23 de junio de 2006 10:59 Para: bio_bulletin_board at bioinformatics.org Asunto: [BiO BB] BioInformatics Workbench project Hi All, I am looking for people that want to help me create a set of functional requirements and technical specifications (for example: flowcharts, classdiagrams, etc) for the development of a complete workbench solution created in C# and .NET. This workbench should be an "easy to use" application which researchers, students and others that are interested can use. The workbench would be an open-source suite that contains all useful tools that are around. The first step in this project would be to define a list of functional requirements, so that we can get an overview what features our new solution should be able to do. So my question is: If you would like to usage a all-in-one bioinformatics application, what do you want to do with it? Any help is welcome. Thanks, Marcel van den Bosch _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- A non-text attachment was scrubbed... Name: flowchart.jpg Type: image/jpeg Size: 71305 bytes Desc: not available URL: From ssal at intracom.gr Fri Jun 23 08:12:04 2006 From: ssal at intracom.gr (ssal at intracom.gr) Date: Fri, 23 Jun 2006 15:12:04 +0300 Subject: [BiO BB] BioInformatics Workbench project In-Reply-To: Message-ID: <200606231153.k5NBrtj27198@hal.intranet.gr> Dear Marcel, C# and .NET is not actually the most preferred language for open source projects. I would propose Java/C/php/python and Linux/MySQL. I think that somewere exists a Linux-Distro with Bioinformatic tools a Web Interface to such tools would be perfect. Regards Sotiris -----Original Message----- From: bio_bulletin_board-bounces+ssal=intracom.gr at bioinformatics.org [mailto:bio_bulletin_board-bounces+ssal=intracom.gr at bioinformatics.org] On Behalf Of Marcel van den Bosch Sent: Friday, June 23, 2006 11:59 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] BioInformatics Workbench project Hi All, I am looking for people that want to help me create a set of functional requirements and technical specifications (for example: flowcharts, classdiagrams, etc) for the development of a complete workbench solution created in C# and .NET. This workbench should be an "easy to use" application which researchers, students and others that are interested can use. The workbench would be an open-source suite that contains all useful tools that are around. The first step in this project would be to define a list of functional requirements, so that we can get an overview what features our new solution should be able to do. So my question is: If you would like to usage a all-in-one bioinformatics application, what do you want to do with it? Any help is welcome. Thanks, Marcel van den Bosch _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From ykalidas at gmail.com Fri Jun 23 11:38:40 2006 From: ykalidas at gmail.com (Kalidas Yeturu) Date: Fri, 23 Jun 2006 21:08:40 +0530 Subject: [BiO BB] SCOP ids from PDB id In-Reply-To: <20060622105550.M35346@nii.res.in> References: <20060622105550.M35346@nii.res.in> Message-ID: <5632703b0606230838n5b1af8cbm8cbe979db54a1247@mail.gmail.com> Hi use the file, "dir.des.scop.txt_1.69"., for obtaining a classification number. For eg., grep "1a4g" dir.des.scop.txt_1.69 will output: 27600 px b.68.1.1 d1a4ga_ 1a4g A: 27601 px b.68.1.1 d1a4gb_ 1a4g B: and you can get the classification number from it. with regards kalidas.y On 6/22/06, Pankaj wrote: > > Hi all, > I have a few PDB ids. > I want to know whether these structures are related or not. > One way was to do it by calculating RMSD among all of them and seeing if > they > r related or not. > Other way was to get their SCOP id's and comapre if they belong to same > SCOP > family. > My question is given a PDB id, how do I get its SCOP id? > Thanking all in advance, > > Pankaj Khurana > Research Scholar > National Institute of Immunology > New Delhi > India > -- > Open WebMail Project (http://openwebmail.org) > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Kalidas Y http://ssl.serc.iisc.ernet.in/~kalidas -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan.rensing at biologie.uni-freiburg.de Fri Jun 23 09:15:31 2006 From: stefan.rensing at biologie.uni-freiburg.de (Stefan Rensing) Date: Fri, 23 Jun 2006 15:15:31 +0200 Subject: [BiO BB] PAML (baseml) In-Reply-To: <006b01c69639$1df29fe0$2f01a8c0@GOLHARMOBILE1> References: <006b01c69639$1df29fe0$2f01a8c0@GOLHARMOBILE1> Message-ID: <449BE973.3020909@biologie.uni-freiburg.de> Ryan, the main_result.txt contains at its end some lines like this: Substitution rate is per time unit Gene 1: 0.023706 +- 0.002073 Gene 2: 0.061812 +- 0.005858 Nodes and Times (JeffNode is for Thorne's multidivtime. ML analysis uses ingroup data only.) Node 7 (Jeffnode 10) Time 10.15223 +- 0.94581 Node 8 (Jeffnode 9) Time 6.74960 +- 0.58392 Node 9 (Jeffnode 8) Time 4.17529 +- 0.27483 Node 10 (Jeffnode 7) Time 3.20000 Node 11 (Jeffnode 6) Time 2.34832 +- 0.20325 rates for 2 genes: 1 0.06181 Dunno if this helps; I have used PAML for calculation of divergence times. Have you tried r8s? http://ginger.ucdavis.edu/r8s/ It offers a lot more options. Best regards, Stefan Ryan Golhar wrote: > Has anyone every used PAML for measuring substitution rates? I'm using > baseml to do this, however the documentation mentions NOTHING about how > to interpret the output files. > > If anyone has used this I could sure you your help... > > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Dr. Stefan Rensing, Group Leader Computational Biology Plant Biotechnology, Faculty of Biology, University of Freiburg Schaenzlestr. 1, D-79104 Freiburg, Fon: +49 761 203-6974, Fax: -6945 http://www.plant-biotech.net/ http://www.cosmoss.org/ stefan.rensing at biologie.uni-freiburg.de "Mr. Musgrave, please don't interrupt me when I'm asking rhetorical questions." From jeff at bioinformatics.org Fri Jun 23 19:10:22 2006 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri, 23 Jun 2006 19:10:22 -0400 Subject: [BiO BB] BioInformatics Workbench project In-Reply-To: <01M3YXJB8BT8AZXUAV@uib.es> References: <01M3YXJB8BT8AZXUAV@uib.es> Message-ID: <449C74DE.9010102@bioinformatics.org> I agree with Oscar. Bioinformatics is a small field but incredibly broad in scope. Plus, "workbench" could mean a lot of things and is largely dependent on the user interface (are you thinking about a desktop or Web application?). You should also consider the fact that there are a couple dozen applications out there that could be (and are) described as "bioinformatics workbenches", some being under well-funded development for years. Here's a sample: Taverna Swami OpenFlow GalaxiaWorkflow Wildfire BIRCH EMBOSS wEMBOSS Portal WSBAW SciCraft Scitegic Pegasys ANGIS W2H Pise SRS I suggest that your first objective would be to identify every "bioinformatics workbench" out there. Your second objective should be to find out what none of them do (or do well). And then propose a project to address that problem. Cheers, Jeff Oscar Moya wrote: > > Your project looks quite interesting but it sounds too broad to me. Could > you give some examples of the kind of tools you would like to include in > your package? Which are the problems you want to solve with your program? [...] -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From marcel at bioinformatics.org Sun Jun 25 15:02:05 2006 From: marcel at bioinformatics.org (Marcel van den Bosch) Date: Sun, 25 Jun 2006 15:02:05 -0400 (EDT) Subject: [BiO BB] BioInformatics Workbench project Message-ID: Hello Jeff, Hello Oscar, I must agree with you that this project has a very broad scope. However part of the project should be to determine what (popular) functionalities a complete workbench should contain and with this information, compose a list of functional requirements. These functional requirements should provide us with enough information to begin working on the technical details. Perhaps if it turns out that all requirements are related to proteomics-area, we can always call it something like the "All-in-one Proteomics Workbench project.." :-) But I think that we shouldn't be doing that until we know the exact requirements and who would like to team-up with the project. The differences between this application and other workbench projects, in my opinion, should be: - Must contain an intuitive user interfaces (taking advantage of standard UI components from the .NET framework) so that the time needed to learn how to use the application should be minimized and the application should be attractive to (biochemistry) students without a lot of computer/informatics experience. - Integration and collaboration of different functions/tools within the workbench. This should allow the user of the application to work more efficiently than a collection of standalone tools and saves a lot of time saving/opening/converting filetypes etc. Pretty much the same idea as the Open Office/Microsoft Office suite.. it just works better then using all standalone applications for example like Wordperfect, Lotus 123 and dBASE. - It allows developers from widely used languages as C++/C#/J#/Visual Basic and Fortran to work on the project or allows them to easily develop a plug-in for it. Ofcourse I am open to suggestions, I received a lot of useful tips by email from interested people. So I of you have some suggestions which might help bringing this idea to life, please let me know. I am also interested in using a agile style system development methodology, so that this project obtains some flexibility in it.s requirements later in the process. This project is too big to do it on my own, so any help is appreciated. The first step should be, in my opinion, to ask people what they would like to have in a workbench. From that point on we can always decide to change things according to the needs. Regards, Marcel From nuraini at cs.usm.my Sun Jun 25 22:04:22 2006 From: nuraini at cs.usm.my (Nur'Aini Abdul Rashid) Date: Mon, 26 Jun 2006 10:04:22 +0800 Subject: [BiO BB] BioInformatics Workbench project In-Reply-To: References: Message-ID: <1151287462.2620.5.camel@yankumi.cs.usm.my> Hello marcel and others , I agree with others that this project has a very broad scope. Perhaps we can partition it into smaller scope and works on those independently depending on the needs of each user in each scope and merge later on. However, there are some basic functions that are needed everywhere such as search and comparison functions which are extensively used at primary, secondary and tertiary level of data. I would like very much to join this project however I must admit that I am good in C but not much of the other languages that you specify. On Sun, 2006-06-25 at 15:02 -0400, Marcel van den Bosch wrote: > Hello Jeff, Hello Oscar, > > I must agree with you that this project has a very broad scope. However > part of the project should be to determine what (popular) functionalities a > complete workbench should contain and with this information, compose a > list of functional requirements. > > These functional requirements should provide us with enough information to > begin working on the technical details. Perhaps if it turns out that all > requirements are related to proteomics-area, we can always call it > something like the "All-in-one Proteomics Workbench project.." :-) > But I think that we shouldn't be doing that until we know the exact > requirements and who would like to team-up with the project. > > The differences between this application and other workbench projects, in > my opinion, should be: > > - Must contain an intuitive user interfaces (taking advantage of standard > UI components from the .NET framework) so that the time needed to learn > how to use the application should be minimized and the application should > be attractive to (biochemistry) students without a lot of > computer/informatics experience. > > - Integration and collaboration of different functions/tools within the > workbench. This should allow the user of the application to work more > efficiently than a collection of standalone tools and saves a lot of time > saving/opening/converting filetypes etc. Pretty much the same idea as the > Open Office/Microsoft Office suite.. it just works better then using all > standalone applications for example like Wordperfect, Lotus 123 and dBASE. > > - It allows developers from widely used languages as C++/C#/J#/Visual > Basic and Fortran to work on the project or allows them to easily develop > a plug-in for it. > > Ofcourse I am open to suggestions, I received a lot of useful tips by > email from interested people. So I of you have some suggestions which > might help bringing this idea to life, please let me know. I am also > interested in using a agile style system development methodology, so that > this project obtains some flexibility in it.s requirements later in the > process. > > This project is too big to do it on my own, so any help is appreciated. > The first step should be, in my opinion, to ask people what they would > like to have in a workbench. From that point on we can always decide > to change things according to the needs. > > Regards, > > Marcel > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From omoya at uib.es Mon Jun 26 06:34:39 2006 From: omoya at uib.es (Oscar Moya) Date: Mon, 26 Jun 2006 12:34:39 +0200 Subject: [BiO BB] BioInformatics Workbench project In-Reply-To: Message-ID: <01M42XBPPX7KB2XBT1@uib.es> Ok, big projects are also possible ;) I would be glad to have to help giving a user point of view (my programming skills are still scarce). Another point that could be considered for the success of such a project: - The workbench should allow some kind of complementarity with applications currently in use. I mean, the user should have the opportunity to keep using their preferred software for some analysis and easily incorporate the results (outputs) of other programs or generate inputs for them. There are several programs that are extensively used, they are really well done and have lots of useful and specific tools. Moreover, when you are used to a program (even if it has very complicated commands) and you trust on it, it is difficult to change to a new one. I think that such point is a key for the acceptability of all-in-one applications. If you are interested, I can prepare a report of the most common analysis in my field, the software available (the most popular, at least), the existing standards in input and output files, what I miss as user or another information that you could find valuable. Such a work could be a good starting point for all the areas touched by your project. My email address is omoya at uib.es. All the best ?scar -----Mensaje original----- De: bio_bulletin_board-bounces+omoya=uib.es at bioinformatics.org [mailto:bio_bulletin_board-bounces+omoya=uib.es at bioinformatics.org] En nombre de Marcel van den Bosch Enviado el: domingo, 25 de junio de 2006 21:02 Para: bio_bulletin_board at bioinformatics.org Asunto: RE: [BiO BB] BioInformatics Workbench project Hello Jeff, Hello Oscar, I must agree with you that this project has a very broad scope. However part of the project should be to determine what (popular) functionalities a complete workbench should contain and with this information, compose a list of functional requirements. These functional requirements should provide us with enough information to begin working on the technical details. Perhaps if it turns out that all requirements are related to proteomics-area, we can always call it something like the "All-in-one Proteomics Workbench project.." :-) But I think that we shouldn't be doing that until we know the exact requirements and who would like to team-up with the project. The differences between this application and other workbench projects, in my opinion, should be: - Must contain an intuitive user interfaces (taking advantage of standard UI components from the .NET framework) so that the time needed to learn how to use the application should be minimized and the application should be attractive to (biochemistry) students without a lot of computer/informatics experience. - Integration and collaboration of different functions/tools within the workbench. This should allow the user of the application to work more efficiently than a collection of standalone tools and saves a lot of time saving/opening/converting filetypes etc. Pretty much the same idea as the Open Office/Microsoft Office suite.. it just works better then using all standalone applications for example like Wordperfect, Lotus 123 and dBASE. - It allows developers from widely used languages as C++/C#/J#/Visual Basic and Fortran to work on the project or allows them to easily develop a plug-in for it. Ofcourse I am open to suggestions, I received a lot of useful tips by email from interested people. So I of you have some suggestions which might help bringing this idea to life, please let me know. I am also interested in using a agile style system development methodology, so that this project obtains some flexibility in it.s requirements later in the process. This project is too big to do it on my own, so any help is appreciated. The first step should be, in my opinion, to ask people what they would like to have in a workbench. From that point on we can always decide to change things according to the needs. Regards, Marcel _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From hamid at ibb.ut.ac.ir Mon Jun 26 06:05:26 2006 From: hamid at ibb.ut.ac.ir (hamid) Date: Mon, 26 Jun 2006 14:35:26 +0430 Subject: [BiO BB] BioInformatics Workbench project In-Reply-To: References: Message-ID: I am interested to contribute in this project. I know LAMP (Linux, Apache, MySQL and PHP) web developer. I think web tools are an essential part of this workbench. /* Hamid Nikbakht, M.Sc of Cell and Molecular Biology, Laboratory of Biophysics and Molecular Biology, Bioinformatics Center, Institute of Biochemistry and Biophysics(IBB), University of Tehran, Tehran,Iran. Tel: +98-21-6111-3322 Fax: +98-21-6640-4680 Alt. E-mail: nikbakht at ibb.ut.ac.ir */ From bikram80 at gmail.com Tue Jun 27 02:12:17 2006 From: bikram80 at gmail.com (Bikram Nayak) Date: Tue, 27 Jun 2006 11:42:17 +0530 Subject: [BiO BB] for bioinformatics query solve? Message-ID: <16f934830606262312qae32e9fv279a713529619a64@mail.gmail.com> i am doing one project in java with weblogic.can u tell me how could i explicitly execute a service of remote object,i.e sequence from interproscan.and import to my system. -- Bikram Nayak. -------------- next part -------------- An HTML attachment was scrubbed... URL: From skhadar at gmail.com Tue Jun 27 03:31:20 2006 From: skhadar at gmail.com (Shameer Khadar) Date: Tue, 27 Jun 2006 13:01:20 +0530 Subject: [BiO BB] for bioinformatics query solve? In-Reply-To: <16f934830606262312qae32e9fv279a713529619a64@mail.gmail.com> References: <16f934830606262312qae32e9fv279a713529619a64@mail.gmail.com> Message-ID: Hi, I think u can use JAVA-AXIS based client programs based on WebServices / SOAP protocol provided by EBI to access InterProcan. I am afraid, it is not based on WebLogic - you may have to switch on Apache Tomcat / Axis - and it is easy too :) Check this URL : http://www.ebi.ac.uk/Tools/webservices/WSInterProScan.html shameer at ncbs.res.in Prof. R. Sowdhamini's Lab The Computational Biology Lab NCBS - TIFR - Bangalore On 6/27/06, Bikram Nayak wrote: > > i am doing one project in java with weblogic.can u tell me how could i > explicitly execute a service of remote object,i.e sequence from > interproscan.and import to my system. > > -- > Bikram Nayak. > > _______________________________________________ > 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 william.hsiao at gmail.com Tue Jun 27 15:52:03 2006 From: william.hsiao at gmail.com (William Hsiao) Date: Tue, 27 Jun 2006 12:52:03 -0700 Subject: [BiO BB] strange error parsing a specific NCBI gff file Message-ID: <679a35b20606271252x1a321756m51d203b28c259d40@mail.gmail.com> Hi all, I've encountered a strange problem while parsing a gff file from NCBI using perl. I'm hoping that someone on the list may have a solution even though this is not a bioperl issue. Maybe someone familiar with gff3 parsing can help :) Essentially, I'm parsing a gff file into a nested hash structure using the following functions: sub parse_gff { my $file = shift; my %hash_gff; open (INFILE, $file) or die "Cannot find file $file\n"; while(){ next if (/^\#/); chomp; my ($seqid, $source, $type, $start, $end, $score, $strand, $phase, $attributes) = split /\t/; my $attri_ref = &process_attributes($attributes); my %record = ('seqid' => $seqid, 'source' => $source, 'type' => $type, 'start' => $start, 'end' => $end, 'score' => $score, 'strand' => $strand, 'phase' => $phase, 'attribute' => $attri_ref); push @{$hash_gff{$type}}, \%record; } close INFILE; print Dumper %hash_gff; return \%hash_gff; } sub process_attributes { my $attr_string = shift; my @attributes = split (/\;/, $attr_string); my %attr; foreach (@attributes){ my ($key, $value) = split /=/; if ($value=~/\:/){ my ($subkey, $subvalue) = split (/:/, $value); $attr{$key}{$subkey}=$subvalue; } else{ $attr{$key}=$value; } } return \%attr; } It works for all the gff files we downloaded from NCBI's microbial genomes refseq ftp repository. However, 3 lines from one particular file NC_005966.gff (of Acinetobacter_sp_ADP1) can not be parsed properly. These lines are: NC_005966.1 RefSeq CDS 635836 636489 . - 0 locus_tag=ACIAD0647;function=adaptation%20to%20stress;function=protection%20%28MultiFun:5.5%29;note=Multifun:5.6%0AEvidence%203%20:%20Function%20proposed%20based%20on%20presence%20of%20conserved%20amino%20acid%20motif%2C%20structural%20feature%20or%20limited%20homolgy;inference=non-experimental%20evidence%2C%20no%20additional%20details%20recorded;transl_table=11;product=putative%20antioxidant%20protein;protein_id=YP_045389.1;db_xref=GI:50083879;db_xref=GeneID:2878732;exon_number=1 NC_005966.1 RefSeq start_codon 636487 636489 . - 0 locus_tag=ACIAD0647;function=adaptation%20to%20stress;function=protection%20%28MultiFun:5.5%29;note=Multifun:5.6%0AEvidence%203%20:%20Function%20proposed%20based%20on%20presence%20of%20conserved%20amino%20acid%20motif%2C%20structural%20feature%20or%20limited%20homolgy;inference=non-experimental%20evidence%2C%20no%20additional%20details%20recorded;transl_table=11;product=putative%20antioxidant%20protein;protein_id=YP_045389.1;db_xref=GI:50083879;db_xref=GeneID:2878732;exon_number=1 NC_005966.1 RefSeq stop_codon 635833 635835 . - 0 locus_tag=ACIAD0647;function=adaptation%20to%20stress;function=protection%20%28MultiFun:5.5%29;note=Multifun:5.6%0AEvidence%203%20:%20Function%20proposed%20based%20on%20presence%20of%20conserved%20amino%20acid%20motif%2C%20structural%20feature%20or%20limited%20homolgy;inference=non-experimental%20evidence%2C%20no%20additional%20details%20recorded;transl_table=11;product=putative%20antioxidant%20protein;protein_id=YP_045389.1;db_xref=GI:50083879;db_xref=GeneID:2878732;exon_number=1 They generate an error: Can't use string ("adaptation%20to%20stress") as a HASH ref while "strict refs" in use. The strange part is that all I have to do is replace the word "function" in front of "=adaptation%20to%20stress;" with another word or simply change it to functions or functio or Function, etc, then the line parses properly. If I retype the word "function", it doesn't solve the problem. For some strange reason, when the word "function" is there, perl tried to use "adaptation%20to%20stress" as the hash key and failed. The word "function" is used in other lines as well so I don't think the problem is not caused by the word alone. Any suggestion on what might be happening would be greatly appreciated. Thank you. Cheers, Will -- William Hsiao PhD Student, Brinkman Laboratory Department of Molecular Biology and Biochemistry Simon Fraser University, 8888 University Dr. Burnaby, BC, Canada V5A 1S6 Phone: 604-291-4206 Fax: 604-291-5583 From akarger at CGR.Harvard.edu Wed Jun 28 10:04:42 2006 From: akarger at CGR.Harvard.edu (Amir Karger) Date: Wed, 28 Jun 2006 10:04:42 -0400 Subject: [BiO BB] RE: BioInformatics Workbench project Message-ID: (Sorry, I don't know how to reply to messages I get in digest form) Marcel, > I must agree with you that this project has a very broad scope. I don't want to sound mean or pessimistic here (so please put an IMO before each sentence that follows), but it still sounds like you are glossing over the hugeness of this project. > However > part of the project should be to determine what (popular) functionalities a > complete workbench should contain and with this information, compose a > list of functional requirements. There are hundreds to possibly thousands of software packages out there in many, overlapping sub-disciplines of biology. Which ones are you planning on supporting? "My workbench will integrate every possible application" only works if you have an extremely lightweight framework - like, say, X and the command line. How many dozens of people were you planning on interviewing in depth to find out user needs? If your functional requirements aren't detailed, your project either won't get very far or won't satisfy actual users' needs. Are you supporting computational biologists? Non-computer-y biologists? Students? If you say "everyone", then you probably need to code 3 separate workbenches. Are these people using it every day, or spending a month in the lab between uses? It makes a big difference in the tradeoff of efficiency (lots of shortcuts, specialized GUI) vs. memorability ("How do I list my projects again?") I suspect most of the existing workbenches took several years to write. Are you (and your development team) prepared for that commitment? > The differences between this application and other workbench projects, in > my opinion, should be: > > - Must contain an intuitive user interfaces Define intuitive. ("Easy to use" isn't precise enough.) What details are you planning on sacrificing to make it easy to use, and will it still be useful for experts? > (taking advantage of standard > UI components from the .NET framework) so that the time needed to learn > how to use the application should be minimized and the application should > be attractive to (biochemistry) students without a lot of > computer/informatics experience. I'm all for standards. But, when starting on a major project, is it really a good idea to pick your tool (.NET) before you've even gotten requirements? I don't know anything about .NET, but has anyone done a study to clarify whether the standard .NET UI components are the best kinds of UI for biologists to be using? Although some aspects of usability are universal (as long as your users are all human), the average biologist is probably much different than the average .NET app user in certain ways. > - Integration and collaboration of different functions/tools within the > workbench. This should allow the user of the application to work more > efficiently than a collection of standalone tools and saves a lot of time > saving/opening/converting filetypes etc. Pretty much the same idea as the > Open Office/Microsoft Office suite.. it just works better then using all > standalone applications for example like Wordperfect, Lotus 123 and dBASE. I'm all for integration, too. On the other hand, the Office suite has the advantage of all being written by the same company (or project teams, in the case of OOo). All these biology profs who hack together GUI-less C codes ("It's just a one-time program that I'm sure no one else will use , so I don't have to code cleanly.") aren't necessarily going to follow all of your coding rules. They may even go and change formats while you're not looking. > - It allows developers from widely used languages as C++/C#/J#/Visual > Basic and Fortran to work on the project or allows them to easily develop > a plug-in for it. Sure. Once you've built a robust, tested framework, and convinced enough people to use it that it's worth installing, learning to use, and writing a plug-in for. > This project is too big to do it on my own, so any help is appreciated. > The first step should be, in my opinion, to ask people what they would > like to have in a workbench. From that point on we can always decide > to change things according to the needs. I know I've sounded very negative here. Maybe you're good enough to actually pull it off. But the open source world is littered with the wreckage of well-intentioned projects that never got off the ground. (I've created - or not successfully created - a few little ones myself.) It's several zillion times faster to start from an existing code base than to start from scratch. This could mean either joining an existing project's development team, or, if you disagree about their future direction, at least copying their code to start your own project. Jeff gave you a large list of projects with widely differing approaches. Are you sure that ALL of them are so inadequate that it's worth starting Yet Another Workbench for Bioinformatics project from scratch? (If you do, you can call it YAWB :) If you don't want to join another project, should you maybe focus on one detail of the interoperability problem? I suspect you'll have a better chance of releasing something that way. Anyway, good luck with whatever you decide. -Amir Karger From jeff at bioinformatics.org Wed Jun 28 11:29:44 2006 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 28 Jun 2006 11:29:44 -0400 Subject: [BiO BB] RE: BioInformatics Workbench project In-Reply-To: References: Message-ID: <44A2A068.4000403@bioinformatics.org> Marcel, just as an example of the head-start that some projects have (you're looking for a list of tools needed), take a look at the EMBOSS applications (more than 100): http://emboss.sourceforge.net/apps/cvs/groups.html Even on the user interface side, lots of work has been done (on Windows, too): http://emboss.sourceforge.net/interfaces/ EMBOSS is about 8 years old. Speaking as someone who has been involved in OSS development for bioinformatics for the same amount of time, I can tell you that existing projects need a lot of help from volunteers. But most aren't getting it. For every 10 projects started, maybe only 1 makes it to maturity and is considered significant. And, for every 10 people that join a mailing list saying that they'll help with a project, maybe only 1 actually does (it's much lower than that in some cases). Amir is right about this. Even Bioinformatics.Org could use some help. Know any PHP? ;-) Cheers, Jeff Amir Karger wrote: [...] > I know I've sounded very negative here. Maybe you're good enough to actually > pull it off. But the open source world is littered with the wreckage of > well-intentioned projects that never got off the ground. (I've created - or > not successfully created - a few little ones myself.) > > It's several zillion times faster to start from an existing code base than > to start from scratch. This could mean either joining an existing project's > development team, or, if you disagree about their future direction, at least > copying their code to start your own project. [...] -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From bader at cbio.mskcc.org Wed Jun 28 16:50:41 2006 From: bader at cbio.mskcc.org (Gary Bader) Date: Wed, 28 Jun 2006 16:50:41 -0400 Subject: [BiO BB] The Cancer Cell Map - a new human cancer pathway database Message-ID: <44A2EBA1.1040900@cbio.mskcc.org> Greetings, [My apologies if you have received a duplicate of this email message...] The Cancer Cell Map is a selected set of human cancer focused pathways. http://cancer.cellmap.org * Biologists can browse and search the Cancer Cell Map pathways. View gene expression data on any pathway. * Computational biologists can download all pathways in BioPAX format for global analysis. * Software developers can build software on top of the Cancer Cell Map using the web service API. * Download and install the cPath pathway database software to create a local mirror of the Cancer Cell Map. * All data is freely available. Released by the Computational Biology Center at Memorial Sloan-Kettering Cancer Center, in collaboration with Gary Bader's lab at the University of Toronto (http://baderlab.org). Pathway collection by the PandeyLab at Johns Hopkins University (http://pandeylab.igm.jhmi.edu) and the Institute of Bioinformatics (http://www.ibioinformatics.org). Cancer Cell Map pathways are also available in the new NetPath database (http://www.netpath.org) created by the PandeyLab and the Institute of Bioinformatics. In addition to 10 cancer pathways, 10 immune signaling pathways are available, all of which are freely available in GenMAPP, PSI-MI and BioPAX formats at http://www.netpath.org. BioPAX is an emerging standard for pathway data exchange (http://www.biopax.org). These pathways are unpublished at this time; please cite these websites until the pathways are described in a publication. From cfp-CIC-2006-a at magno-congreso.cic.ipn.mx Fri Jun 30 02:52:49 2006 From: cfp-CIC-2006-a at magno-congreso.cic.ipn.mx (Alexander Gelbukh (CIC-2006)) Date: Fri, 30 Jun 2006 01:52:49 -0500 Subject: [BiO BB] CFP: CIC-2006, 15th International Conference on Computing, published by IEEE CS (one week reminder) Message-ID: <05ca01c69c11$cd20e520$9314cc94@micron> 15th International Conference on Computing CIC 2006 November 21 to 24, 2006 Mexico City, Mexico http://magno-congreso.cic.ipn.mx/CIC-2006 Proceedings: IEEE CS Press. Deadline: July 1 expression of interest (recommended), July 7 full papers. CALL FOR PAPERS *** PUBLICATION *** Papers accepted for oral session will be published by IEEE CS Press. Papers accepted for poster session will be published in a journal "Research in Computing Science," ISSN 1665-9899. Extended versions of selected papers will be published in the journal "Computacion y Sistemas," ISSN 1405-5546. Submissions are received via the webpage, see guidelines there. Direct submission page is www.easychair.org/CIC2006. *** IMPORTANT DATES *** July 1: expression of interest (abstract) -- recommended. July 7: full text for registered papers. *** TOPICS *** All areas of Computer Science and Engineering, see webpage. PLEASE CIRCULATE this CFP among your students and colleagues. We apologize if you receive this CFP more than once. It is sent in good faith of its interest for you as a CS expert or student.