From structbio at gmail.com Mon Dec 4 19:20:12 2006 From: structbio at gmail.com (Struct Bio) Date: Mon, 4 Dec 2006 19:20:12 -0500 Subject: [BiO BB] ProtBuD: A comparative database of biological units in the Protein Data Bank (PDB) Message-ID: <4fb297440612041620n29c82f92t3367d8ee5a6594d6@mail.gmail.com> We have developed ProtBuD, a database that contains information on the contents of asymmetric units (ASUs) and hypothetical biological units (BUs) as obtained from the PDB and the Protein Quaternary Server (PQS) from the EBI (http://pqs.ebi.ac.uk). A query consisting of a PDB entry code (e.g. 1TUP) retrieves ASU and BU information across the family or superfamily as defined by SCOP and PSI-BLAST relationships. The database can also be queried by SCOP family or superfamily code (e.g. b.2.5.2) or by a pair of such designations to search for multi-domain proteins or complexes of proteins. The database can also be used to search for specific content across a family or superfamily, such as complexes with ions, ligands, or nucleic acids. The biological unit from the PDB and/or PQS differ from the asymmetric unit for 52% of X-ray structures. The PQS and PDB BUs disagree with each other for 18% of X-ray entries. For 14% of entries, the PDB BU is a substructure of the PQS BU or vice versa. For 1.3% of entries, the PQS and PDB entries differ and one is not a substructure of the other (i.e., they contain different interfaces). For 3.3%, PQS lists an interface as a possible crystallization artifact ("XPACK"). Availability: It is free to researchers in both non-profit and commercial institutions. The database is provided as a standalone program (recommended) and a web server from: http://dunbrack.fccc.edu/ProtBuD.php Reference: Qifang Xu, Adrian Canutescu, Roland Dunbrack, Bioinformatics, vol. 22, pp. 2876-2882 (2006). Roland Dunbrack Fox Chase Cancer Center Philadelphia PA 19111 USA Roland.Dunbrack at fccc.edu From joets at moulon.inra.fr Wed Dec 6 11:30:36 2006 From: joets at moulon.inra.fr (Johann JOETS) Date: Wed, 6 Dec 2006 17:30:36 +0100 Subject: [BiO BB] blast alert soft Message-ID: <005001c71953$dcf85270$3372668a@Bioinfo1> Hi ! I'm looking for software that can run blast search from time to time automatically and alert user when new homologous sequence appears. It would be better if it could be installed locally. Thanks for your suggestions ! Regards. Johann JOETS UMR de Genetique Vegetale Ferme du Moulon 91 190 Gif sur Yvette France 33(0)169332378 From jeff at bioinformatics.org Wed Dec 6 19:12:23 2006 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 06 Dec 2006 19:12:23 -0500 Subject: [BiO BB] Course: Advanced Bioinformatics Programming: Perl & R for Biologists, Level 2 Message-ID: <45775C67.90101@bioinformatics.org> (Apologies for multiple copies of this announcement.) Bioinformatics.Org is pleased to introduce an advanced and extended version of its "Perl and R for Biologists" course. LOCALE: Cambridge, Massachusetts DATES: January 16-19, 2007 OVERVIEW: This course will help biologists learn how to use Perl as a scripting language to automate certain tasks in their research, and how to use R as a statistical scripting language for data analysis. It includes an introduction to Perl and R and may be taken instead of "Introduction to Bioinformatics Programming: Perl and R for Biologists, Level 1," or as a refresher course on the basics. The course also covers advanced topics and projects, all in the context of biological research. Armed with some knowledge and hands-on experience with these tools, scientists will be able to perform more sophisticated software development tasks and to phrase research questions in the context of these tools. As a result, they will be able to appreciate and use computers better in their organization, and communicate better with their IT group. TOPICS: Students will learn how to write Perl and R scripts using various data structures, loops and file I/O constructs. They will also learn scripting with the Perl DBI and how to write multi-function scripts and convert them into Perl modules and packages. Examples will include high-throughput BLAST output, BioPerl, MySQL database packages for Perl, Bioconductor packages for R, and Affymetrix CEL files. SCHEDULE: This course will run January 16-19 and will be divided into 8 sessions of approximately 3.5 hours each. Instruction and exercises will begin at 8:30 AM and end at 5:00 PM. FOR MORE INFORMATION: To find out more information on the course, including the registration process, please see the course schedule page: http://edu.bioinformatics.org/06c Cheers, Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From idh at poulet.org Thu Dec 7 08:24:09 2006 From: idh at poulet.org (Yannick Wurm) Date: Thu, 7 Dec 2006 14:24:09 +0100 Subject: [BiO BB] Gene prediction References: <24EE8E9C-0D65-4B0A-9174-E10642156123@unil.ch> Message-ID: Hi, we all know that gene predictions can be far from reliable. Which is why recent genome projects, such as the Honey bee, used several gene predictions: ab initio predictions, homology-based predictions, EST- based prediction... They used GLEAN3 to combine the different predictions into one confident "Official Gene Set". I am exploring my favorite - currently unannotated - genome. Does anyone know of a web-tool which might do something similar on a much smaller scale? (I basically just want the CDS sequences for a small number of genes). If not, this could be a great opportunity for someone.... Input: my small genomic sequence of interest (maybe 10 or 20kb) + ESTs + other homologous sequences I may have Program fetches more homologous sequences from Genbank. Aligns everything it can to my sequence of interest Program uses genscan or whatever to predict exons. Program figures out a "consensus" protein sequence and determins introns/exons. Any ideas? Comments? Cheers, yannick -------------------------------------------- yannick . wurm @ unil . ch Ant Genomics, Ecology & Evolution @ Lausanne http://www.unil.ch/dee/page28685_fr.html From insight.robin at gmail.com Thu Dec 7 21:48:19 2006 From: insight.robin at gmail.com (Rob C) Date: Thu, 7 Dec 2006 21:48:19 -0500 Subject: [BiO BB] Gene prediction In-Reply-To: References: <24EE8E9C-0D65-4B0A-9174-E10642156123@unil.ch> Message-ID: I am interested in this problem. We are developing a tool to facilitate cross-Website and cross-database data analysis, and hope the bioinformatics community can get some benefit from it. However, I am not an expert in bioinformatics and have no clue how useful our tool is. The basic idea is: we developed visual interfaces to help the integration of Web data from distributed sites. In the simplest way, one can just record whatever s/he did on the Web, and repeat the Web exploration anytime later. In the more complex scenery, one can visually program it to extract data from one site, fill in form data in another site, compute data on the fly and save the extracted data into databases. An example is demonstrated in the following irobot file: http://irobotsoft.com/robots/blastx.irb (it requires installation of the irobot software, which is free). If you open it and run it, it will do a BLAST search for a given protein, extract the matching sequences from GenBank, search for conserved domain from CDART database, and save the results in an xml file "save.xml". I am wondering if there is any real world problem that may require the integration of Web data like the one demonstrated above. And additional functionality that may be required to solve larger problems. Thanks, R On 12/7/06, Yannick Wurm wrote: > > Hi, > we all know that gene predictions can be far from reliable. Which is > why recent genome projects, such as the Honey bee, used several gene > predictions: ab initio predictions, homology-based predictions, EST- > based prediction... They used GLEAN3 to combine the different > predictions into one confident "Official Gene Set". > > I am exploring my favorite - currently unannotated - genome. Does > anyone know of a web-tool which might do something similar on a much > smaller scale? (I basically just want the CDS sequences for a small > number of genes). If not, this could be a great opportunity for > someone.... > Input: > my small genomic sequence of interest (maybe 10 or 20kb) + ESTs + > other homologous sequences I may have > Program fetches more homologous sequences from Genbank. > Aligns everything it can to my sequence of interest > Program uses genscan or whatever to predict exons. > > Program figures out a "consensus" protein sequence and determins > introns/exons. > > Any ideas? Comments? > > Cheers, > yannick > > > > -------------------------------------------- > yannick . wurm @ unil . ch > Ant Genomics, Ecology & Evolution @ Lausanne > http://www.unil.ch/dee/page28685_fr.html > > > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From aloraine at gmail.com Fri Dec 8 03:37:13 2006 From: aloraine at gmail.com (Ann Loraine) Date: Fri, 8 Dec 2006 02:37:13 -0600 Subject: [BiO BB] question regarding unicode, biopython Seq object, DAS Message-ID: <83722dde0612080037i33884c20jafcb4b24ac7b6815@mail.gmail.com> Hello, I'm attempting to get sequence data from a DAS server (UCSC, DAS1) and am having what appears to be a unicode-related problem - if you have any insights or advice, I'd be grateful for the help. I'm running biopython v. 1.42 on Mac OS X 10.3.9. My sax parser delivers character (sequence) data as unicode, but when I make a Seq object from the unicode string and then try to reverse complement the sequence, I get an exception: TypeError: character mapping must return integer, None or unicode So I tried this: >>> from Bio.Alphabet import IUPAC >>> from Bio.Seq import Seq >>> s = Seq(u'atcg',IUPAC.unambiguous_dna) >>> s.reverse_complement() Traceback (most recent call last): File "", line 1, in ? File "/usr/local/lib/python2.4/site-packages/Bio/Seq.py", line 117, in reverse_complement s = self.data[-1::-1].translate(ttable) TypeError: character mapping must return integer, None or unicode >>> s = Seq('atcg',IUPAC.unambiguous_dna) # note: no longer unicode >>> s.reverse_complement() Seq('cgat', IUPACUnambiguousDNA()) An example access of the UCSC DAS1 site follows. In my code I'm using a SAX parser to get the data, but this demonstrates a bit of how the DAS aspect works: >>> u = 'http://genome.cse.ucsc.edu/cgi-bin/das/hg17/dna?segment=1:158288275,158302415' >>> import urllib >>> fh = urllib.urlopen(u) >>> fh.readline() '\n' >>> fh.readline() '\n' >>> fh.readline() '\n' >>> fh.readline() '\n' >>> fh.readline() 'gtctcttaaaacccactggacgttggcacagtgctgggatgactatggag\n' ...and etc. Yours, Ann -- Ann Loraine Assistant Professor Departments of Genetics, Biostatistics, and Section on Statistical Genetics University of Alabama at Birmingham http://www.ssg.uab.edu http://www.transvar.org From dalesan at gmail.com Tue Dec 12 15:19:01 2006 From: dalesan at gmail.com (Dale Richardson) Date: Tue, 12 Dec 2006 21:19:01 +0100 Subject: [BiO BB] Re: Quickly retrieving cross-referenced records from NCBI Message-ID: <3E154C4F-250F-4908-973A-B5F7C6B8FF24@gmail.com> Hello All, Forgive me for posting, but this question is hard to condense into a good google search. I am wondering if there is a quick way to batch retrieve all coding sequences (mRNA sequences) linked to a particular NCBI RefSeq Protein identifier. For example, if I have a list of 10 sequences with the following protein refseq IDs: XP_698519.1 XP_697978.1 and so on.. How can I retrieve the cross-referenced XM_ identifiers for the coding sequences based on such protein accessions? Must one write some kind of script to accomplish this or is there a quicker way? thanks, dale richardson university of cologne From dankoc at gmail.com Tue Dec 12 13:37:52 2006 From: dankoc at gmail.com (Charles Danko) Date: Tue, 12 Dec 2006 13:37:52 -0500 Subject: [BiO BB] Reading DNA ambiguity codes with WuBlast blastn 2.0 Message-ID: <8adccabf0612121037t1c934d1al9cbb3e687ecd3ff5@mail.gmail.com> Hi, Does anyone know of a method to compare DNA template sequences that contain IUPAC ambiguity codes (i.e. W=A/T) to a database using WuBlast blastn 2.0? I've been through the docs, and havent found anything on ambiguity code support besides N (any base). Thanks very much! Charles From ybolo001 at student.ucr.edu Wed Dec 13 13:30:25 2006 From: ybolo001 at student.ucr.edu (Eugene Bolotin) Date: Wed, 13 Dec 2006 10:30:25 -0800 Subject: [BiO BB] Re: Quickly retrieving cross-referenced records from NCBI In-Reply-To: <3E154C4F-250F-4908-973A-B5F7C6B8FF24@gmail.com> References: <3E154C4F-250F-4908-973A-B5F7C6B8FF24@gmail.com> Message-ID: <941fcc750612131030y6cd3b9d4ga0d2c734e8be25c2@mail.gmail.com> The quickest way is UCSC table browser, batch retreive. Read up on that. On 12/12/06, Dale Richardson wrote: > > Hello All, > > Forgive me for posting, but this question is hard to condense into a > good google search. I am wondering if there is a quick way to batch > retrieve all coding sequences (mRNA sequences) linked to a particular > NCBI RefSeq Protein identifier. For example, if I have a list of 10 > sequences with the following protein refseq IDs: > > XP_698519.1 > XP_697978.1 > > and so on.. > > How can I retrieve the cross-referenced XM_ identifiers for the > coding sequences based on such protein accessions? Must one write > some kind of script to accomplish this or is there a quicker way? > > thanks, > > dale richardson > university of cologne > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Eugene Bolotin Ph.D. candidate Genetics Genomics and Bioinformatics University of California Riverside ybolo001 at student.ucr.edu Dr. Frances Sladek Lab From pandey.gaurav at gmail.com Wed Dec 13 23:37:19 2006 From: pandey.gaurav at gmail.com (Gaurav Pandey) Date: Wed, 13 Dec 2006 22:37:19 -0600 Subject: [BiO BB] New Survey: Computational Approaches for Protein Function Prediction Message-ID: <627ca1900612132037p7b9e400fg9654996c40126ecb@mail.gmail.com> [Apologies if you receive this more than once] Dear Colleague, We are pleased to share with you a recent review of several hundred papers in the field of computational protein function prediction: Title: Computational Approaches for Protein Function Prediction: A Survey Authors: Gaurav Pandey , Vipin Kumarand Michael Steinbach Available at: http://www.cs.umn.edu/~kumar/papers/survey.php Abstract Proteins are the most essential and versatile macromolecules of life, and the knowledge of their functions is a crucial link in the development of new drugs, better crops, and even the development of synthetic biochemicals such as biofuels. Experimental procedures for protein function prediction are inherently low throughput and are thus unable to annotate a non-trivial fraction of proteins that are becoming available due to rapid advances in genome sequencing technology. This has motivated the development of computational techniques that utilize a variety of high-throughput experimental data for protein function prediction, such as protein and genome sequences, gene expression data, protein interaction networks and phylogenetic profiles. Indeed, in a short period of a decade, several hundred articles have been published on this topic. This review aims to discuss this wide spectrum of approaches by categorizing them in terms of the data type they use for predicting function, and thus identify the trends and needs of this very important field. The survey is expected to be useful for computational biologists and bioinformaticians aiming to get an overview of the field of computational function prediction, and identify areas that can benefit from further research. Your comments on the article, or any part thereof, are welcome. Thanks and best regards Gaurav Pandey (gaurav at cs.umn.edu) Vipin Kumar (kumar at cs.umn.edu) Michael Steinbach (steinbac at cs.umn.edu) From p.balaji at gmail.com Thu Dec 14 12:11:20 2006 From: p.balaji at gmail.com (Balaji Parameswaran) Date: Thu, 14 Dec 2006 22:41:20 +0530 Subject: [BiO BB] Yeast - Human Homologs Message-ID: <881c02220612140911i35c2f71ficd166c1dbdbe74d7@mail.gmail.com> Hello all, I am working with a set of genes from the yeast genome. I want to retrive the corresponding human homologs for those genes, can anyone suggest a simple way to batch-retrieve human homologs of all the yeast genes under consideration ? Thanks in advance Balaji From ethan.strauss at promega.com Thu Dec 14 13:53:40 2006 From: ethan.strauss at promega.com (Ethan Strauss) Date: Thu, 14 Dec 2006 12:53:40 -0600 Subject: [BiO BB] Yeast - Human Homologs In-Reply-To: <881c02220612140911i35c2f71ficd166c1dbdbe74d7@mail.gmail.com> Message-ID: Hi, Assuming that you have accession numbers or similar, you could use the eSearch and eLink utilities from NCBI (http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html) to find the human homologs. I don't know of a simple way to do it without a little code. Perhaps someone else does. Ethan Ethan Strauss Ph.D. Bioinformatics Scientist Promega Corporation 2800 Woods Hollow Rd. Madison, WI 53711 608-274-4330 800-356-9526 ethan.strauss at promega.com -----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 Balaji Parameswaran Sent: Thursday, December 14, 2006 11:11 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Yeast - Human Homologs Hello all, I am working with a set of genes from the yeast genome. I want to retrive the corresponding human homologs for those genes, can anyone suggest a simple way to batch-retrieve human homologs of all the yeast genes under consideration ? Thanks in advance Balaji _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From Michael.Muratet at operon.com Thu Dec 14 13:50:08 2006 From: Michael.Muratet at operon.com (Michael Muratet US-Huntsville) Date: Thu, 14 Dec 2006 12:50:08 -0600 Subject: [BiO BB] Yeast - Human Homologs In-Reply-To: <881c02220612140911i35c2f71ficd166c1dbdbe74d7@mail.gmail.com> Message-ID: Balaji You might try downloading the yeast core database and perl APIs from Ensembl. You can get yeast-human homologs easily with a few lines of perl. Good luck 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 Balaji Parameswaran Sent: Thursday, December 14, 2006 11:11 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Yeast - Human Homologs Hello all, I am working with a set of genes from the yeast genome. I want to retrive the corresponding human homologs for those genes, can anyone suggest a simple way to batch-retrieve human homologs of all the yeast genes under consideration ? Thanks in advance Balaji _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From hararid at bgu.ac.il Thu Dec 14 16:49:20 2006 From: hararid at bgu.ac.il (Daniel Harari) Date: Thu, 14 Dec 2006 21:49:20 GMT Subject: [BiO BB] Yeast - Human Homologs In-Reply-To: <881c02220612140911i35c2f71ficd166c1dbdbe74d7@mail.gmail.com> References: <881c02220612140911i35c2f71ficd166c1dbdbe74d7@mail.gmail.com> Message-ID: To compare orthologues between two species, including human-yeast, may I suggest trying Inparanoid: http://inparanoid.cgb.ki.se/ For multispecies comparisons, you may prefer to use NCBI's Homologene: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene Regarding Homologene, if you can't extract the data easily via the Web browser, you will find a tab linking to the Homologene FTP download sites, and you can access the desired tables directly.? Extracting meanig from this data will require some code writing. Regards, Daniel ----- Original Message ----- From: Balaji Parameswaran Date: Thursday, December 14, 2006 20:42 Subject: [BiO BB] Yeast - Human Homologs To: bio_bulletin_board at bioinformatics.org > Hello all, > ? I am working with a set of genes from the yeast genome. I > want to retrive > the corresponding human homologs for those genes, can anyone > suggest a > simple way to batch-retrieve human homologs of all the yeast > genes under > consideration ? > Thanks in advance > Balaji > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.orghttps://bioinformatics.org/mailman/listinfo/bio_bulletin_board > ? From insight.robin at gmail.com Sun Dec 17 12:27:09 2006 From: insight.robin at gmail.com (Rob C) Date: Sun, 17 Dec 2006 12:27:09 -0500 Subject: [BiO BB] Yeast - Human Homologs In-Reply-To: References: <881c02220612140911i35c2f71ficd166c1dbdbe74d7@mail.gmail.com> Message-ID: I created a tool for you to batch-download matches from the NCBI's Homologene. Follow this link: http://irobotsoft.org/bb/YaBB.pl?num=1166375573 > From deletto at unisa.it Thu Dec 14 14:59:35 2006 From: deletto at unisa.it (deletto at unisa.it) Date: Thu, 14 Dec 2006 20:59:35 +0100 Subject: [BiO BB] 3'-UTR database Message-ID: <20061214205935.0evzbtuxgc4os0sc@webmail.unisa.it> Hi All, Where can I find a 3'UTR database, on internet? Thanks a lot, Davide ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From ldufur at scsk12.org Thu Dec 14 18:03:33 2006 From: ldufur at scsk12.org (Lisa DuFur) Date: Thu, 14 Dec 2006 17:03:33 -0600 Subject: [BiO BB] Spooling DNA Message-ID: Hi, I am a teacher at Houston High School in Germantown TN. I did DNA extraction of strawberries today and it worked great except for one thing. I didn?t get the long strands of DNA, only clumps. Is there a trick to getting those long wonderful strands of DNA? Thanks for your help, Lisa -- Lisa DuFur Shelby County Schools From ulimard at yahoo.com.br Thu Dec 14 22:37:06 2006 From: ulimard at yahoo.com.br (Ulisses Dias) Date: Fri, 15 Dec 2006 03:37:06 +0000 (GMT) Subject: [BiO BB] Gene Ontology - Validating classifier In-Reply-To: Message-ID: <20061215033706.1909.qmail@web56608.mail.re3.yahoo.com> Hi! I created a system to predict the function of a protein using GO terms. Anyone could sugest a method to use the cross fold validation to perform the tests? I know that I must to redefine the recall and precision but I have troubles in doing so. Other question is that I'm trying a way to split the data ensuring fold balance and fold isolation using WEKA, anyone knows an algorithm that could help me? Thanks Ulisses Dias --------------------------------- Yahoo! Search M?sica para ver e ouvir: You're Beautiful, do James Blunt From hararid at bgu.ac.il Tue Dec 19 04:17:35 2006 From: hararid at bgu.ac.il (Daniel Harari) Date: Tue, 19 Dec 2006 09:17:35 GMT Subject: [BiO BB] 3'-UTR database In-Reply-To: <20061214205935.0evzbtuxgc4os0sc@webmail.unisa.it> References: <20061214205935.0evzbtuxgc4os0sc@webmail.unisa.it> Message-ID: Dear Davide, There is a UTR database and set of tools provided by an Italian group.? See links. Daniel http://www.ba.itb.cnr.it/BIG/PatSearch/UTRdb.pdf http://www.ba.itb.cnr.it/UTR/ ----- Original Message ----- From: deletto at unisa.it Date: Monday, December 18, 2006 1:01 Subject: [BiO BB] 3'-UTR database To: bio_bulletin_board at bioinformatics.org > Hi All, > Where can I find a 3'UTR database, on internet? > > Thanks a lot, > Davide > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.orghttps://bioinformatics.org/mailman/listinfo/bio_bulletin_board > ? From hararid at bgu.ac.il Tue Dec 19 04:20:40 2006 From: hararid at bgu.ac.il (Daniel Harari) Date: Tue, 19 Dec 2006 09:20:40 GMT Subject: [BiO BB] Spooling DNA In-Reply-To: References: Message-ID: Dear Lisa, Especially when there is a lot of DNA to precipitate, sometimes the precipitation process is sudden and ~ immediate.? In this case, you don't get to see DNA spooling but rather DNA clumping. So your classroom experiment probably worked very well (or too well). Daniel ----- Original Message ----- From: Lisa DuFur? Date: Monday, December 18, 2006 1:01 Subject: [BiO?BB] Spooling DNA To: bio_bulletin_board at bioinformatics.org > Hi, > > I am a teacher at Houston High School in Germantown TN. I did > DNA extraction > of strawberries today and it worked great except for one thing. > I didn?t get > the long strands of DNA, only clumps. Is there a trick to > getting those long > wonderful strands of DNA? > > Thanks for your help, > > Lisa > -- > > Lisa DuFur? > Shelby County Schools > > > > > _______________________________________________ > General Forum at Bioinformatics.Org?- > BiO_Bulletin_Board at bioinformatics.orghttps://bioinformatics.org/mailman/listinfo/bio_bulletin_board > ? From me_brajesh at yahoo.co.in Tue Dec 19 06:52:46 2006 From: me_brajesh at yahoo.co.in (brajesh kaistha) Date: Tue, 19 Dec 2006 11:52:46 +0000 (GMT) Subject: [BiO BB] 3'-UTR database In-Reply-To: <20061214205935.0evzbtuxgc4os0sc@webmail.unisa.it> Message-ID: <554160.52302.qm@web8514.mail.in.yahoo.com> Hi Davide There is something called UTR database where u can find the UTR sequences of various organisms. The URL is " http://www.ba.itb.cnr.it/UTR/ " Cheers, Brajesh Kaistha --- deletto at unisa.it wrote: > Hi All, > Where can I find a 3'UTR database, on internet? > > Thanks a lot, > Davide > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet > Messaging Program. > > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > Thanks and regards...... Sincerely, Brajesh ------------------------------------------------------------- BRAJESH KAISTHA M.Tech.(Bioinformatics) Room No: 408, Boys Hostel (Hall -2) Indian Institute of Information Technology Deoghat, Jhalwa, Allahabad Uttar Pradesh 211 012 (INDIA) Mobile No.# : 91-9935020205 Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php From richard.squires at utsouthwestern.edu Tue Dec 19 12:09:06 2006 From: richard.squires at utsouthwestern.edu (Burke Squires) Date: Tue, 19 Dec 2006 11:09:06 -0600 Subject: [BiO BB] Compiling emboss 4.0 for Mac OS X In-Reply-To: References: Message-ID: <8D885752-C389-4EBA-9B4D-AA184CFFC705@utsouthwestern.edu> Hello, Has anyone had success in compiling emboss 4.0 for Mac OS X 10.4? If so, do you have the how you did it? I am getting the following errors when executing ./configure: ... config.status: creating doc/tutorials/Makefile config.status: error: cannot find input file: doc/tutorials/Makefile.in Thanks! Burke From Stan.Gaj at BIGCAT.unimaas.nl Wed Dec 20 06:02:29 2006 From: Stan.Gaj at BIGCAT.unimaas.nl (Gaj Stan (BIGCAT)) Date: Wed, 20 Dec 2006 12:02:29 +0100 Subject: [BiO BB] Re: Quickly retrieving cross-referenced records from NCBI In-Reply-To: <941fcc750612131030y6cd3b9d4ga0d2c734e8be25c2@mail.gmail.com> Message-ID: <1C6586068DF1054DA3899159C38B32C9071E2D80@um-mail0136.unimaas.nl> Dear Dale, I encountered the same question a few weeks ago, but my focus was the other way around: go from NM to NP. For that I've written a Perl script that I've adjusted to fit your needs (so going for NP to NM). If I'm correct, RefSeq splits it's database in three parts: genomic, mRNA and protein. For this script to work, you need a) to download a species-specific RefSeq mRNA database (ends with .rna.gbff) for the NCBI ftp and b) to have your own file of convertable IDs, sorted in a list-form.. Note that this script will NOT detect version numbers: e.g. XP_12345.1 needs to be converted to XP_12345 in your list before it does it's job! Although the code is far from perfect, it fulfills your question perfectly (-; Best wishes, Stan -----Original Message----- From: bio_bulletin_board-bounces+stan.gaj=bigcat.unimaas.nl at bioinformatics.org [mailto:bio_bulletin_board-bounces+stan.gaj=bigcat.unimaas.nl at bioinforma tics.org] On Behalf Of Eugene Bolotin Sent: 13 December 2006 19:30 To: General Forum at Bioinformatics.Org Subject: Re: [BiO BB] Re: Quickly retrieving cross-referenced records from NCBI The quickest way is UCSC table browser, batch retreive. Read up on that. On 12/12/06, Dale Richardson wrote: > > Hello All, > > Forgive me for posting, but this question is hard to condense into a > good google search. I am wondering if there is a quick way to batch > retrieve all coding sequences (mRNA sequences) linked to a particular > NCBI RefSeq Protein identifier. For example, if I have a list of 10 > sequences with the following protein refseq IDs: > > XP_698519.1 > XP_697978.1 > > and so on.. > > How can I retrieve the cross-referenced XM_ identifiers for the > coding sequences based on such protein accessions? Must one write > some kind of script to accomplish this or is there a quicker way? > > thanks, > > dale richardson > university of cologne > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Eugene Bolotin Ph.D. candidate Genetics Genomics and Bioinformatics University of California Riverside ybolo001 at student.ucr.edu Dr. Frances Sladek Lab _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From jeff at bioinformatics.org Wed Dec 20 17:18:26 2006 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 20 Dec 2006 17:18:26 -0500 Subject: [BiO BB] Re: Quickly retrieving cross-referenced records from NCBI In-Reply-To: <1C6586068DF1054DA3899159C38B32C9071E2D80@um-mail0136.unimaas.nl> References: <1C6586068DF1054DA3899159C38B32C9071E2D80@um-mail0136.unimaas.nl> Message-ID: <4589B6B2.6080400@bioinformatics.org> Stan, the attached script got removed. Please resend it in-line (in the message body), or send a link. Thanks, Jeff Gaj Stan (BIGCAT) wrote: > Dear Dale, > > I encountered the same question a few weeks ago, but my focus was the > other way around: go from NM to NP. For that I've written a Perl script > that I've adjusted to fit your needs (so going for NP to NM). > > If I'm correct, RefSeq splits it's database in three parts: genomic, > mRNA and protein. For this script to work, you need a) to download a > species-specific RefSeq mRNA database (ends with .rna.gbff) for the NCBI > ftp and b) to have your own file of convertable IDs, sorted in a > list-form.. > Note that this script will NOT detect version numbers: e.g. XP_12345.1 > needs to be converted to XP_12345 in your list before it does it's job! > > Although the code is far from perfect, it fulfills your question > perfectly (-; > > Best wishes, > > Stan -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From dalesan at gmail.com Wed Dec 20 22:32:17 2006 From: dalesan at gmail.com (Dale Richardson) Date: Thu, 21 Dec 2006 04:32:17 +0100 Subject: [BiO BB] Re: Quickly retrieving cross-referenced records from NCBI In-Reply-To: <1C6586068DF1054DA3899159C38B32C9071E2D80@um-mail0136.unimaas.nl> References: <1C6586068DF1054DA3899159C38B32C9071E2D80@um-mail0136.unimaas.nl> Message-ID: Hi Stan, Thanks for this! I will definitely keep a hold of it. However, I think there is yet another way to retrieve such cross-ref'd records: For example, if I input a set of XP_ accessions and want to get the XM_ accessions one can simply select, "Nucleotide links" from the pulldown menu at NCBI (where GenPept, FASTA and other such options are listed). Thanks for your tips tho (and to everyone else as well)! Hope everyone has a great holiday season. -dale On Dec 20, 2006, at 12:02 PM, Gaj Stan (BIGCAT) wrote: > Dear Dale, > > I encountered the same question a few weeks ago, but my focus was the > other way around: go from NM to NP. For that I've written a Perl > script > that I've adjusted to fit your needs (so going for NP to NM). > > If I'm correct, RefSeq splits it's database in three parts: genomic, > mRNA and protein. For this script to work, you need a) to download a > species-specific RefSeq mRNA database (ends with .rna.gbff) for the > NCBI > ftp and b) to have your own file of convertable IDs, sorted in a > list-form.. > Note that this script will NOT detect version numbers: e.g. XP_12345.1 > needs to be converted to XP_12345 in your list before it does it's > job! > > Although the code is far from perfect, it fulfills your question > perfectly (-; > > Best wishes, > > Stan > > > -----Original Message----- > From: > bio_bulletin_board-bounces > +stan.gaj=bigcat.unimaas.nl at bioinformatics.org > [mailto:bio_bulletin_board-bounces > +stan.gaj=bigcat.unimaas.nl at bioinforma > tics.org] On Behalf Of Eugene Bolotin > Sent: 13 December 2006 19:30 > To: General Forum at Bioinformatics.Org > Subject: Re: [BiO BB] Re: Quickly retrieving cross-referenced records > from NCBI > > The quickest way is UCSC table browser, batch retreive. Read up on > that. > > > On 12/12/06, Dale Richardson wrote: >> >> Hello All, >> >> Forgive me for posting, but this question is hard to condense into a >> good google search. I am wondering if there is a quick way to batch >> retrieve all coding sequences (mRNA sequences) linked to a particular >> NCBI RefSeq Protein identifier. For example, if I have a list of 10 >> sequences with the following protein refseq IDs: >> >> XP_698519.1 >> XP_697978.1 >> >> and so on.. >> >> How can I retrieve the cross-referenced XM_ identifiers for the >> coding sequences based on such protein accessions? Must one write >> some kind of script to accomplish this or is there a quicker way? >> >> thanks, >> >> dale richardson >> university of cologne >> >> _______________________________________________ >> General Forum at Bioinformatics.Org - >> BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> > > > > -- > Eugene Bolotin > Ph.D. candidate > Genetics Genomics and Bioinformatics > University of California Riverside > ybolo001 at student.ucr.edu > Dr. Frances Sladek Lab > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From codeshepherd at gmail.com Thu Dec 21 03:06:59 2006 From: codeshepherd at gmail.com (Deepan) Date: Thu, 21 Dec 2006 16:06:59 +0800 Subject: [BiO BB] Compiling emboss 4.0 for Mac OS X In-Reply-To: <8D885752-C389-4EBA-9B4D-AA184CFFC705@utsouthwestern.edu> References: <8D885752-C389-4EBA-9B4D-AA184CFFC705@utsouthwestern.edu> Message-ID: <1166688419.2737.20.camel@codeworld> On Tue, 2006-12-19 at 11:09 -0600, Burke Squires wrote: > Hello, > > Has anyone had success in compiling emboss 4.0 for Mac OS X 10.4? If > so, do you have the how you did it? > > I am getting the following errors when executing ./configure: > > ... > config.status: creating doc/tutorials/Makefile > config.status: error: cannot find input file: doc/tutorials/Makefile.in > > This suggests that you have a corrupted download. Do you find those files in place. I mean do you find a Makefile.in in doc/tutorials folder? You will find a file by the name INSTALL or README once you untar or unzip the package. you will find necessary instructions in that. > Thanks! > > Burke > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- ----------------------------------------------- Regards Deepan Chakravarthy N http://www.codeshepherd.com/ +65-96770940 Software Engineer, Nova Global Pte Ltd, Technical & Scientific Computing Solutions, #05-04 Keypoint, 371 Beach Road, Singapore. web: http://www.novaglobal.com.sg/ Have Fun, Play Sudoku :) http://sudoku-solver.net/ From Stan.Gaj at BIGCAT.unimaas.nl Thu Dec 21 03:22:49 2006 From: Stan.Gaj at BIGCAT.unimaas.nl (Gaj Stan (BIGCAT)) Date: Thu, 21 Dec 2006 09:22:49 +0100 Subject: [BiO BB] Re: Quickly retrieving cross-referenced records from NCBI In-Reply-To: Message-ID: <1C6586068DF1054DA3899159C38B32C9071E2E00@um-mail0136.unimaas.nl> No problem. Well, I didn't know the trick through NCBI. So I learned a bit out of this as well. (-; On the other hand, I'd like to do those 'smaller' tasks myself, so I understand the processes behind it and know for sure that it happened in a correct manner. But that's just a personal view on it! (-; Oh, and just for completeness sake, I noticed that the maillist does not support attachments, so I've uploaded the script (if you or someone else might ever need it *cough*) to http://ftp2.bigcat.unimaas.nl/~stan.gaj/scripts/refseq_converter_np2nm.p l Best wishes to you all for 2007! Stan -----Original Message----- From: bio_bulletin_board-bounces+stan.gaj=bigcat.unimaas.nl at bioinformatics.org [mailto:bio_bulletin_board-bounces+stan.gaj=bigcat.unimaas.nl at bioinforma tics.org] On Behalf Of Dale Richardson Sent: 21 December 2006 04:32 To: General Forum at Bioinformatics.Org Subject: Re: [BiO BB] Re: Quickly retrieving cross-referenced records from NCBI Hi Stan, Thanks for this! I will definitely keep a hold of it. However, I think there is yet another way to retrieve such cross-ref'd records: For example, if I input a set of XP_ accessions and want to get the XM_ accessions one can simply select, "Nucleotide links" from the pulldown menu at NCBI (where GenPept, FASTA and other such options are listed). Thanks for your tips tho (and to everyone else as well)! Hope everyone has a great holiday season. -dale On Dec 20, 2006, at 12:02 PM, Gaj Stan (BIGCAT) wrote: > Dear Dale, > > I encountered the same question a few weeks ago, but my focus was the > other way around: go from NM to NP. For that I've written a Perl > script > that I've adjusted to fit your needs (so going for NP to NM). > > If I'm correct, RefSeq splits it's database in three parts: genomic, > mRNA and protein. For this script to work, you need a) to download a > species-specific RefSeq mRNA database (ends with .rna.gbff) for the > NCBI > ftp and b) to have your own file of convertable IDs, sorted in a > list-form.. > Note that this script will NOT detect version numbers: e.g. XP_12345.1 > needs to be converted to XP_12345 in your list before it does it's > job! > > Although the code is far from perfect, it fulfills your question > perfectly (-; > > Best wishes, > > Stan > > > -----Original Message----- > From: > bio_bulletin_board-bounces > +stan.gaj=bigcat.unimaas.nl at bioinformatics.org > [mailto:bio_bulletin_board-bounces > +stan.gaj=bigcat.unimaas.nl at bioinforma > tics.org] On Behalf Of Eugene Bolotin > Sent: 13 December 2006 19:30 > To: General Forum at Bioinformatics.Org > Subject: Re: [BiO BB] Re: Quickly retrieving cross-referenced records > from NCBI > > The quickest way is UCSC table browser, batch retreive. Read up on > that. > > > On 12/12/06, Dale Richardson wrote: >> >> Hello All, >> >> Forgive me for posting, but this question is hard to condense into a >> good google search. I am wondering if there is a quick way to batch >> retrieve all coding sequences (mRNA sequences) linked to a particular >> NCBI RefSeq Protein identifier. For example, if I have a list of 10 >> sequences with the following protein refseq IDs: >> >> XP_698519.1 >> XP_697978.1 >> >> and so on.. >> >> How can I retrieve the cross-referenced XM_ identifiers for the >> coding sequences based on such protein accessions? Must one write >> some kind of script to accomplish this or is there a quicker way? >> >> thanks, >> >> dale richardson >> university of cologne >> >> _______________________________________________ >> General Forum at Bioinformatics.Org - >> BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> > > > > -- > Eugene Bolotin > Ph.D. candidate > Genetics Genomics and Bioinformatics > University of California Riverside > ybolo001 at student.ucr.edu > Dr. Frances Sladek Lab > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From stg at inf.ed.ac.uk Thu Dec 21 08:51:06 2006 From: stg at inf.ed.ac.uk (Stephen Gilmore) Date: Thu, 21 Dec 2006 13:51:06 +0000 Subject: [BiO BB] [cmsb-2007] Call for papers CMSB07 Message-ID: <458A914A.4090003@inf.ed.ac.uk> International Conference on COMPUTATIONAL METHODS IN SYSTEMS BIOLOGY 20th and 21st September 2007 Edinburgh, Scotland http://conferences.inf.ed.ac.uk/cmsb07/ The CMSB (Computational Methods in Systems Biology) conference series was established in 2003 to help catalyze the convergence of modellers, physicists, mathematicians, and theoretical computer scientists from fields such as language design, concurrency theory, program verification, and molecular biologists, physicians, neuroscientists interested in a systems-level understanding of cellular physiology and pathology. CMSB'07 solicits original research articles (including significant works-in-progress), surveys of current research and posters. These may cover theoretical or applied contributions that are motivated by a biological question and can demonstrate either actual or potential usefulness towards answering that question. They may also cover models of computation inspired by biological processes; the motivation may be as much computational as biological. Particularly relevant case studies and open issues from the biological side that demands modeling of systems are of interest as well. The introduction of formal models should be supported by theoretical arguments about the model and/or on the analyses that they enable, by comparisons with other network models, and/or by examples of representation and analysis of a biological system. Topics of interest include, among others: 1. Biological systems and networks: inference, properties, modeling, dynamics, simulation and reverse engineering 2. Formal methods for drug discovery and design 3. Methods to predict biological network behavior from incomplete information 4. Models including symbolic evolution and learning 5. Models of self-assembly 6. Detailed case-studies on how a biological question was successfully addressed using formal models 7. Emergence of properties in complex biological systems 8. Theoretical comparisons between different formal models of cellular processes 9. Differential, discrete and/or stochastic modeling-language frameworks 10. Quantitative formal languages 11. Biologically-inspired extensions to concurrency theory, constraint programming, logical methods or language equivalences 12. Computer models in nano-sciences applied to biological domains 13. Definition and study of theoretical properties of biologically-inspired formal languages 14. Biological data bases and exchange formats for biological data and standards History 2006 held in Trento, chaired by Corrado Priami 2005 held in Edinburgh, chaired by Gordon Plotkin. 2004 held in Paris, co-chaired by Vincent Danos and Vincent Schachter 2003 held in Trento, chaired by Corrado Priami Paper and poster submission guidelines Authors are invited to submit original research papers or survey papers of no more than 15 pages in PDF format using the LNCS templates, available at the url below http://www.springer.com/sgw/cda/frontpage/0,11855,5-164-2-72376-0,00.html We also accept poster proposals in the form of a text-only abstract describing the poster contents. Papers and posters descriptions should be sent by e-mail to cmsb07-papers at inf.ed.ac.uk The subject line should be CMSB Paper: (Title of Paper). The body of the e-mail should contain the title, authors and affiliations, an abstract, and the themes to which the paper/poster refers according to the topics of interest list. If no theme is listed, please insert some keywords. All submissions will be reviewed by the program committee. Accepted papers will be included in the proceedings available at the conference. Publication as an LNBI volume by Springer is under negotiation. Important Dates (deadlines are strict): Submission of papers: May, 7 Notification of paper acceptance: June, 4 Revised version of papers due: July, 2 Submission of posters: July, 10 Notification of poster acceptance: July, 30 Venue The conference will be held in Edinburgh (Scotland) at the e-Science Institute. The dates are 20th and 21st September 2007. Committees Steering Committee * Finn Drabl?s, Norwegian University of Science and Technology, Trondheim (Norway) * Monika Heiner, TU Cottbus (Germany) * Patrick Lincoln, Stanford Research International (US) * Satoru Miyano, University of Tokyo (Japan) * Gordon Plotkin, University of Edinburgh (UK) * Corrado Priami, The Microsoft Research -- University of Trento Centre for Computational and Systems Biology (Italy) * Magali Roux-Rouqui?, CNRS-UPMC (France) * Vincent Schachter, Genoscope, Evry (France) * Adelinde Uhrmacher, University of Rostock (Germany) Program Committee * Alexander Bockmayr, Freie Universit?t Berlin (Germany) * Muffy Calder (co-chair), University of Glasgow (UK) * Luca Cardelli, Microsoft Research Cambridge (UK) * Vincent Danos, CNRS, Universit? Denis Diderot (France) * Pierpaolo Degano, Universit? di Pisa (Italy) * Finn Drabl?s, Norwegian University of Science and Technology, Trondheim (Norway) * Fran?ois Fages, INRIA Rocquencourt (France) * Anthony Finkelstein, University College London (UK) * Stephen Gilmore (co-chair), University of Edinburgh (UK) * David Harel, Weizmann Institute (Israel) * Monika Heiner, TU Cottbus (Germany) * Walter Kolch, Beatson Institute for Cancer Research (UK) * Ina Koch, Technische Fachhochschule Berlin (Germany) * Gethin Norman, University of Birmingham (UK) * Corrado Priami, The Microsoft Research -- University of Trento Centre for Computational and Systems Biology (Italy) * Stephen Ramsey, Institute for Systems Biology, Seattle (USA) * Adelinde Uhrmacher, University of Rostock (Germany) Organising committee * Muffy Calder, University of Glasgow (UK) * Stephen Gilmore, University of Edinburgh (UK) (Apologies if you receive multiple copies of this message) _______________________________________________ cmsb-2007 mailing list cmsb-2007 at inf.ed.ac.uk http://lists.inf.ed.ac.uk/mailman/listinfo/cmsb-2007 From structbio at gmail.com Thu Dec 21 14:08:40 2006 From: structbio at gmail.com (Struct Bio) Date: Thu, 21 Dec 2006 14:08:40 -0500 Subject: [BiO BB] BioDownloader: Bioinformatics File Downloads/Updates in Several Clicks Message-ID: <4fb297440612211108w63b512b8k88f0e348d3172598@mail.gmail.com> Dear colleagues, Please try our new free software product: BioDownloader is an application for downloading and/or updating files from ftp/http servers. The program has unique features that are specifically designed to deal with bioinformatics data files and servers: - optimized to work with vast amount of data and very large file sets (~ 10,000 - 100,000). - allows the selective retrieval of only the required files (file masks, ls-lR parsing, recursive search, updates) - has a built-in repository containing the settings for the most common bioinformatics download needs - built-in wizard for batch post-processing of downloaded files (archive extraction, file conversion, etc.) Availability: BioDownloader is free to researchers in both non-profit and commercial institutions. It is provided as a standalone application from: http://dunbrack.fccc.edu/BioDownloader/BioDownloader.php (with screenshots and detailed description) Maxim Shapovalov Roland Dunbrack Fox Chase Cancer Center Philadelphia PA 19111 USA Maxim . Shapovalov at yahoo . com Roland . Dunbrack at gmail . com From codeshepherd at gmail.com Fri Dec 22 00:33:07 2006 From: codeshepherd at gmail.com (Deepan) Date: Fri, 22 Dec 2006 13:33:07 +0800 Subject: [BiO BB] bio game / bioinformatics game /fun Message-ID: <1166765587.2691.2.camel@codeworld> Does anyone have any interesting ideas about games wrt to biology/bioinformatics ? If you have any good ideas, or pointers I would like to create a web game just for fun. I was thinking about some kind of game to program a vector and infect a culture or designing of vectors or bacterial genome blah blah blah.. -- ----------------------------------------------- Regards Deepan Chakravarthy N http://www.codeshepherd.com/ +65-96770940 Software Engineer, Nova Global Pte Ltd, Technical & Scientific Computing Solutions, #05-04 Keypoint, 371 Beach Road, Singapore. web: http://www.novaglobal.com.sg/ Have Fun, Play Sudoku :) http://sudoku-solver.net/ From bsmagic at gmail.com Fri Dec 22 01:45:54 2006 From: bsmagic at gmail.com (Sheng Wang) Date: Fri, 22 Dec 2006 14:45:54 +0800 Subject: [BiO BB] Re: Quickly retrieving cross-referenced records Message-ID: <793f8aed0612212245x4ea55210r127b99adf576cde8@mail.gmail.com> Why not use Entrez Batch Retrieval Service: http://www.ncbi.nlm.nih.gov/entrez/query/static/advancedentrez.html > Subject: Re: [BiO BB] Re: Quickly retrieving cross-referenced records > from NCBI > > The quickest way is UCSC table browser, batch retreive. Read up on > that. > > > On 12/12/06, Dale Richardson wrote: >> >> Hello All, >> >> Forgive me for posting, but this question is hard to condense into a >> good google search. I am wondering if there is a quick way to batch >> retrieve all coding sequences (mRNA sequences) linked to a particular >> NCBI RefSeq Protein identifier. For example, if I have a list of 10 >> sequences with the following protein refseq IDs: >> >> XP_698519.1 >> XP_697978.1 >> >> and so on.. >> >> How can I retrieve the cross-referenced XM_ identifiers for the >> coding sequences based on such protein accessions? Must one write >> some kind of script to accomplish this or is there a quicker way? >> >> thanks, >> >> dale richardson >> university of cologne From dmb at mrc-dunn.cam.ac.uk Fri Dec 22 03:13:58 2006 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 22 Dec 2006 09:13:58 +0100 Subject: [BiO BB] bio game / bioinformatics game /fun In-Reply-To: <1166765587.2691.2.camel@codeworld> References: <1166765587.2691.2.camel@codeworld> Message-ID: <458B93C6.6010403@mrc-dunn.cam.ac.uk> Deepan wrote: > Does anyone have any interesting ideas about games wrt to > biology/bioinformatics ? > If you have any good ideas, or pointers I would like to create a web > game just for fun. I was thinking about some kind of game to program a > vector and infect a culture or designing of vectors or bacterial genome > blah blah blah.. > > Sim 'virus' or Sim 'bug' - that would be really great! How about a 'first person perspective' view of protein structure? Take Doom / Quake and map the floor of the game onto the surface of your favorite structure. Then you could explore the active site 'on foot' and carry a ligand into the receptor to get to level 2. (Watch out for the slippery hydrophobic cluster!) From marchywka at hotmail.com Fri Dec 22 10:56:03 2006 From: marchywka at hotmail.com (Mike Marchywka) Date: Fri, 22 Dec 2006 10:56:03 -0500 Subject: [BiO BB] bio game / bioinformatics game /fun In-Reply-To: <458B93C6.6010403@mrc-dunn.cam.ac.uk> Message-ID: Actually, does someone know of an opensource or free graphics rendering program that can be used with scripts for prototyping these kinds of ideas? I downloaded this thing: http://www.csim.com/models/vpt/viewer/format2.html and wrote some perl to take the pdb file for a COMPND Ptp1b With The Catalytic Cysteine Oxidized To A COMPND 2 Sulfenyl-Amide Bond and display selected atoms using the above viewer. It worked ok- I could put the viewpoint at the oxidized cysteine and see what other things could still get to the residue. However, before investing a lot of time in scripts to support this viewer, I thought someone here may have some better suggestions. It doesn't have to be fancy but transparency and shadows would be nice ( being able to move lightsources and view point interactively with tolerable CPU usage a big plus ). Thanks. ( note new address as of 10-06) Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165r ( NOTE MORE NEWER NUMBER ) 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only >From: Dan Bolser >Reply-To: "General Forum at Bioinformatics.Org" > >To: codeshepherd at gmail.com,"General Forum at Bioinformatics.Org" > >Subject: Re: [BiO BB] bio game / bioinformatics game /fun >Date: Fri, 22 Dec 2006 09:13:58 +0100 > >Deepan wrote: >>Does anyone have any interesting ideas about games wrt to >>biology/bioinformatics ? If you have any good ideas, or pointers I would >>like to create a web >>game just for fun. I was thinking about some kind of game to program a >>vector and infect a culture or designing of vectors or bacterial genome >>blah blah blah.. >> >> > >Sim 'virus' or Sim 'bug' - that would be really great! > >How about a 'first person perspective' view of protein structure? Take Doom >/ Quake and map the floor of the game onto the surface of your favorite >structure. Then you could explore the active site 'on foot' and carry a >ligand into the receptor to get to level 2. (Watch out for the slippery >hydrophobic cluster!) > > > > > > >_______________________________________________ >General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ Get FREE Web site and company branded e-mail from Microsoft Office Live http://clk.atdmt.com/MRT/go/mcrssaub0050001411mrt/direct/01/ From dalesan at gmail.com Mon Dec 25 19:01:42 2006 From: dalesan at gmail.com (Dale Richardson) Date: Mon, 25 Dec 2006 18:01:42 -0600 Subject: [BiO BB] Bioinformatics.org server down? In-Reply-To: References: Message-ID: <2377F6EC-A36E-4E45-9AE0-63386E19747F@gmail.com> Anyone able to access the bioinformatics.org server? It's been down for the past two days for me... Thanks, -dale From ykalidas at gmail.com Sun Dec 24 11:11:09 2006 From: ykalidas at gmail.com (Kalidas Yeturu) Date: Sun, 24 Dec 2006 21:41:09 +0530 Subject: [BiO BB] bio game / bioinformatics game /fun In-Reply-To: References: <458B93C6.6010403@mrc-dunn.cam.ac.uk> Message-ID: <5632703b0612240811v4d75733axcaf5e95455d3e1f@mail.gmail.com> Hi Mike and Deepan, My suggestion is OpenGL, though I have not experimented much (but for sample programs) is a feasible idea? Further, regarding the gaming software - it can be an interactive graphics s/w (JRE/Jmol) like shooting a ligand at a binding site, or traversal of a peptide in a galaxy of hydrophobic bombs etc. ;-) In such a scenario I would like to inform that I had culled out segments of code from autodock-3.0 and created a C-stand-alone-module to suite to applying torsions at specific bonds and generating PDB formatted-output after each torsion. So this module can take care of any dynamics to be incorporated in graphics.. Regards Kalidas. Y On 12/22/06, Mike Marchywka wrote: > > Actually, does someone know of an opensource or free graphics rendering > program > that can be used with scripts for prototyping these kinds of ideas? > > I downloaded this thing: > http://www.csim.com/models/vpt/viewer/format2.html > and wrote some perl to take the pdb file for a > > COMPND Ptp1b With The Catalytic Cysteine Oxidized To A > COMPND 2 Sulfenyl-Amide Bond > > and display selected atoms using the above viewer. It worked ok- I could > put the viewpoint at the oxidized cysteine and see what other things > could still get to the residue. However, before investing a lot of time > in scripts to support this viewer, I thought someone here may have > some better suggestions. It doesn't have to be fancy but transparency and > shadows would be nice ( being able to move lightsources and view point > interactively with tolerable CPU usage a big plus ). > > > Thanks. > > > > > ( note new address as of 10-06) > Mike Marchywka > 586 Saint James Walk > Marietta GA 30067-7165r > ( NOTE MORE NEWER NUMBER ) > 404-788-1216 (C)<- leave message > 989-348-4796 (P)<- emergency only > > > > > > >From: Dan Bolser > >Reply-To: "General Forum at Bioinformatics.Org" > > > >To: codeshepherd at gmail.com,"General Forum at Bioinformatics.Org" > > > >Subject: Re: [BiO BB] bio game / bioinformatics game /fun > >Date: Fri, 22 Dec 2006 09:13:58 +0100 > > > >Deepan wrote: > >>Does anyone have any interesting ideas about games wrt to > >>biology/bioinformatics ? If you have any good ideas, or pointers I would > >>like to create a web > >>game just for fun. I was thinking about some kind of game to program a > >>vector and infect a culture or designing of vectors or bacterial genome > >>blah blah blah.. > >> > >> > > > >Sim 'virus' or Sim 'bug' - that would be really great! > > > >How about a 'first person perspective' view of protein structure? Take > Doom > >/ Quake and map the floor of the game onto the surface of your favorite > >structure. Then you could explore the active site 'on foot' and carry a > >ligand into the receptor to get to level 2. (Watch out for the slippery > >hydrophobic cluster!) > > > > > > > > > > > > > >_______________________________________________ > >General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > _________________________________________________________________ > Get FREE Web site and company branded e-mail from Microsoft Office Live > http://clk.atdmt.com/MRT/go/mcrssaub0050001411mrt/direct/01/ > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Kalidas Y http://ssl.serc.iisc.ernet.in/~kalidas From marchywka at hotmail.com Tue Dec 26 14:00:57 2006 From: marchywka at hotmail.com (Mike Marchywka) Date: Tue, 26 Dec 2006 14:00:57 -0500 Subject: [BiO BB] bio game / bioinformatics game /fun In-Reply-To: <1167103150.2619.1.camel@codeworld> Message-ID: Thanks. It doesn't have to have any features specialized to molecules but they would be a plus as long as it could also function as a general rendering and interaction engine. I started my search looking for some way to display 3D data and allow user interaction ( rotate for example). Sure, it would be nice if certain artistic devices similar to the stuff in Cn3D were available, but mostly I was looking for ways to prototype analysis ideas ( imagine you are sitting on the interesting atom of a complicated enzyme and want to "visually" verify some calculation you made? How much room is there really at an active site? And do my metrics for fitting a sqaure peg in a round hole really capture the situation? ). I guess what I may be trying to determine are things like the following: 1) Are there any "holes" big enough for solvent or reactants to find me at oxidized sulfur of my prior example? 2) If I used the coordinates of a pdb file as starting point, and made up some simple potentials, could I write a perl script ( probably with some complied code :) ) to watch the molecular dynamics in response to various things? I don't have any immediate objectives I've set on- lots of ideas- but I would like to see how easy it is to do the visualization part. If it is easy, perhaps I could do some "screening" with scripts. Thanks! ( note new address as of 10-06) Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165r ( NOTE MORE NEWER NUMBER ) 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only >From: Deepan >Reply-To: codeshepherd at gmail.com >To: Mike Marchywka , viswanathanc at gmail.com >CC: bio_bulletin_board at bioinformatics.org >Subject: Re: [BiO BB] bio game / bioinformatics game /fun >Date: Tue, 26 Dec 2006 11:19:10 +0800 > >Hi Mike, > you may want to work with Vishwanath, He has wrote molecule viewers >like Rasmol, in C using OpenGL, He calls it as Vismol. > > > >On Fri, 2006-12-22 at 10:56 -0500, Mike Marchywka wrote: > > Actually, does someone know of an opensource or free graphics rendering > > program > > that can be used with scripts for prototyping these kinds of ideas? > > > > I downloaded this thing: > > http://www.csim.com/models/vpt/viewer/format2.html > > and wrote some perl to take the pdb file for a > > > > COMPND Ptp1b With The Catalytic Cysteine Oxidized To A > > COMPND 2 Sulfenyl-Amide Bond > > > > and display selected atoms using the above viewer. It worked ok- I could > > put the viewpoint at the oxidized cysteine and see what other things > > could still get to the residue. However, before investing a lot of time > > in scripts to support this viewer, I thought someone here may have > > some better suggestions. It doesn't have to be fancy but transparency >and > > shadows would be nice ( being able to move lightsources and view point > > interactively with tolerable CPU usage a big plus ). > > > > > > Thanks. > > > > > > > > > > ( note new address as of 10-06) > > Mike Marchywka > > 586 Saint James Walk > > Marietta GA 30067-7165r > > ( NOTE MORE NEWER NUMBER ) > > 404-788-1216 (C)<- leave message > > 989-348-4796 (P)<- emergency only > > > > > > > > > >Deepan wrote: > > >>Does anyone have any interesting ideas about games wrt to > > >>biology/bioinformatics ? If you have any good ideas, or pointers I >would > > >>like to create a web > > >>game just for fun. I was thinking about some kind of game to program a > > >>vector and infect a culture or designing of vectors or bacterial >genome > > >>blah blah blah.. > > >> > > >> > > > > > >Sim 'virus' or Sim 'bug' - that would be really great! > > > > > >How about a 'first person perspective' view of protein structure? Take >Doom > > >/ Quake and map the floor of the game onto the surface of your favorite > > >structure. Then you could explore the active site 'on foot' and carry a > > >ligand into the receptor to get to level 2. (Watch out for the slippery > > >hydrophobic cluster!) > > > > > > > > > > > > > > ----------------------------------------------- > > Regards > > Deepan Chakravarthy N > > http://www.codeshepherd.com/ > > http://sudoku-solver.net/ > _________________________________________________________________ Get live scores and news about your team: Add the Live.com Football Page www.live.com/?addtemplate=football&icid=T001MSN30A0701 From skhadar at gmail.com Mon Dec 25 04:13:23 2006 From: skhadar at gmail.com (Shameer Khadar) Date: Mon, 25 Dec 2006 14:43:23 +0530 Subject: [BiO BB] TFBS Mapping Message-ID: Hi I am looking for a solution to draw boxes/arrows on a scale to represent TFBS on a promoter sequence with numbers and scale. Is there any programming resource that can do this? -- Shameer From codeshepherd at gmail.com Mon Dec 25 22:19:10 2006 From: codeshepherd at gmail.com (Deepan) Date: Tue, 26 Dec 2006 11:19:10 +0800 Subject: [BiO BB] bio game / bioinformatics game /fun In-Reply-To: References: Message-ID: <1167103150.2619.1.camel@codeworld> Hi Mike, you may want to work with Vishwanath, He has wrote molecule viewers like Rasmol, in C using OpenGL, He calls it as Vismol. On Fri, 2006-12-22 at 10:56 -0500, Mike Marchywka wrote: > Actually, does someone know of an opensource or free graphics rendering > program > that can be used with scripts for prototyping these kinds of ideas? > > I downloaded this thing: > http://www.csim.com/models/vpt/viewer/format2.html > and wrote some perl to take the pdb file for a > > COMPND Ptp1b With The Catalytic Cysteine Oxidized To A > COMPND 2 Sulfenyl-Amide Bond > > and display selected atoms using the above viewer. It worked ok- I could > put the viewpoint at the oxidized cysteine and see what other things > could still get to the residue. However, before investing a lot of time > in scripts to support this viewer, I thought someone here may have > some better suggestions. It doesn't have to be fancy but transparency and > shadows would be nice ( being able to move lightsources and view point > interactively with tolerable CPU usage a big plus ). > > > Thanks. > > > > > ( note new address as of 10-06) > Mike Marchywka > 586 Saint James Walk > Marietta GA 30067-7165r > ( NOTE MORE NEWER NUMBER ) > 404-788-1216 (C)<- leave message > 989-348-4796 (P)<- emergency only > > > > >Deepan wrote: > >>Does anyone have any interesting ideas about games wrt to > >>biology/bioinformatics ? If you have any good ideas, or pointers I would > >>like to create a web > >>game just for fun. I was thinking about some kind of game to program a > >>vector and infect a culture or designing of vectors or bacterial genome > >>blah blah blah.. > >> > >> > > > >Sim 'virus' or Sim 'bug' - that would be really great! > > > >How about a 'first person perspective' view of protein structure? Take Doom > >/ Quake and map the floor of the game onto the surface of your favorite > >structure. Then you could explore the active site 'on foot' and carry a > >ligand into the receptor to get to level 2. (Watch out for the slippery > >hydrophobic cluster!) > > > > > > > > ----------------------------------------------- > Regards > Deepan Chakravarthy N > http://www.codeshepherd.com/ > http://sudoku-solver.net/ From skhadar at gmail.com Wed Dec 27 05:19:46 2006 From: skhadar at gmail.com (Shameer Khadar) Date: Wed, 27 Dec 2006 15:49:46 +0530 Subject: [BiO BB] Perl Script to search NR database Message-ID: Hi, Is there any efficient (in terms of perfomance and memmory) script/program available to do some text search on NR database. Please let me know, Thanks -- Shameer From kiran.soorya at gmail.com Mon Dec 25 05:41:18 2006 From: kiran.soorya at gmail.com (soorya kiran) Date: Mon, 25 Dec 2006 02:41:18 -0800 Subject: [BiO BB] atomic coordinates of the proteins to predict protein tertiary structure using adaptive neuro-fuzzy systems Message-ID: Sub: atomic coordinates of the proteins to predict protein tertiary structure using adaptive neuro-fuzzy systems We are trying to predict protein tertiary structure using adaptive neuro-fuzzy systems. This method comes in the category of homology modeling, since we are using homologous proteins for prediction. We are facing a few problems in deriving the training data. As an example, consider a situation where I use 2 proteins (PDB Ids: 1MYJ and 1YMB) to predict the structure of the protein 'Human Myoglobin' (PDB Id: 2MM1). I am attaching the co-ordinates of the first alpha carbons herewith. For 1MYJ, the first few alpha carbon have atomic co-ordinates as follows: GLY 48.763 -12.39 28.42 LEU 52.541 -11.96 28.764 SER 54.79 -13.074 25.979 ASP 56.15 -16.567 25.988 GLY 59.289 -14.893 27.105 GLU 57.708 -13.153 30.06 TRP 56.174 -16.476 31.235 GLN 59.566 -17.977 31.117 For 1YMB, the co-ordinates of the first few alpha carbon atoms are as follows: GLY -3.12 15.454 14.959 LEU -0.482 14.622 17.641 SER -1.126 13.415 21.177 ASP 0.851 14.53 24.209 GLY 2.401 11.015 24.161 GLU 3.737 11.867 20.724 TRP 4.724 15.486 21.478 GLN 6.75 14.065 24.424 For 2MM1, the atomic co-ordinates of the first few atomic coordinates are as follows: GLY -4.704 17.705 14.942 LEU -1.187 18.608 16.091 SER -0.042 17.772 19.588 ASP 0.651 20.497 22.117 GLY 4.297 19.54 21.663 GLU 3.879 19.913 17.893 TRP 2.244 23.408 18.097 GLN 5.159 24.505 20.293 You can notice that even though the amino acids are the same, their atomic co-ordinates are completely different. This is not because of the amino acids which follows in the sequence, since all these 3 proteins have very similar sequence. I infer this is because, the atomic co-ordinates may not absolute and cannot be taken as such for training. We faced this issue while using this data for training neural networks, since neural networks won't know *which co-ordinates* to predict. Can you suggest any means by which we can get the atomic coordinates of the proteins used for training, after alignment? That means, all the proteins used for training, should be aligned first and then, we need to get the co-ordinates so that we can use those data for training. Our understanding is there are many tools for aligning the alpha carbon atoms of proteins, but they do not give the atomic coordinates after alignment." Thanks and regards, Srijith V. M. From dmb at mrc-dunn.cam.ac.uk Wed Dec 27 05:45:06 2006 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Wed, 27 Dec 2006 11:45:06 +0100 Subject: [BiO BB] bio game / bioinformatics game /fun In-Reply-To: <1166765587.2691.2.camel@codeworld> References: <1166765587.2691.2.camel@codeworld> Message-ID: <45924EB2.6080008@mrc-dunn.cam.ac.uk> Deepan wrote: > Does anyone have any interesting ideas about games wrt to > biology/bioinformatics ? > If you have any good ideas, or pointers I would like to create a web > game just for fun. I was thinking about some kind of game to program a > vector and infect a culture or designing of vectors or bacterial genome > blah blah blah.. > > Here are some more random ideas... Part 1 Level 1, you are ATP sized... run around the proteins surface to carry the ligand in to the active site. Level 2, you are electron sized... fly around the atom universe to deliver electrons to the active site. Level 3, you are 'protein sized'... assemble the electron transport chain to deliver energy to the cell. Part 2 Level 4, you are ATP sized... run around fixing bonds before the protein is denatured. Level 5, you are electron sized... bounce around the iron sulfur clusters Level 6, etc... Level 1/4 == packman meets doom Level 2 == elite / space simulation game Level 3/6 == many puzzle games Level 5 == pinball From jeff at bioinformatics.org Wed Dec 27 09:13:18 2006 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 27 Dec 2006 09:13:18 -0500 Subject: [BiO BB] Bioinformatics.org server down? In-Reply-To: <2377F6EC-A36E-4E45-9AE0-63386E19747F@gmail.com> References: <2377F6EC-A36E-4E45-9AE0-63386E19747F@gmail.com> Message-ID: <45927F7E.2020405@bioinformatics.org> Sorry, Santa must have tripped over the power cord on Christmas Eve while all of his helpers were out of town ;-) Jeff Dale Richardson wrote: > Anyone able to access the bioinformatics.org server? It's been down for > the past two days for me... -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From leo at corn.ab.a.u-tokyo.ac.jp Wed Dec 27 12:06:56 2006 From: leo at corn.ab.a.u-tokyo.ac.jp (Leonardo Martins) Date: Thu, 28 Dec 2006 02:06:56 +0900 Subject: [BiO BB] TFBS Mapping In-Reply-To: References: Message-ID: <20061227170656.GA12369@lbm.ab.a.u-tokyo.ac.jp> As spoken by Shameer Khadar: > Hi > I am looking for a solution to draw boxes/arrows on a scale to > represent TFBS on a promoter sequence with numbers and scale. Is there > any programming resource that can do this? > -- > Shameer Did you take a look at the Bio::Graphics module of bioperl ( http://www.bioperl.org/wiki/HOWTO:Graphics ) ? It involves some programming, but the examples from the HOWTO are of great help. Sincerely, Leo -- -- Leonardo de Oliveira Martins Mobile: 080-3395-6334 ???????????????? ???????? Biometrics Laboratory at the University of Tokyo, Japan ---------------------------------------------------------- From marchywka at hotmail.com Wed Dec 27 13:52:51 2006 From: marchywka at hotmail.com (Mike Marchywka) Date: Wed, 27 Dec 2006 13:52:51 -0500 Subject: [BiO BB] atomic coordinates of the proteins to predict proteintertiary structure using adaptive neuro-fuzzy systems In-Reply-To: Message-ID: If you really get stuck, this same problem comes up in just about all related fields- machine vision was dealing with a 2D problem in the 80's ( how do you get a translationally and rotationally tolerant measure-of-widgetness from a picture?). Image analysis and recognition literature may be heplful and, in any case, I think most of the stuff from all fields is on citeseer: http://citeseer.ist.psu.edu/ ( note new address as of 10-06) Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165r ( NOTE MORE NEWER NUMBER ) 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only >From: "soorya kiran" >Reply-To: "General Forum at Bioinformatics.Org" > >To: bio_bulletin_board at bioinformatics.org >Subject: [BiO BB] atomic coordinates of the proteins to predict >proteintertiary structure using adaptive neuro-fuzzy systems >Date: Mon, 25 Dec 2006 02:41:18 -0800 > >Sub: atomic coordinates of the proteins to predict protein tertiary >structure using adaptive neuro-fuzzy systems > >We are trying to predict protein tertiary structure using adaptive >neuro-fuzzy systems. This method comes in the category of homology >modeling, >since we are using homologous proteins for prediction. > > > >We are facing a few problems in deriving the training data. > > > >As an example, consider a situation where I use 2 proteins (PDB Ids: 1MYJ >and 1YMB) to predict the structure of the protein 'Human Myoglobin' (PDB >Id: >2MM1). > > > >I am attaching the co-ordinates of the first alpha carbons herewith. > > > >For 1MYJ, the first few alpha carbon have atomic co-ordinates as follows: > > > >GLY > >48.763 > >-12.39 > >28.42 > >LEU > >52.541 > >-11.96 > >28.764 > >SER > >54.79 > >-13.074 > >25.979 > >ASP > >56.15 > >-16.567 > >25.988 > >GLY > >59.289 > >-14.893 > >27.105 > >GLU > >57.708 > >-13.153 > >30.06 > >TRP > >56.174 > >-16.476 > >31.235 > >GLN > >59.566 > >-17.977 > >31.117 > > > >For 1YMB, the co-ordinates of the first few alpha carbon atoms are as >follows: > > > >GLY > >-3.12 > >15.454 > >14.959 > >LEU > >-0.482 > >14.622 > >17.641 > >SER > >-1.126 > >13.415 > >21.177 > >ASP > >0.851 > >14.53 > >24.209 > >GLY > >2.401 > >11.015 > >24.161 > >GLU > >3.737 > >11.867 > >20.724 > >TRP > >4.724 > >15.486 > >21.478 > >GLN > >6.75 > >14.065 > >24.424 > > > > > >For 2MM1, the atomic co-ordinates of the first few atomic coordinates are >as >follows: > > > >GLY > >-4.704 > >17.705 > >14.942 > >LEU > >-1.187 > >18.608 > >16.091 > >SER > >-0.042 > >17.772 > >19.588 > >ASP > >0.651 > >20.497 > >22.117 > >GLY > >4.297 > >19.54 > >21.663 > >GLU > >3.879 > >19.913 > >17.893 > >TRP > >2.244 > >23.408 > >18.097 > >GLN > >5.159 > >24.505 > >20.293 > > > >You can notice that even though the amino acids are the same, their atomic >co-ordinates are completely different. This is not because of the amino >acids which follows in the sequence, since all these 3 proteins have very >similar sequence. > > > >I infer this is because, the atomic co-ordinates may not absolute and >cannot >be taken as such for training. We faced this issue while using this data >for >training neural networks, since neural networks won't know *which >co-ordinates* to predict. > > > >Can you suggest any means by which we can get the atomic coordinates of the >proteins used for training, after alignment? > > > >That means, all the proteins used for training, should be aligned first and >then, we need to get the co-ordinates so that we can use those data for >training. > > > >Our understanding is there are many tools for aligning the alpha carbon >atoms of proteins, but they do not give the atomic coordinates after >alignment." > > > >Thanks and regards, > > >Srijith V. M. >_______________________________________________ >General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ Get FREE Web site and company branded e-mail from Microsoft Office Live http://clk.atdmt.com/MRT/go/mcrssaub0050001411mrt/direct/01/ From landman at scalableinformatics.com Wed Dec 27 23:39:26 2006 From: landman at scalableinformatics.com (Joe Landman) Date: Wed, 27 Dec 2006 23:39:26 -0500 Subject: [BiO BB] large HMMer searches Message-ID: <45934A7E.8020408@scalableinformatics.com> Hi folks: We are working on testing some high performance HMMer search capability (hmmsearch, etc). We are in need of some very large test cases to stress our system, and see how well it scales. If you have a set of large (highly subjective of course) tests, or tests that simply are out of reach of your existing {hmm|pfam}search capability, due to lack of processing power, and would be willing to share them with us so we can see what if anything we can do with them, please contact me off-line. Thanks! Joe -- Joseph Landman, Ph.D Founder and CEO Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://www.scalableinformatics.com phone: +1 734 786 8423 fax : +1 734 786 8452 cell : +1 734 612 4615 From dalesan at gmail.com Wed Dec 27 15:43:45 2006 From: dalesan at gmail.com (Dale Richardson) Date: Wed, 27 Dec 2006 14:43:45 -0600 Subject: [BiO BB] Bioinformatics.org server down? In-Reply-To: <45927F7E.2020405@bioinformatics.org> References: <2377F6EC-A36E-4E45-9AE0-63386E19747F@gmail.com> <45927F7E.2020405@bioinformatics.org> Message-ID: <27A63AEF-D2A9-41C5-A380-18A42D5639A9@gmail.com> Not a problem. I was just concerned as the registration deadline for the CS101 class is fast approaching.. dale On Dec 27, 2006, at 8:13 AM, J.W. Bizzaro wrote: > Sorry, Santa must have tripped over the power cord on Christmas Eve > while all of his helpers were out of town ;-) Jeff > > Dale Richardson wrote: >> Anyone able to access the bioinformatics.org server? It's been >> down for the past two days for me... > > -- > J.W. Bizzaro > Bioinformatics Organization, Inc. (Bioinformatics.Org) > E-mail: jeff at bioinformatics.org > Phone: +1 508 890 8600 > -- > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From asidhu at biomap.org Thu Dec 28 06:23:21 2006 From: asidhu at biomap.org (Amandeep S. Sidhu) Date: Thu, 28 Dec 2006 22:23:21 +1100 Subject: [BiO BB] CFP: 2nd Ontologies for Biomedical Systems Track with IEEE CBMS 2007 Message-ID: <1167305001.4593a9292a145@mail.opentransfer.com> 2nd Special Track on Ontologies for Biomedical Systems for 20th IEEE International Symposium on Computer-Based Medical Systems http://cbms07.biomap.org/ Biomedical Ontologies have developed in an uncoordinated way, often reflecting mere relations of 'association' between what are called 'concepts', and serving primarily the purposes of information extraction from on-line biomedical literature and databases. In this track we will broadly cover current research on development biomedical ontologies, and various issues in biomedical informatics addressed by these ontologies. Track will consist of papers in a biomedical informatics sub discipline, refereed by international program committee. Papers selected for this special track should report on significant unpublished work suitable for publication as a conference paper. This track will broadly address following areas: * Conceptual Models for Biological and Medical Data * Biomedical Data Integration, Analysis and Interoperability * Support of Ontologies for Biological Information Retrieval and Web Services * Tools for Development and Management of Biomedical Ontologies Last year the special track on ONTOLOGIES FOR BIOMEDICAL SYSTEMS at CBMS 2006 got a good response and some high quality papers. We have accepted 8 of 17 papers submitted to the track. More information about this track can be found at: http://cbms06.biomap.org/ In recent years, we have learned a great deal about the criteria which must be satisfied if ontology is to allow true information integration and automatic reasoning across data and information derived from different sources. The goal of this track is to survey existing biomedical ontologies and reform them in such a way as to allow true information integration in biomedical domain. Authors are invited to submit original papers exploring the theories, techniques, and applications of biomedical ontologies. Papers are invited (but not limited) to the following themes: * Biomedical Ontologies for Genetics, Proteomics, Diseases, Privacy etc. * Conceptual Models for Biological and Medical Data * Semantics in Biological Data Modeling * Use of semantics to manage Interoperation in Biomedical Databases * Semantic Web technologies and formalisms for Biomedical Data * Ontology representation and exchange languages for bioinformatics * Biomedical Ontologies and OWL * Biological Data Integration and Management using Ontologies * Biomedical Data Engineering using Ontologies * Application of Biomedical Ontologies for Heterogeneous Database Access * Query Optimization Techniques for Biomedical Database using Ontologies * Support of Ontologies for Biological Information Retrieval and Web Services * Change Management in Biomedical Ontologies * Tools for Development and Management of Biomedical Ontologies Special Issue and Edited Book For second year, we will be running a Special Issue of International Journal of Bioinformatics Research and Applications (IJBRA) on "Ontologies for Bioinformatics II" in early 2008.Current issue of Ontologies for Bioinformatics, to be published in 2007 received 24 papers of which 8 are accepted. High Quality submissions will be published as book chapters in book entitled "Biomedical Data and Applications", as a part of Series of Studies in Computational Intelligence of Springer in late 2007. Important Dates January 31, 2007 Submission of a 3-page paper summary March 15, 2007 Notification of acceptance April 15, 2007 Final camera-ready paper (6 pages, maximum) due April 15, 2007 Pre-registration deadline Paper Submission and Publication Submitted papers have to be original, containing new and original results. There are two possibilities for initially submitting a paper: * A full paper (6 pages). It is strongly encouraged to submit a full paper, which enables reviewers to assess it more objectively and authors to substantially improve the paper based on the review feedback. In this way, the high quality of this conference series can be adequately maintained and/or improved. * A summary (3 pages). CBMS 2007 serves also as a forum for exchanging interesting and novel results of a work in progress and in this manner provides participants with an opportunity to come up-to-date on important issues. In this way, the 3-pages summaries are also accepted in the case that a full paper can not be delivered until the deadline. There are two possibilities for presenting an accepted paper: oral presentation (regular papers) or poster presentation (short papers). Authors can also indicate their preference when submitting a paper. The final decision will be made by the Program Committee based on the reviews. All papers will be peer-reviewed by at least two reviewers. Submission implies the willingness of at least one of the authors to register and present the paper at the CBMS 2007 Symposium. All papers will be peer reviewed by at least two independent referees. All accepted papers will be included in the conference proceedings. Additionally, selected high quality papers may be invited to submit a substantially extended version for the special issue of an international medical informatics journal (Journal of Medical Systems, International Journal of Medical Informatics, IEEE Transactions on Information Technology in Biomedicine,Computer methods and programs in biomedicine). At least one of authors must pre-register to have the paper published in the proceedings. If you only plan to attend and are not submitting a paper, pre-registration is still strongly encouraged. This conference is space-limited, and registration may not be available on-site. For further questions, please contact technical program chair: cbms07 at biomap.org Track Chairs * Tharam S. Dillon (University of Technology Sydney, Australia) * Elizabeth Chang (Curtin University of Technology, Australia) Technical Program Chairs * Amandeep S. Sidhu (University of Technology Sydney, Australia) * Jake Chen (Indiana University, USA) -- Amandeep S. Sidhu, MIEEE, MACM, MACS, MISCB Senior Researcher (Bioinformatics) Room CB10.04.130 Faculty of Information Technology University of Technology, Sydney PO Box 123 Broadway, NSW 2007, Australia UTS Email: asidhu"AT SIGN"it.uts.edu.au Personal Email: asidhu"AT SIGN"biomap.org Personal Web: http://www.amandeep.org/ Project Web: http://www.proteinontology.info/ Ph: +61 2 9514 4469 Fax: +61 2 9514 1807 Mobile: +61 448897900 From sariego9 at yahoo.com Fri Dec 29 11:05:08 2006 From: sariego9 at yahoo.com (Diego Martinez) Date: Fri, 29 Dec 2006 08:05:08 -0800 (PST) Subject: [BiO BB] large HMMer searches Message-ID: <20061229160508.37333.qmail@web32511.mail.mud.yahoo.com> Hello Joe, We sometimes run pfam on entire small euk. genomes, would you like one of those to try? Diego ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .=$=. .=$=. .=$=. .=$=. .=$=. .=$=. @ @ | | | @ | | | @ @ | | | @ | | | @ @ | | | @ | | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | | @ | | | @ @ | | | @ | | | @ @ | | | @ | | | @ @ | ~' `~$~' `~$~' `~$~' `~$~' `~$~' `~ ----- Original Message ---- From: Joe Landman To: bio_bulletin_board at bioinformatics.org; bioclusters at bioinformatics.org Sent: Wednesday, December 27, 2006 9:39:26 PM Subject: [BiO BB] large HMMer searches Hi folks: We are working on testing some high performance HMMer search capability (hmmsearch, etc). We are in need of some very large test cases to stress our system, and see how well it scales. If you have a set of large (highly subjective of course) tests, or tests that simply are out of reach of your existing {hmm|pfam}search capability, due to lack of processing power, and would be willing to share them with us so we can see what if anything we can do with them, please contact me off-line. Thanks! Joe -- Joseph Landman, Ph.D Founder and CEO Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://www.scalableinformatics.com phone: +1 734 786 8423 fax : +1 734 786 8452 cell : +1 734 612 4615 _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From marco.severgnini at itb.cnr.it Fri Dec 29 09:30:56 2006 From: marco.severgnini at itb.cnr.it (Marco Severgnini) Date: Fri, 29 Dec 2006 15:30:56 +0100 Subject: [BiO BB] help Message-ID: <459526A0.7050103@itb.cnr.it> About the thread [BiO BB] help posted by chirag nepal on March 1, 2006, I would like to say that I had the same problem. I contacted the Blast support @ NCBI and got this reply message: " You can ignore those messages as you already noticed. Unfortunately, there is no switch for end users to use to rid of them. Regards, Tao Tao, PhD NCBI User Service" I hope my post can be of any help... Regrads, Marco Severgnini ITB - CNR room 25, floor 7 via f.lli Cervi, 93 20090, Segrate Milano ITALY tel: +39 02 26422705 fax: +39 02 26422770 e-mail: marco.severgnini at itb.cnr.it From landman at scalableinformatics.com Fri Dec 29 11:28:03 2006 From: landman at scalableinformatics.com (Joe Landman) Date: Fri, 29 Dec 2006 11:28:03 -0500 Subject: [BiO BB] large HMMer searches In-Reply-To: <20061229160508.37333.qmail@web32511.mail.mud.yahoo.com> References: <20061229160508.37333.qmail@web32511.mail.mud.yahoo.com> Message-ID: <45954213.4080902@scalableinformatics.com> Diego Martinez wrote: > Hello Joe, > > We sometimes run pfam on entire small euk. genomes, > would you like one of those to try? > > Diego Hi Diego: That would be great. If you can give us a rough idea of the execution time of the original, and the platform it was running on, and which eukaryotes, this would help as well. Thanks! Joe -- 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 skhadar at gmail.com Sat Dec 30 13:35:52 2006 From: skhadar at gmail.com (Shameer Khadar) Date: Sat, 30 Dec 2006 10:35:52 -0800 Subject: [BiO BB] Help : How to interoperate between a WebServer and a Cluster ? Message-ID: Dear All, Currently we are developing an Integrated Web Server for protein sequence and structure analysis. We are planning to provide a dedicated cluster to support the server. I need help to set up a web application that can manage the web server and our cluster. For example if the user is submitting a huge set of sequence for MSA, the program should take care of the process and pass it on to the cluster and display the status of the job (que and other details). I know this is possible and people are doing it for example (Robetta Server). It will be great, If any of the BioIT techies around can help me out with some help :)) We are using Ganglia as the server management tool. Web Server is apache running on CentOS4 . Thanks in Advance and Happy New Year to all... -- S Khadar From xiaowei.jiang at msn.com Sun Dec 31 21:16:55 2006 From: xiaowei.jiang at msn.com (Xiaowei Jiang) Date: Mon, 1 Jan 2007 03:16:55 +0100 Subject: [BiO BB] RE: Help : How to interoperate between a WebServer and a Cluster In-Reply-To: <20061231170052.CE76836959D@primary.bioinformatics.org> Message-ID: Dear I was interested in clustering systems three years agao when I was studying operating systems. I knew at that moment the Red Hat enterprise cluster system or sth can do this kind of job (shoud be free for the system), and also there was a microsoft windows system can also do this job. The thing is I am not in this field any more. So there might be great changes from time to time. I suggest that you go to the Red Hat community and search for details. I believe that you can find something interesting there and the Red Hat clustering system might be your solution. Kind regards, Xiaowei Jiang -----Original Message----- ---------------------------------------------------------------------- Message: 1 Date: Sat, 30 Dec 2006 10:35:52 -0800 From: "Shameer Khadar" Subject: [BiO BB] Help : How to interoperate between a WebServer and a Cluster ? To: "General Forum at Bioinformatics.Org" Message-ID: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Dear All, Currently we are developing an Integrated Web Server for protein sequence and structure analysis. We are planning to provide a dedicated cluster to support the server. I need help to set up a web application that can manage the web server and our cluster. For example if the user is submitting a huge set of sequence for MSA, the program should take care of the process and pass it on to the cluster and display the status of the job (que and other details). I know this is possible and people are doing it for example (Robetta Server). It will be great, If any of the BioIT techies around can help me out with some help :)) We are using Ganglia as the server management tool. Web Server is apache running on CentOS4 . Thanks in Advance and Happy New Year to all... -- S Khadar ------------------------------ _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board End of BiO_Bulletin_Board Digest, Vol 26, Issue 18 ************************************************** From maria.mirto at unile.it Sat Dec 30 11:27:44 2006 From: maria.mirto at unile.it (Maria Mirto) Date: Sat, 30 Dec 2006 17:27:44 +0100 (CET) Subject: [BiO BB] CFP: (IEEE CBMS2007) 3rd Special Track on Grids for Biomedicine and Bioinformatics Message-ID: <1200.10.0.13.90.1167496064.squirrel@webmail2.unile.it> Dear all, Please find attached the Call For Papers for: 20th IEEE Symposium on Computer-Based Medical Systems (CBMS) - Track on Grids for Biomedicine and Bioinformatics. Maribor, Slovenia 20-22 June 2007 http://sara.unile.it/cbms2007/cfp.htm http://datadog.unile.it/cbms2007/cfp.htm http://cbms2007.uni-mb.si/ sponsored by IEEE Computer Society The main goal of the track is to discuss well-known and emerging bio data-intensive systems in the context of Grids and to analyse technologies and methodologies useful to develop such systems in these environments. In particular, this Conference Track aims at offering a forum of discussion where young researchers and PhD students could present their research activities, either at an early or mature phase. Best regards, Maria Mirto. PhD Maria Mirto National Nanotechnology Laboratory (NNL/CNR-INFM) - www.nnl.it Euromediterranean Center for Climate Changes - https://www.cmcc.it SPACI Consortium - www.spaci.it Via per Monteroni - 73100 Lecce (Italy) email: maria.mirto at unile.it web: www.cact.unile.it/staff/mirto office: (+39) 0832.29.7304-8123 fax: (+39) 0832.29.7279 ******************************************************************************** We apologize if you received multiple copies of this Call for Papers. Please feel free to distribute it to those who might be interested. ******************************************************************************** -------------------------------------------------------------------------------- Special Track on Grids for Biomedicine and Bioinformatics. CBMS 2007: IEEE on Computer-Based Medical Systems (CBMS) Sponsored by the IEEE Computer Society June 20-22, 2007 Maribor, Slovenia -------------------------------------------------------------------------------- Call for Papers http://sara.unile.it/cbms2007/cfp.htm http://datadog.unile.it/cbms2007/cfp.htm http://cbms2007.uni-mb.si/ ***************** Biomedicine and Bioinformatics are quickly evolving into a research field that encompasses the use of all kinds of biomedical information, from genetic and proteomic data to image data associated with particular patients in clinical settings. Biomedical Informatics comprises the fields of Bioinformatics (e.g., genomics and proteomics) and Medical Informatics (e.g., medical image analysis), and deals with issues related to the access to information technology in medicine, the analysis of genomics data, security, interoperability and integration of data-intensive biomedical applications. What is missing today is: ? the full integration of these methods and technologies to enhance all phases of health care, including diagnosis, prognosis, etc.; ? the dissemination of such methods in the clinical practice, whenever they are developed, deployed and maintained. The grid paradigm offers CPU and data handling capabilities and allows users and laboratories to share their facilities (computing and data storage resources, instruments, knowledge, etc.) through high bandwidth networks between dynamically formed Virtual Organizations. Grid middleware currently offers basic services for Grid management, and application development and deployment. To face the complexity of novel, cooperative, distributed Health and Bioinformatics applications, new specialized Grid services have to be developed: in such a way Grids can be deployed to address the needs of the biomedical community. Grid middleware, used as the integrative middleware, has matured from its prototypical state to an expanding network of Grid services. With that, it has started to be enthusiastically embraced by the Biomedical Informatics community for its use in complex interactive computational environments that provide integrated facilities to scientists for ubiquitous computation, efficient data access, and high quality visualization, generally known as Problem Solving Environments (PSEs). The main goal of the track is to discuss well-known and emerging bio data-intensive systems in the context of Grids and to analyse technologies and methodologies useful to develop such systems in these environments. TOPICS OF INTEREST include, but are not limited to: ? Grid Infrastructures for Biomedical Data Analysis and Management ? Problem Solving Environments for Biomedical and Bioinformatics Applications ? GRID based application in life science ? Workflow application for complex analysis processes ? High Throughput for in-silico virtual screening ? Grid Computing Infrastructures, Middleware and Tools for Healthcare ? Grid Computing Biomedical Services ? Collaboration Technologies ? Databases and the Grid in the Biomedical Field ? Extracting Knowledge from Biomedical Data Grids ? Data Grids for Bioinformatics ? Grid Architectures for Interactive Biomedical Applications ? Grid Architectures and Solutions for Data-Intensive Biomedical Applications ? Grid-based Biomedical Informatics Interoperability ? Security in Biomedical Data Grids ? Semantic Grids for Multimedia Biomedical Data ? Ubiquitous Access to Grid-enabled Applications in Biomedicine ? High-performance Computing for Data-Centric Biomedical Applications ? Grid-based Visualization of Biomedical Data ? Integration of Grid-enabled Applications into Clinical Practice IMPORTANT DATES January 31, 2007 Submission of (6-page, maximum) paper March 15, 2007 Notification of acceptance April 15, 2007 Final camera-ready paper due April 15, 2007 Pre-registration deadline Paper Submission and Publication Submitted papers have to be original, containing new and original results. There are two possibilities for initially submitting a paper: * A full paper (6 pages). It is strongly encouraged to submit a full paper, which enables reviewers to assess it more objectively and authors to substantially improve the paper based on the review feedback. In this way, the high quality of this conference series can be adequately maintained and/or improved. * A summary (3 pages). CBMS 2007 serves also as a forum for exchanging interesting and novel results of a work in progress and in this manner provides participants with an opportunity to come up-to-date on important issues. In this way, the 3-pages summaries are also accepted in the case that a full paper can not be delivered until the deadline. There are two possibilities for presenting an accepted paper: oral presentation (regular papers) or poster presentation (short papers). Authors can also indicate their preference when submitting a paper. The final decision will be made by the Program Committee based on the reviews. All papers will be peer-reviewed by at least two reviewers. Submission implies the willingness of at least one of the authors to register and present the paper at the CBMS 2007 Symposium. All papers will be peer reviewed by at least two independent referees. All accepted papers will be included in the conference proceedings. At least one of authors must pre-register to have the paper published in the proceedings. If you only plan to attend and are not submitting a paper, pre-registration is still strongly encouraged. This conference is space-limited, and registration may not be available on-site. For further questions, please contact: maria.mirto at unile.it Track Chairs * Giovanni Aloisio (University of Lecce, Italy) * Maria Mirto (University of Lecce, Italy) * Almerico Murli (University of Naples, Italy) * Alfredo Tirado-Ramos (University of Amsterdam, The Netherlands) Track Program Committee * Dave S. Angulo DePaul University, USA * Robert G. Belleman University of Amsterdam, The Netherlands * Christian Barillot Campus de Beaulieu, France * Vincent Breton CNRS/IN2P3, LPC Clermont-Ferrand, France * Marian Bubak Institute of Computer Science, Poland * Mario Cannataro University "Magna Gr?cia" of Catanzaro, Italy * Sandro Fiore University of Lecce, Italy * Andreas R. Formiconi Dept. of Clinical Pathophysiology - University of Florence, Italy * Carole Goble University of Manchester, UK * Concettina Guerra University of Padova, Italy * Vicente Hernandez Universidad Politecnica de Valencia * Dieter Kranzlmueller Joh. Kepler University Linz, Austria * Yannick Legre CNRS/IN2P3 France * Nick Mankovich Philips Medical Systems, USA * Robert L. Martino National Institutes of Health, USA * Silvia D. Olabarriaga University of Amsterdam, The Netherlands * Cecilia Saccone ITB/CNR Institute of Biomedical Technologies of Bari, Italy * Fabrizio Silvestri Information Science and Technology Institute (ISTI), CNR Pisa, Italy * Peter M.A. Sloot University of Amsterdam, The Netherlands * Tony Solomonides University of West of England, UK -- PhD Maria Mirto National Nanotechnology Laboratory (NNL/CNR-INFM) - www.nnl.it Euromediterranean Center for Climate Changes - https://www.cmcc.it SPACI Consortium - www.spaci.it Via per Monteroni - 73100 Lecce (Italy) email: maria.mirto at unile.it web: www.cact.unile.it/staff/mirto office: (+39) 0832.29.7304-8123 fax: (+39) 0832.29.7279 From rb at hcl.in Sat Dec 30 22:54:30 2006 From: rb at hcl.in (Balamurugan.R) Date: Sun, 31 Dec 2006 09:24:30 +0530 Subject: [BiO BB] Help : How to interoperate between a WebServer and aCluster ? In-Reply-To: Message-ID: <200612310350.kBV3ox7Q007366@mispmo.hcl.in> Hi Shameer, If you already have a cluster setup and running and you also have a dedicated web server that can reach the head node of your cluster in the network, then your job is simple. All you have to do is install and cluster resource manager and scheduler. Below is a list of few open source tools you could use. 1. TORQUE 2. SLURM If what you wish is a simple FIFO queue and no complications, then the choice would be SLURM. It is very simple to port and install SLURM on a linux cluster. Just three steps. 1. Install SLURM. 2. At the web server, convert the query into a linux shell script that can run independently. 3. Submit the job to the head node of the cluster using srun command of the SLURM utility. You can check with the documentation of this utility at www.llnl.gov/linux/slurm Hope this helps. Happy new year! Best Regards, Balamurugan.R, HCL Infosystems Ltd. _____ | RS 107/5, 6 & 7, Sedarapet | Puducherry -605111, India. | | *Office : 0413-2677585 | *Extn: 120 | Email: rb at hcl.in | _____ This e-Mail may contain proprietary and confidential information and is sent for the intended recipient(s) only. If by an addressing or transmission error this mail has been misdirected to you, you are requested to delete this mail immediately. You are also hereby notified that any use, any form of reproduction, dissemination, copying, disclosure, modification, distribution and/or publication of this e-mail message, contents or its attachment other than by its intended recipient(s) is strictly prohibited. -----Original Message----- From: bio_bulletin_board-bounces+rb=hcl.in at bioinformatics.org [mailto:bio_bulletin_board-bounces+rb=hcl.in at bioinformatics.org] On Behalf Of Shameer Khadar Sent: Sunday, December 31, 2006 12:06 AM To: General Forum at Bioinformatics.Org Subject: [BiO BB] Help : How to interoperate between a WebServer and aCluster ? Dear All, Currently we are developing an Integrated Web Server for protein sequence and structure analysis. We are planning to provide a dedicated cluster to support the server. I need help to set up a web application that can manage the web server and our cluster. For example if the user is submitting a huge set of sequence for MSA, the program should take care of the process and pass it on to the cluster and display the status of the job (que and other details). I know this is possible and people are doing it for example (Robetta Server). It will be great, If any of the BioIT techies around can help me out with some help :)) We are using Ganglia as the server management tool. Web Server is apache running on CentOS4 . Thanks in Advance and Happy New Year to all... -- S Khadar _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board