From hershel.safer at weizmann.ac.il Tue Aug 1 06:08:07 2006 From: hershel.safer at weizmann.ac.il (Hershel Safer) Date: Tue, 01 Aug 2006 13:08:07 +0300 Subject: [BiO BB] DATE CHANGE - European Conf. on ComputationalBiology (ECCB) In-Reply-To: References: Message-ID: <44CF2807.6080908@weizmann.ac.il> We will have a forum for late-breaking results, and we may also accept more posters. We're still working out the details and will post them when they are set. Please check the website, www.eccb06.org, for details in a few weeks. Thanks, Hershel Sarah Wang wrote: > Do you still accept poster presentations if the meeting date is changed? I'm > interested in a poster presentation at the conference, if it's held in > January. > > Best > > Sarah > > On 7/30/06 5:18 AM, "Hershel Safer" wrote: > > >> We appreciate the concern that some people have expressed regarding the >> security situation in Israel and how it will affect the safety of >> participants in the 5th European Conference on Computational Biology >> (ECCB ?06). In order to host a high-quality conference that people will >> feel comfortable attending, we are delaying the conference to January >> 21-24, 2007. >> >> The conference schedule will remain unchanged to the greatest extent >> possible. We are in the process of contacting all the speakers to verify >> that they will be able to participate on the new dates. The scientific >> program is available for viewing on the web at www.eccb06.org >> , and any changes will be displayed there. >> >> Many people will have achieved new results during the intervening >> months. We are planning an additional session for presenting >> late-breaking results; we will send an announcement once the details >> have been worked out. >> >> We realize that some people have already made travel plans, and in >> particular may have to pay penalties to reschedule their airline >> tickets. Travel to Eilat should be somewhat less expensive in January >> than in September, which should help offset the change fee. In addition, >> hotel prices will be approximately 10% lower; detailed prices will be >> posted on the website when they are available. Overall, the change in >> dates should have at most a small effect on the cost of participation. >> >> People who have already registered for the conference can simply >> maintain their reservations, and hotel reservations made via the >> conference website will be moved to the corresponding dates in January; >> confirmations will be sent shortly. >> >> The early-registration deadline will be extended to Tuesday, November >> 21, 2006. Anybody who has already registered at the regular registration >> rate will be charged only the early-registration fee. >> >> The new dates will, unfortunately, be inconvenient for some people who >> planned to participate in September. Cancellations received by August >> 31, 2006, will be processed without a cancellation fee. Thereafter, the >> standard policy will apply; cancellations until three weeks before the >> start of the conference will be charged a $30 processing fee. >> >> The weather in Eilat is very pleasant in January, averaging 22C (72F). >> Always pleasant as a Red Sea resort, Eilat is especially attractive >> during the northern-hemisphere winter months. >> >> Eilat itself is safe, both in terms of street crime and terrorist >> activity. Travel from Ben Gurion International Airport to Eilat is also >> safe and has been continuing without interruption. The post-conference >> tours go only to safe areas. >> >> Details about matters related to the date change are being added to the >> FAQ page on the conference website. Please contact the Secretariat >> (eccb06 at diesenhaus.com) if you have questions that are not answered in >> the FAQ. >> >> We apologize that events beyond our control have caused us to change the >> conference dates and for the inconvenience that this will cause you. We >> nevertheless look forward to seeing you in Eilat for an exciting >> conference in January 2007! >> >> Best regards, >> Hershel Safer and Haim Wolfson >> ECCB Conference Chairs >> >> _______________________________________________ >> 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 > > -- Hershel M. Safer, Ph.D. Chair, 5th European Conference on Computational Biology (ECCB '06) Head, Bioinformatics Core Facility Weizmann Institute of Science PO Box 26, Rehovot 76100, Israel v: +972-8-934-3456 | f: +972-8-934-6006 | skype: hsafer e: hershel.safer at weizmann.ac.il | hsafer at alum.mit.edu w: http://bioportal.weizmann.ac.il | http://alum.mit.edu/www/hsafer *************************************************** Plan now for ECCB '06! 5th European Conference on Computational Biology Eilat, Israel, January 21-24, 2007 Visit www.eccb06.org for details From rajkumar.bondugula at gmail.com Tue Aug 1 18:20:58 2006 From: rajkumar.bondugula at gmail.com (Raj) Date: Tue, 1 Aug 2006 17:20:58 -0500 Subject: [BiO BB] Help with RMSD calculation Message-ID: <353b2b10608011520q4c3f74c6r1b51c60f5ba26f24@mail.gmail.com> Does anyone have a script or algorithm that can calculate the minimum RMSD if C-alpha co-ordinates of two protein fragments are given? I mean, the algorithm should rotate and translate the first set of co-ordinates until it results in minimum RMSD with the second set of points. Thank you, Raj From hararid at bgu.ac.il Wed Aug 2 02:17:09 2006 From: hararid at bgu.ac.il (Daniel Harari) Date: Wed, 02 Aug 2006 06:17:09 GMT Subject: [BiO BB] Heat Maps In-Reply-To: <353b2b10608011520q4c3f74c6r1b51c60f5ba26f24@mail.gmail.com> References: <353b2b10608011520q4c3f74c6r1b51c60f5ba26f24@mail.gmail.com> Message-ID: Thanks for responses to my request for user-friendly heat-map software.? I have come across another potential solution which might be of interest to some users.? Microsoft is allowing people to freely download their 2007 beta version of Office Professional Plus . They have done a pretty extensive face lift with Excel.? It offers amongst other new functionality, heat maps: If you can stomach a beta version of a Microsoft product: http://www.microsoft.com/office/preview/beta/getthebeta.mspx?showIntro=n Thanks to Ron Ophir (Weizmann Inst.) for the suggestion. Daniel ? -------------- next part -------------- An HTML attachment was scrubbed... URL: From skhadar at gmail.com Wed Aug 2 02:45:45 2006 From: skhadar at gmail.com (Shameer Khadar) Date: Wed, 2 Aug 2006 12:15:45 +0530 Subject: [BiO BB] Help with RMSD calculation In-Reply-To: <353b2b10608011520q4c3f74c6r1b51c60f5ba26f24@mail.gmail.com> References: <353b2b10608011520q4c3f74c6r1b51c60f5ba26f24@mail.gmail.com> Message-ID: Hi Raj, You can do it even with out scripts/algos ! Try using any standard protein visualisation tool like Chimera or VMD both of them have option for RMSD calculation (no matter if it is a fragment or a full proteins). STRAP - Java Web Start (http://www.charite.de/bioinf/strap/) will be another easy option, where you can do this. Cheers, Shameer Khadar Prof. R. Sowdhamini's Lab NCBS - TIFR On 8/2/06, Raj wrote: > > Does anyone have a script or algorithm that can calculate the minimum > RMSD if C-alpha co-ordinates of two protein fragments are given? I > mean, the algorithm should rotate and translate the first set of > co-ordinates until it results in minimum RMSD with the second set of > points. > > Thank you, > Raj > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sourangshu at csa.iisc.ernet.in Wed Aug 2 02:19:34 2006 From: sourangshu at csa.iisc.ernet.in (Sourangshu Bhattacharya) Date: Wed, 2 Aug 2006 11:49:34 +0530 (IST) Subject: [BiO BB] Help with RMSD calculation In-Reply-To: <353b2b10608011520q4c3f74c6r1b51c60f5ba26f24@mail.gmail.com> References: <353b2b10608011520q4c3f74c6r1b51c60f5ba26f24@mail.gmail.com> Message-ID: Hi, You should try some of the protein structure comparison algorithm e.g. DALI or CE ... HTH Sourangshu Sourangshu Bhattacharya PhD Student, Dept. of Computer Science & Automation, IISc, Bangalore. http://people.csa.iisc.ernet.in/sourangshu On Tue, 1 Aug 2006, Raj wrote: > Does anyone have a script or algorithm that can calculate the minimum > RMSD if C-alpha co-ordinates of two protein fragments are given? I > mean, the algorithm should rotate and translate the first set of > co-ordinates until it results in minimum RMSD with the second set of > points. > > Thank you, > Raj > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From christoph.gille at charite.de Wed Aug 2 08:26:01 2006 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Wed, 2 Aug 2006 14:26:01 +0200 (CEST) Subject: [BiO BB] Help with RMSD calculation In-Reply-To: <353b2b10608011520q4c3f74c6r1b51c60f5ba26f24@mail.gmail.com> References: <353b2b10608011520q4c3f74c6r1b51c60f5ba26f24@mail.gmail.com> Message-ID: <64066.84.190.45.17.1154521561.squirrel@webmail.charite.de> > Does anyone have a script or algorithm that can calculate the minimum > RMSD if C-alpha co-ordinates of two protein fragments are given? I > mean, the algorithm should rotate and translate the first set of I recommend TM_align, which is a fast Fortran program. I have a Java wrapper which takes care of downloading, compiling the Fortran and executing. You can also use CE/CL. But this is slower and the user interface is more difficult. I have also a Java interface for CE. From xiaowei.jiang at msn.com Wed Aug 2 14:30:10 2006 From: xiaowei.jiang at msn.com (Xiaowei JIANG) Date: Wed, 2 Aug 2006 20:30:10 +0200 Subject: [BiO BB] about JMP Genomics statistical platform In-Reply-To: <20060802160133.7A26A368465@primary.bioinformatics.org> Message-ID: Dear all, Does anyone has the experience using JMP Genomics toolkit, if so, what do you think of this environment specificly according to your experience? I am currently writing a case study report for this new platform. Thank you in advance. For more information please refer to http://www.jmp.com/software/genomics/index.shtml Best regards, Xiaowei JIANG ---------------------------------------- University Center for Statistics Faculty of Science Katholieke Universiteit Leuven,Belgium ucs.kuleuven.be ---------------------------------------- MSc Statistics/Mathematics 2005-2006 MSc Bioinformatics, BEng Computer Science ---------------------------------------- Disclaimer:http://www.kuleuven.be/cwis/email_disclaimer.htm From marty.gollery at gmail.com Wed Aug 2 16:07:54 2006 From: marty.gollery at gmail.com (Martin Gollery) Date: Wed, 2 Aug 2006 13:07:54 -0700 Subject: [BiO BB] about JMP Genomics statistical platform In-Reply-To: References: <20060802160133.7A26A368465@primary.bioinformatics.org> Message-ID: We have used JMP extensively, and find it very useful. the academic price is quite reasonable. Unfortunately, I had to let my JMP expert go, due to a lack of funding... Marty On 8/2/06, Xiaowei JIANG wrote: > > Dear all, > > Does anyone has the experience using JMP Genomics toolkit, if so, what do > you think of this environment specificly according to your experience? > > I am currently writing a case study report for this new platform. > > Thank you in advance. > > For more information please refer to > http://www.jmp.com/software/genomics/index.shtml > > > > Best regards, > Xiaowei JIANG > ---------------------------------------- > University Center for Statistics > Faculty of Science > Katholieke Universiteit Leuven,Belgium > ucs.kuleuven.be > ---------------------------------------- > MSc Statistics/Mathematics 2005-2006 > MSc Bioinformatics, BEng Computer Science > ---------------------------------------- > Disclaimer:http://www.kuleuven.be/cwis/email_disclaimer.htm > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- -- Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ----------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From Reactome-Knowledgebase at reactome.org Thu Aug 3 10:39:31 2006 From: Reactome-Knowledgebase at reactome.org (Reactome-Knowledgebase at reactome.org) Date: Thu, 3 Aug 2006 10:39:31 -0400 Subject: [BiO BB] Reactome version 18 released! Message-ID: <8011E5ED-F049-48BD-8F9E-032EB419DAF8@cshl.edu> The Reactome Knowledgebase team (Lincoln Stein's group at CSHL and Ewan Birney's group at European Bioinformatics Institute) is proud to announce the release of Reactome Version 18, accessible at http://www.reactome.org! Reactome is a curated knowledgebase of biological processes in humans. It covers processes ranging from basic pathways of metabolism to complex events such as hormonal signaling and apoptosis. The information in Reactome is provided by expert bench biologists, and edited and managed as a relational database by the Reactome staff. New material is peer-reviewed and revised as necessary before publication to the web. Reactome entries are linked to corresponding ones in NCBI EntrezGene, RefSeq, OMIM, Ensembl genome annotations, UCSC Genome Browser, KEGG, ChEBI and Gene Ontology (GO). New modules include the signaling cascade mediated by Toll-like receptor 2, Maintenance of Telomeres, Entry and Binding under HIV Life Cycle and the pathways of Complement Activation. Reactions and pathways chosen by the user are now highlighted prominently in the reaction map at the top of each web page. Updated release statistics and the Editorial Calendar are available. A new web display feature allows the user to choose the focus species annotations - curated (for human) and electronically inferred (for 22 other species). Stable identifiers have been introduced to facilitate the tracking of data objects over successive releases of Reactome. As before, Reactome data can be exported in SMBL, Prot?g?, and BioPAX level 2 formats. Like everything in Reactome, these downloaded and exported materials can be reused and redistributed freely. For questions and comments please reply to this message or write to help at reactome.org -Gopal Gopinathrao Reactome, CSHL -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeff at bioinformatics.org Sat Aug 5 18:22:21 2006 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Sat, 05 Aug 2006 18:22:21 -0400 Subject: [BiO BB] BioEdu mailing list Message-ID: <44D51A1D.6010808@bioinformatics.org> Greetings, BioEdu is a new mailing list created for discussions about education in bioinformatics in general, but it will also include discussions about the educational resources at Bioinformatics.Org (bioedu.org or edu.bioinformatics.org). You can subscribe to BioEdu through the mailing list website: https://bioinformatics.org/mailman/listinfo/bioedu Cheers, Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From xiaowei.jiang at msn.com Sun Aug 6 12:59:14 2006 From: xiaowei.jiang at msn.com (Xiaowei JIANG) Date: Sun, 6 Aug 2006 18:59:14 +0200 Subject: [BiO BB] Re: about JMP Genomics statistical platform (Martin Gollery) In-Reply-To: <20060803160126.9348A3684E0@primary.bioinformatics.org> Message-ID: Hi Martin and fellows, Thanks for your reply. Yeah, JMP is really a good tool that it can give you a user friendly environment. Click and go style. Compared with SAS itself, JMP is more popular for non-expert users (programming). The point is We need to evaluate their three new modules, namely, JMP Genetics, JMP Microarray,JMP Proteomics. Do they really hear from the scientists who are working in the field? Or do they really make a streamline tool which can work in a way as they stated? Etc... Kind regards, Xiaowei JIANG -----Original Message----- Message: 2 Date: Wed, 2 Aug 2006 13:07:54 -0700 From: "Martin Gollery" Subject: Re: [BiO BB] about JMP Genomics statistical platform To: "General Forum at Bioinformatics.Org" Message-ID: Content-Type: text/plain; charset="iso-8859-1" We have used JMP extensively, and find it very useful. the academic price is quite reasonable. Unfortunately, I had to let my JMP expert go, due to a lack of funding... Marty On 8/2/06, Xiaowei JIANG wrote: > > Dear all, > > Does anyone has the experience using JMP Genomics toolkit, if so, what > do you think of this environment specificly according to your experience? > > I am currently writing a case study report for this new platform. > > Thank you in advance. > > For more information please refer to > http://www.jmp.com/software/genomics/index.shtml > > > > Best regards, > Xiaowei JIANG > ---------------------------------------- > University Center for Statistics > Faculty of Science > Katholieke Universiteit Leuven,Belgium ucs.kuleuven.be > ---------------------------------------- > MSc Statistics/Mathematics 2005-2006 > MSc Bioinformatics, BEng Computer Science > ---------------------------------------- > Disclaimer:http://www.kuleuven.be/cwis/email_disclaimer.htm > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- -- Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ----------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://bioinformatics.org/pipermail/bio_bulletin_board/attachments/20060802/ 7c5e51ab/attachment-0001.html ------------------------------ Message: 3 Date: Thu, 3 Aug 2006 10:39:31 -0400 From: Reactome-Knowledgebase at reactome.org Subject: [BiO BB] Reactome version 18 released! To: reactome-announce at reactome.org Message-ID: <8011E5ED-F049-48BD-8F9E-032EB419DAF8 at cshl.edu> Content-Type: text/plain; charset="iso-8859-1" The Reactome Knowledgebase team (Lincoln Stein's group at CSHL and Ewan Birney's group at European Bioinformatics Institute) is proud to announce the release of Reactome Version 18, accessible at http://www.reactome.org! Reactome is a curated knowledgebase of biological processes in humans. It covers processes ranging from basic pathways of metabolism to complex events such as hormonal signaling and apoptosis. The information in Reactome is provided by expert bench biologists, and edited and managed as a relational database by the Reactome staff. New material is peer-reviewed and revised as necessary before publication to the web. Reactome entries are linked to corresponding ones in NCBI EntrezGene, RefSeq, OMIM, Ensembl genome annotations, UCSC Genome Browser, KEGG, ChEBI and Gene Ontology (GO). New modules include the signaling cascade mediated by Toll-like receptor 2, Maintenance of Telomeres, Entry and Binding under HIV Life Cycle and the pathways of Complement Activation. Reactions and pathways chosen by the user are now highlighted prominently in the reaction map at the top of each web page. Updated release statistics and the Editorial Calendar are available. A new web display feature allows the user to choose the focus species annotations - curated (for human) and electronically inferred (for 22 other species). Stable identifiers have been introduced to facilitate the tracking of data objects over successive releases of Reactome. As before, Reactome data can be exported in SMBL, Prot?g?, and BioPAX level 2 formats. Like everything in Reactome, these downloaded and exported materials can be reused and redistributed freely. For questions and comments please reply to this message or write to help at reactome.org -Gopal Gopinathrao Reactome, CSHL -------------- next part -------------- An HTML attachment was scrubbed... URL: http://bioinformatics.org/pipermail/bio_bulletin_board/attachments/20060803/ 027a31b8/attachment-0001.html ------------------------------ _______________________________________________ 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 22, Issue 3 ************************************************* From janynan at gmail.com Mon Aug 7 09:04:25 2006 From: janynan at gmail.com (Nannan) Date: Mon, 7 Aug 2006 14:04:25 +0100 Subject: [BiO BB] Get Swiss-Port ID from protein names Message-ID: <56cee34a0608070604l68e27e3evf219bb72ec9f6067@mail.gmail.com> Hello, I have a list of proteins (around 70), I need to get their Swissport IDs. I don't want to do it manually. Any idea of doing it? Many thanks, Nan -------------- next part -------------- An HTML attachment was scrubbed... URL: From rainer.winnenburg at bbsrc.ac.uk Mon Aug 7 11:53:11 2006 From: rainer.winnenburg at bbsrc.ac.uk (rainer winnenburg (RRes-Roth)) Date: Mon, 7 Aug 2006 16:53:11 +0100 Subject: [BiO BB] 3rd Integrative Bioinformatics Workshop - REGISTER WORKSHOP AND ACCOMMODATION NOW! Message-ID: *** CALL FOR POSTERS AND PARTICIPATION *** *** REGISTER WORKSHOP AND ACCOMMODATION NOW! *** 3rd Integrative Bioinformatics Workshop September 4-6, 2006 Rothamsted Research, Harpenden, Hertfordshire, United Kingdom http://www.rothamsted.bbsrc.ac.uk/bab/conf/ibiof/ IMPORTANT DATES (please note that the dates have been revised!!!) August 14: Registration for participation deadline August 21: Poster submission deadline INVITED SPEAKERS Dr Steve Gardner, Chief Technology Officer, Biowisdom, UK Semantic Integration, SRS and the Meaning of Life (Sciences) Dr Gunaretnam Rajagopal, Deputy Director, Bioinformatics Institute, Singapore BioComputing at Biopolis - Opening New Frontiers at the Interface of Computing, Biology and Medicine Dr Tom Oinn, Taverna project leader, EBI, UK Services, Semantics and Workflows in eScience Prof Pedro Mendes, Virginia Bioinformatics Institute, USA Top-down Modeling of Biochemical Networks, a Grand Challenge of Systems Biology PRELIMINARY PROGRAMME Monday 4th September 2006 11:30 Registration desk opens 12:30 Lunch (buffet style) 13:10 Welcome followed by some administrivia Session 1 - Database Integration and Integrative Databases 13:20 (keynote) Semantic Integration, SRS and the Meaning of Life (Sciences) Steve Gardner (Biowisdom, UK) 14:00 CoryneRegNet 2: An Integrative Bioinformatics Approach for Reconstruction and Comparison of Transcriptional Regulatory Networks in Prokaryotes Baumbach, J; Brinkrolf, K; Wittkop, T; Tauch, A; Rahmann, S 14:25 Analysing Microarray Data using the Multi-functional Immune Ontologiser Khalid, S; Fraser, K; Khan, M; Wang, P; Liu, X; Li, S 14:50 The BioRS(TM) Integration and Retrieval System: An open system for distributed data integration Kaps, A; Dyshlevoi, K; Heumann, K; Jost, R; Kontodinas, I; Wolff, M; Hani, J 15:15 Integration of Protein and Protein-Protein Interaction Data: Feasibility Report using Microsoft .NET Stra?er, W; Siegl, D; ?nder, K; Bauer, J 15:40 Coffee break 16:00 BN++ - A Biological Information System K?ntzer, J; Blum, T; Gerasch, A; Backes, C; Hildebrandt, A; Kaufmann, M; Kohlbacher, O; Lenhof, HP 16:25 MILAN - A medical information-system linking agents to metabolic networks Prins, B; Hofest?dt, R 16:50 Data Cleaning and Semantic Improvement in Biological Databases Apiletti, D; Bruno, G; Ficarra, E; Baralis, E 17:15 Drinks and Poster Session Tuesday 5th September 2006 09:30 Coach from recommended hotel Session 2 - Integrative Systems Biology (Modelling and Simulation) 10:00 (keynote) Title to be announced Pedro Mendes (Virginia Bioinformatics Institute, USA) 11:05 BASIS: an internet resource for network modelling Gillespie, CS; Wilkinson, DJ; Shanley, DP; Proctor, CJ; Boys, RJ; Kirkwood, TBL 11:30 Coffee break 12:10 The implications for Bioinformatics of integration across physical scales Hodgman, TC; Ugartechea-Chirino, Y; Tansley, G; Dryden, I 12:35 A Graphical Notation to Describe the Logical Interactions of Biological Pathways Moodie, SL; Sorokin, A; Goryanin, I; Ghazal, P 13:00 Exact and Approximate Stochastic Simulations of the MAPK Pathway and Comparisons of Simulations' Results Purutcuoglu, V; Wit, E 13:25 Lunch (buffet style) Session 3 Integrative Systems Biology (Networks) 14:20 keynote BioComputing at Biopolis - Opening New Frontiers at the Interface of Computing, Biology and Medicine Gunaretnam Rajagopal (Bioinformatics Institute, Singapore) 15:00 Statistical Embedding in Complex Biosystems Capobianco, E 15:25 An assessment of machine and statistical learning approaches to inferring networks of protein-protein interactions Azuaje, F 15:50 Multi-model inference of network properties from incomplete data Stumpf, MPH; Thorne, T 16:15 Coffee break Session 4 Data Analysis and Interpretation (Transcriptomics) 16:30 Co-expressed gene groups analysis (CGGA): An automatic tool for the interpretation of microarray experiments Martinez, R; Pasquier, N; Collard, M; Lopez, L; Pasquier, C 16:55 Combining biomedical knowledge and transcriptomic data to extract new knowledge on genes Gu?rin, E; Marquet, G; Chabalier, J; Troadec, M-B; Guguen-Guillouzo, C; Lor?al, O; Burgun, A; Moussouni, F 17:20 Inference of Gene Coexpression Networks by Integrative Analysis across Microarray Experiments Elo, LL; Lahesmaa, R; Aittokallio, T 17:45 Modelling Microarray Data: Interpreting and communicating the biological results Pittelkow, YE; Wilson, SR 18:10 Targeted Projection Pursuit Tool for Gene Expression Visualisation Faith, J; Brockway, M 18:35 Poster session and Bar opens 19:30 Conference dinner Wednesday 6th September 2006 09:30 Coach from recommended hotel Session 5 Data Analysis and Interpretation 10:00 (keynote) Services, Semantics and Workflows in eScience Tom Oinn (European Bioinformatics Institute, UK) 10:40 Metabolite profiles as a reflection of physiological status - a methodological validation Steinfath, M; Repsilber, D; Hische, M; Schauer, N; Fernie, A; Selbig, J 11:05 A First Step towards Learning which uORFs Regulate Gene Expression Selpi, S; Bryant, CH; Kemp, GJL; Cvijovic, M 11:30 Coffee break 11:50 Prediction of transcription factor binding to DNA using rule induction methods Huss, M; Nordstr?m, K 12:15 Functional diversity within protein superfamilies Casbon, J; Saqi, M 12:40 Closing remarks 12:50 Lunch (buffet style) Depart ORGANISING COMMITTEE Julio Collado-Vides UNAM, Mexico Ralf Hofest?dt Bielefeld University, Germany Paul Kersey EBI, UK Jacob Koehler RRes, UK Chris Rawlings RRes, UK Uwe Scholz IPK Gatersleben, Germany Paul Verrier RRes, UK CONTACT Karen Morris, BAB Division, Rothamsted Research, West Common, Harpenden, Herts. AL5 2JQ, UK karen.morris at bbsrc.ac.uk tel: 01582 763133 ext 2813 fax: 01582 467907 From christoph.gille at charite.de Mon Aug 7 18:26:50 2006 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Tue, 8 Aug 2006 00:26:50 +0200 (CEST) Subject: [BiO BB] Get Swiss-Port ID from protein names In-Reply-To: <56cee34a0608070604l68e27e3evf219bb72ec9f6067@mail.gmail.com> References: <56cee34a0608070604l68e27e3evf219bb72ec9f6067@mail.gmail.com> Message-ID: <62060.84.190.51.190.1154989610.squirrel@webmail.charite.de> >I have a list of proteins (around 70), I need to get their Swissport IDs. I >don't want to do it manually. Any idea of doing it? I understand that you have the sequences ? U could download the Swissprot database as one single file. Transform this large swissprot file such that there is one line per entry starting with the ID and containing the entire sequence like HSLV_ECOLI MADFSDFFFASFSDFFAFASDAFSD .... HSLV_BACSY MADYSEFFFASFSDFFGFASDAFSD .... You may need basic text processing skills using sed, grep, tr. Then you can then search in this transformed swissprot file with fgrep with the 70 sequences as query to identify the respective entry. From amonti at unich.it Tue Aug 8 07:28:57 2006 From: amonti at unich.it (Andrea Monti - Universita' di Chieti) Date: Tue, 08 Aug 2006 13:28:57 +0200 Subject: [BiO BB] copyright and bioinformatics instesection In-Reply-To: <20060728113845.A9B8253690@smtp.caspur.it> References: <20060728113845.A9B8253690@smtp.caspur.it> Message-ID: <44D87579.9020204@unich.it> Hallo All, Here http://www.ictlex.net/?p=545 is an article to be published on the "Cyberspace and Law" Legal Quarterly Review (chaired by prof. Giovanni Ziccardi, universita' Statale, Milan (IT)), analysing the relationship between bioinformatics and copyright law evolution. Hope this might be of some interest for the list. Best regards. Andrea Monti mail to amonti at unich.it From J.Hane at murdoch.edu.au Tue Aug 8 09:44:35 2006 From: J.Hane at murdoch.edu.au (James Hane) Date: Tue, 8 Aug 2006 21:44:35 +0800 Subject: [BiO BB] Linking Metabolomics data with Gene Ontology Message-ID: Hi, I was wondering if anyone knows of any ways of integrating metabolite ontology and gene ontology or KEGG ids? That is, if I had a list of metabolites and list of genes, is there a way of visualising pathways with identified genes and metabolites present? Thanks, James Hane From janynan at gmail.com Wed Aug 9 15:29:34 2006 From: janynan at gmail.com (Nannan) Date: Wed, 9 Aug 2006 20:29:34 +0100 Subject: [BiO BB] Get Swiss-Port ID from protein names In-Reply-To: <62060.84.190.51.190.1154989610.squirrel@webmail.charite.de> References: <56cee34a0608070604l68e27e3evf219bb72ec9f6067@mail.gmail.com> <62060.84.190.51.190.1154989610.squirrel@webmail.charite.de> Message-ID: <56cee34a0608091229q1e39a1efobb7fb835a9871cd7@mail.gmail.com> Unfortunately, I only have some weak descriptions of protein (protein name). Is there any way of getting their Swissport IDs? Nan On 8/7/06, Dr. Christoph Gille wrote: > > >I have a list of proteins (around 70), I need to get their Swissport IDs. > I > >don't want to do it manually. Any idea of doing it? > I understand that you have the sequences ? > U could download the Swissprot database as one single file. > Transform this large swissprot file such that there is one line per > entry starting with the ID and containing the entire sequence > like > HSLV_ECOLI MADFSDFFFASFSDFFAFASDAFSD .... > HSLV_BACSY MADYSEFFFASFSDFFGFASDAFSD .... > You may need basic text processing skills using sed, grep, tr. > Then you can then search in this transformed swissprot file > with fgrep with the 70 sequences as query to identify the respective > entry. > > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ljosa at cs.ucsb.edu Tue Aug 8 11:45:35 2006 From: ljosa at cs.ucsb.edu (Vebjorn Ljosa) Date: Tue, 8 Aug 2006 08:45:35 -0700 Subject: [BiO BB] Call for Participation: BioImage Informatics 2006, Santa Barbara, Sept 7-8, 2006 Message-ID: <20060808154535.GB8201@cs.ucsb.edu> ---------------------- CALL FOR PARTICIPATION ---------------------- 2006 Workshop on Multiscale Biological Imaging, Data Mining & Informatics Santa Barbara, CA, USA, September 7-8, 2006 http://www.bioimageinformatics.org/2006/ Important dates: - August 13: Deadline for reserving discounted hotel rooms - August 20: Early registration deadline - September 7-8: Workshop This workshop aims at bringing together interdisciplinary researchers to identify problems and present answers to multiscale bioimage data mining and informatics using cutting edge imaging technology (including fluorescence imaging, electron microscopy imaging, etc.) and quantitative analysis methods (including image data analysis, computer vision, data mining, machine learning, as well as other informatics methods). Registration: http://www.bioimageinformatics.org/2006/registration.html (Students, postdocs, and faculty qualify for discounted rates.) Lodging: http://www.bioimageinformatics.org/2006/lodging.html Transportation: http://www.bioimageinformatics.org/2006/transportation.html ------------- KEYNOTE _____________ * Paul Matsudaira (MIT) "High Content and Quantitative Cell Imaging" ------------- INVITED TALKS ------------- * Fanqing Chen (Lawrence Berkeley National Laboratory) "Using Quantum Dots for Biological Applications" * Jim Duncan (Yale University, School of Medicine) "Segmentation and Quantification of Microtubules from TIRF Microscopy" * Thomas Goddard (University of California, San Francisco) "Interactive Analysis of Density Maps using UCSF Chimera" * Ilya Goldberg (National Institute on Aging) "The OME Image Analysis System in the Real World: From Single-Image Hacking to Managed Distributed Work-flows" * Pengyu Hong (Brandeis University) "Interactive Analysis of High-Content Cellular Images via Relevant Feedback" * Bryan Jones (University of Utah) * Fuhui Long (Janelia Farm Research Campus, Howard Hughes Medical Institute) "Building A Digital Cell Atlas for C. elegans Larvae" * Maryann E. Martone (University of California, San Diego) "From Molecules to Brains: Multiscale Imaging of the Nervous System" * Jeffrey Price (Burnham Institute for Medical Research and Vala Sciences Inc.) * Michael F. Schmid (Baylor College of Medicine) "Aligning and Averaging Single Particles from a Tomogram" * Oliver Staadt (University of California, Davis) "Interactive Visualization for Biological Imaging" * Yuli Wang (University of Massachusetts Medical School) "Computer as A Microscopist ? Applications of Informatic Tools to Fluorescence Cell Imaging" ------------------ PEER-REVIWED TALKS ------------------ * "Model Based Dynamics Analysis in Microtubule Videos" by Alphan Altinok and Stuart Feinstein * "Calculating Derivative Displacement Fields from Confocal Fluorescence Microscopy Data" by Tigran Bacarian, Marcus Heisler, Eva-Maria Schoetz, and Eric Mjolsness * "Analysis of Confocal Microscope Images from Retina Detachment Experiments Using Texture Bases Features" by Zhiqiang Bi * "Utility of Multispectral Imaging for Analysis of Routine Clinical Histopathology Imagery" by Laura Boucheron, Neal Harvey, and B.S. Manjunath * "Automatic Extraction of 3D Nuclear Bounding Surfaces from CLSM Imagery of Developing Arabidopsis Flowers by Michael Burl, Adrienne Roeder, Carolyn Ohno, Eric Mjolsness, and Elliot Meyerowitz * "Quantifying Structural Distortions in Retinal Tissue Before and After Injury" by Jiyun Byun, Mark Verardo, Nhat Vu, Dmitry Fedorov, Geoffrey Lewis, Steven Fisher, and B.S. Manjunath * "Graph Theoretic Analysis of Functional Magnetic Resonance Imaging" by Guillermo Cecchi * "A Multiscale Image Representation Using Multiresolution Triangulations" by Alexandre Cunha, Ivo Dinov, and Arthur Toga * "Imaging Dopamine D3 Receptors (D3R) in Non-human Primate Brain Using [C-11]PHNO and PET" by Dah-Ren Hwang, Raj Narendran, Mark Slifstein, Yuying Hwang, and Marc Laruelle * "Per-Cell Classification for Exploring High-Throughput, High-Content Image-Based Screens" by Thouis Jones, Anne Carpenter, David Sabatini, and Polina Golland * "Probabilistic Segmentation of Horizontal Cells" by Vebjorn Ljosa and Ambuj K. Singh * "Biological Image Classification with Random Subwindows and Extra-Trees" by Raphael Maree, Pierre Geurts, and Louis Wehenkel * "BioSig: An Imaging Bioinformatics for Mapping Multidimensional Responses" by Bahram Parvin * "High Performance Computing Environment for 4D Image Analysis" by Ravi Rao * "Molecular Informatics and the Role of Pattern Analysis" by Rahul Singh * "Automatic Recognition and Annotation of Gene Expression Patterns of Fly Embryos" by Jie Zhou, and Hanchuan Peng --------------- We hope to see you in Santa Barbara in September! Manfred Auer - Lawrence Berkeley National Laboratory (PC Co-chair) Hanchuan Peng - Howard Hughes Medical Institute (PC Co-chair) Ambuj Singh - University of California, Santa Barbara (PC Co-chair) From areed at imdc.org Tue Aug 8 13:29:31 2006 From: areed at imdc.org (Ann Reed) Date: Tue, 8 Aug 2006 12:29:31 -0500 Subject: [BiO BB] Tuition-free online bioinformatics training from UIC Message-ID: <7BDF6464945AB045B845C2AB588B9B40249CA7@tachyon.imdc.org> BiTmaP, Bioinformatics Training Program is seeking students for the Spring 2007 semester. The application deadline is October 6, 2006 and instruction begins on January 16, 2007. All tuition and course materials are paid for by a generous grant from the U.S. Dept. of Labor. BiTmaP courses are accredited and provided by the University of Illinois at Chicago (UIC). BiTmaP consists of online lectures and industry seminars that focus on standard bioinformatics principles and protocols used widely throughout industry and academia. Students complete 3 of the following 4 courses and earn 12-graduate level credits and a certificate in bioinformatics from UIC. BiTmaP courses are: Introduction to Bioinformatics, Biostatistics, Functional Computational Genomics and Microarray, Molecular Modeling in Bioinformatics. Minimum qualifications for applicants: 1. U.S. Citizenship or Permanent Residency 2. Minimum B.S. degree, preferably in C.S. 3. Minimum 3.0 or B average GPA 4. Aptitude, enthusiasm or interest in moving to a career in the life sciences. To pre-qualify for tuition sponsorship, send a resume or CV to apply at bitmapchicago.com. For more information, please visit http://www.bitmapchicago.com/ or email areed at bitmapchicago.com. This program is intended to help re-train American workers, so U.S. citizenship or permanent residency is required. Ann Reed Director, BiTmaP: Bioinformatics Training Program Chicago Technology Park 312.243.1289 www.BiTmaPchicago.com Director, BiTmaP: Bioinformatics Training Program www.BiTmaPchicago.com 312.243.1289 -------------- next part -------------- An HTML attachment was scrubbed... URL: From kanagasa at i2r.a-star.edu.sg Wed Aug 9 22:23:40 2006 From: kanagasa at i2r.a-star.edu.sg (Kanagasabai Rajaraman) Date: Thu, 10 Aug 2006 10:23:40 +0800 Subject: [BiO BB] Linking Metabolomics data with Gene Ontology References: Message-ID: <162B8AFBFBBB2148A9A1B8F9C5753428328B07@mailbe01.teak.local.net> Hi You might want to take a look at our Metabolome explorer system: http://research.i2r.a-star.edu.sg/DRAGON/ME2/ It's Arabidopsis specific but ideas there may be helpful. This work has been published in 'Plant physiology': http://www.plantphysiol.org/cgi/content/abstract/138/4/1914 -Raja ________________________________ From: bio_bulletin_board-bounces+kanagasa=i2r.a-star.edu.sg at bioinformatics.org on behalf of James Hane Sent: Tue 8/8/2006 9:44 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Linking Metabolomics data with Gene Ontology Hi, I was wondering if anyone knows of any ways of integrating metabolite ontology and gene ontology or KEGG ids? That is, if I had a list of metabolites and list of genes, is there a way of visualising pathways with identified genes and metabolites present? Thanks, James Hane _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board ------------ Institute For Infocomm Research - Disclaimer ------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. -------------------------------------------------------- From schreibe at ipk-gatersleben.de Thu Aug 10 02:34:32 2006 From: schreibe at ipk-gatersleben.de (Falk Schreiber) Date: Thu, 10 Aug 2006 08:34:32 +0200 Subject: [BiO BB] Linking Metabolomics data with Gene Ontology In-Reply-To: References: Message-ID: <44DAD378.7000008@ipk-gatersleben.de> Dear James, You might want to take a look at the Vanted system which also allows you to visualize time series data or data from different lines within KEGG, GO and other networks/hierarchies, see http://vanted.ipk-gatersleben.de/ and the paper in BMC Bioinformatics http://www.biomedcentral.com/1471-2105/7/109 Kind regards Falk Schreiber James Hane wrote: > Hi, I was wondering if anyone knows of any ways of integrating > metabolite ontology and gene ontology or KEGG ids? That is, if I had a > list of metabolites and list of genes, is there a way of visualising > pathways with identified genes and metabolites present? > > Thanks, > James Hane > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From xiaowei.jiang at msn.com Thu Aug 10 04:14:37 2006 From: xiaowei.jiang at msn.com (Xiaowei JIANG) Date: Thu, 10 Aug 2006 10:14:37 +0200 Subject: [BiO BB] About Aglient microarray raw data set In-Reply-To: <20060809234931.4954D3683AA@primary.bioinformatics.org> Message-ID: Dear fellows, Does anyone have the experience using Aglient microarray raw data set. If so, can you give me an example of this data set. For instance, variable_name1 variable_name2 variable_name3 ... data1 data2 data3 ... ... ... ... ... ... ... ... ... I need to know the exact raw data format, I tried some searches in Google, still haven't got it yet. Thank you in advance. Kind regards, Xiaowei JIANG From Alex.Bossers at wur.nl Thu Aug 10 08:20:52 2006 From: Alex.Bossers at wur.nl (Bossers, Alex) Date: Thu, 10 Aug 2006 14:20:52 +0200 Subject: [BiO BB] Starting point EST annotation/grouping Message-ID: <839C6D97DA4B564882F385F1DA46742C037F8CB5@slely0004.wurnet.nl> Dear all, I am looking for a point where to start in "annotating" our groups of ESTs/genes.... Briefly; I have a DB containing my 13k ESTs. I clustered/assembled them after cleaning using the Tiger TGICL tools. Now I have a "unigene list" of contigs and singletons (about 7k features). BLAST made it possible to "annotate" about half of the sequences further with known (useful) information. Now I want to do the following (at best using (semi) automated conditions (web based or linux based tools)); 1. I would like to know how many genes of which groups/classes are available and which genes of my set belong to it (i.e. Apoptosis, development, immunology,........ This is to get an overview of the genes present and how complete the repertoire is we finally put onto our microarray. 2. Are some of these genes normally tissue specific? Any help to get me started into the right direction is appreciated, Alex -------------- next part -------------- An HTML attachment was scrubbed... URL: From wangwp at UDel.Edu Thu Aug 10 09:09:25 2006 From: wangwp at UDel.Edu (Weiping) Date: Thu, 10 Aug 2006 09:09:25 -0400 Subject: [BiO BB] Questions about ssDNA and protein Docking Message-ID: <000a01c6bc7e$34553b60$52b5af80@wangweiping> Do anyone have experience about ssDNA and protein Docking? what software you would suggest? Thanks Annie From Alex.Bossers at wur.nl Fri Aug 11 02:02:16 2006 From: Alex.Bossers at wur.nl (Bossers, Alex) Date: Fri, 11 Aug 2006 08:02:16 +0200 Subject: [BiO BB] Starting point EST annotation/grouping Message-ID: <839C6D97DA4B564882F385F1DA46742C037F8CBC@slely0004.wurnet.nl> Ahmed, No I did not use the PHRED/PHRAP/CONSED package for this (I did try it but found the TGICL suite more appropriate for ESTs). http://www.tigr.org/tdb/tgi/software/ For basecalling I used a windows platform based caller since PHRED at that time did not support our used dyes for sequencing.. :( Thereafter the TGICL basically uses megablast to cluster all sequences into groups and than assembles it using the cap3 assembler. Clustering and assembling is always difficult to explain. As far as I understand the clustering of large groups of sequences speeds up the second step; assembling. Basically you end up with contigs (having more than one sequence) or singletons. With unigene list I mean a list of all different genes present in my sample of 13k. Like the Gene indices lists of species present at TIGR. http://www.tigr.org/tdb/tgi/index.shtml Now the next steps. Alex _____ Van: ahmed.moustafa at gmail.com [mailto:ahmed.moustafa at gmail.com] Namens Ahmed Moustafa Verzonden: donderdag 10 augustus 2006 23:53 Aan: Bossers, Alex Onderwerp: Re: [BiO BB] Starting point EST annotation/grouping Hi Alex, Regarding the steps that you mentioned to process ESTs, I would like to ask you: (1) What is the difference between clustering and assembling the ESTs? (2) What is a unigene? BTW, are you using the Phred/Phrap/Consed suite? Thanks in advance! Ahmed On 8/10/06, Bossers, Alex wrote: Dear all, I am looking for a point where to start in "annotating" our groups of ESTs/genes.... Briefly; I have a DB containing my 13k ESTs. I clustered/assembled them after cleaning using the Tiger TGICL tools. Now I have a "unigene list" of contigs and singletons (about 7k features). BLAST made it possible to "annotate" about half of the sequences further with known (useful) information. Now I want to do the following (at best using (semi) automated conditions (web based or linux based tools)); 1. I would like to know how many genes of which groups/classes are available and which genes of my set belong to it (i.e. Apoptosis, development, immunology,........ This is to get an overview of the genes present and how complete the repertoire is we finally put onto our microarray. 2. Are some of these genes normally tissue specific? Any help to get me started into the right direction is appreciated, Alex _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- An HTML attachment was scrubbed... URL: From ahmed at pobox.com Fri Aug 11 17:00:15 2006 From: ahmed at pobox.com (Ahmed Moustafa) Date: Fri, 11 Aug 2006 16:00:15 -0500 Subject: [BiO BB] Starting point EST annotation/grouping In-Reply-To: <839C6D97DA4B564882F385F1DA46742C037F8CBC@slely0004.wurnet.nl> References: <839C6D97DA4B564882F385F1DA46742C037F8CBC@slely0004.wurnet.nl> Message-ID: <5da6cfe20608111400m4953e95ewe7e836c54fd4298e@mail.gmail.com> Hi Alex, Thank you so much for your reply. How do you generate the unigene list after assembling the ESTs? Thanks again! Ahmed On 8/11/06, Bossers, Alex wrote: > > Ahmed, > > > > No I did not use the PHRED/PHRAP/CONSED package for this (I did try it but > found the TGICL suite more appropriate for ESTs). > > http://www.tigr.org/tdb/tgi/software/ > > For basecalling I used a windows platform based caller since PHRED at that > time did not support our used dyes for sequencing.. :( > > Thereafter the TGICL basically uses megablast to cluster all sequences > into groups and than assembles it using the cap3 assembler. > > > > Clustering and assembling is always difficult to explain. As far as I > understand the clustering of large groups of sequences speeds up the second > step; assembling. Basically you end up with contigs (having more than one > sequence) or singletons. > > > > With unigene list I mean a list of all different genes present in my > sample of 13k. Like the Gene indices lists of species present at TIGR. > http://www.tigr.org/tdb/tgi/index.shtml > > > > > > Now the next steps. > > > > Alex > -------------- next part -------------- An HTML attachment was scrubbed... URL: From rborpuzari at yahoo.com Sat Aug 12 07:56:36 2006 From: rborpuzari at yahoo.com (Rajib Borpuzari) Date: Sat, 12 Aug 2006 04:56:36 -0700 (PDT) Subject: [BiO BB] New setup Bioinformatics Message-ID: <20060812115636.99079.qmail@web54707.mail.yahoo.com> Dear Member, I want to setup new bioinformatics centre in a institute through that to create database of almost 2000 Germplasm.Therefore you may please give me answer for following queries. 1.Initial infrastructure requirement. 2.Software to create database. 3.Total cost of in Indian rupee. Thanking you. With best regards, R.Borpuzari __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From rainer.winnenburg at bbsrc.ac.uk Mon Aug 14 05:49:00 2006 From: rainer.winnenburg at bbsrc.ac.uk (rainer winnenburg (RRes-Roth)) Date: Mon, 14 Aug 2006 10:49:00 +0100 Subject: [BiO BB] 3rd Integrative Bioinformatics Workshop - REGISTRATION CLOSES TODAY!! Message-ID: *** FINAL CALL FOR PARTICIPATION *** *** REGISTER FOR WORKSHOP AND BOOK ACCOMMODATION NOW! *** *** REGISTRATION CLOSES TODAY *** 3rd Integrative Bioinformatics Workshop September 4-6, 2006 Rothamsted Research, Harpenden, Hertfordshire, United Kingdom http://www.rothamsted.bbsrc.ac.uk/bab/conf/ibiof/ IMPORTANT DATES (please note that the dates have been revised!!!) August 14: Registration for participation deadline August 21: Poster submission deadline INVITED SPEAKERS Dr Steve Gardner, Chief Technology Officer, Biowisdom, UK Semantic Integration, SRS and the Meaning of Life (Sciences) Dr Gunaretnam Rajagopal, Deputy Director, Bioinformatics Institute, Singapore BioComputing at Biopolis - Opening New Frontiers at the Interface of Computing, Biology and Medicine Dr Tom Oinn, Taverna project leader, EBI, UK Services, Semantics and Workflows in eScience Prof Pedro Mendes, Virginia Bioinformatics Institute, USA Top-down Modeling of Biochemical Networks, a Grand Challenge of Systems Biology PROGRAMME Monday 4th September 2006 11:30 Registration desk opens 12:30 Lunch (buffet style) 13:10 Welcome followed by some administrivia Session 1 Database Integration and Integrative Databases 13:20 keynote Semantic Integration, SRS and the Meaning of Life (Sciences) Steve Gardner (Biowisdom, UK) 14:00 CoryneRegNet 2: An Integrative Bioinformatics Approach for Reconstruction and Comparison of Transcriptional Regulatory Networks in Prokaryotes Baumbach, J; Brinkrolf, K; Wittkop, T; Tauch, A; Rahmann, S 14:25 Analysing Microarray Data using the Multi-functional Immune Ontologiser Khalid, S; Fraser, K; Khan, M; Wang, P; Liu, X; Li, S 14:50 The BioRS(TM) Integration and Retrieval System: An open system for distributed data integration Kaps, A; Dyshlevoi, K; Heumann, K; Jost, R; Kontodinas, I; Wolff, M; Hani, J 15:15 Integration of Protein and Protein-Protein Interaction Data: Feasibility Report using Microsoft .NET Stra?er, W; Siegl, D; ?nder, K; Bauer, J 15:40 Coffee break 16:00 BN++ - A Biological Information System K?ntzer, J; Blum, T; Gerasch, A; Backes, C; Hildebrandt, A; Kaufmann, M; Kohlbacher, O; Lenhof, HP 16:25 MILAN - A medical information-system linking agents to metabolic networks Prins, B; Hofest?dt, R 16:50 Data Cleaning and Semantic Improvement in Biological Databases Apiletti, D; Bruno, G; Ficarra, E; Baralis, E 17:15 Drinks and Poster Session 18:45 Coach to Holiday Inn Hotel Tuesday 5th September 2006 09:30 Coach from Holiday Inn Hotel Session 2 Integrative Systems Biology - Modelling and Simulation 10:00 keynote Top-down Modeling of Biochemical Networks, a Grand Challenge of Systems Biology Pedro Mendes (Virginia Bioinformatics Institute, USA) 10:40 BASIS: an internet resource for network modelling Gillespie, CS; Wilkinson, DJ; Shanley, DP; Proctor, CJ; Boys, RJ; Kirkwood, TBL 11:05 Coffee break 11:20 The implications for Bioinformatics of integration across physical scales Hodgman, TC; Ugartechea-Chirino, Y; Tansley, G; Dryden, I 11:45 A Graphical Notation to Describe the Logical Interactions of Biological Pathways Moodie, SL; Sorokin, A; Goryanin, I; Ghazal, P 12:10 Exact and Approximate Stochastic Simulations of the MAPK Pathway and Comparisons of Simulations' Results Purutcuoglu, V; Wit, E 12:35 Lunch (buffet style) Session 3 Integrative Systems Biology - Networks 13:30 keynote BioComputing at Biopolis - Opening New Frontiers at the Interface of Computing, Biology and Medicine Gunaretnam Rajagopal (Bioinformatics Institute, Singapore) 14:10 Statistical Embedding in Complex Biosystems Capobianco, E 14:35 An assessment of machine and statistical learning approaches to inferring networks of protein-protein interactions Azuaje, F 14:50 Multi-model inference of network properties from incomplete data Stumpf, MPH; Thorne, T 15:15 Coffee break Session 4 Data Analysis and Interpretation - Transcriptomics 15:45 Co-expressed gene groups analysis (CGGA): An automatic tool for the interpretation of microarray experiments Martinez, R; Pasquier, N; Collard, M; Lopez, L; Pasquier, C 16:10 Combining biomedical knowledge and transcriptomic data to extract new knowledge on genes Gu?rin, E; Marquet, G; Chabalier, J; Troadec, M-B; Guguen-Guillouzo, C; Lor?al, O; Burgun, A; Moussouni, F 16:35 Inference of Gene Coexpression Networks by Integrative Analysis across Microarray Experiments Elo, LL; Lahesmaa, R; Aittokallio, T 17:00 Modelling Microarray Data: Interpreting and communicating the biological results Pittelkow, YE; Wilson, SR 17:25 Targeted Projection Pursuit Tool for Gene Expression Visualisation Faith, J; Brockway, M 17:50 Poster session and Bar opens 19:00 Coach to workshop dinner and Holiday Inn Hotel 22:00 Coach from workshop dinner to Holiday Inn Hotel 19:30 Conference dinner Wednesday 6th September 2006 09:30 Coach from Holiday Inn Hotel Session 5 Data Analysis and Interpretation 10:00 keynote Services, Semantics and Workflows in eScience Tom Oinn (European Bioinformatics Institute, UK) 10:40 Metabolite profiles as a reflection of physiological status - a methodological validation Steinfath, M; Repsilber, D; Hische, M; Schauer, N; Fernie, A; Selbig, J 11:05 A First Step towards Learning which uORFs Regulate Gene Expression Selpi; Bryant, CH; Kemp, GJL; Cvijovic, M 11:30 Coffee break 11:50 Prediction of transcription factor binding to DNA using rule induction methods Huss, M; Nordstr?m, K 12:15 Functional diversity within protein superfamilies Casbon, J; Saqi, M 12:40 Closing remarks 12:50 Lunch (buffet style) Depart ORGANISING COMMITTEE Julio Collado-Vides UNAM, Mexico Ralf Hofest?dt Bielefeld University, Germany Paul Kersey EBI, UK Jacob Koehler RRes, UK Chris Rawlings RRes, UK Uwe Scholz IPK Gatersleben, Germany Paul Verrier RRes, UK CONTACT Karen Morris, BAB Division, Rothamsted Research, West Common, Harpenden, Herts. AL5 2JQ, UK karen.morris at bbsrc.ac.uk tel: 01582 763133 ext 2813 fax: 01582 467907 From Roland.Dunbrack at fccc.edu Sat Aug 12 16:48:15 2006 From: Roland.Dunbrack at fccc.edu (Roland Dunbrack) Date: Sat, 12 Aug 2006 16:48:15 -0400 Subject: [BiO BB] ArboDraw: a program for visualization of phylogenetic trees Message-ID: <2160d370708a283821cb24d6f4d72240@fccc.edu> We have developed a program for creating and saving images of phylogenetic trees, called ArboDraw. The program can input a tree in standard Newick format (used by Clustal W and other programs) or a FASTA-formatted file used as input to the MUSCLE alignment program (R. Edgar, 2004), included and automatically installed with ArboDraw. The image of the tree can be changed in many ways -- fonts, horizontal and vertical scales, and different branches can be rendered in different colors. Annotations from the FASTA file can be viewed on mouseover of the sequence labels, and these labels and annotations can be edited by right-click. The program is currently available for Windows, and is free to both commercial and academic users. The installation begins with a single click of the download package. It is available from: http://dunbrack.fccc.edu/ArboDraw I hope you find it useful. Roland Dunbrack **************************************** * Roland L. Dunbrack, Jr. * Member * Institute for Cancer Research * Fox Chase Cancer Center * 333 Cottman Avenue * Philadelphia PA 19111 * (215) 728-2434 * (215) 728-2412 (fax) * Roland.Dunbrack @ fccc.edu * http://dunbrack.fccc.edu (research) * http://dunbrack.org (genealogy) **************************************** -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1335 bytes Desc: not available URL: From Alex.Bossers at wur.nl Tue Aug 15 01:20:11 2006 From: Alex.Bossers at wur.nl (Bossers, Alex) Date: Tue, 15 Aug 2006 07:20:11 +0200 Subject: [BiO BB] Starting point EST annotation/grouping Message-ID: <839C6D97DA4B564882F385F1DA46742C037F8CC0@slely0004.wurnet.nl> Ahmed, In our case the unigenelist is the list we ended-up with after assembling (so basically the singletons and contigs). To make it more complete into a unigenelist we did a second round of clustering assembling after we added the entries with which we had a BLAST hit at nr/nt database (excluding the BAC clones etc). Hereby we also grouped contigs/singletons that where not overlapping in our dataset yet. Alex _____ Van: bio_bulletin_board-bounces+alex.bossers=wur.nl at bioinformatics.org [mailto:bio_bulletin_board-bounces+alex.bossers=wur.nl at bioinformatics.or g] Namens Ahmed Moustafa Verzonden: vrijdag 11 augustus 2006 23:00 Aan: Bossers, Alex CC: bio_bulletin_board at bioinformatics.org Onderwerp: Re: [BiO BB] Starting point EST annotation/grouping Hi Alex, Thank you so much for your reply. How do you generate the unigene list after assembling the ESTs? Thanks again! Ahmed On 8/11/06, Bossers, Alex wrote: Ahmed, No I did not use the PHRED/PHRAP/CONSED package for this (I did try it but found the TGICL suite more appropriate for ESTs). http://www.tigr.org/tdb/tgi/software/ For basecalling I used a windows platform based caller since PHRED at that time did not support our used dyes for sequencing.. :( Thereafter the TGICL basically uses megablast to cluster all sequences into groups and than assembles it using the cap3 assembler. Clustering and assembling is always difficult to explain. As far as I understand the clustering of large groups of sequences speeds up the second step; assembling. Basically you end up with contigs (having more than one sequence) or singletons. With unigene list I mean a list of all different genes present in my sample of 13k. Like the Gene indices lists of species present at TIGR. http://www.tigr.org/tdb/tgi/index.shtml Now the next steps. Alex -------------- next part -------------- An HTML attachment was scrubbed... URL: From kim at chop.swmed.edu Tue Aug 15 12:08:21 2006 From: kim at chop.swmed.edu (Bong-Hyun Kim) Date: Tue, 15 Aug 2006 11:08:21 -0500 Subject: [BiO BB] =?utf-8?q?Dallas_Area_Bioinformatics_and_Computational_?= =?utf-8?q?Biology_Workshop_=E2=80=93_2006?= Message-ID: <4cd067f00608150908v21c6c910ga749cdb041888c1e@mail.gmail.com> August 29, 2006 8:00 am ? 7:30 pm 6000 Harry Hines Blvd., NG3 Conference Room Over the last decade, the human genome project has fueled a revolution in biomedical research by supporting the development of high throughput methodologies that have resulted in the generation of massive quantities of research data regarding normal biological processes and how these processes are altered during disease pathogenesis. Associated with this technological revolution has been a paradigm shift in the nature of biomedical research in which reductionistic, hypothesis-driven research is being augmented with approaches designed to understand how biological components interact in complex networks. Two related biological disciplines have emerged from the need to understand the massive amounts of data being generated from these high throughput technologies ? bioinformatics and computational biology. The National Institutes of Health defines bioinformatics as "research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those that acquire, store, organize, archive, analyze or visualize such data", and computational biology as "the development and application of data-analytical and theoretical methods, mathematical modeling and computation simulation techniques to the study of biological, behavioral, and social systems", with the latter typically focusing on algorithm development and specific computational methods. Thus, bioinformatics utilizes principles in information sciences to make the vast amount of diverse biological data understandable, while computational biology uses mathematical and computational approaches to address theoretical and experimental questions in biology. Both of these disciplines are rooted in life sciences as well as information sciences and technologies, and draw from mathematics and statistics, computer science, physics, engineering, biology and behavioral sciences. The Dallas Area contains several academic institutions with strengths in one or more of these core disciplines. There is considerable justification for bringing these various groups together to encourage the development of collaborative projects in bioinformatics and computational biology that build upon these strengths. url: http://webpath.swmed.edu/dab/DABinfo.html Goal: To discuss common interest and develop collaborative projects in bioinformatics and computational biology. Date: August 29, 2006 Time: 8:00 am ? 7:30 pm Location: 6000 Harry Hines Blvd., NG3 Conference Room Schedule: 8:00 ? 8:30 Registration 8:30 ? 10:00 Session 1 10:00 ? 10:30 Break 10:30 ? 12:00 Session 2 12:00 ? 1:00 Lunch 1:00 ? 2:30 Poster Session 2:30 ? 4:00 Session 3 4:00 ? 4:30 Break 4:30 ? 6:00 Session 4 6:00 ? 7:30 Reception Presentations: Oral and poster presentations will be chosen from abstracts submitted for consideration by the workshop organizing committee. Contact: Email Jennifer Cai jennifer.cai at utsouthwestern.edu From rb at hcl.in Wed Aug 16 01:02:05 2006 From: rb at hcl.in (Balamurugan R) Date: Wed, 16 Aug 2006 10:32:05 +0530 Subject: [BiO BB] New setup Bioinformatics In-Reply-To: <20060812115636.99079.qmail@web54707.mail.yahoo.com> References: <20060812115636.99079.qmail@web54707.mail.yahoo.com> Message-ID: <20060816045318.M95213@hcl.in> On Sat, 12 Aug 2006 04:56:36 -0700 (PDT), Rajib Borpuzari wrote > Dear Member, > > I want to setup new bioinformatics centre in a > institute through that to create database of almost > 2000 Germplasm.Therefore you may please give me answer > for following queries. > > 1.Initial infrastructure requirement. Depends on how you want to setup your lab. HARDWARE: a. Atleast a workstation or a server machine to host your database. b. you may require some Desktop machines as client (depends on the number of intended users in the lab). > 2.Software to create database. If you opt for all linux solution then you get postgresql (GNU) and MYSQL(LGPL) versions of databases that you could use. > 3.Total cost of in Indian rupee. With all Linux solution, you will be spending only for your hardware and probably for your internet connectivity ofcourse. > > Thanking you. > With best regards, > R.Borpuzari Best Regards, Balamurugan.R Bioinformatics Solutions Group HCL Infosystems Ltd. Pondicherry. From P.Curley at westminster.ac.uk Wed Aug 16 14:49:58 2006 From: P.Curley at westminster.ac.uk (paul) Date: Wed, 16 Aug 2006 11:49:58 -0700 Subject: [BiO BB] Printing/editing Jalview output? In-Reply-To: <2D921CDF-1B24-4AB8-B744-9C3E8E18F98C@utoronto.ca> Message-ID: Hi Folks, Stupid question, but does anyone know how to print out the Jalview output (as available at the EBI) of Clustal MSAs - at present I take a screen capture, but this is not much use when the sequences are very long. Also looking at the overall alignments is difficult when the sequemces are long as it involves lots of scrolling left and right, so it would be nice to have a paper copy to look at the alignmetn by eye. Appreciate any suggestions. Thanks againa and best regards, Paul From ahoffsta at alumnos.inf.utfsm.cl Wed Aug 16 18:34:23 2006 From: ahoffsta at alumnos.inf.utfsm.cl (Arturo Alejandro Hoffstadt Urrutia) Date: Wed, 16 Aug 2006 18:34:23 -0400 Subject: [BiO BB] New setup Bioinformatics In-Reply-To: <20060816045318.M95213@hcl.in> References: <20060812115636.99079.qmail@web54707.mail.yahoo.com> <20060816045318.M95213@hcl.in> Message-ID: <200608161834.24883.ahoffsta@alumnos.inf.utfsm.cl> El Mi?rcoles, 16 de Agosto de 2006 01:02, Balamurugan R escribi?: > On Sat, 12 Aug 2006 04:56:36 -0700 (PDT), Rajib Borpuzari wrote > > > Dear Member, > > > > I want to setup new bioinformatics centre in a > > institute through that to create database of almost > > 2000 Germplasm.Therefore you may please give me answer > > for following queries. > > > > 1.Initial infrastructure requirement. > > Depends on how you want to setup your lab. > > HARDWARE: > a. Atleast a workstation or a server machine to host your database. > b. you may require some Desktop machines as client (depends on the number > of intended users in the lab). > > > 2.Software to create database. > > If you opt for all linux solution then you get postgresql (GNU) and > MYSQL(LGPL) versions of databases that you could use. IMHO, I would use PostgreSQL, because I currently use MySQL and PostgreSQL en different applications, and MySQL has a very dissapointing administration and privileges system. It makes administrating it a real nightmare... > > > 3.Total cost of in Indian rupee. > > With all Linux solution, you will be spending only for your hardware and > probably for your internet connectivity ofcourse. > > > Thanking you. > > With best regards, > > R.Borpuzari > > Best Regards, > Balamurugan.R > Bioinformatics Solutions Group > HCL Infosystems Ltd. > Pondicherry. > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Arturo Alejandro Hoffstadt Urrutia Estudiante de Ingenier?a Civil Inform?tica ahoffsta at alumnos.inf.utfsm.cl "La magia existe, solo debes buscar mejor" From godinn at bgu.ac.il Thu Aug 17 03:32:53 2006 From: godinn at bgu.ac.il (Noa Godin) Date: Thu, 17 Aug 2006 07:32:53 GMT Subject: [BiO BB] Printing/editing Jalview output? In-Reply-To: References: <2D921CDF-1B24-4AB8-B744-9C3E8E18F98C@utoronto.ca> Message-ID: Hi, In the lower File menu you have an export option to 3 file formats : png(picture), HTML and eps(text). Good luck, Noa Godin ----- Original Message ----- From: paul Date: Wednesday, August 16, 2006 21:37 Subject: [BiO BB] Printing/editing Jalview output? To: "The general forum at Bioinformatics.Org" Cc: amritasivasankar at hotmail.com > Hi Folks, > > Stupid question, but does anyone know how to print out the > Jalview output > (as available at the EBI) of Clustal MSAs - at present I take a screen > capture, but this is not much use when the sequences are very > long. Also > looking at the overall alignments is difficult when the > sequemces are long > as it involves lots of scrolling left and right, so it would be > nice to have > a paper copy to look at the alignmetn by eye. > > Appreciate any suggestions. > > Thanks againa and best regards, > > Paul > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.orghttps://bioinformatics.org/mailman/listinfo/bio_bulletin_board > ? -------------- next part -------------- An HTML attachment was scrubbed... URL: From dgw106 at york.ac.uk Thu Aug 17 06:13:14 2006 From: dgw106 at york.ac.uk (DGW) Date: Thu, 17 Aug 2006 11:13:14 +0100 Subject: [BiO BB] Printing/editing Jalview output? In-Reply-To: References: Message-ID: <44E4413A.5050505@york.ac.uk> Hi Paul, If you download a local version of Jalview (up to version 2.08.1 now, I think) you have more features to play with, including the option to wrap alignments. You can get a high quality paper copy by exporting postscript or a PNG format bitmap and printing that. Hope this helps, David paul wrote: >Hi Folks, > >Stupid question, but does anyone know how to print out the Jalview output >(as available at the EBI) of Clustal MSAs - at present I take a screen >capture, but this is not much use when the sequences are very long. Also >looking at the overall alignments is difficult when the sequemces are long >as it involves lots of scrolling left and right, so it would be nice to have >a paper copy to look at the alignmetn by eye. > >Appreciate any suggestions. > >Thanks againa and best regards, > >Paul > >_______________________________________________ >General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From bsmagic at gmail.com Fri Aug 18 01:42:24 2006 From: bsmagic at gmail.com (Sheng Wang) Date: Fri, 18 Aug 2006 13:42:24 +0800 Subject: [BiO BB] Two Servers for New setup Bioinformatics Message-ID: <793f8aed0608172242s52e6a77am8105fdcb412e98da@mail.gmail.com> Besides the suggestion in title, "One for Data, Another For Computation". You may also need a stuff as bioinformatics technique support. He/She may help you solve many small but anoising problems. > Message: 1 > Date: Wed, 16 Aug 2006 10:32:05 +0530 > From: "Balamurugan R" > Subject: Re: [BiO BB] New setup Bioinformatics > To: "General Forum at Bioinformatics.Org" > > Message-ID: <20060816045318.M95213 at hcl.in> > Content-Type: text/plain; charset=iso-8859-1 > > On Sat, 12 Aug 2006 04:56:36 -0700 (PDT), Rajib Borpuzari wrote > > Dear Member, > > > > I want to setup new bioinformatics centre in a > > institute through that to create database of almost > > 2000 Germplasm.Therefore you may please give me answer > > for following queries. > > > > 1.Initial infrastructure requirement. > Depends on how you want to setup your lab. > > HARDWARE: > a. Atleast a workstation or a server machine to host your database. > b. you may require some Desktop machines as client (depends on the number of > intended users in the lab). > > > > 2.Software to create database. > If you opt for all linux solution then you get postgresql (GNU) and > MYSQL(LGPL) versions of databases that you could use. > > > 3.Total cost of in Indian rupee. > With all Linux solution, you will be spending only for your hardware and > probably for your internet connectivity ofcourse. > > > > > Thanking you. > > With best regards, > > R.Borpuzari > > Best Regards, > Balamurugan.R > Bioinformatics Solutions Group > HCL Infosystems Ltd. > Pondicherry. > > -- Best Regards, Sheng From P.Curley at westminster.ac.uk Fri Aug 18 14:32:57 2006 From: P.Curley at westminster.ac.uk (paul) Date: Fri, 18 Aug 2006 11:32:57 -0700 Subject: [BiO BB] Printing/editing Jalview output? In-Reply-To: <44E4413A.5050505@york.ac.uk> Message-ID: Hi Folks, Thanks for all the suggestions - really much appreciated. I'll give them a shot when I get a chance. Best Regards, Paul -----Original Message----- From: bio_bulletin_board-bounces+p.curley=wmin.ac.uk at bioinformatics.org [mailto:bio_bulletin_board-bounces+p.curley=wmin.ac.uk at bioinformatics.or g]On Behalf Of DGW Sent: Thursday, August 17, 2006 3:13 AM To: General Forum at Bioinformatics.Org Subject: Re: [BiO BB] Printing/editing Jalview output? Hi Paul, If you download a local version of Jalview (up to version 2.08.1 now, I think) you have more features to play with, including the option to wrap alignments. You can get a high quality paper copy by exporting postscript or a PNG format bitmap and printing that. Hope this helps, David paul wrote: >Hi Folks, > >Stupid question, but does anyone know how to print out the Jalview output >(as available at the EBI) of Clustal MSAs - at present I take a screen >capture, but this is not much use when the sequences are very long. Also >looking at the overall alignments is difficult when the sequemces are long >as it involves lots of scrolling left and right, so it would be nice to have >a paper copy to look at the alignmetn by eye. > >Appreciate any suggestions. > >Thanks againa and best regards, > >Paul > >_______________________________________________ >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 cupton at uvic.ca Fri Aug 18 12:32:38 2006 From: cupton at uvic.ca (Chris Upton) Date: Fri, 18 Aug 2006 09:32:38 -0700 Subject: [BiO BB] Re: Printing/editing Jalview output? Message-ID: <6AA89945-145F-4A52-8F5A-54327B5D6504@uvic.ca> Hi, You could always use a different interface. Try our program Base-By-Base http://athena.bioc.uvic.ca/ see left column of web page If you have large alignments, I'd suggest just feeding your pre- aligned sequences into BBB. Can produce jpgs from this prog.... + many other features. Cheers, Chris Chris Upton Ph.D. Associate Professor Biochemistry and Microbiology Tel. 250-721-6507 University of Victoria Fax 250-721-8855 P.O. Box 3055 STN CSC Victoria, BC V8W 3P6 Canada web.uvic.ca/~cupton www.virology.ca bioinfoblog.wordpress.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From christoph.gille at charite.de Sat Aug 19 09:56:41 2006 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Sat, 19 Aug 2006 15:56:41 +0200 (CEST) Subject: [BiO BB] Macintosh Fortran Message-ID: <61932.84.190.59.233.1155995801.squirrel@webmail.charite.de> Hi, could somebody with a Macintosh OSX be so kind and compile a very short Fortran program for me. Many thanks Christoph From a.gopee at utm.intnet.mu Mon Aug 21 02:54:21 2006 From: a.gopee at utm.intnet.mu (Ajit Gopee) Date: Mon, 21 Aug 2006 10:54:21 +0400 Subject: [BiO BB] Any Research title for PhD? Message-ID: <001301c6c4ef$2936c180$d40d7bca@Gopee> Hello all of you... I possess a MSc in IT (Bioinformatics) from UK and now would like to do a PhD in Bioinformatics.... Any one can suggest a possible PhD Title for research in the field of protein structure - function determination, molecular modelling, data mining in bioinformatics or any other interesting title from your research areas in bioinformatics? I thank you a lot... Please also advise any web site/magazine/papers where I can look for potential PhD titles in Bioinformatics... Regards Mr Ajit Gopee Lecturer School Of Business Informatics and Software Engineering University of Technology, Mauritius Tel: 2347624 Fax: 234-1747 Website: www.utm.ac.mu -------------- next part -------------- An HTML attachment was scrubbed... URL: From forward at hongyu.org Mon Aug 21 15:34:50 2006 From: forward at hongyu.org (Hongyu Zhang) Date: Mon, 21 Aug 2006 12:34:50 -0700 (PDT) Subject: [BiO BB] NCBI NR size history Message-ID: <20060821193450.37643.qmail@web51415.mail.yahoo.com> I am trying to find the history of NCBI NR file size increasement, but couldn't find it anywhere in the NCBI website or Google. could anyone please let know where I can get it? I remember I saw it somewhere before. Hongyu Zhang, Ph.D. Computational biologist, Ceres Inc. Cell: (805)405-5394, Fax: (805)322-2137 -------------- next part -------------- An HTML attachment was scrubbed... URL: From wilfred at sdsc.edu Mon Aug 21 19:26:18 2006 From: wilfred at sdsc.edu (Wilfred Li) Date: Mon, 21 Aug 2006 16:26:18 -0700 Subject: [BiO BB] NCBI NR size history In-Reply-To: <20060821193450.37643.qmail@web51415.mail.yahoo.com> Message-ID: <452F37AE49199D49B1702D7D45038C4D6B1002@et.ad.sdsc.edu> I had some data collected on the number of protein sequences in NR between May 2000 to May 2003, and it's shown in Figure 2 of this New Generation Computing paper. Unfortunately I can't find the raw numbers, and don't have anything more recent after that. http://nbcr.net/users/wilfred/publications/2003_Encyc_Grid_Software_NGC. pdf If someone had periodically downloaded NR, and kept an archive of the major releases, one can probably do a quick count from that. I know we haven't kept a record of it except for the most recent version. Regards, Wilfred ________________________________ From: bio_bulletin_board-bounces+wilfred=sdsc.edu at bioinformatics.org [mailto:bio_bulletin_board-bounces+wilfred=sdsc.edu at bioinformatics.org] On Behalf Of Hongyu Zhang Sent: Monday, August 21, 2006 12:35 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] NCBI NR size history I am trying to find the history of NCBI NR file size increasement, but couldn't find it anywhere in the NCBI website or Google. could anyone please let know where I can get it? I remember I saw it somewhere before. Hongyu Zhang, Ph.D. Computational biologist, Ceres Inc. Cell: (805)405-5394, Fax: (805)322-2137 -------------- next part -------------- An HTML attachment was scrubbed... URL: From ethan.strauss at promega.com Tue Aug 22 10:36:20 2006 From: ethan.strauss at promega.com (Ethan Strauss) Date: Tue, 22 Aug 2006 09:36:20 -0500 Subject: [BiO BB] NCBI NR size history In-Reply-To: <20060821193450.37643.qmail@web51415.mail.yahoo.com> Message-ID: Hi, The current release notes (ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt) has a bunch of stats including Genbank size. I don't see NR specifically, but perhaps something in this file would be useful. 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 ________________________________ 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 Hongyu Zhang Sent: Monday, August 21, 2006 2:35 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] NCBI NR size history I am trying to find the history of NCBI NR file size increasement, but couldn't find it anywhere in the NCBI website or Google. could anyone please let know where I can get it? I remember I saw it somewhere before. Hongyu Zhang, Ph.D. Computational biologist, Ceres Inc. Cell: (805)405-5394, Fax: (805)322-2137 -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.gopee at utm.intnet.mu Thu Aug 24 03:41:48 2006 From: a.gopee at utm.intnet.mu (Ajit Gopee) Date: Thu, 24 Aug 2006 11:41:48 +0400 Subject: [BiO BB] Any Research title for PhD? Message-ID: <001e01c6c750$c8e8d110$1b0510ac@Gopee> >>> Hello all of you... >>> >>> I possess a MSc in IT (Bioinformatics) from UK and now would like to do >>> a >>> PhD in Bioinformatics.... >>> Can any one suggest a possible PhD Title for research in the field of >>> protein structure - function determination, molecular modelling, data >>> mining in bioinformatics or any other interesting title from your >>> research >>> areas in bioinformatics? >>> I thank you a lot... >>> Please also advise any web site/magazine/papers where I can look for >>> potential PhD titles in Bioinformatics... >>> >>> Regards >>> >>> >>> Mr Ajit Gopee >>> Lecturer >>> School Of Business Informatics and Software Engineering >>> University of Technology, Mauritius >>> Tel: 2347624 Fax: 234-1747 Website: www.utm.ac.mu >>> >>> >>> > From hararid at bgu.ac.il Thu Aug 24 07:11:16 2006 From: hararid at bgu.ac.il (Daniel Harari) Date: Thu, 24 Aug 2006 11:11:16 GMT Subject: [BiO BB] Any Research title for PhD? In-Reply-To: <001301c6c4ef$2936c180$d40d7bca@Gopee> References: <001301c6c4ef$2936c180$d40d7bca@Gopee> Message-ID: Dear Ajit, I think you have put the cart ahead of the horse here. A standard protocol: 1.?? Find a laboratory which specializes in a field of bioinformatics that interests you. 2.?? Read up and learn about the focus of the research group and stay within this arena. Join group if of? ????? interest 3.?? If your supervisor does not provide you with a suggested topic, choose your own. 4.?? Choose a research title. If you are going to do this all on your own, without supervision, think twice about doing a PhD in the place that you have chosen (or in the subject that you have chosen).? The thesis title should be sufficiently general in which to allow to to change projects mid-stream, should your initial project falter.? This happens in science quite often. Good luck. Daniel ----- Original Message ----- From: Ajit Gopee Date: Monday, August 21, 2006 19:38 Subject: [BiO BB] Any Research title for PhD? To: "The general forum at Bioinformatics.Org" > Hello all of you... > > I possess a MSc in IT (Bioinformatics) from UK and now would > like to do a PhD in Bioinformatics.... > Any one can suggest a possible PhD Title for research in the > field of protein structure - function? determination, > molecular modelling, data mining in bioinformatics or any other > interesting title from your research areas in bioinformatics? > I thank you a lot... > Please also advise any web site/magazine/papers where I can look > for potential PhD titles in Bioinformatics... > > Regards > > > Mr Ajit Gopee > Lecturer > School Of Business Informatics and Software Engineering > University of Technology, Mauritius > Tel: 2347624??? Fax: 234-1747?? > Website: www.utm.ac.mu > > ? -------------- next part -------------- An HTML attachment was scrubbed... URL: From dgw106 at york.ac.uk Thu Aug 24 08:01:06 2006 From: dgw106 at york.ac.uk (DGW) Date: Thu, 24 Aug 2006 13:01:06 +0100 Subject: [BiO BB] Any Research title for PhD? In-Reply-To: <001e01c6c750$c8e8d110$1b0510ac@Gopee> References: <001e01c6c750$c8e8d110$1b0510ac@Gopee> Message-ID: <44ED9502.1060903@york.ac.uk> Dear Ajit, You may try http://www.findaphd.com/ to look for PhD projects in the UK and elsewhere (particularly Europe). The sister site http://www.findapostdoc.com/ may be useful for somebody too. You might also be lucky with http://www.newscientistjobs.com/. There are studentships advertised there too. Best wishes, David Ajit Gopee wrote: > >>>> Hello all of you... >>>> >>>> I possess a MSc in IT (Bioinformatics) from UK and now would like >>>> to do a >>>> PhD in Bioinformatics.... >>>> Can any one suggest a possible PhD Title for research in the field of >>>> protein structure - function determination, molecular modelling, data >>>> mining in bioinformatics or any other interesting title from your >>>> research >>>> areas in bioinformatics? >>>> I thank you a lot... >>>> Please also advise any web site/magazine/papers where I can look for >>>> potential PhD titles in Bioinformatics... >>>> >>>> Regards >>>> >>>> >>>> Mr Ajit Gopee >>>> Lecturer >>>> School Of Business Informatics and Software Engineering >>>> University of Technology, Mauritius >>>> Tel: 2347624 Fax: 234-1747 Website: www.utm.ac.mu >>>> >>>> >>>> >> > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From idoerg at burnham.org Fri Aug 25 15:06:52 2006 From: idoerg at burnham.org (Iddo Friedberg) Date: Fri, 25 Aug 2006 12:06:52 -0700 Subject: [BiO BB] Last minute reminder: the second automated function prediction meeting Message-ID: <44EF4A4C.4030406@burnham.org> An HTML attachment was scrubbed... URL: From frcerqueira at gmail.com Mon Aug 28 06:28:04 2006 From: frcerqueira at gmail.com (Fabio Cerqueira) Date: Mon, 28 Aug 2006 12:28:04 +0200 Subject: [BiO BB] java library for mass spec Message-ID: <50fceb2c0608280328l77638beg8ab7ab5d0a013a24@mail.gmail.com> Hello, does anyone know a good java library for manipulation of Mass Spectrometry data? I have found "ProteomeCommons.org IO Framework 6.0" but the documentation is poor and I'am having some unexpected difficult to read a raw MS file. Thanks, . Fabio . -------------- next part -------------- An HTML attachment was scrubbed... URL: From varvenne at genoway.com Mon Aug 28 05:34:28 2006 From: varvenne at genoway.com (Benoit VARVENNE) Date: Mon, 28 Aug 2006 11:34:28 +0200 Subject: [BiO BB] Restriction sites frequencies in mouse genome Message-ID: Dear Members, I am a new member of this mailing-list and i don't know if such a post will draw the attention of anyone here. So excuse me in advance if my subject is not appropriate. I am searching for a way to calculate restriction sites frequency in mouse genome (so sequences from 6 to 13bp). I have already tried to do so using blast (or blast-like) tools and configuring them as needed but it gave no results, because of too numerous hits i think. I would be very greatful if someone could help me on this topic. Thanks a lot for your help, Best regards, Beno?t Varvenne, Bioinformatics pearson in charge, Genoway Lyon - France From gary at primary.bioinformatics.org Mon Aug 28 08:37:08 2006 From: gary at primary.bioinformatics.org (Gary Van Domselaar) Date: Mon, 28 Aug 2006 08:37:08 -0400 (EDT) Subject: [BiO BB] Restriction sites frequencies in mouse genome In-Reply-To: References: Message-ID: Hi Beno, If you Perl programming capability, you should use the bioperl libraries: http://bioperl.org http://www.bioperl.org/wiki/Bptutorial.pl http://www.bioperl.org/wiki/Bptutorial.pl#III.3.4_Identifying_restriction_enzyme_sites_.28Bio::Restriction.29 You may also be able to calculate restriction site frequencies with bioinformatics software programs like LaserGene plus Excel. Regards, g. -- Gary Van Domselaar, PhD Head of Bioinformatics National Microbiology Laboratory Public Health Agency of Canada 1015 Arlington St., Winnipeg, MB, Canada R3E 3R2 Suite H3570 Ph: (204)-784-5994 Fax: (204)-789-2018 gary_van_domselaar at phac-aspc.gc.ca gary.vandomselaar at gmail.com Associate Director, Bioinformatics.Org gary at bioinformatics.org On Mon, 28 Aug 2006, Benoit VARVENNE wrote: > Dear Members, > > I am a new member of this mailing-list and i don't know if such a post will > draw the attention of anyone here. So excuse me in advance if my subject is > not appropriate. > I am searching for a way to calculate restriction sites frequency in mouse > genome (so sequences from 6 to 13bp). I have already tried to do so using > blast (or blast-like) tools and configuring them as needed but it gave no > results, because of too numerous hits i think. > > I would be very greatful if someone could help me on this topic. > > Thanks a lot for your help, > Best regards, > > Beno?t Varvenne, > Bioinformatics pearson in charge, > Genoway Lyon - France > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Gary Van Domselaar, PhD Associate Director, Bioinformatics.Org gary at bioinformatics.org From varvenne at genoway.com Mon Aug 28 08:59:18 2006 From: varvenne at genoway.com (Benoit VARVENNE) Date: Mon, 28 Aug 2006 14:59:18 +0200 Subject: [BiO BB] Restriction sites frequencies in mouse genome In-Reply-To: Message-ID: Hello Gary, Thanks a lot for your suggestions. I've got Perl programming capabilities and i'm already used to Bioperl package but the aim is to perform operations using already existing softwares which allow me calculate frequencies (so number of hits...) without any additive programming and using web tools (software+genome). The problem encountered is that all softwares i've already found (including LaserGene i think) seem to be useful for finding restriction sites in sequences given in parameter (so not in a whole genome). If i found such a solution i'm going to post it here if someone's interested. Thanks again for your very quick answer, Best regards, Beno?t Varvenne Bioinformatics pearson in charge, Genoway Lyon - France Le 28/08/06 14:37, ??Gary Van Domselaar?? a ?crit?: > > Hi Beno, > > If you Perl programming capability, you should use the bioperl libraries: > http://bioperl.org > http://www.bioperl.org/wiki/Bptutorial.pl > http://www.bioperl.org/wiki/Bptutorial.pl#III.3.4_Identifying_restriction_enzy > me_sites_.28Bio::Restriction.29 > > You may also be able to calculate restriction site frequencies with > bioinformatics software programs like LaserGene plus Excel. > > Regards, > > g. > -- > Gary Van Domselaar, PhD > Head of Bioinformatics > National Microbiology Laboratory > Public Health Agency of Canada > 1015 Arlington St., Winnipeg, MB, Canada R3E 3R2 > > Suite H3570 > Ph: (204)-784-5994 Fax: (204)-789-2018 > gary_van_domselaar at phac-aspc.gc.ca > gary.vandomselaar at gmail.com > > > Associate Director, Bioinformatics.Org > gary at bioinformatics.org > > > > > On Mon, 28 Aug 2006, Benoit VARVENNE wrote: > >> Dear Members, >> >> I am a new member of this mailing-list and i don't know if such a post will >> draw the attention of anyone here. So excuse me in advance if my subject is >> not appropriate. >> I am searching for a way to calculate restriction sites frequency in mouse >> genome (so sequences from 6 to 13bp). I have already tried to do so using >> blast (or blast-like) tools and configuring them as needed but it gave no >> results, because of too numerous hits i think. >> >> I would be very greatful if someone could help me on this topic. >> >> Thanks a lot for your help, >> Best regards, >> >> Beno?t Varvenne, >> Bioinformatics pearson in charge, >> Genoway Lyon - France >> >> _______________________________________________ >> 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 Mon Aug 28 09:02:19 2006 From: hararid at bgu.ac.il (Daniel Harari) Date: Mon, 28 Aug 2006 13:02:19 GMT Subject: [BiO BB] Restriction sites frequencies in mouse genome In-Reply-To: References: Message-ID: Genoway, EMBOSS has a number of restriction enzyme analyses programs: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/nucleic_restriction_group.html Try RESTRICT. Also the GCG software package (Accelyris) offers some similar capabilities (but is commercial).? I hope that you are aware that genomic sequences between different mouse srtains can sometimes vary considerably. Good luck. Daniel ----- Original Message ----- From: Benoit VARVENNE Date: Monday, August 28, 2006 14:16 Subject: [BiO BB] Restriction sites frequencies in mouse genome To: bio_bulletin_board at bioinformatics.org > Dear Members, > > I am a new member of this mailing-list and i don't know if such > a post will > draw the attention of anyone here. So excuse me in advance if my > subject is > not appropriate. > I am searching for a way to calculate restriction sites > frequency in mouse > genome (so sequences from 6 to 13bp). I have already tried to do > so using > blast (or blast-like) tools and configuring them as needed but > it gave no > results, because of too numerous hits i think. > > I would be very greatful if someone could help me on this topic. > > Thanks a lot for your help, > Best regards, > > Beno?t Varvenne, > Bioinformatics pearson in charge, > Genoway Lyon - France > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.orghttps://bioinformatics.org/mailman/listinfo/bio_bulletin_board > ? -------------- next part -------------- An HTML attachment was scrubbed... URL: From marty.gollery at gmail.com Mon Aug 28 09:30:42 2006 From: marty.gollery at gmail.com (Martin Gollery) Date: Mon, 28 Aug 2006 06:30:42 -0700 Subject: [BiO BB] Restriction sites frequencies in mouse genome In-Reply-To: References: Message-ID: You are correct, BLAST is limited in the number of HSP extensions, and so will not be appropriate for this type of search. I could run it for you with TeraBlast, which has no such restrictions, but I think restrict from EMBOSS will be the best tool for this. Marty On 8/28/06, Benoit VARVENNE wrote: > > Dear Members, > > I am a new member of this mailing-list and i don't know if such a post > will > draw the attention of anyone here. So excuse me in advance if my subject > is > not appropriate. > I am searching for a way to calculate restriction sites frequency in mouse > genome (so sequences from 6 to 13bp). I have already tried to do so using > blast (or blast-like) tools and configuring them as needed but it gave no > results, because of too numerous hits i think. > > I would be very greatful if someone could help me on this topic. > > Thanks a lot for your help, > Best regards, > > Beno?t Varvenne, > Bioinformatics pearson in charge, > Genoway Lyon - France > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- -- Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ----------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From boris.steipe at utoronto.ca Mon Aug 28 10:59:42 2006 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Mon, 28 Aug 2006 10:59:42 -0400 Subject: [BiO BB] Restriction sites frequencies in mouse genome In-Reply-To: References: Message-ID: However if it's only frequency for a single (or a handful) restriction sequences, a Perl one-liner or even grep will help (but you have to be careful about your input file format and consider non- palindromic sites,multiple occurrences in one line, overlapping occurrences and occurences that break across lines). If that's what you need, I can post a solution. HTH Boris On 28 Aug 2006, at 09:30, Martin Gollery wrote: > [...] > I am searching for a way to calculate restriction sites frequency > in mouse > genome (so sequences from 6 to 13bp). [...] > > Thanks a lot for your help, > Best regards, > > Beno?t Varvenne, > Bioinformatics pearson in charge, > Genoway Lyon - France > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > -- > -- > Martin Gollery > Associate Director > Center For Bioinformatics > University of Nevada at Reno > Dept. of Biochemistry / MS330 > 775-784-7042 > ----------- > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From rmurawski at physics.tamu.edu Mon Aug 28 14:05:02 2006 From: rmurawski at physics.tamu.edu (Robert Murawski) Date: Mon, 28 Aug 2006 13:05:02 -0500 (CDT) Subject: [BiO BB] help with ghemical-gms on fc4 Message-ID: Greetings I am trying to compile ghemical-gms-1.01.06 on a system running Fedora Core 4 with gcc-4.0.2-8.fc4 installed. configure stops with the following error message checking for main in -lg2c... no checking for main in -lf2c... no configure: error: Cannot find either g2c or f2c library could you please help? thanks Robert From mheusel at gmail.com Mon Aug 28 15:55:51 2006 From: mheusel at gmail.com (Martin Heusel) Date: Mon, 28 Aug 2006 21:55:51 +0200 Subject: [BiO BB] help with ghemical-gms on fc4 In-Reply-To: References: Message-ID: <6127fc200608281255x5e40d042sa451a52c89d8cc35@mail.gmail.com> On 28/08/06, Robert Murawski wrote: > Greetings > > I am trying to compile > ghemical-gms-1.01.06 > on a system running Fedora Core 4 > with gcc-4.0.2-8.fc4 installed. > > configure stops with the following error message > > checking for main in -lg2c... no > checking for main in -lf2c... no > configure: error: Cannot find either g2c or f2c library Hi, maybe missing Fortran libraries/compiler or the links are not correct. Here are some infos http://www.bo.infn.it/alice/alice-doc/mll-doc/ali-inst/node40.html regards Martin From J.Hane at murdoch.edu.au Tue Aug 29 02:18:20 2006 From: J.Hane at murdoch.edu.au (James Hane) Date: Tue, 29 Aug 2006 14:18:20 +0800 Subject: [BiO BB] Gene prediction training program binary request Message-ID: Hi I was wondering if anyone has successfully compiled the training binaries for Genezilla and or GlimmerHMM for linux x86_64? If so could you please be kind enough to mail them to me? You will have my eternal gratitude. It doesn't even really have to be x86_64. Many thanks in advance, James Hane From J.Hane at murdoch.edu.au Tue Aug 29 02:33:00 2006 From: J.Hane at murdoch.edu.au (James Hane) Date: Tue, 29 Aug 2006 14:33:00 +0800 Subject: [BiO BB] RE: Gene prediction training program binary request Message-ID: Sorry, I forgot to add that if anyone has built the Genezilla/GlimmerHMM binaries for cygwin I would greatly appreciate it if they could share it with me also. Cheers, James -----Original Message----- From: James Hane Sent: Tuesday, 29 August 2006 2:18 PM To: 'bio_bulletin_board at bioinformatics.org' Subject: Gene prediction training program binary request Hi I was wondering if anyone has successfully compiled the training binaries for Genezilla and or GlimmerHMM for linux x86_64? If so could you please be kind enough to mail them to me? You will have my eternal gratitude. It doesn't even really have to be x86_64. Many thanks in advance, James Hane From varvenne at genoway.com Tue Aug 29 08:35:44 2006 From: varvenne at genoway.com (Benoit VARVENNE) Date: Tue, 29 Aug 2006 14:35:44 +0200 Subject: [BiO BB] Restriction sites frequencies in mouse genome In-Reply-To: Message-ID: Hello everybody, Thanks to all for your ideas and suggestions. I think i'm going to consider perl programming to calculate restriction sites frequency as softwares mentionned in your mails (+softwares i found) don't seem to be useful for a whole genome scale. Programming was to be avoid for this study but it seems to be the only solution. I'm really surprised not being able to find such an already done study. Thanks again, Regards, Beno?t Varvenne, Bioinformatics pearson in charge, Genoway Lyon - France. Le 28/08/06 11:34, ??Benoit VARVENNE?? a ?crit?: > Dear Members, > > I am a new member of this mailing-list and i don't know if such a post will > draw the attention of anyone here. So excuse me in advance if my subject is > not appropriate. > I am searching for a way to calculate restriction sites frequency in mouse > genome (so sequences from 6 to 13bp). I have already tried to do so using > blast (or blast-like) tools and configuring them as needed but it gave no > results, because of too numerous hits i think. > > I would be very greatful if someone could help me on this topic. > > Thanks a lot for your help, > Best regards, > > Beno?t Varvenne, > Bioinformatics pearson in charge, > Genoway Lyon - France > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From skhadar at gmail.com Wed Aug 30 01:29:30 2006 From: skhadar at gmail.com (Shameer Khadar) Date: Wed, 30 Aug 2006 10:59:30 +0530 Subject: [BiO BB] java library for mass spec In-Reply-To: <50fceb2c0608280328l77638beg8ab7ab5d0a013a24@mail.gmail.com> References: <50fceb2c0608280328l77638beg8ab7ab5d0a013a24@mail.gmail.com> Message-ID: Hi, Why dont you check with the BioJava ? I am not sure about - but still you can give a try. !!! http://www.biojava.org/docs/api/index.html On 8/28/06, Fabio Cerqueira wrote: > > Hello, > > does anyone know a good java library for manipulation of Mass > Spectrometry data? > > I have found "ProteomeCommons.org IO Framework 6.0" but > the documentation is poor and I'am having some unexpected difficult to > read a raw MS file. > > Thanks, > > . Fabio . > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From rich at thevillas.eclipse.co.uk Wed Aug 30 08:01:47 2006 From: rich at thevillas.eclipse.co.uk (rich) Date: Wed, 30 Aug 2006 13:01:47 +0100 Subject: [BiO BB] megablast and blastp index errors Message-ID: <44F57E2B.1030800@thevillas.eclipse.co.uk> Hi, I created a blastable db with formatdb (2.2.10): formatdb -i astral100 I can run blastall -p blastp and it works fine but when I run megablast I get [megablast] WARNING: Could not find index files for database astral100 Any ideas? Thanks Rich From dgw106 at york.ac.uk Wed Aug 30 10:14:02 2006 From: dgw106 at york.ac.uk (DGW) Date: Wed, 30 Aug 2006 15:14:02 +0100 Subject: [BiO BB] megablast and blastp index errors In-Reply-To: <44F57E2B.1030800@thevillas.eclipse.co.uk> References: <44F57E2B.1030800@thevillas.eclipse.co.uk> Message-ID: <44F59D2A.3040006@york.ac.uk> Hi Rich, I'm not totally sure about this, but you might need to pass the option -o T to formatdb. See if the following works: formatdb -i -o T astral100 without the -o option the program fastacmd won't work (as far as I remember). Perhaps the same is true for megablast... Cheers David rich wrote: > Hi, > > I created a blastable db with formatdb (2.2.10): > > formatdb -i astral100 > > I can run blastall -p blastp and it works fine > but when I run megablast I get > > [megablast] WARNING: Could not find index files for database astral100 > > Any ideas? > Thanks > Rich > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From marty.gollery at gmail.com Wed Aug 30 10:09:01 2006 From: marty.gollery at gmail.com (Martin Gollery) Date: Wed, 30 Aug 2006 07:09:01 -0700 Subject: [BiO BB] megablast and blastp index errors In-Reply-To: <44F57E2B.1030800@thevillas.eclipse.co.uk> References: <44F57E2B.1030800@thevillas.eclipse.co.uk> Message-ID: astral100 is a protein database- Megablast is only for nucleotides, and so it is looking for astral100.nin which is not there. Marty Gollery On 8/30/06, rich wrote: > > Hi, > > I created a blastable db with formatdb (2.2.10): > > formatdb -i astral100 > > I can run blastall -p blastp and it works fine > but when I run megablast I get > > [megablast] WARNING: Could not find index files for database astral100 > > Any ideas? > Thanks > Rich > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- -- Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ----------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From landman at scalableinformatics.com Wed Aug 30 10:27:06 2006 From: landman at scalableinformatics.com (Joe Landman) Date: Wed, 30 Aug 2006 10:27:06 -0400 Subject: [BiO BB] megablast and blastp index errors In-Reply-To: <44F59D2A.3040006@york.ac.uk> References: <44F57E2B.1030800@thevillas.eclipse.co.uk> <44F59D2A.3040006@york.ac.uk> Message-ID: <44F5A03A.5070903@scalableinformatics.com> Hi David DGW wrote: > Hi Rich, > I'm not totally sure about this, but you might need to pass the option > -o T to formatdb. See if the following works: > > formatdb -i -o T astral100 Yes. Without it, it seems to forget to write some files. Joe > > without the -o option the program fastacmd won't work (as far as I > remember). Perhaps the same is true for megablast... > > Cheers > David > > rich wrote: >> Hi, >> >> I created a blastable db with formatdb (2.2.10): >> >> formatdb -i astral100 >> >> I can run blastall -p blastp and it works fine >> but when I run megablast I get >> >> [megablast] WARNING: Could not find index files for database astral100 >> >> Any ideas? >> Thanks >> Rich >> _______________________________________________ >> 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 -- 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 rich at thevillas.eclipse.co.uk Wed Aug 30 12:06:11 2006 From: rich at thevillas.eclipse.co.uk (rich) Date: Wed, 30 Aug 2006 17:06:11 +0100 Subject: [BiO BB] megablast and blastp index errors In-Reply-To: <44F59D2A.3040006@york.ac.uk> References: <44F57E2B.1030800@thevillas.eclipse.co.uk> <44F59D2A.3040006@york.ac.uk> Message-ID: <44F5B773.9000908@thevillas.eclipse.co.uk> Hi David, yes, I wondered about that and tried it initially but to no avail. Very strange. Thanks Rich DGW wrote: > Hi Rich, > I'm not totally sure about this, but you might need to pass the option > -o T to formatdb. See if the following works: > > formatdb -i -o T astral100 > > without the -o option the program fastacmd won't work (as far as I > remember). Perhaps the same is true for megablast... > > Cheers > David > > rich wrote: >> Hi, >> >> I created a blastable db with formatdb (2.2.10): >> >> formatdb -i astral100 >> >> I can run blastall -p blastp and it works fine >> but when I run megablast I get >> >> [megablast] WARNING: Could not find index files for database astral100 >> >> Any ideas? >> Thanks >> Rich >> _______________________________________________ >> 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 asidhu at biomap.org Wed Aug 30 13:27:33 2006 From: asidhu at biomap.org (Amandeep S. Sidhu) Date: Thu, 31 Aug 2006 03:27:33 +1000 (EST) Subject: [BiO BB] 1st CFP: IJBRA Special Issue on Ontologies for Bioinformatics Message-ID: <51742.144.136.103.92.1156958853.squirrel@biomap.org> ********************************************************************** We apologize if you received multiple copies of this CFP. Please feel free to distribute it to those who might be interested ********************************************************************** International Journal of Bioinformatics Research and Applications (IJBRA) Special Issue on "Ontologies for Bioinformatics" To be Published as Volume 3, Issue 1 in 2007 https://www.inderscience.com/browse/index.php?journalcode=ijbra Special Issue on Ontologies for Bioinformatics http://ijbra.biomap.org/ Call for Papers 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 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 issue 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 to both the sessions exploring the theories, techniques, and applications of biomedical ontologies. Papers are invited (but not limited) to the following themes: * Conceptual Models for Biological and Medical Data. * Semantic Biological Data Modeling. * Use of semantics to manage Interoperation in Biomedical Databases. * Semantic Web technologies and formalisms for Biomedical Data. * OWL and Biomedical Ontologies. * Biomedical Data Engineering using Ontologies. * Biological Data Integration using Ontologies. * Application of Biomedical Ontologies for Heterogeneous Database Access. * Application of Biomedical Ontologies for Issues in Privacy and Security. * 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. Important Dates September 30, 2006 Call for Submissions November 20, 2006 Notification of acceptance December 15, 2006 Final camera-ready paper due January 15, 2006 Issue Deadline Paper Submission Submission and Review Guidelines * No hardcopy submissions are being accepted. * Electronic submissions of original technical research papers will be preferred in PDF format. * Submitted papers should not have been previously published nor be currently under consideration for publication elsewhere. * Include one cover sheet, stating the issue title (Special Issue on Ontologies for Bioinformatics), paper title, authors, keywords, corresponding author's information. * Author names should appear only on the cover sheet, not on the paper. * All papers are refereed through a double blind process. Submission Procedures All submissions will be done electronically via the online submission system for this issue: http://biomap.it.uts.edu.au/ijbra07/ If you have any problems with submission please email: ijbra at biomap.org Templates Please note that the format of submission will be in IJBRA template format. Both MS-Word and Latex format templates are available. Submissions are highly encouraged in this format. A guide for authors, sample copies and other relevant information for submitting papers are available on the Submission Guidelines web-page. Co-Editors * Tharam S. Dillon (University of Technology Sydney, Australia) * Elizabeth Chang (Curtin University of Technology, Australia) * Amandeep S. Sidhu (University of Technology Sydney, Australia) * Jake Chen (Indiana University, USA) Special Issue Review Board * Tharam S. Dillon (University of Technology Sydney, Australia) * Elizabeth Chang (Curtin University of Technology, Australia) * Amandeep S. Sidhu (University of Technology Sydney, Australia) * Philip E. Bourne (University of California San Diego) * Martin Senger (European Bioinformatics Institute) * Midori Harris (European Bioinformatics Institute) * Robert Meersman (Vrije Universiteit Brussel, Belgium) * Mustafa Jarrar (Vrije Universiteit Brussel, Belgium) * Ernesto Damiani (Computer Science Department, Milan University, Italy) * Ling Feng (University of Twente, Netherlands) * Jake Chen (Indiana University, USA) * Suzanna Lewis (Berkeley Drosophila Genome Project) * Mihaela Ulieru (University of New Brunswick, Canada) * Hans-Dieter Ehrich (Technical University of Braunschweig, Germany) * Fabio Porto (Database Laboratory, EPFL, Switzerland) * Rajugan Rajagopalapillai (University of Technology Sydney, Australia) * Manish Bhide (IBM India Research Lab, India) * Paul Kennedy (University of Technology Sydney, Australia) * Wenny Rahayu (La Trobe University, Australia) * Farookh K. Hussain (Curtin University of Technology, Australia) * Pornpit Wongthongtham (Curtin University of Technology, Australia) * Maja Hadzic (Curtin University of Technology, Australia) From idoerg at burnham.org Wed Aug 30 19:22:18 2006 From: idoerg at burnham.org (Iddo Friedberg) Date: Wed, 30 Aug 2006 16:22:18 -0700 Subject: [BiO BB] Webcast of the Automated Function Prediction meeting Message-ID: <44F61DAA.7080009@burnham.org> Keynote talks in the AFP 2006 are being webcast. Note that the times are Pacific (GMT-8) http://www.calit2.net/events/popup.php?id=840 Iddo -- Iddo Friedberg, Ph.D. Burnham Institute for Medical Research 10901 N. Torrey Pines Rd. La Jolla, CA 92037 Tel: (858) 646 3100 x3516 Fax: (858) 795 5249 ** NEW ** http://iddo-friedberg.org http://BioFunctionPrediction.org From idoerg at burnham.org Thu Aug 31 03:16:58 2006 From: idoerg at burnham.org (Iddo Friedberg) Date: Thu, 31 Aug 2006 00:16:58 -0700 Subject: [BiO BB] Webcast of the Automated Function Prediction meeting: correciton Message-ID: <44F68CEA.1040802@burnham.org> New and correct URL: http://biofunctionprediction.org/AFP/afp2006-webcasts/ -- Iddo Friedberg, Ph.D. Burnham Institute for Medical Research 10901 N. Torrey Pines Rd. La Jolla, CA 92037 Tel: (858) 646 3100 x3516 Fax: (858) 795 5249 ** NEW ** http://iddo-friedberg.org http://BioFunctionPrediction.org From rich at thevillas.eclipse.co.uk Thu Aug 31 06:28:07 2006 From: rich at thevillas.eclipse.co.uk (rich) Date: Thu, 31 Aug 2006 11:28:07 +0100 Subject: [BiO BB] megablast and blastp index errors In-Reply-To: References: <44F57E2B.1030800@thevillas.eclipse.co.uk> Message-ID: <44F6B9B7.3070103@thevillas.eclipse.co.uk> Ha! Of course, thanks. I just assumed. As an aside, taking the same input file I wanted to use for megablast (one file with multiple a number of fasta entries) and running blastall -p blastp seems to work in a similar manner as megablast ie taking one entry at a time and blasting against the db. I didn't realise blastall would take multiple entries as input cheers Rich Martin Gollery wrote: > astral100 is a protein database- Megablast is only for nucleotides, > and so it is looking for astral100.nin which is not there. > > Marty Gollery > > On 8/30/06, * rich* > wrote: > > Hi, > > I created a blastable db with formatdb (2.2.10): > > formatdb -i astral100 > > I can run blastall -p blastp and it works fine > but when I run megablast I get > > [megablast] WARNING: Could not find index files for database > astral100 > > Any ideas? > Thanks > Rich > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > -- > -- > Martin Gollery > Associate Director > Center For Bioinformatics > University of Nevada at Reno > Dept. of Biochemistry / MS330 > 775-784-7042 > ----------- > ------------------------------------------------------------------------ > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From smagarwal at yahoo.com Thu Aug 31 09:25:51 2006 From: smagarwal at yahoo.com (Subhash Agarwal) Date: Thu, 31 Aug 2006 14:25:51 +0100 (BST) Subject: [BiO BB] Exon information Message-ID: <20060831132552.71854.qmail@web31505.mail.mud.yahoo.com> Hi all Can anybody let me know how to find, how many exons a human gene has (For example NP_001080 present in NCBI) and its coding coordinates. Thanks Subhash --------------------------------- Here's a new way to find what you're looking for - Yahoo! Answers Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8. Get it NOW -------------- next part -------------- An HTML attachment was scrubbed... URL: From marty.gollery at gmail.com Thu Aug 31 09:42:45 2006 From: marty.gollery at gmail.com (Martin Gollery) Date: Thu, 31 Aug 2006 06:42:45 -0700 Subject: [BiO BB] megablast and blastp index errors In-Reply-To: <44F6B9B7.3070103@thevillas.eclipse.co.uk> References: <44F57E2B.1030800@thevillas.eclipse.co.uk> <44F6B9B7.3070103@thevillas.eclipse.co.uk> Message-ID: No problem. Yes, you can run multiple entries at a time with the comand line, but with the newest version it does not run them one at a time, as the old version did, but all at once. Then it parses out the results later. This means that it is much faster- ten times faster, in some cases because the database only has to be loaded once. Marty On 8/31/06, rich wrote: > > > Ha! Of course, thanks. I just assumed. > As an aside, taking the same input file I wanted to use for megablast > (one file with multiple a number of fasta entries) and running > blastall -p blastp > seems to work in a similar manner as megablast ie taking one entry at a > time and blasting against the db. I didn't realise blastall would take > multiple entries as input > > cheers > Rich > > Martin Gollery wrote: > > astral100 is a protein database- Megablast is only for nucleotides, > > and so it is looking for astral100.nin which is not there. > > > > Marty Gollery > > > > On 8/30/06, * rich* > > wrote: > > > > Hi, > > > > I created a blastable db with formatdb (2.2.10): > > > > formatdb -i astral100 > > > > I can run blastall -p blastp and it works fine > > but when I run megablast I get > > > > [megablast] WARNING: Could not find index files for database > > astral100 > > > > Any ideas? > > Thanks > > Rich > > _______________________________________________ > > General Forum at Bioinformatics.Org - > > BiO_Bulletin_Board at bioinformatics.org > > > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > > > > > -- > > -- > > Martin Gollery > > Associate Director > > Center For Bioinformatics > > University of Nevada at Reno > > Dept. of Biochemistry / MS330 > > 775-784-7042 > > ----------- > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > -- -- Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ----------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From aloraine at gmail.com Thu Aug 31 18:25:37 2006 From: aloraine at gmail.com (Ann Loraine) Date: Thu, 31 Aug 2006 17:25:37 -0500 Subject: [BiO BB] Exon information In-Reply-To: <20060831132552.71854.qmail@web31505.mail.mud.yahoo.com> References: <20060831132552.71854.qmail@web31505.mail.mud.yahoo.com> Message-ID: <83722dde0608311525j54e2583crfeace36a3b52a181@mail.gmail.com> Dear Subhash, You can get this information using the Table Browser download tool at the UC Santa Cruz Genome Informatics Web site. It will allow you to download a data file that gives the genomic coordinates for mRNA-to-genome alignments. To start, I would recommend you use a RefSeq data set, since these tend to be full-length sequences and many have been vetted by expert curators. To figure out which mRNA accessions go with which genes, you can use gene2accession, a data file available from the Entrez Gene ftp site. Of course there may be more direct approaches which other participants on this list may suggest. Best of luck, Ann Loraine On 8/31/06, Subhash Agarwal wrote: > > Hi all > > Can anybody let me know how to find, how many exons a human gene has (For > example NP_001080 present in NCBI) and its coding coordinates. > > Thanks > > Subhash > > > ________________________________ > Here's a new way to find what you're looking for - Yahoo! Answers > Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8. Get > it NOW > > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > -- Ann Loraine Assistant Professor Section on Statistical Genetics University of Alabama at Birmingham http://www.ssg.uab.edu http://www.transvar.org From golharam at umdnj.edu Thu Aug 31 21:48:22 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 31 Aug 2006 21:48:22 -0400 Subject: [BiO BB] Exon information In-Reply-To: <20060831132552.71854.qmail@web31505.mail.mud.yahoo.com> Message-ID: <02b001c6cd68$b671ec10$2f01a8c0@GOLHARMOBILE1> Entrez Gene should have this information. If it doesn't then the simpliest way is to map to protein to the genome using Splign. Basically, obtain the CDS for the protein, and align the CDS to the genome using Splign. Splign will determine the location of the exons. You can use this information to extract the coordinates or number of exons. -----Original Message----- From: bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org [mailto:bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org ] On Behalf Of Subhash Agarwal Sent: Thursday, August 31, 2006 9:26 AM To: bioinformatics.org Subject: [BiO BB] Exon information Hi all Can anybody let me know how to find, how many exons a human gene has (For example NP_001080 present in NCBI) and its coding coordinates. Thanks Subhash _____ Here's a new way to find what you're looking for - Yahoo! Answers Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8. Get it NOW -------------- next part -------------- An HTML attachment was scrubbed... URL: