From ritu.bioinfo at gmail.com Mon Apr 2 01:11:17 2007 From: ritu.bioinfo at gmail.com (ritu chaudhary) Date: Mon, 2 Apr 2007 10:41:17 +0530 Subject: [BiO BB] plz help-DOCK 6.1 In-Reply-To: <2e1edeb10703310419g57edec4dlb7a3b8e323e124a1@mail.gmail.com> References: <2e1edeb10703310419g57edec4dlb7a3b8e323e124a1@mail.gmail.com> Message-ID: <2e1edeb10704012211t24b9cd32k4a838fbe964a0b60@mail.gmail.com> > > I am working on project entitled *"Virtual Screening of Inhibitors > against NS3 Protease of Dengue Virus"* using software *Dock 6.1*.Sir i > have to perform Docking of 1bef.pdb to about 1000 compounds of NCL > library. i read all the tutorials given at site > http://dock.compbio.ucsf.edu/DOCK_6/index.htm > and i used them for running dock 6 but those tutorials are for docking > single ligand to the receptor.and i want to dock a database containing > 10,000 compounds.so plzzzzzzzzzzzzzz tell me that tutorial which is for > docking a library of compounds to single 3-D receptor mol. > please help me. > i have prepared receptor mol by running SPHGEN and it has generated 27 > clusters and now i have to generate spheres on the surface of receptor so > which tutorial should i follow for that > I will be really thankful. > > Ritu Chaudhary > M.Sc BIOINFORMATICS > CCSHAU > HISAR > INDIA > > > > > > From gary at primary.bioinformatics.org Mon Apr 2 10:24:08 2007 From: gary at primary.bioinformatics.org (Gary Van Domselaar) Date: Mon, 2 Apr 2007 10:24:08 -0400 (EDT) Subject: [BiO BB] plz help-DOCK 6.1 In-Reply-To: <2e1edeb10704012211t24b9cd32k4a838fbe964a0b60@mail.gmail.com> References: <2e1edeb10703310419g57edec4dlb7a3b8e323e124a1@mail.gmail.com> <2e1edeb10704012211t24b9cd32k4a838fbe964a0b60@mail.gmail.com> Message-ID: Hi ritu, Wow, you sure sound desperate. You should check out the ZINC database (designed to work with dock), it will give you the prepped small molecules for running with DOCK. http://blaster.docking.org/zinc/ And may have better subsets than NCI (you do mean NCI don't you?) for screening against NS3 protease. Zinc and Dock also having their own mailing lists that might serve you better in answering this question. http://blur.compbio.ucsf.edu/mailman/listinfo Kindest Regards, g. -- Gary Van Domselaar, PhD Associate Director, Bioinformatics.Org gary at bioinformatics.org On Mon, 2 Apr 2007, ritu chaudhary wrote: > >> >> I am working on project entitled *"Virtual Screening of Inhibitors >> against NS3 Protease of Dengue Virus"* using software *Dock 6.1*.Sir i >> have to perform Docking of 1bef.pdb to about 1000 compounds of NCL >> library. i read all the tutorials given at site >> http://dock.compbio.ucsf.edu/DOCK_6/index.htm >> and i used them for running dock 6 but those tutorials are for docking >> single ligand to the receptor.and i want to dock a database containing >> 10,000 compounds.so plzzzzzzzzzzzzzz tell me that tutorial which is for >> docking a library of compounds to single 3-D receptor mol. >> please help me. >> i have prepared receptor mol by running SPHGEN and it has generated 27 >> clusters and now i have to generate spheres on the surface of receptor so >> which tutorial should i follow for that >> I will be really thankful. >> >> Ritu Chaudhary >> M.Sc BIOINFORMATICS >> CCSHAU >> HISAR >> INDIA >> >> >> >> >> >> > _______________________________________________ > 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 marchywka at hotmail.com Mon Apr 2 10:49:05 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Mon, 02 Apr 2007 10:49:05 -0400 Subject: [BiO BB] plz help-DOCK 6.1 In-Reply-To: Message-ID: Is there a list of these things somewhere- like a wiki page? Specifically limitations versus needs for prediction,modelling, and visualization? I've got my opengl/c++ molecule viewer almost working ( the UI and scripting ability took more effort than the "real" stuff) and now I need something useful to do with it. Right now I'm not sure it has any benefit over RasMol- I can draw some nice pictures with "artisitic" potential surfaces but maybe I can find something scientifically interesting. In as much as cavity visualization was an early objective, maybe I can find a way to do some active site or interaction predictions. I had asked earlier about more realistic potential surfaces and assumed the lack of response indicated lack of interest in the area. Obviously visuals don't do predictions but they can be good tools for testing/evaluating these things. Thanks. >From: Gary Van Domselaar >Reply-To: "General Forum at Bioinformatics.Org" > >To: ritu chaudhary >CC: bio_bulletin_board at bioinformatics.org >Subject: Re: [BiO BB] plz help-DOCK 6.1 >Date: Mon, 2 Apr 2007 10:24:08 -0400 (EDT) > > >Hi ritu, > > >Wow, you sure sound desperate. > >You should check out the ZINC database (designed to work with dock), it >will give you the prepped small molecules for running with DOCK. >http://blaster.docking.org/zinc/ > >And may have better subsets than NCI (you do mean NCI don't you?) for >screening against NS3 protease. > >Zinc and Dock also having their own mailing lists that might serve you >better in answering this question. >http://blur.compbio.ucsf.edu/mailman/listinfo > >Kindest Regards, > >g. >-- >Gary Van Domselaar, PhD >Associate Director, Bioinformatics.Org >gary at bioinformatics.org > > >On Mon, 2 Apr 2007, ritu chaudhary wrote: > >> >>> >>> I am working on project entitled *"Virtual Screening of Inhibitors >>>against NS3 Protease of Dengue Virus"* using software *Dock 6.1*.Sir i >>>have to perform Docking of 1bef.pdb to about 1000 compounds of NCL >>>library. i read all the tutorials given at site >>>http://dock.compbio.ucsf.edu/DOCK_6/index.htm >>>and i used them for running dock 6 but those tutorials are for docking >>>single ligand to the receptor.and i want to dock a database containing >>>10,000 compounds.so plzzzzzzzzzzzzzz tell me that tutorial which is for >>>docking a library of compounds to single 3-D receptor mol. >>>please help me. >>>i have prepared receptor mol by running SPHGEN and it has generated 27 >>>clusters and now i have to generate spheres on the surface of receptor so >>>which tutorial should i follow for that >>>I will be really thankful. >>> >>>Ritu Chaudhary >>>M.Sc BIOINFORMATICS >>>CCSHAU >>>HISAR >>>INDIA >>> >>> >>> >>> >>> >>> >>_______________________________________________ >>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 >_______________________________________________ >General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ Exercise your brain! Try Flexicon. http://games.msn.com/en/flexicon/default.htm?icid=flexicon_hmemailtaglinemarch07 From nuin at genedrift.org Mon Apr 2 10:28:28 2007 From: nuin at genedrift.org (Paulo Nuin) Date: Mon, 02 Apr 2007 10:28:28 -0400 Subject: [BiO BB] mxtextools In-Reply-To: <1175371076.6587.3.camel@linux-eslv.site> References: <1175371076.6587.3.camel@linux-eslv.site> Message-ID: <4611130C.4090408@genedrift.org> Hi I installed mxtexttools in order to use BioPython and the installation and BioPython tests were fine. HTH Paulo Tim wrote: > Hi, > I have installed Suse 10.2 linux on my computer which came packaged with > Python 2.5. I notice on the mxtexttools website that their is only a tar > file up to python 2.4 . Has anyone tried the 2.4 texttools with python > 2.5. Is it compatible? > > Thanks, > Tim > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > From pmr at ebi.ac.uk Mon Apr 2 11:52:16 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 02 Apr 2007 16:52:16 +0100 Subject: [BiO BB] php and seqret In-Reply-To: <33a85e2f0703290709t6081254cx5670dbfdd95b749b@mail.gmail.com> References: <33a85e2f0703290709t6081254cx5670dbfdd95b749b@mail.gmail.com> Message-ID: <461126B0.20706@ebi.ac.uk> Kim Clarke wrote: > Hi folks, > I'm a first year bioinformatics undergraduate nearing completion of my > first > year project. A quick question...I am writing a very simple web server > using > basic html and php. One section of the php deals with calling Seqret > (EMBOSS) using exec(). Seqret is stored on the same file server and the > command line instruction when ran in a terminal works fine. here is the > snippet of code: > > //exec("touch $pass_c"); > exec("seqret embl:$accession $pass_c"); > > both $accession and $pass_c work fine. Can anyone with experience of PHP > and > EMBOSS help me? is it a problem with file permissions? if you add "-debug" to the command line, seqret will write a file seqret.dbg in the current directory (wherever it runs) that will give you more clues. My guess is that it is not finding the database definitions. Two applications you can try are: embossversion -full (lists all the defined paths) showdb -full (lists all the available databases) if the emboss.default file or the .embossrc file for the user running the php are not found, you may be missing a definition for embl. Hope that helps. Ask again if you need more clues. Peter Rice EMBOSS developer From aas_lakyari at yahoo.com Tue Apr 3 07:29:11 2007 From: aas_lakyari at yahoo.com (Azhar Ali Shah Syed) Date: Tue, 3 Apr 2007 04:29:11 -0700 (PDT) Subject: [BiO BB] Visualization Software Message-ID: <470298.2525.qm@web56311.mail.re3.yahoo.com> I am currently planning to run protein 3d strcutre comparison calculations in a cluster or grid environemnt. Could any one recommend the data strcture and visualization software for results of the comparison? thanks in advance Azhar Azhar Ali Shah Syed, PhD Research Scholar, ASAP Research Group, School of Computer Science & IT, University of Nottingham, Jubilee Campus, Wollaton Road, Nottingham NG8 1BB, UK. Cell: +44 7847389539 E-mail: aas at cs.nott.ac.uk Web: http://www.cs.nott.ac.uk/~aas/ --------------------------------- Looking for earth-friendly autos? Browse Top Cars by "Green Rating" at Yahoo! Autos' Green Center. From asidhu at biomap.org Sat Apr 7 16:48:38 2007 From: asidhu at biomap.org (Amandeep S. Sidhu) Date: Sun, 08 Apr 2007 06:48:38 +1000 Subject: [BiO BB] Call for Chapters: Biomedical Data and Applications by Springer Message-ID: <1175978918.461803a6b927a@mail.opentransfer.com> *********************************************************** Call for Book Chapters Biomedical Data and Applications http://biomed.biomap.org/ *********************************************************** Editors: Amandeep S. Sidhu, Tharam S. Dillon, Elizabeth Chang Digital Ecosystems and Business Intelligence, Curtin University of Technology, Perth, Australia Volume: Studies in Computational Intelligence Series Publisher: Springer http://www.springer.com/series/7092/ ************************************************************ Deadline: 15 June 2007 ************************************************************ Introduction: The goal of this book is to cover biomedical data and applications identifying new issues and directions for future research in biomedical domain. The book will become a useful guide for researchers, practitioners, and graduate-level students interested in learning state-of-the-art development in biomedical data management, data-intensive bioinformatics systems, and other miscellaneous biological database applications. The content of this book is at an introductory and medium technical level. ************************************************************* Topics: Chapters in the book will broadly address following areas: * Conceptual Models for Biological and Medical Data * Data Representation and Visualization * Biomedical Databases and Data Integration * Biomedical Data Analysis and Interoperability * Biological Query Processing, Query Optimization, and Information Retrieval * Biomedical Ontologies and taxonomies * Ontology-driven Biomedical Systems * Computational Methods for Microarray analysis, Protein and RNA structure prediction * Feature selection and pattern discovery in biological data * Modelling Biological Pathways * Health Care Information Systems * Electronic Health Records * Biomedical Data Privacy and Security * Clinical Assessment and Patient Diagnosis * Disease Control and Prevention * Data mining applications in bioinformatics, biomedicine, health care and other biomedical domain areas **************************************************************** Publication: The Book will be published in Studies in Computational Intelligence of Springer in Late 2007. Studies in Computational Intelligence Series publishes new developments and advances in the various areas of computational intelligence. **************************************************************** Submission Instructions: Papers should be original and should not be submitted for publication or published elsewhere. All papers are to be submitted electronically (PDF or MS word format preferred) by email to: Amandeep.Sidhu at cbs.curtin.edu.ai For details on how to prepare the manuscripts and style files refer to: http://www.springer.com/west/home/new+&+forthcoming+titles+(default)?SGWID=4-40356-69-173623546-0&detailsPage=contentItemPage&contentItemId=149813&CIPageCounter=CI_FOR_AUTHORS_AND_EDITORS_PAGE1 **************************************************************** Important Dates: June 15, 2007 Last day to email a letter of intent (including a tentative title, short summary of proposed topic, and a list of authors) July 31, 2007 Deadline to submit a full book chapter paper August 30, 2007 Notification of acceptance with referee comments and revision comments September 30, 2007 Deadline to submit final version of the accepted chapters in camera-ready Springer format **************************************************************** Editors: Amandeep S. Sidhu, Prof. Tharam S. Dillon, Prof. Elizabeth Chang Digital Ecosystems & Business Intelligence Institute, Curtin University of Technology, Australia http://debii.curtin.edu.au/ **************************************************************** -- From marchywka at hotmail.com Sat Apr 7 18:04:19 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Sat, 07 Apr 2007 18:04:19 -0400 Subject: [BiO BB] Call for Chapters: Biomedical Data and Applications bySpringer In-Reply-To: <1175978918.461803a6b927a@mail.opentransfer.com> Message-ID: This is a bit off topic but, in reply to this request for chapters, > Digital Ecosystems and Business Intelligence, Curtin University of >Technology, let me cite an earlier post I made: http://bioinformatics.org/pipermail/bio_bulletin_board/2006-May/003249.html Those of you looking for interesting things to do may want to look at the recent action surrounding Dendreon. They have questionable clinical data and confusing results regarding the MOA of their cancer vaccine. The value of the company depends of course on determining if their product actually does anything and how to best optimize and generalize the approach. There has been little additional science from the company and the method is reasonably well disclosed in some patents. So, there could be opportunities here for someone to prove that their product works or doesn't work based on identification of the precise MOA. http://www.fda.gov/ohrms/dockets/ac/07/briefing/2007-4291B1-00-index.htm Business intelligence in this case could be some blast searches and epitope predictions :) The immediate concern from the FDA was clinical data but a precise MOA could "explain" why some patients responded and others didn't. Modelling of prognostic factors and disease trajectory, indepedent of the MOA, could also be interesting bioinformatics areas with immediate commercial application. >From: "Amandeep S. Sidhu" >Reply-To: "General Forum at Bioinformatics.Org" > >To: bio_bulletin_board at bioinformatics.org >Subject: [BiO BB] Call for Chapters: Biomedical Data and Applications >bySpringer >Date: Sun, 08 Apr 2007 06:48:38 +1000 > >*********************************************************** >Call for Book Chapters > >Biomedical Data and Applications > >http://biomed.biomap.org/ > >*********************************************************** > >Editors: Amandeep S. Sidhu, Tharam S. Dillon, Elizabeth Chang > Digital Ecosystems and Business Intelligence, Curtin University of >Technology, >Perth, Australia > >Volume: Studies in Computational Intelligence Series > >Publisher: Springer _________________________________________________________________ The average US Credit Score is 675. The cost to see yours: $0 by Experian. http://www.freecreditreport.com/pm/default.aspx?sc=660600&bcd=EMAILFOOTERAVERAGE From TAN_Tsu_Soo at nyp.gov.sg Thu Apr 5 00:44:13 2007 From: TAN_Tsu_Soo at nyp.gov.sg (Tsu Soo TAN) Date: Thu, 5 Apr 2007 12:44:13 +0800 Subject: [BiO BB] Visualization Software [2] In-Reply-To: <20070404160139.96AC3368776@primary.bioinformatics.org> Message-ID: Accelrys offers their DS Viewer free, for both MS Windows and Linux platforms. They've just announced the latest release. You just need to register at their website and you can download the software. Tan Tsu Soo Bioinformatics Group Nanyang Polytechnic Date: Tue, 3 Apr 2007 04:29:11 -0700 (PDT) From: Azhar Ali Shah Syed Subject: [BiO BB] Visualization Software To: bio_bulletin_board at bioinformatics.org Message-ID: <470298.2525.qm at web56311.mail.re3.yahoo.com> Content-Type: text/plain; charset=iso-8859-1 I am currently planning to run protein 3d strcutre comparison calculations in a cluster or grid environemnt. Could any one recommend the data strcture and visualization software for results of the comparison? thanks in advance Azhar Azhar Ali Shah Syed, PhD Research Scholar, ASAP Research Group, School of Computer Science & IT, University of Nottingham, Jubilee Campus, Wollaton Road, Nottingham NG8 1BB, UK. Cell: +44 7847389539 E-mail: aas at cs.nott.ac.uk Web: http://www.cs.nott.ac.uk/~aas/ From hlapp at gmx.net Thu Apr 5 17:36:52 2007 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 5 Apr 2007 17:36:52 -0400 Subject: [BiO BB] Computational Phyloinformatics Course at NESCent Message-ID: Computational Phyloinformatics: A Course at NESCent. 9 - 19 July 2007 The National Evolutionary Synthesis Center (Durham, NC, USA) http://www.nescent.org/summer_course Computational Phyloinformatics is a new course that aims to give students practical knowledge and hands-on skills in phyloinformatics. SYNOPSIS Biologists are faced with ever larger datasets, more complex evolutionary models, and more elaborate analytical methods. Seldom is it sufficient to run a dataset through an off-the-shelf program on a desktop PC; increasingly, biologists need to write scripts to interface with internet services and databases, build analytical pipelines, customize analyses, and distribute computation over multiple processors. This course is designed to give graduate students, post-docs, and researchers in phylogenetics who have an interest in writing programs and scripting analyses the skills needed to tackle the grand challenges posed by the Assembling the Tree of Life program, Evo- Devo, Metagenomics, Phylogenomics, and other emerging research areas. Students will learn how to build and compute with phylogenetic databases; they will learn "power-user" skills for scripting analyses in Mesquite and HyPhy. Students choose between either a Java- or a Perl-based environment for learning how to write basic phylogeny programs: parsing NEXUS files; traversing and computing over trees; and making practical use of phylogenetic libraries (e.g. PAL, JEBL, BioJava; BioPerl, Bio::Phylo, CIPRES interface). These skills will be learned in a biological context, touching on a diverse array of topics such as automated base calling, ancestral state and continuous character reconstruction, model selection, parametric bootstrapping, etc. INSTRUCTORS Organizer: William Piel (william.piel at yale.edu) Hilmar Lapp David Maddison Wayne Maddison Jeff Oliver Sergei L. Kosakovsky Pond Stephen Smith Arlin Stoltzfus Rutger Vos PREREQUISITES Biology: A solid understanding of phylogenetics -- for example, having already taken the Workshop on Molecular Evolution (http:// www.molecularevolution.org/) or equivalent coursework or experience. Computing: Prior experience with either Perl or Java; or, having read and studied the recommended books on either language (see web site). Students will be using Mac OSX computers in the course, so should have experience with basic Unix shell commands. FEES Tuition is $500.00. Housing is $440 for single occupancy, $220 for double occupancy in housing provided at Duke University. Travel awards of up to $620 each are available to subsidize travel expenses for applicants from underrepresented groups. HOW TO APPLY Students may apply through the website (www.nescent.org/ summer_course). You will be asked to provide a resume, two references, a brief description of your computational and phylogenetic background, and your reasons for taking the course. Applications are due by April 15, 2007. International students may wish to apply for Travel awards from the Society of Systematic Biologists (due date: March 31, 2007, see website for details). William Piel From sswang at berkeley.edu Thu Apr 5 19:30:08 2007 From: sswang at berkeley.edu (Sarah Wang) Date: Thu, 05 Apr 2007 16:30:08 -0700 Subject: [BiO BB] Some questions about Kegg Message-ID: Hi, I have been trying to reconstruct the pathways with the text files from Kegg ftp site. But there are some questions puzzling me to get explicit relationships among KO number, EC number, orthologous genes and reaction ID, map ID. I did figured some out, but some seem missing. Is there anybody who is familiar with Kegg or in a group also using Kegg data? I wish to get some quick consulting, at least know how others tackle these. It is very urgent for my work. Any help would be greatly appreciated! Thanks Sarah From ci-bio2007 at disi.unige.it Fri Apr 6 04:51:28 2007 From: ci-bio2007 at disi.unige.it (ci-bio2007) Date: Fri, 6 Apr 2007 10:51:28 +0200 Subject: [BiO BB] CFA: Post-IJCNN 2007 workshop on COMPUTATIONAL INTELLIGENCE APPROACHES FOR THE ANALYSIS OF BIOINFORMATICS DATA Message-ID: <200704061051.39154.ci-bio2007@disi.unige.it> CALL FOR ABSTRACTS ----------------------------------------------------------------------------------------------------------- International Joint Conference on Neural Networks 2007 POST-CONFERENCE WORKSHOP ON COMPUTATIONAL INTELLIGENCE APPROACHES FOR THE ANALYSIS OF BIOINFORMATICS DATA CI-BIO 2007 http://ci-bio2007.disi.unige.it/ August 17th, 2007 Renaissance Orlando Resort at SeaWorld, Florida, USA SPONSORED BY THE INNS BIOINFORMATICS SIG SCOPE & TOPICS Bioinformatics is a fast growing scientific area aimed at managing, analyzing and interpreting information from biological data, sequences and structures. In the past few years, many Computational Intelligence approaches have been successfully applied to the solution of complex problems typical of this field, including signal and image processing, clustering, feature selection, data visualization, and data mining. CI-BIO 2007 will present surveys and contributed papers covering different areas where neural, fuzzy, and genetic approaches have been successfully applied to the analysis of Bioinformatics data. INTERNATIONAL PROGRAM COMMITTEE Pierre Baldi, University of California, Irvine, CA, USA Jake Chen, Purdue University Indianapolis, IN, USA Alexessander Couto Alves, University of Porto, Purtugal Alexandru Floares, Oncological Institute Cluj-Napoca, Romania Jon Garibaldi, University of Nottingham, UK Luciano Milanesi, CNR-ITB, Milano, Italy David Alejandro Pelta, University of Granada, Spain Leif Peterson, The Methodist Hospital, Houston, TX, USA Giorgio Valentini, University of Milan, Italy Jean-Philippe Vert, Ecole des mines de Paris, France INVITED SPEAKER Mark A. Kon, Department of Mathematics and Statistics, Boston University CONTRIBUTION TO THE WORKSHOP We request two kinds of contributions: * surveys papers giving overviews of innovative Computational Intelligence approaches to a specific Bioinformatics area * standard papers presenting new results not already presented at the IJCNN 2007. Standard papers accepted as oral will be presented in a slot of 15-20 min, while survey papers will have a slot of 30-60 min for oral presentation (details will be communicated to the authors by the end of June). Submission of Contributions Extended abstracts submission for the Workshop Notes Extended abstracts no longer than 2 pages must be prepared in Latex following the same style of IJCNN 2007 papers (IEEEtran.cls and a sample tex file are available here). By 10 May 2007 the authors must submit the PDF file with an email to ci-bio2007 at disi.unige.it In the email they must specify: (1) Paper title; (2) Survey/Standard paper (3) Keywords; (4) Authors names and affiliations; (5) Corresponding author's name and contact details, including telephone/fax numbers and e-mail address. ON-LINE PAPER PUBLICATION The authors of accepted abstracts must prepare the final paper in Latex following the same style of IJCNN 2007 papers (IEEEtran.cls and a sample tex file are available here). Papers must be submitted by 15 June 2007 in PDF format with an email to ci-bio2007 at disi.unige.it The papers will be published on-line on this web site. POST-WORKSHOP PUBLICATION We are making agreements with the editor of an international scientific journal in order to publish a special journal issue including extended versions of a selection of papers presented at CI-BIO workshop. IMPORTANT DATES Extended abstract submission deadline: 10 May 2007 Notification of acceptance: 20 May 2007 Accepted papers due: 15 June 2007 Slides of presentations due: 1 July 2007 Workshop: 17 August 2007 Best regards, Francesco Masulli, Univ. Genova (Italy) Roberto Tagliaferri, Univ. Salerno (Italy) CI-BIO 2007 organizers - ************************************************************************* CI-BIO 2007 WORKSHOP ON COMPUTATIONAL INTELLIGENCE APPROACHES FOR THE ANALYSIS OF BIOINFORMATICS DATA http://ci-bio2007.disi.unige.it/ email: ci-bio2007 at disi.unige.it August 17th, 2007 Renaissance Orlando Resort at SeaWorld, Florida, USA ************************************************************************* From marchywka at hotmail.com Mon Apr 9 13:17:13 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Mon, 09 Apr 2007 13:17:13 -0400 Subject: [BiO BB] Visualization Software [2] In-Reply-To: Message-ID: I mentioned I wrote my own but someone put me on to this, sorry if it was already posted on this list as I have been switching among many: http://www.cgl.ucsf.edu/chimera/ >From: Tsu Soo TAN >Reply-To: "General Forum at Bioinformatics.Org" > >To: bio_bulletin_board at bioinformatics.org >Subject: [BiO BB] Visualization Software [2] >Date: Thu, 5 Apr 2007 12:44:13 +0800 > >Accelrys offers their DS Viewer free, for both MS Windows and Linux >platforms. They've just announced the latest release. >You just need to register at their website and you can download the >software. > >Tan Tsu Soo >Bioinformatics Group >Nanyang Polytechnic > > _________________________________________________________________ Exercise your brain! Try Flexicon. http://games.msn.com/en/flexicon/default.htm?icid=flexicon_hmemailtaglineapril07 From a_s_soares at yahoo.com.br Mon Apr 9 18:34:23 2007 From: a_s_soares at yahoo.com.br (Alexsandro Soares) Date: Mon, 9 Apr 2007 15:34:23 -0700 (PDT) Subject: [BiO BB] Genetic Algorithm Message-ID: <467973.42697.qm@web51610.mail.re2.yahoo.com> Hi, I have started work on the clustering of DNA sequences. I`m trying genetic algorithms and I would like to know about the recent publications using this technique to build phylogenetic trees. Thanks in advance for any answer. Cheers, Alex __________________________________________________ Fale com seus amigos de gra?a com o novo Yahoo! Messenger http://br.messenger.yahoo.com/ From Sterten at aol.com Mon Apr 9 22:16:06 2007 From: Sterten at aol.com (Sterten at aol.com) Date: Mon, 9 Apr 2007 22:16:06 EDT Subject: [BiO BB] influenza databases Message-ID: is someone working to improve the influenza databases from genbank,lanl (i.e. H5N1) ? is someone writing software to process these databases for all kinds of statistics ? is someone interested to exchange (partial) flu databases in improved, computer readable format ? I'd like to get updates of the whole database (~50000 records, 70MB,10MB compressed) and work with them offline rather than using the online tools. Guenter From richard.squires at utsouthwestern.edu Tue Apr 10 21:29:53 2007 From: richard.squires at utsouthwestern.edu (rsquir) Date: Tue, 10 Apr 2007 20:29:53 -0500 Subject: [BiO BB] influenza databases In-Reply-To: References: Message-ID: <50D0BE3E-67DC-495A-BD0B-2FE8C3D20831@utsouthwestern.edu> Hello Guenter, In short, yes we are! I am the person responsible for the influenza component of the BioHealthBase Bioinformatic Resource Center (BRC). We are a free integrated bioinformatics resource supporting influenza researchers. We are currently working on including the crucial improvements to GenBank sequence curation that you refer to. We also include a number of other data types including curated and predicted epitopes and polymorphism analysis. We are always on the look out for additional high quality data to incorporate into the system. I would like to hear any ideas you have. Our website is http://www.BioHealthBase.org Please contact me at richard.squires at utsouthwestern.edu with questions and comments. Thanks for the interest! Burke Squires On Apr 9, 2007, at 9:16 PM, Sterten at aol.com wrote: > > is someone working to improve the influenza databases from > genbank,lanl > (i.e. H5N1) ? > is someone writing software to process these databases for all > kinds of > statistics ? > is someone interested to exchange (partial) flu databases in improved, > computer readable format ? > > I'd like to get updates of the whole database (~50000 records, 70MB, > 10MB > compressed) > and work with them offline rather than using the online tools. > > > Guenter > > > > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board ------------------- Burke Squires BioHealthBase BRC, Influenza Specialist UT Southwestern Medical Center at Dallas richard.squires at utsouthwestern.edu Office (214) 648-4952 From asidhu at biomap.org Wed Apr 11 16:07:56 2007 From: asidhu at biomap.org (Amandeep S. Sidhu) Date: Thu, 12 Apr 2007 06:07:56 +1000 Subject: [BiO BB] CFP: 2007 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2007) Message-ID: <1176322076.461d401cc0e53@mail.opentransfer.com> 2007 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2007) (co-located with IEEE/WCI/ACM WI-IAT 07 and IEEE GrC 07) http://www.cis.drexel.edu/faculty/thu/bibm/index.php.htm San Jose, CA, USA Nov 2-4, 2007 IEEE BIBM 2007 will provide a general forum for disseminating the latest research in bioinformatics and biomedicine. It is a multidisciplinary conference that brings together academic and industrial scientists from computer science, biology, chemistry, medicine, mathematics and statistics. It will exchange research results and address open issues in all aspects of bioinformatics and biomedicine and provide a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling, simulation, ontology and other computational methods, as applied to life science problems, with emphasis on applications in high throughput data-rich areas in biology, biomedical engineering. IEEE BIBM 2007 intends to attract a balanced combination of computer scientists, biologists, biomedical engineers, chemist, data analyzer, statistician. Topics of interests We are soliciting high quality original research papers (including significant works-in-progress) in any aspect of bioinformatics and biomedicine. New computational techniques and methods in machine learning; data mining; text analysis; pattern recognition; knowledge representation; databases; data modeling; combinatorics; stochastic modeling; string and graph algorithms; linguistic methods; robotics; constraint satisfaction; data visualization; parallel computation; data integration; modeling and simulation and heir application in life science domain are especially encouraged. Relevant topics included, but are not limited to: ? Biological Data Mining ? High Performance Bio-computing ? Genomics, Comparative Genomics ? Biological Databases & Data Integration ? Biological Data Visualization ? Evolution and Phylogeny ? Molecular sequence analysis ? Healthcare Informatics ? Recognition of genes and regulatory elements ? Molecular evolution ? Proteomics, Protein structure, Computational proteomics ? Gene networks, Computational genetics ? Combinatorial libraries and drug design ? Computational systems biology ? Microarray design and data analysis ? BioOntologies ? Sequence Analysis ? Structural and functional genomics ? Synthetic Biological Systems ? Pathways, Networks , Systems Biology ? Text Mining & Information Extraction ? Transcriptomics ? BioMedical Devices with Embedded Computers ? Signal and Image Processing in BioMedicine ? BioMedical Image Segmentation and Compression ? BioMedical Intelligence and Data Warehousing ? BioMedical Databases & Information Systems , BioMedical Information ? Multimedia Biomedical Databases ? Intelligent Biomedical Knowledge Discovery ? Modeling signalling network ? Temporal and spatial mining of clinic data including medical images MEETING ORGANIZATION: GENERAL CO-CHAIRS: Prof. Yi Pan Department of Computer Science Georgia State University 34 Peachtree Street, Suite 1450 Atlanta, GA 30302-4110, USA Prof. Carmelina Ruggiero Editor-in-chief of IEEE Trans. on NanoBioscience Professor of Bioengineering DIST University of Genoa Via Opera Pia 13 Genoa, 16145, Italy Prof. Aydin Tozeren Distinguished Professor and Director, Center for Integrated Bioinformatics, School of Biomedical Engineering, Science & Health Systems Drexel University, Philadelphia, PA 19104, USA PROGRAM CO-CHAIRS: Prof. Xiaohua Hu College of Information Science & Technology Drexel University Philadelphia, PA 19104 USA Prof. Zoran Obradovic Center for Information Science and Technology, Temple University, 303 Wachman Hall (038-24), 1805 N. Broad St., Philadelphia, PA 19122, USA. Prof. Ion Mandoiu Computer Science & Engineering Department University of Connecticut 371 Fairfield Way, Unit 2155 Storrs, CT 06269-2155 Office: ITEB 261 WORKSHOP CHAIRS: Jinyan Li Institute for Infocomm Research, Singapore Xue-Wen Chen Univ. of Kansas, USA Tharam S. Dillon Curtin University of Technology, Australia TUTORIAL CHAIR: Sun Kim Indiana University, USA LOCAL ACCOMMODATION CO-CHAIRS: David Scot Taylor San Jos? State University, USA Tom Qi Zhang Google, USA PUBLICITY CO-CHAIRS: Amandeep S. Sidhu Curtin University of Technology, Australia Shuigeng Zhou Fudan University, China IEEE BIBM CO-CHAIRS/DIRECTORS: Xiaohua Hu Drexel University, USA Yi Pan Georgia State University, USA IEEE BIBM STEERING COMMITTEE: Xiaohua Hu Drexel University, USA Vipin Kumar Univ. of Minnesota, USA Michael Ng HongKong Baptist University, China Zoran Obradovic Temple University, USA Yi Pan Georgia State University, USA Jose Principe Univ. of Florida, USA Carmelina Ruggiero DIST University of Genoa, Italy Niilo Saranummi VTT Information Technology, Finland Shusaku Tsumoto Shimane University, Japan SUBMISSION REQUIREMENTS: Please submit a full length paper (not exceeding 5000 words) thorough the online submission system (we will use the same cyber chair system as the IEEE/WCI-ACM WI-IAT 2007 and IEEE GrC 2007 conference) Electronic submissions (in PDF or Postscript format) are required. Selected participants will be asked to submit their revised papers in a format to be specified at the time of acceptance. The Best papers selected from the IEEE BIBM 07 will be published as a special issue in related IEEE Transactions and other journals such as IJDMB, IJBRA etc. IMPORTANT DATES: Paper submission: June 10, 2007 Notification: August 1, 2007 Camera-ready due: August 20, 2007 -- From danielucg at yahoo.com.br Thu Apr 12 23:01:28 2007 From: danielucg at yahoo.com.br (Daniel Xavier de Sousa) Date: Thu, 12 Apr 2007 20:01:28 -0700 (PDT) Subject: [BiO BB] length OR similarity Message-ID: <20070413030130.18410.qmail@web52411.mail.re2.yahoo.com> Hi people, Please, I have one doubt. For same database on BLAST, which spends more time: length of query OR similarity (contend) of query? For example: Sequence A is biggest than sequence B. But sequence B is more similarity than sequence A. Which they will spend more time? And, it is the same BLASTP and BLASTN for this? This is a relation with: => Make lookup table of ?words? for query AND Scan database for hits (word match/seed) AND => Extend alignment both directions Thanks, Daniel Xavier ***************************************************************** * Daniel Xavier de Sousa * * Mestrando em Inform?tica - PUC-Rio * * E-MAIL : dsousaARROBAinf.puc-rio.br * * Fone : +55 21 35271500 - 4543 * **************************************************************** __________________________________________________ Fale com seus amigos de gra?a com o novo Yahoo! Messenger http://br.messenger.yahoo.com/ From danielucg at yahoo.com.br Mon Apr 16 08:35:44 2007 From: danielucg at yahoo.com.br (Daniel Xavier de Sousa) Date: Mon, 16 Apr 2007 05:35:44 -0700 (PDT) Subject: [BiO BB] Simirity of sequence Message-ID: <20070416123544.26823.qmail@web52404.mail.re2.yahoo.com> Hi people, Please, I have one doubt. For same database on BLAST, which spends more time: length of query OR similarity (contend) of query? For example: Sequence A is biggest than sequence B. But sequence B is more similarity than sequence A. Which they will spend more time? And, it is the same BLASTP and BLASTN for this? This is a relation with: => Make lookup table of ?words? for query AND Scan database for hits (word match/seed) AND => Extend alignment both directions Thanks, Daniel Xavier ***************************************************************** * Daniel Xavier de Sousa * * Mestrando em Inform?tica - PUC-Rio * * E-MAIL : dsousaARROBAinf.puc-rio.br * * Fone : +55 21 35271500 - 4543 * **************************************************************** __________________________________________________ Fale com seus amigos de gra?a com o novo Yahoo! Messenger http://br.messenger.yahoo.com/ From idoerg at burnham.org Mon Apr 16 18:29:07 2007 From: idoerg at burnham.org (Iddo Friedberg) Date: Mon, 16 Apr 2007 15:29:07 -0700 Subject: [BiO BB] AFP - BioSapiens Joint SIG at ECCB 2007: Second call for submissions Message-ID: <4623F8B3.7030508@burnham.org> Please post & forward.. thanks! Joint AFP-Biosapiens SIG http://2007.BioFunctionPrediction.org The Automated Function Prediction (AFP) SIG and the Biosapiens European network of excellence in genome annotation are teaming up to hold a two-day Special Interest Group (SIG) meeting July 19-20, 2007 alongside ISMB/ECCB 2007. The abstract submission site is now open. Two page abstracts for posters or short talks will be accepted until May 1, 2007. Please go to: http://2007.BioFunctionPrediction.org and click on "submissions" to submit your abstracts. The deluge of genomic information is challenging biologists to annotate this data, from locating genes in the raw data through to predicting the function from protein sequence and structure. AFP and Biosapiens share many common goals, and this year we have decided to join forces for a SIG that will deal with a wide scope of gene, protein, and genomic annotations. Talks are sought in, but not limited to: * Various aspects of gene and protein function prediction o Function prediction using sequence based methods. This would include "classic" methods such as detection of functional motifs and inferring function from sequence similarity. o Function from genomic information: prediction by genomic location; locus comparison with other organisms; function gain and loss. o Phylogeny based methods o Function from molecular interactions o Function from structure o Function prediction using combined methods o "Meta-talks" discussing the limitations and horizons of computational function prediction. o Assessing function prediction programs * Genomic annotation o Gene finding o Genome visualization o Collaborative annotation o Cooperation between experimental and computational biologists Confirmed speakers include: * Janet Thornton, European Bioinformatics Institute, Cambridge, UK * David Jones University College, London, UK * Rob Russell EMBL, Heidelberg, Germany * Christine Orengo, University College London, UK * Alfonso Valencia, Centro Nacional de Biotecnologia, Madrid, Spain * Ewan Birney, European Bioinformatics Institute, Cambridge, UK * Shoshana Wodak, University of Toronto, Canada * Russ Altman, Stanford University, USA Organizers: Iddo Friedberg, Burnham Institute for Medical Research, La Jolla, CA, USA Adam Godzik, Burnham Institute for Medical Research and University of California, San Diego Christine Orengo, University College, London Important dates: May 1 2007: Talk and poster abstracts due May 21 2007: notification of acceptance May 28, 2007: final abstracts due July 19-20, 2007: AFP-Biosapiens SIG alongside ISMB/ECCB 2007 in Vienna, Austria. Contact us: afp.biosap.2007 at gmail.com For more information: http://2007.BioFunctionPrediction.org Iddo Friedberg, co-chair AFP / Biosapiens 2007 -- Iddo Friedberg, Ph.D. Burnham Institute for Medical Research 10901 N. Torrey Pines Rd. La Jolla, CA 92037, USA T: +1 858 646 3100 x3516 http://iddo-friedberg.org http://BioFunctionPrediction.org From paolo.romano at istge.it Tue Apr 17 11:35:00 2007 From: paolo.romano at istge.it (Paolo Romano) Date: Tue, 17 Apr 2007 17:35:00 +0200 Subject: [BiO BB] CfP: NETTAB 2007 Semantic Web for Bioinformatics: deadline extended Message-ID: <200704171542.l3HFgadY016828@ibm43p.biotech.ist.unige.it> Apologies, if you're receiving multiple copies. ---------------------------------------------------------------- Dear bionformaticians, computer scientists, molecular biologists, in answer to requests from colleagues and also with the view of an overlapping of deadlines with the Annual Meeting of the Bioinformatics Italian Society (BItS), the deadline for submission of posters has been postponed. NEW DEADLINES ARE: Submission of posters: May 8, 2007 Early Registration: May 18, 2007 BEST PAPERS AND POSTERS WILL BE PUBLISHED BY BMC BIOINFORMATICS Here are essential information on the workshop. 7th International Workshop NETTAB 2007 June 12-15, 2006 Department of Computer Science, University of Pisa, Pisa http://www.nettab.org/2007/ FOCUS THEME A Semantic Web for Bioinformatics: Goals, Tools, Systems, Applications NETTAB 2007 is not limited to the main focus theme, but it also includes general sessions on as specified below. Goals of a Semantic Web for Bioinformatics: Standards, Technologies, Tools for the Semantic Web Systems for a Semantic Web for Bioinformatics: Existing and perspective applications of the Semantic Web for Bioinformatics Algorithms in Bioinformatics Formal Methods for Systems Biology Network Tools and Applications in Bioinformatics You are welcome to submit your contributions through the MyReview system at the following URL: http://www.nettab.org/2007/myreview/ . This is a two steps submission procedure. You will have to submit first an abstract and later the paper. You are invited to prepare your contribution according to instructions available in the NETTAB 2007 web site and at http://www.biomedcentral.com/bmcbioinformatics/ifora/ (specially, see "Preparing main manuscript text" section). See the workshop's web site for more details about the preparation of the papers. On this occasion, we are glad to confirm you that best papers and best posters from NETTAB 2007 will be published in a Special Issue of BMC Bioinformatics in 2007. When submitting your poster through the MyReview system, please specify if you also intend to submit for the publication in the journal. The referees will evaluate your poster in view of its publication and you will then be invited to revise your submission and submit it for the selection for the journal. Deadline will be around end of June, begin of July. The workshop will engage itself to pay part of the cost of the publication, but please be advised that depending on the final budget of the workshop you could be requested to partially contribute to publication costs, which have been set to 600 British pounds per paper. For any further information or clarification, please contact the organization by email at info at nettab.org . Looking forward to seeing you all in Tuscany. Best regards. On behalf of the Organizing Committee Paolo Romano Paolo Romano (paolo.romano at istge.it) Bioinformatics and Structural Proteomics National Cancer Research Institute (IST) Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 Fax: +39-010-5737-295 From akarger at CGR.Harvard.edu Fri Apr 20 10:00:35 2007 From: akarger at CGR.Harvard.edu (Amir Karger) Date: Fri, 20 Apr 2007 10:00:35 -0400 Subject: [BiO BB] "The" mRNA for a gene Message-ID: I'd like to get exactly one "representative" transcript (Ensembl ENST or GenBank mRNA, say) for every gene. Due to alternative splicing and other messy biology, Ensembl and GenBank will often have lots of mRNA's associated with single genes. But I think it's true that for most genes, we know of one "main" protein that that gene makes, and one isoform of that protein will be the most studied. Swiss-PROT gives me just one mRNA for BRCA1_HUMAN, which is nice, but for 1433E_HUMAN it gives me 7 mRNAs, which have different lengths! Does anyone know of a place I could get something like this? I'm happy to do some coding if necessary. The results don't have to be perfect. I'm just trying to do something high-throughput that gives one believable result per gene. Thanks, - Amir Karger Research Computing Life Sciences Division Harvard University 617-496-0626 From golharam at umdnj.edu Fri Apr 20 19:41:43 2007 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 20 Apr 2007 19:41:43 -0400 Subject: [BiO BB] "The" mRNA for a gene In-Reply-To: Message-ID: <005801c783a5$73d415b0$f6028a0a@PICO> Amir, You can't always rely on 1 mRNA to represent a gene due to splice variants, etc. Your best bet is to use the RefSeq NM_ sequence and only use the coding portion ie from start to stop codon. The RefSeq NM_ sequence will give you a single reference sequence per gene. In the GenBank entry, pull out the CDS portion. That will give you what you are looking for. Ryan -----Original Message----- From: bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org [mailto:bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org] On Behalf Of Amir Karger Sent: Friday, April 20, 2007 10:01 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] "The" mRNA for a gene I'd like to get exactly one "representative" transcript (Ensembl ENST or GenBank mRNA, say) for every gene. Due to alternative splicing and other messy biology, Ensembl and GenBank will often have lots of mRNA's associated with single genes. But I think it's true that for most genes, we know of one "main" protein that that gene makes, and one isoform of that protein will be the most studied. Swiss-PROT gives me just one mRNA for BRCA1_HUMAN, which is nice, but for 1433E_HUMAN it gives me 7 mRNAs, which have different lengths! Does anyone know of a place I could get something like this? I'm happy to do some coding if necessary. The results don't have to be perfect. I'm just trying to do something high-throughput that gives one believable result per gene. Thanks, - Amir Karger Research Computing Life Sciences Division Harvard University 617-496-0626 _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From codeshepherd at gmail.com Sat Apr 21 05:08:59 2007 From: codeshepherd at gmail.com (Deepan) Date: Sat, 21 Apr 2007 17:08:59 +0800 Subject: [BiO BB] php and seqret In-Reply-To: <33a85e2f0703290709t6081254cx5670dbfdd95b749b@mail.gmail.com> References: <33a85e2f0703290709t6081254cx5670dbfdd95b749b@mail.gmail.com> Message-ID: <1177146540.2595.0.camel@localhost> On Thu, 2007-03-29 at 15:09 +0100, Kim Clarke wrote: > Hi folks, > I'm a first year bioinformatics undergraduate nearing completion of my first > year project. A quick question...I am writing a very simple web server using > basic html and php. One section of the php deals with calling Seqret > (EMBOSS) using exec(). Seqret is stored on the same file server and the > command line instruction when ran in a terminal works fine. here is the > snippet of code: > > //exec("touch $pass_c"); > exec("seqret embl:$accession $pass_c"); > > both $accession and $pass_c work fine. Can anyone with experience of PHP and > EMBOSS help me? is it a problem with file permissions? > > Kim Kim, What is the problem you face? What errors do you get? What do you find in log files? -- ----------------------------------------------- Regards Deepan Chakravarthy N http://www.codeshepherd.com/ http://sudoku-solver.net/ Deciphering the source code of life... From idoerg at burnham.org Mon Apr 23 12:36:37 2007 From: idoerg at burnham.org (Iddo Friedberg) Date: Mon, 23 Apr 2007 09:36:37 -0700 Subject: [BiO BB] Final week for submissions: AFP - BioSapiens Joint SIG at ECCB 2007 Message-ID: <462CE095.5030903@burnham.org> (Please forward as appropriate) Joint AFP-Biosapiens SIG Last week to submit your work! http://2007.BioFunctionPrediction.org The Automated Function Prediction (AFP) SIG and the Biosapiens European network of excellence in genome annotation are teaming up to hold a two-day Special Interest Group (SIG) meeting July 19-20, 2007 alongside ISMB/ECCB 2007 in Vienna Austria. The abstract submission site is now open. Two page abstracts for posters or short talks will be accepted until May 1, 2007. Please go to: http://2007.BioFunctionPrediction.org/node/2 to submit your abstracts. The deluge of genomic information is challenging biologists to annotate this data, from locating genes in the raw data through to predicting the function from protein sequence and structure. AFP and Biosapiens share many common goals, and this year we have decided to join forces for a SIG that will deal with a wide scope of gene, protein, and genomic annotations. Talks are sought in, but not limited to: * Various aspects of gene and protein function prediction o Function prediction using sequence based methods. This would include "classic" methods such as detection of functional motifs and inferring function from sequence similarity. o Function from genomic information: prediction by genomic location; locus comparison with other organisms; function gain and loss. o Phylogeny based methods o Function from molecular interactions o Function from structure o Function prediction using combined methods o "Meta-talks" discussing the limitations and horizons of computational function prediction. o Assessing function prediction programs * Genomic annotation o Gene finding o Genome visualization o Collaborative annotation o Cooperation between experimental and computational biologists Confirmed speakers include: * Janet Thornton, European Bioinformatics Institute, Cambridge, UK * David Jones University College, London, UK * Rob Russell EMBL, Heidelberg, Germany * Christine Orengo, University College London, UK * Alfonso Valencia, Centro Nacional de Biotecnologia, Madrid, Spain * Ewan Birney, European Bioinformatics Institute, Cambridge, UK * Shoshana Wodak, University of Toronto, Canada * Russ Altman, Stanford University, USA Organizers: Iddo Friedberg, Burnham Institute for Medical Research, La Jolla, CA, USA Adam Godzik, Burnham Institute for Medical Research and University of California, San Diego Christine Orengo, University College, London Important dates: May 1 2007: Talk and poster abstracts due May 21 2007: notification of acceptance May 28, 2007: final abstracts due July 19-20, 2007: AFP-Biosapiens SIG alongside ISMB/ECCB 2007 in Vienna, Austria. Contact us: afp.biosap.2007 at gmail.com For more information: http://2007.BioFunctionPrediction.org -- Iddo Friedberg, Ph.D. Burnham Institute for Medical Research 10901 N. Torrey Pines Rd. La Jolla, CA 92037, USA T: +1 858 646 3100 x3516 http://iddo-friedberg.org http://BioFunctionPrediction.org From marchywka at hotmail.com Tue Apr 24 11:36:19 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Tue, 24 Apr 2007 11:36:19 -0400 Subject: [BiO BB] peptide identification tools question In-Reply-To: <470298.2525.qm@web56311.mail.re3.yahoo.com> Message-ID: Hi, I was looking into various issues surrounding 5HT. There seems to be a lot confusion on its role in depression and valvular heart disease among other things. I did a blast search on SERT and then tried to make a frequency table of peptide hits using a simple text processing script. While line breaks and other artifacts are surely messing up the details, I did find a couple of interesting peptides I wanted to investigate. Just out of curiousity, what tools would I use to investigate the longer more frequent peptides? I ran a blast search on LGNVWRFPY and tried to use the conserved domain search but the blast search didn't return anything surprising and I didn't find anything related in conserved domain results but I wasn't sure I knew how to use the output. Are these peptides well known or just likely artifacts and how would I tell? Thanks. $ cat sert_peptides |more 816 PY 766 LG 502 LPW 495 VW 482 LL 464 FF 462 AV 437 GG 410 YY 395 TS 384 LGNVWRFPY 377 YL 376 CY 357 SF 352 FI 350 DA 347 LGN 345 YG 339 VA 333 WNT 328 NGGGAFL 315 YP 315 IF ( note new address as of 10-06) Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165r ( NOTE MORE NEWER NUMBER ) 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only _________________________________________________________________ Mortgage rates near historic lows. Refinance $200,000 loan for as low as $771/month* https://www2.nextag.com/goto.jsp?product=100000035&url=%2fst.jsp&tm=y&search=mortgage_text_links_88_h27f8&disc=y&vers=689&s=4056&p=5117 From danielucg at yahoo.com.br Thu Apr 26 11:08:56 2007 From: danielucg at yahoo.com.br (Daniel Xavier de Sousa) Date: Thu, 26 Apr 2007 08:08:56 -0700 (PDT) Subject: [BiO BB] Can you explain theses results? Message-ID: <933937.26619.qm@web52411.mail.re2.yahoo.com> Hi for all Please, you would see theses tests in serial machine, but important to cluster. What do you think about it? Please look theses tests using BLASTP: Length Seq Query -- HITs -- TIME 10000 -- 3 -- 8min51sec 10000 -- 500 -- 7min41sec ---------------------------------- Length Seq Query -- HITs -- TIME 9000 -- 2 -- 7min11sec 9000 -- 500 -- 6min49sec ---------------------------------- Length Seq Query -- HITs -- TIME 3000 -- 3 -- 2min54sec 3000 -- 500 -- 2min52sec Theses times are very strange. You can see which the sequence of 10000 bases and 3 hits get more time than another sequence of 10000 bases but with 500 hits. So, I can conclude: BLASTP is not sensitive to similarity, difference of BLASTN. But the most important, why this happened? Can anybody explain theses results? Thanks for all Daniel ***************************************************************** * Daniel Xavier de Sousa * * Mestrando em Inform?tica - PUC-Rio * * E-MAIL : dsousaARROBAinf.puc-rio.br * * Fone : +55 21 35271500 - 4543 * **************************************************************** __________________________________________________ Fale com seus amigos de gra?a com o novo Yahoo! Messenger http://br.messenger.yahoo.com/ From varvenne at genoway.com Thu Apr 26 11:28:40 2007 From: varvenne at genoway.com (Benoit VARVENNE) Date: Thu, 26 Apr 2007 17:28:40 +0200 Subject: [BiO BB] Can you explain theses results? In-Reply-To: <933937.26619.qm@web52411.mail.re2.yahoo.com> Message-ID: Hi Daniel, Have you thought about the limit of hits while running a Blast ? I mean that the default limit is (I think) 500hits for a query so, if you reach this limit, the Blast is stopped and the results returned. I think this can explain that there is less time of execution when you reach these 500hits. While running a remote Blast, I think this limit can be changed but I don't remember what's the option. Hope this will help, Cheers Beno?t -- Benoit Varvenne, Bioinformatics, GenOway - Lyon (France) Le 26/04/07 17:08, ??Daniel Xavier de Sousa?? a ?crit?: > Hi for all > > Please, you would see theses tests in serial machine, but important to > cluster. > What do you think about it? > > Please look theses tests using BLASTP: > > Length Seq Query -- HITs -- TIME > 10000 -- 3 -- 8min51sec > 10000 -- 500 -- 7min41sec > ---------------------------------- > Length Seq Query -- HITs -- TIME > 9000 -- 2 -- > 7min11sec > 9000 -- 500 -- 6min49sec > ---------------------------------- > Length Seq Query -- HITs -- TIME > 3000 -- 3 -- 2min54sec > 3000 -- 500 -- 2min52sec > > Theses > times are very strange. You can see which the sequence of 10000 bases > and 3 hits get more time than another sequence of 10000 bases but with > 500 hits. So, I can conclude: BLASTP is not sensitive to similarity, > difference of BLASTN. > > But the most important, why this happened? Can anybody explain theses results? > > Thanks for all > Daniel > > > ***************************************************************** > * Daniel Xavier de Sousa * > * Mestrando em Inform?tica - PUC-Rio * > * E-MAIL : dsousaARROBAinf.puc-rio.br * > * Fone : +55 21 35271500 - 4543 * > **************************************************************** > > > > __________________________________________________ > Fale com seus amigos de gra?a com o novo Yahoo! Messenger > http://br.messenger.yahoo.com/ > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From Michael.Muratet at operon.com Thu Apr 26 12:05:09 2007 From: Michael.Muratet at operon.com (Michael Muratet US-Huntsville) Date: Thu, 26 Apr 2007 11:05:09 -0500 Subject: [BiO BB] Can you explain theses results? In-Reply-To: <933937.26619.qm@web52411.mail.re2.yahoo.com> Message-ID: > > Hi for all > > Please, you would see theses tests in serial machine, but important to > cluster. > What do you think about it? > > Please look theses tests using BLASTP: > > Length Seq Query -- HITs -- TIME > 10000 -- 3 -- 8min51sec > 10000 -- 500 -- 7min41sec > ---------------------------------- > Length Seq Query -- HITs -- TIME > 9000 -- 2 -- > 7min11sec > 9000 -- 500 -- 6min49sec > ---------------------------------- > Length Seq Query -- HITs -- TIME > 3000 -- 3 -- 2min54sec > 3000 -- 500 -- 2min52sec > > Theses > times are very strange. You can see which the sequence of 10000 bases > and 3 hits get more time than another sequence of 10000 bases but with > 500 hits. So, I can conclude: BLASTP is not sensitive to similarity, > difference of BLASTN. > > But the most important, why this happened? Can anybody explain theses > results? > Daniel Without knowledge of the parameters and data you used I can offer you a couple of comments. The BLAST heuristic operates in a several steps. First, the query and the targets are broken up into tokens based on the word size you select. The default size is ll for nucleotides and 4 for proteins (I think--check the man page). The targets are then searched for tokens that match tokens in the query. The matches are used to seed alignments performed with the Smith-Waterman algorithm. The bottom line is that how long a given run takes is a complicated function of the parameters and the data. I recall there was a paper in Bioinformatics that calculated the computational complexity, but I can't lay my hands on it at the moment. You'll notice that the time is dominated by query length, i.e., the time it takes to search for matches. The difference in the time for hits depends on how long the hits were. There's a good description of blast in the book Bioinformatics by David Mount. I would also recommend the book Blast by Korf, Yandell, and Bedell. It has a whole chapter on setting parameters for various types of searches. (You should never just use the defaults unless, of course, they are correct for the search you are doing ;-) ). Also, there are several different implementations of blast (NCBI and WUBLAST being the two most popular, I think) that perform differently under different circumstances. There is a parallelized version called mpiBlast and at least one hardware-accelerated version that I know of. Good Luck Mike From bhakti.dwivedi at gmail.com Thu Apr 26 12:41:35 2007 From: bhakti.dwivedi at gmail.com (Bhakti Dwivedi) Date: Thu, 26 Apr 2007 11:41:35 -0500 Subject: [BiO BB] how transition to transversion rate ratio (kappa) related to phylogenetic accuracy? Message-ID: Hello everyone, What could be your opinion on the relationship between transition to transversion rate ratio (kappa) and phylogenetic accuracy? Does the accuracy always decrease with increase in kappa? Can you think of a situation where we could see an increase in accuracy with increase in kappa. If so, then when and why? Thank you. Bhakti From danielucg at yahoo.com.br Thu Apr 26 13:14:22 2007 From: danielucg at yahoo.com.br (Daniel Xavier de Sousa) Date: Thu, 26 Apr 2007 10:14:22 -0700 (PDT) Subject: Res: [BiO BB] Can you explain theses results? Message-ID: <228482.78859.qm@web52412.mail.re2.yahoo.com> Hi Mike, Thanks for your reply. I know this steps of blast, and is because theses I think to be strange theses results. I believe which for 2 sequence of same length, but one more similar than other, the most similar get more time to process. But when I run BLASTP this is not happen. I used default parameter of NCBI_BLAST, in serial machine. The database was all NR. What do you think about? Daniel ***************************************************************** * Daniel Xavier de Sousa * * Mestrando em Inform?tica - PUC-Rio * * E-MAIL : dsousaARROBAinf.puc-rio.br * * Fone : +55 21 35271500 - 4543 * **************************************************************** ----- Mensagem original ---- De: Michael Muratet US-Huntsville Para: General Forum at Bioinformatics.Org Enviadas: Quinta-feira, 26 de Abril de 2007 13:05:09 Assunto: RE: [BiO BB] Can you explain theses results? > > Hi for all > > Please, you would see theses tests in serial machine, but important to > cluster. > What do you think about it? > > Please look theses tests using BLASTP: > > Length Seq Query -- HITs -- TIME > 10000 -- 3 -- 8min51sec > 10000 -- 500 -- 7min41sec > ---------------------------------- > Length Seq Query -- HITs -- TIME > 9000 -- 2 -- > 7min11sec > 9000 -- 500 -- 6min49sec > ---------------------------------- > Length Seq Query -- HITs -- TIME > 3000 -- 3 -- 2min54sec > 3000 -- 500 -- 2min52sec > > Theses > times are very strange. You can see which the sequence of 10000 bases > and 3 hits get more time than another sequence of 10000 bases but with > 500 hits. So, I can conclude: BLASTP is not sensitive to similarity, > difference of BLASTN. > > But the most important, why this happened? Can anybody explain theses > results? > Daniel Without knowledge of the parameters and data you used I can offer you a couple of comments. The BLAST heuristic operates in a several steps. First, the query and the targets are broken up into tokens based on the word size you select. The default size is ll for nucleotides and 4 for proteins (I think--check the man page). The targets are then searched for tokens that match tokens in the query. The matches are used to seed alignments performed with the Smith-Waterman algorithm. The bottom line is that how long a given run takes is a complicated function of the parameters and the data. I recall there was a paper in Bioinformatics that calculated the computational complexity, but I can't lay my hands on it at the moment. You'll notice that the time is dominated by query length, i.e., the time it takes to search for matches. The difference in the time for hits depends on how long the hits were. There's a good description of blast in the book Bioinformatics by David Mount. I would also recommend the book Blast by Korf, Yandell, and Bedell. It has a whole chapter on setting parameters for various types of searches. (You should never just use the defaults unless, of course, they are correct for the search you are doing ;-) ). Also, there are several different implementations of blast (NCBI and WUBLAST being the two most popular, I think) that perform differently under different circumstances. There is a parallelized version called mpiBlast and at least one hardware-accelerated version that I know of. Good Luck Mike _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board __________________________________________________ Fale com seus amigos de gra?a com o novo Yahoo! Messenger http://br.messenger.yahoo.com/ From phoebe at deakin.edu.au Thu Apr 26 19:21:53 2007 From: phoebe at deakin.edu.au (Phoebe Chen) Date: Fri, 27 Apr 2007 09:21:53 +1000 Subject: [BiO BB] FIRST CALL FOR PAPERS - APBC 2008 Message-ID: <5.1.1.5.2.20070427091012.053444e0@mail.deakin.edu.au> ************************************************** FIRST CALL FOR PAPERS - APBC 2008 The Sixth Asia-Pacific Bioinformatics Conference, APBC2008, will be held in Kyoto, Japan, during 14-17 January 2008. See http://bic.kyoto-u.ac.jp/apbc2008/ **************************************************** The Asia-Pacific Bioinformatics Conference series is an annual forum for exploring research, development, and novel applications bioinformatics. The aim of this conference is to bring together researchers, professionals, and industrial practitioners for interaction and exchange of knowledge and ideas. We invite submissions that address conceptual and practical issues of bioinformatics. IMPORTANT DATES Submission of papers 20 July 2007 Notification of paper acceptance 17 September 2007 Submission of posters 30 September 2007 Camera-ready copy & Author registration 30 September 2007 Notification of poster acceptance 20 October 2007 Conference 14-17 January 2008 From mariopradeep at gmail.com Fri Apr 27 10:39:08 2007 From: mariopradeep at gmail.com (pradeep chowriappa) Date: Fri, 27 Apr 2007 09:39:08 -0500 Subject: [BiO BB] Protein Surface Extraction Message-ID: Hi, I am new to this list. I am currently involved in Active site identification over the surface of a protein and would like to know the different mesh based protein surface extraction tools available. Thanks in advance Mario From christoph.gille at charite.de Sat Apr 28 05:04:10 2007 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Sat, 28 Apr 2007 11:04:10 +0200 (CEST) Subject: [BiO BB] Protein Surface Extraction In-Reply-To: References: Message-ID: <63108.84.190.19.190.1177751050.squirrel@webmail.charite.de> A former colleague developed a system called alpha-shape. I could send the package if you like. > Hi, > > I am new to this list. I am currently involved in Active site identification > over the surface of a protein and would like to know the different mesh > based protein surface extraction tools available. > > Thanks in advance > > Mario From mariopradeep at gmail.com Sat Apr 28 10:42:27 2007 From: mariopradeep at gmail.com (pradeep chowriappa) Date: Sat, 28 Apr 2007 09:42:27 -0500 Subject: [BiO BB] Protein Surface Extraction In-Reply-To: <63108.84.190.19.190.1177751050.squirrel@webmail.charite.de> References: <63108.84.190.19.190.1177751050.squirrel@webmail.charite.de> Message-ID: Certainly! it would help. Thanx On 4/28/07, Dr. Christoph Gille wrote: > > A former colleague developed a system called alpha-shape. > I could send the package if you like. > > > Hi, > > > > I am new to this list. I am currently involved in Active site > identification > > over the surface of a protein and would like to know the different mesh > > based protein surface extraction tools available. > > > > Thanks in advance > > > > Mario > > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Pradeep Chowriappa, Lab Manager, DMRL, Louisiana Tech University. From lichunjiang at sibs.ac.cn Sat Apr 28 05:22:08 2007 From: lichunjiang at sibs.ac.cn (lichunjiang) Date: Sat, 28 Apr 2007 17:22:08 +0800 (CST) Subject: [BiO BB] discrepancy between probe sets for same gene in microarray Message-ID: <4596.10.10.118.126.1177752128.squirrel@webmail.sibs.ac.cn> Dear colleagues, ?????? I’m now dealing with microarray data and I encounter a problem as following: Quite sometime multiple probe sets are adopted for a same gene, while data produced with these multiple probe sets does not agree with each other well, sometimes, they are quite different even shows a contrary change trends. I wonder how does this happen and what should do to deal with the problem. Thanks for your help! Cheers, ? Lichun ? -- lichunjiang at sibs.ac.cn Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences From forward at hongyu.org Mon Apr 30 12:54:31 2007 From: forward at hongyu.org (Hongyu Zhang) Date: Mon, 30 Apr 2007 09:54:31 -0700 (PDT) Subject: [BiO BB] GCG gap program and emboss Message-ID: <87614.55710.qm@web51403.mail.re2.yahoo.com> Dear all, I am wondering which program in the EMBOSS package is closest to the GCG gap program? and how similar is their performance in terms of sequence alignment and score? Thanks! Hongyu From crishnakh at gmail.com Mon Apr 30 13:02:53 2007 From: crishnakh at gmail.com (Francisco G.P.) Date: Mon, 30 Apr 2007 19:02:53 +0200 Subject: [BiO BB] hi, I'm Fran from Spain and I'm trying to make a website about bioinformatics & biology tools (web based) Message-ID: <4636213D.2050206@gmail.com> Hi, my name is Fran and I'd like to talk about bioScripts (http://www.bioscripts.net). It's a website about bioinformatic and biology, and it grows slowly because I'm alone in the proyect. I'd like to make a dictionary of biology terms (BioDic, http://www.bioscripts.net/biodic/) that include terms in other languajes, it is working in beta version, and only in Spanish but coming soon I'll try to implement other languajes, I need more time to make all the things I want. Ther are a lot of proyects I want to continue as "Yerbarium" a system to menage your colecctions of plants, a data base to introduce plants from all kind of places and his determinations keys (sorry for my english, i'm spanish). Other proyects are "Randorium", BioQuotes, Biotheory, BioInfo (a Biowiki), BioBio (biographies)... and more. If someone is interested in this proyect and want to participate, only have to send me a e-mail... PD: Sorry for my English, I'm spanish (again)