From pascual at cnb.csic.es Fri Jan 2 16:43:37 2009 From: pascual at cnb.csic.es (Alberto Pascual Montano) Date: Fri, 2 Jan 2009 22:43:37 +0100 Subject: [BiO BB] gene expression software for mere biologists? References: <200812221039.40453.harry.mangalam@uci.edu><003201c964d1$949476f0$bdbd64d0$@ac.il><200812231422.50130.harry.mangalam@uci.edu> <005d01c965cf$7e682580$7b387080$@ac.il> Message-ID: <80C0A96D444A40E7A904627CADA70F9C@pitts> Tibco Spotfire has recently released Integromics Biomarker Discovery for their new software platform: http://spotfire.tibco.com/news/press_releases/detail.cfm?id=7597 You can check the product at: http://www.integromics.com/IBD.php Regards, Alberto ----- Original Message ----- From: "Vered Caspi" To: "'Harry Mangalam'" ; "'General Forum at Bioinformatics.Org'" Sent: Wednesday, December 24, 2008 2:57 PM Subject: Re: [BiO BB] gene expression software for mere biologists? > Dear Harry, > >>Does Spotfire still support gene expression? > It seems they do. > > I am using SpotFire DecisionSite for Functional Genomics: > http://spotfire.tibco.com/products/decisionsite_functional_genomics.cfm > > They also have a newer software with more advanced statistics for > microarray analysis: > SpotFire DecisionSite for Microarray Analysis: > http://spotfire.tibco.com/solutions/life_sciences/biomarker_discovery.cfm > > With best regards, > Vered > > ______________________________________________________________ > Vered Caspi, Ph.D. > Bioinformatics Core Facility, Head > National Institute for Biotechnology in the Negev > Building 39, room 214 > Ben-Gurion University of the Negev > Beer-Sheva 84105, Israel > > Email: veredcc at bgu.ac.il > Tel: 08-6479034 054-7915969 > Fax: 08-6472983 > > http://bioinfo.bgu.ac.il > ______________________________________________________________ > > -----Original Message----- > From: Harry Mangalam [mailto:harry.mangalam at uci.edu] > Sent: Wednesday, December 24, 2008 12:23 AM > To: bbb at bioinformatics.org > Cc: Vered Caspi > Subject: Re: [BiO BB] gene expression software for mere biologists? > > Thanks very much for taking the time to comment. > > Does Spotfire still support gene expression? I went to their website > but couldn't find anything related - it looks like they're trying to > become SAS (business intelligence, decision support) just as SAS is > trying to be Spotfire (with JMP/Genomics). > > Expander looks interesting - the > 1st time I've heard of it. > > hjm > > > On Monday 22 December 2008, Vered Caspi wrote: >> Hello, >> I highly recommend Partek, Spotfire (both commercial), Expander >> (mainly clustering and functional analysis) and GSEA (functional >> analysis) Vered >> >> ______________________________________________________________ >> Vered Caspi, Ph.D. >> Bioinformatics Core Facility, Head >> National Institute for Biotechnology in the Negev >> Building 39, room 214 >> Ben-Gurion University of the Negev >> Beer-Sheva 84105, Israel >> >> Email: veredcc at bgu.ac.il >> Tel: 08-6479034 054-7915969 >> Fax: 08-6472983 >> >> http://bioinfo.bgu.ac.il >> ______________________________________________________________ >> >> -----Original Message----- >> From: bbb-bounces at bioinformatics.org >> [mailto:bbb-bounces at bioinformatics.org] On Behalf Of Harry Mangalam >> Sent: Monday, December 22, 2008 8:40 PM >> To: BBB >> Subject: [BiO BB] gene expression software for mere biologists? >> >> Hi All, >> >> This may be a difficult query for this group to answer as the >> readership is canted heavily in the geek direction, but what gene >> expression software are you and your users relying on for gene >> expression and pathway analysis? >> >> I tilt heavily towards R/Bioconductor and other free software, so >> I'm aware of the advantages of it, but we have non-commandline tool >> researchers who are in need of tools they can use to examine the >> results of gene expression studies. >> >> This is something of a no-win - those tools that are very easy to >> use tend to hide the very complexity that the user has to address, >> and so the 'ease of use' / 'ease of thought' tends to weaken an >> already iffy analysis. >> >> That said, are there tools (commercial or free) that provide fairly >> good tradeoffs between power and ease of use for a non-geek >> biologist user. ie runs on Mac & Windows and is mostly GUI? (If >> you have experience in introducing such users to R, I'd also be >> interested in your experiences). >> >> Due to some aggressive pushing from the local SAS consulting group, >> we are in the startup phase of a campus-wide, 1 year trial of >> JMP/Genomics. JMP is a fairly cheap, nicely designed, >> multiplatform GUI stats package from SAS. The Genomics part tho is >> an expensive add-on that runs only on Windows and depends on an >> optional, even more expensive Pathways package from InGenuity. The >> local research community does not have a problem paying for such >> software if it truly does work easily and well. If you have used >> it and have an opinion or evaluation, I'd love to hear from you via >> email or phone. >> >> Harry > > > > -- > Harry Mangalam - Research Computing, NACS, E2148, Engineering Gateway, > UC Irvine 92697 949 824-0084(o), 949 285-4487(c) > --- > Good judgment comes from experience; > Experience comes from bad judgment. [F. Brooks.] > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb From alexander.kel at biobase-international.com Sat Jan 3 07:32:29 2009 From: alexander.kel at biobase-international.com (Alexander Kel) Date: Sat, 3 Jan 2009 13:32:29 +0100 Subject: [BiO BB] gene expression software for mere biologists? In-Reply-To: <200812221039.40453.harry.mangalam@uci.edu> References: <200812221039.40453.harry.mangalam@uci.edu> Message-ID: <89c69d9b0901030432j5e1f1775i69967458673b28c1@mail.gmail.com> Hi Harry, you may try the software called ExPlain http://www.biobase.de/index.php?id=286 There is a free trial at: http://www.biobase.de/index.php?id=456 My team from Russia and Germany have developed it. Perhaps, you will like it. If you have any question dont hesitate to drop me a line. All the best, Alexander Kel Alexander Kel, PhD SVP R&D BIOBASE GmbH, Halchtersche Strasse 33 D-38304 Wolfenbuettel Phone: +49 (0) 5331-8584-41 Fax: +49 (0) 5331-8584-70 www.biobase.de ake at biobase.de On Mon, Dec 22, 2008 at 7:39 PM, Harry Mangalam wrote: > Hi All, > > This may be a difficult query for this group to answer as the > readership is canted heavily in the geek direction, but what gene > expression software are you and your users relying on for gene > expression and pathway analysis? > > I tilt heavily towards R/Bioconductor and other free software, so I'm > aware of the advantages of it, but we have non-commandline tool > researchers who are in need of tools they can use to examine the > results of gene expression studies. > > This is something of a no-win - those tools that are very easy to use > tend to hide the very complexity that the user has to address, and so > the 'ease of use' / 'ease of thought' tends to weaken an already iffy > analysis. > > That said, are there tools (commercial or free) that provide fairly > good tradeoffs between power and ease of use for a non-geek biologist > user. ie runs on Mac & Windows and is mostly GUI? (If you have > experience in introducing such users to R, I'd also be interested in > your experiences). > > Due to some aggressive pushing from the local SAS consulting group, we > are in the startup phase of a campus-wide, 1 year trial of > JMP/Genomics. JMP is a fairly cheap, nicely designed, multiplatform > GUI stats package from SAS. The Genomics part tho is an expensive > add-on that runs only on Windows and depends on an optional, even > more expensive Pathways package from InGenuity. The local research > community does not have a problem paying for such software if it > truly does work easily and well. If you have used it and have an > opinion or evaluation, I'd love to hear from you via email or phone. > > Harry > > -- > Harry Mangalam - Research Computing, NACS, E2148, Engineering Gateway, > UC Irvine 92697 949 824-0084(o), 949 285-4487(c) > --- > Good judgment comes from experience; > Experience comes from bad judgment. [F. Brooks.] > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- From dan.bolser at gmail.com Mon Jan 5 15:39:16 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 5 Jan 2009 20:39:16 +0000 Subject: [BiO BB] Difference between Protein Interaction Network (PIN) and Protein-Protein Interaction Network (PPIN) In-Reply-To: <215bd4440812222025s375b949ft1e221feb3fb05ae8@mail.gmail.com> References: <215bd4440812222025s375b949ft1e221feb3fb05ae8@mail.gmail.com> Message-ID: <2c8757af0901051239x44375702x83b7e4c33cbaa47a@mail.gmail.com> 2008/12/23 Ashwathy : > dear friends, > please help me to find answer to some queries.... > > Is there any difference between Protein Interaction Network (PIN) and > Protein-Protein Interaction Network (PPIN) ? > If so please help me to find what the difference is.. No, its just two different names for the same idea. > and also, > is there any advantages other than finding the connectivity of the protein, > by investigating the PIN? I mean whether it is possible to explore the > attributes (both structural and functional) of a protein through it's PIN? Yes, there are lots of ideas. For example, some people say that highly connected proteins are more likely to be essential, or evolve slower. The 'guilt by association' method is a way to infer protein function or structure from the known function or structure of its interacting partners. There are lots of papers (sorry I didn't reference any here). Dan. > Aswathi > Centre for Bioinformatics > Kerala University > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From smcardwe at ucalgary.ca Mon Jan 12 14:13:42 2009 From: smcardwe at ucalgary.ca (Susanne Cardwell) Date: Mon, 12 Jan 2009 12:13:42 -0700 Subject: [BiO BB] Applied Computational Genomics Course Message-ID: <5D9E5650B3CF4F83AB5475820809AF81@coe022> Dear Sir or Madam, The Bioinformatics Platform (BIP) is offering the Applied Computational Genomics Course (ACGC) to Bioinformatics/ Biology researchers and students as well as to doctors and residences. The ACGC runs full-days from July 14th to July 20th in Calgary, Alberta, Canada. Featuring instruction from some of the best bioinformaticians across Canada on software applications such as BioMoby, Birch, Bluejay, Helpdesk, and more, we are confident that this course will be of benefit to you, your staff and colleagues, or any graduate students you may know. For additional information, please visit our website at http://www.gcbioinformatics.ca/training or contact Administrative Coordinator Susanne Cardwell at smcardwe at ucalgary.ca. Also, if possible, we are asking your assistance to help advertise ACGC via your email, newsletters, or website. Please see the brief description of the ACGC below which I am hoping you will circulate (by posting) throughout your faculty, department, or place of work. If you would like to have a one-page poster or a four-page handout to distribute or to keep for your own purposes, please do not hesitate to email me at smcardwe at ucalgary.ca or training at gcbioinformatics.ca with "ACGC" in the subject line. I would be more that happy to provide you with more information. Feel free to contact me at smcardwe at ucalgary.ca (Subject: ACGC Course Information) with any questions, comments, or feedback. Thank you in advance for your assistance! Susanne Marie Cardwell, Administrative Coordinator Bioinformatics Platform Genome Alberta ACGC dedicated to EMPOWERING biologists, bioinformaticians, students, and researchers to become POWER USERS of the Bioinformatics Platform. Leverage the power of Unix for managing data; learn to write quick Perl scripts that get the job done; become proficient in using bioinformatics software and services. This week long course, running from July 14th to July 20th in Calgary, Alberta, will assist researchers, students, doctors, and residences to increase their efficiency in problem solving by introducing them to the tools and services of the Bioinformatics Platform, including: * The advantages of using a UNIX environment, * BIRCH (Biological Research Computer Hierarchy), * Bluejay * BioMoby, * Help Desk services and programs * And more The course fee is $1250.00 for early bird (before June 1st) Canadian registrants; $1500.00 for early bird non-Canadian registrants; $1750.00 for late Canadian registrants (on or after June 1st): and $2000.00 for late non-Canadian registrants. Snack breaks, lunches, and course materials are included in the above listed fee structure. After the course, attendees of the ACGC will have FREE internet access to all the Bioinformatics Platform tools and databases used in this course. For additional information, posters, or a registration form, please email Susanne Cardwell at smcardwe at ucalgary.ca. Alternatively, for more information (or to access the registration form), please visit http://www.gcbioinformatics.ca/training. From nolanfyh at gmail.com Sun Jan 18 04:53:18 2009 From: nolanfyh at gmail.com (Fan Yanhui) Date: Sun, 18 Jan 2009 17:53:18 +0800 Subject: [BiO BB] How to align orthologous introns? Message-ID: <949af86e0901180153l42c17079ub192b30e60c95c6b@mail.gmail.com> Dear all, I am going to do multiple alignment of orthologous introns, which software should I use? Clustal W or R-coffee or some other better softwares? Thanks! Yanhui Fan From jprudhomme at healthtech.com Tue Jan 20 11:36:09 2009 From: jprudhomme at healthtech.com (Jim Prudhomme) Date: Tue, 20 Jan 2009 11:36:09 -0500 Subject: [BiO BB] Integrated R&D Informatics Systems Message-ID: <00c401c97b1d$33e20bd0$9ba62370$@com> Advance Registration Discount Ends this Friday! Cambridge Healthtech Institute's Inaugural Adopting Integrated R&D Informatics Systems Data Management & Integration - How Far Have We Come? February 25-27, 2009 | Moscone North Convention Center | San Francisco, California Track 9 at CHI's 16th International Molecular Medicne Tri-Conference (www.Tri-Conference.com) * PDF Brochure http://www.tri-conference.com/dload_ird_brochure.asp * Register by January 23 and Save up to $200 https://chidb.com/register/2009/mmtc/reg.asp * Four Additional Ways To Save! - 25% discount for Tri-Conference alumni - 25% discount for BayBio members - Save $75 by staying at the host hotel - Save $50 by submitting a poster - deadline January 23, 2009 * Brand New - Tri-Conference Event Blog www.tri-conference.com/triblog.asp AGENDA-AT-GLANCE: Wednesday, February 25 PLENARY KEYNOTE Therapy Development in a Networked World Jay M. Tenenbaum, Ph.D., Chairman and Chief Scientist, CollabRx, Inc. Scientific Workflows as Productivity Tools for Drug Discovery John Shon, MD, Ph.D., Site Head, In Silico Sciences, Roche The Role of Informatics and Genomics to Drive Innovation in Pharma Jakob DeVlieg, Ph.D., Global Head Molecular Design & Informatics, Molecular Design & Informatics, Schering-Plough Evolution of an Innovation Model to Support Pharma R&D Martin D. Leach, Ph.D., Executive Director, MRL IT Basic Research & Biomarkers, Merck & Co. Inc. RIS? ? Research Informatics System at RIS? Ajay Shah, Ph.D., M.B.A., P.M.P., Director, Research Informatics, Elan Pharmaceuticals Inc. Resource Management Strategies Impacting Systems Integration in R&D David M. Sedlock, Ph.D.. Senior Director, R&D Systems, Millennium Pharmaceuticals The TAKEDA Oncology Company Democratized Serendipity: Leveraging Consumer-Oriented Technologies into Better R&D and Better Health Care Decisions Joseph A. Cerro, President, The Schooner Group, LLC Executive Panel: Integrated R&D, How Far Have We Come? Moderator: Susan J. Ward, Ph.D.,Executive Advisor, Biotechnology & Pharma Panelists: All of the above speakers Breakout Discussions in the Exhibit Hall Translational Informatics Moderator: John Russell * When you?re new to the translational informatics game, where?s the best place to start? * If you?re well into a project, how are you measuring results? * What organizational barriers and what technology challenges should you expect? * What?s the best approach for getting budget for new products? * How much of the enabling technology (hardware and software) can you buy and how much do you have to build yourself? * Does anyone have favorite tools in use today, and what make them effective? Knowledge Management Moderator: Susan Ward, Ph.D., Executive Advisor, Biotechnology & Pharma * How to capture, integrate, and make data accessible when and to whom it is needed * Capture and integrate gene-related information, & distribute the data across the company * Optimal or realistic decision making Effective Integration Strategies Moderator: Joseph A. Cerro, President & Founder, Schooner Group LLC * Driving Productivity * Driving Workflows * Managing resources * Managing costs Thursday, February 26 PLENARY KEYNOTE Tissue Engineering Strategies for Musculoskeletal Regenerative Medicine in Civilian and Military Applications Michael J. Yaszemski, Ph.D., M.D., Brigadier General, United States Air Force Reserves, Professor, Orthopedic Surgery and Biomedical Engineering, College of Medicine, Mayo Clinic Enterprise Information Integration to Inform Biomarker Discovery and Development: Clinical Patient, Biosample and Omics Data Gary Mallow, Ph.D., Director, Biomarker Programs, Information Services for Basic Research, Merck & Co., Inc. A Nationwide Network to Enable Translational Research Ken Buetow, Ph.D., NCI Associate Director, Bioinformatics and Information Technology and Director, Center for Biomedical Informatics and Information Technology, National Cancer Institute Translating Between Pre-clinical Data and Clinical Outcomes: Successes and Challenges Anastasia M. Khoury Christianson, Ph.D., Senior Director and Global Discipline Leader, Biomedical Informatics, AstraZeneca R&D Wilmington How to get the Most Out of Published Findings: Improving Information Flow and Knowledge Enrichment Throughout Discovery Ilya Mazo, Ph.D., President, Ariadne Scientific Informatics: The Integration of Information and Process to Achieve Knowledge Re-Use Frank K. Brown, Ph.D., Vice President & Chief Science Officer, Accelrys Integrated Informatics - Are We There Yet? Sandor Szalma, Ph.D., Director, R&D Informatics, Centocor R&D Inc. Panel: Bridging the Divide Moderator: John Russell PLENARY KEYNOTE Engineering Cells to Death James A. Wells, Ph.D., Professor and Chair of Pharmaceutical Chemistry, and Professor of Cellular & Molecular Pharmacology, University of California, San Francisco PLENARY KEYNOTE Brave New Age of Personalized Medicine David Ewing Duncan, Chief Correspondent, NPR Talk?s ?Biotech Nation? and Best Selling Author ?Masterminds? Tales from the Edge: Advanced Approaches to Knowledge Integration & Search Speaker to be announced, Roche Pharmaceuticals A Strategy for Internal-External Data and Information Integration Jason M. Johnson, Ph.D., Senior Director, Molecular Informatics, Merck & Co., Inc. Accelerating Research Through Information Exploitation Leslie S. Sloan, Ph.D., Senior Program Manager, Chemistry Research Informatics, Pfizer, Inc. Integrating Public and Private Data Reece Hart, Ph.D., Scientific Manager, Research Computing & Informatics, Genentech Inc. Friday, February 27 The Genomic Data Pipeline: Collecting, Cleaning, Analyzing, Integrating, Sharing Jeanette Papp, Ph.D., Associate Professor, Human Genetics, University of California, Los Angeles Surviving the Data Deluge: Informatics for Next Generation Sequencing Toby Bloom, Ph.D, Director of Informatics, Genome Sequencing Platform, The Broad Institute Integrating Public Genomics Data into Pharmaceutical R&D Hans-Martin Will, Ph.D., Senior Director, Genomics R&D, Rosetta Biosoftware Search Strategies for Correlating Combined Public and Internal Large-Scale Studies Ilya Kupershmidt, Cofounder and Vice President Products, NextBio Platform for the FDA Genetic Data Submission and Review Process Weida Tong, Ph.D., Director, Center for Toxicoinformatics, National Center for Toxicological Research, U.S. Food and Drug Administration Lilly?s Transition from Paper to Electronic Lab Notebooks Keith DeVries, Ph.D., Director, Chemical Product, R&D, Eli Lilly and Company, Lilly Research Labs Integration of Chemical Genomics and Structural Biology Informatics: Novel Insights into the Kinase Gene Family? Stephan Sch?rer, Ph.D., Department of Pharmacology, Miller School of Medicine & Center for Computational Science, University of Miami Techniques for Effective Integrated Access to Large Compound-oriented Drug Discovery Databases Michael, Lajiness, Ph.D., Research Scientist, Structural and Computational Sciences, Eli Lilly & Company PRE-CONFERENCE SHORT COURSE* Best Practices in Translational Medicine, Drug Discovery, and Informatics Tuesday, February 24 - 2:00 - 5:00 pm This course provides you with an inside look at several of the outstanding Best Practices presented as a part of the 2008 Bio-IT World Best Practices competition. Speakers will present their best practices, give updates to the program and discuss pushing innovation, increasing ROI, and implementing strategies that are the best in the industry. The forum will be invaluable for building the innovative partnerships and strategies that will keep pushing the industry forward. *Separate registration is required. Sponsorship & Exhibit Opportunities are Available For details, contact: Carol Dinerstein at 781-972-5471, dinerstein at healthtech.com OR John Stroup at 781-972-5483, stroup at healthtech.com Group Discounts are Available For details, contact: David Cunningham at 781-972-5472, cunningham at healthtech.com www.tri-conference.com/09_ird.asp Posted by: James Prudhomme Marketing Manager Cambridge Healthtech Institute 250 First Avenue, Suite 300 Needham, MA 02494 Direct: 781-972-5486 Fax: 781-972-5425 www.healthtech.com From djwild at indiana.edu Tue Jan 20 11:57:31 2009 From: djwild at indiana.edu (David Wild) Date: Tue, 20 Jan 2009 11:57:31 -0500 Subject: [BiO BB] Journal of Cheminformatics - Call for Papers Message-ID: <5eda63310901200857o498e9099we9e115e6d908d6ec@mail.gmail.com> Dear colleagues We are delighted to announce that the Journal of Cheminformatics is accepting submissions at www.jcheminf.com. Journal of Cheminformatics is a new Open Access journal published by Chemistry Central (www.chemistrycentral.com). The Editors-in-Chief for the journal are: Christoph Steinbeck, Head of Cheminformatics and Metabolism at the European Bioinformatics Institute, and David J. Wild, Assistant Professor of Informatics at the Indiana University School of Informatics. The journal is supported by a prestigious international Editorial Board ( http://www.jcheminf.com/edboard/). The Journal of Cheminformatics is devoted to the dissemination of new and original knowledge in all branches of cheminformatics and molecular modelling including but not limited to:- - chemical information systems, software and databases, and molecular modelling - chemical structure representations and their use in structure, substructure, and similarity searching of chemical substance and chemical reaction databases - computer and molecular graphics, computer-aided molecular design, expert systems, QSAR, and data mining techniques The Journal of Cheminformatics will publish high quality peer-reviewed research of specific interest to the cheminformatics community. As well as providing open access to published articles, the journal will strive to respond to emerging electronic technologies to enhance the display of scientific data. The new journal will benefit the scientific community by providing a valuable forum for the dissemination of research in cheminformatics. The multi-disciplinary nature of cheminformatics research makes the benefits of open access particularly attractive, as it ensures that researchers working on different aspects will all have shared access to the latest research. You are invited to submit your research to Journal of Cheminformatics at www.jcheminf.com. The journal offers high-quality peer review, online submission and immediate publication on acceptance. There is currently no article-processing charge due on manuscripts submitted before 30th April 2009. For more information about the journal, please contact editorial at jcheminf.com or visit the journal website www.jcheminf.com. Best wishes, Christoph Steinbeck Head of Cheminformatics & Metabolism European Bioinformatics Institute steinbeck at ebi.ac.uk David J Wild Assistant Professor of Informatics Indiana University djwild at indiana.edu Editors-in-Chief ? Journal of Cheminformatics From jeff at bioinformatics.org Tue Jan 20 16:49:01 2009 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Tue, 20 Jan 2009 16:49:01 -0500 Subject: [BiO BB] Reminder: dChip Boston Message-ID: <497646CD.4010500@bioinformatics.org> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- dChip for Gene Expression and SNP Microarray Data Analysis Boston, Massachusetts January 26-28, 2009 http://wiki.bioinformatics.org/BI201C_dChip -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- (Please share this with others who might be interested.) The Bioinformatics Organization (Bioinformatics.Org) will hold a 3-day workshop on gene expression analysis and SNP microarray data analysis using the dChip software (www.dchip.org) developed by Harvard University Associate Professor Cheng Li. This hands-on course in Boston will teach the workings of the dChip application and cover topics such as importing arrays, performing normalization, model based expression calculations, gene and SNP filtering, clustering, linkage, LOH and copy number analysis. COURSE OUTLINE: Session 1: Gene Expression Analysis: Preparing to import CEL and CHP exported txt files, with basic actions such as normalization and model-based expression index calculations. Re-importing saved "DCP" files and importing expression indices from saved text files. Use of array list file, sample information file, dChip data file list. Session 2: Gene Expression Analysis: Case studies with comparison of two groups, gene filtering and clustering Session 3: Gene Expression Analysis: Case studies with ANOVA, correlation, enrichment and classification Session 4: Gene Expression Analysis: Resampling, manipulating trees, gene function enrichment, pathways, FDR, combine comparisons Session 5: SNP Array Analysis: Preparing to import CEL and CHP exported txt files, with basic actions such as normalization and model-based expression index calculations for copy number analysis; re-importing saved "DCP" files and importing genotypes and SNP signals from saved text files; use of array list file and sample information file. Session 6: SNP Array Analysis: LOH and copy number analysis with sample data; export. Session 7: SNP Array Analysis: Intricacies of copy number and LOH analysis, parameters used Session 8: SNP Array Analysis: Allele sharing analysis, linkage analysis; automation in dChip INSTRUCTORS: Prof. Cheng Li, Dana Farber Cancer Institute and Harvard School of Public Health, author of dChip Shailender Nagpal, Bioinformatics Organization and Tanisha Systems FOR MORE INFORMATION: http://wiki.bioinformatics.org/BI201C_dChip (Course TAA) Cheers, Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 978 562 4800 -- From idoerg at gmail.com Wed Jan 21 17:13:11 2009 From: idoerg at gmail.com (Iddo Friedberg) Date: Wed, 21 Jan 2009 14:13:11 -0800 Subject: [BiO BB] SCALABLAST download Message-ID: This is a bit embarrassing... can anybody tell me where I can download SCALABLAST? Or is it stilllsomething internal to PNL? Thanks, Iddo -- Iddo Friedberg, Ph.D. Atkinson Hall, mail code 0446 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0446, USA T: +1 (858) 534-0570 http://iddo-friedberg.org From gigi at biocomp.unibo.it Thu Jan 22 08:50:56 2009 From: gigi at biocomp.unibo.it (Pier Luigi Martelli) Date: Thu, 22 Jan 2009 14:50:56 +0100 Subject: [BiO BB] COMPBIO'09 call for papers: extended deadline Message-ID: <497879C0.8030206@biocomp.unibo.it> Announcement: Paper submission deadline extended to February 6th. ---------------------------------------------------------------------------------------------------------------------- Please consider to contribute and encourage your team members and fellow scientists to contribute to the following event. Breaking Frontiers of Computational Biology 2009 http://www.cs.unibo.it/~margara/compbio/index2.html Held in conjunction with 2009 ACM International Conference on Computing Frontiers http://www.computingfrontiers.org 18-20 May 2009 - Ischia, Italy In the post-genomic era the vast mass of biological data is growing more than ever before. The creation of automatic tools and techniques to organize, analyze and, most of all, unravel the underlying information is one of the most searched and less well solved problems in biological and computational sciences. Pushing forward current boundaries between existing solutions and innovative ideas is the only way to fill the gap between what we know and what we understand. The main goal of this workshop is to provide to researchers from computational and biological disciplines a meeting point to present and discuss their ideas and innovative solutions to old unsolved problems and new challenges concerning computational issues in biology, with a particular focus on heuristic and approximated algorithms, machine learning and other soft computing methods. Authors are invited to submit papers in one of the following technical areas: ? Automatic methods for analysis of biological data: sequence analysis, promoter analysis and identification of transcription factor binding sites, gene expression data analysis, alternative splicing analysis ? Methods for the unsupervised analysis, validation of structures discovered in bio-molecular data ? Prediction of protein structures ? Methods for comparative genomics ? Algorithms for molecular evolution and phylogenetic analysis ? Mathematical modelling and simulation of biological systems ? Heterogeneous data integration and data fusion for diagnostics ? Bio-molecular databases and data mining ? Software tools for bioinformatics From mourad12345678 at yahoo.com Fri Jan 23 20:23:10 2009 From: mourad12345678 at yahoo.com (Mourad Elloumi) Date: Fri, 23 Jan 2009 17:23:10 -0800 (PST) Subject: [BiO BB] BIOKDD'09 / DEXA'09 CfP Message-ID: <405829.74147.qm@web31503.mail.mud.yahoo.com> CALL FOR PAPERS Higher School of Sciences and Technologies of Tunis (Tunisia) And Faculty of Applied Sciences, Bucharest (Romania) Organize Biological Knowledge Discovery from Databases (BIOKDD'09) Workshop held in parallel with 20th International Conference on Database and Expert Systems Applications (DEXA'09) www.dexa.org University of Linz, Austria August 31 - September 4, 2009 With the development of Biology during the last decades, we are witnessing an exponential growth of both the volume and the complexity of biological databases. For example, the Human Genome Project provided the sequence of the 3 billion DNA bases that constitute the human genome. And, consequently, we are provided too with the sequences of about 100,000 proteins. Therefore, we are entering the post-genomic era : After having focused so much efforts on the accumulation of biological data in databases, we have now to focus as much efforts, and even more, on the analysis of these data. Analyzing this huge volume of biological data stored in databases is a challenging task because, not only, of its complexity and its multiple numerous correlated factors, but also, because of the continuous evolution of our understanding of the biological structural and evolutionary mechanisms. Knowledge Discovery from Databases (KDD) is a response to these new trends. You are invited to submit a draft paper in PDF format before February 28, 2009 via DEXA'09 ConfDriver. Papers should not exceed 5 pages in IEEE format www.ieee.org/ web/publications /authors/ transjnl/ index.html All accepted papers will be published in the proceedings of DEXA?09 Workshops with IEEE CSP. One of the authors of an accepted paper must register to DEXA?09 conference and present the paper at BIOKDD?09 workshop. Program Committee: Mourad Elloumi, University of Tunis, Tunisia, (PC Chair) Cristian Toma, Politehnica University, Bucharest, Romania (PC Co-Chair) Jin-Kao Hao, University of Angers, France Beatrice Duval, University of Angers, France Abdelouahid Lyhyaoui. Abdelmalek Essaadi University, Tanger, Morocco El-Ghazali Talbi, University of Sciences and Techniques of Lille, France Xiangchao Gan, University of Oxford, UK Kathleen Steinh?fel, King's College London, UK Dragan Bosnacki, Eindhoven University of Technology, Netherlands Important Dates: Submission of Full Papers: February 28, 2009 Notification of Acceptance: May 10, 2009 Camera-ready Copies: May 31, 2009 From hlapp at gmx.net Mon Jan 26 22:52:59 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 26 Jan 2009 22:52:59 -0500 Subject: [BiO BB] Evolutionary Database Interoperability Hackathon Message-ID: <77FD397E-1571-4466-A127-35280EA16274@gmx.net> NESCent Hackathon on Evolutionary Database Interoperability OPEN CALL FOR PARTICIPATION The National Evolutionary Synthesis Center (NESCent; http:// nescent.org) is sponsoring an "Evolutionary Database Interoperability" hackathon aimed at enhancing the value (and raising the profile) of important community resources for evolutionary and biodiversity data by increasing their accessibility to users and software. We are broadly soliciting applications for participation from the community. More information about the event is available online at http://evoinfo.nescent.org/Database_Interop_Hackathon . A hackathon is an event at which a group of programmers who otherwise do not have the opportunity to interact on a routine basis meet with users and domain experts to collaboratively develop working code that is of utility to the community as a whole. The Database Interoperability Hackathon will bring together developers from a number of emerging standards for evolutionary data exchange (NeXML; http://nexml.org ), data and metadata semantics (CDAO; http://www.evolutionaryontology.org ), and programmatic access of evolutionary data providers (PhyloWS; http://evoinfo.nescent.org/PhyloWS) with database programmers and metadata experts from a variety of evolutionary and biodiversity community resources. In addition, the mix of people will include programmers of embeddable widgets, mash-up and aggregation applications that can showcase the value of the effort for research applications. We also welcome comments and suggestions for issues in database interoperability that could be addressed at the event but are not yet on our radar. Please email the organizers at hackathon3 at nescent.org with any suggestions you have. GOALS AND ACTIVITIES The focus of the programming aspect of the meeting will be to promote interoperability among online evolutionary databases through the following core set of activities. 1) Mapping the data and operation semantics of the participating online resources to an ontology, CDAO. 2) Implement a NeXML transformation for participating online resources as a formally defined query input and data output. 3) Implementation of programmable web-service interfaces following the emerging PhyloWS standard. 4) Showcase some of the possibilities that can arise from achieving data provider interoperability through small integration and/or mash- up oriented prototype applications. Supporting activities will include discussing input from end-users, discussing compliance with emerging reporting standards (MIAPA) and documentation of solutions and open problems on the hackathon wiki. ORGANIZATION The event will be 5 days in duration and will take place at NESCent in Durham, North Carolina, on March 9-13, 2009. Participant travel, accommodation, expenses for meals, etc, will be paid by NESCent. Logistical and travel details will be communicated to accepted and confirmed participants. The specific development targets will be selected by the participants through a hackathon wiki, a mailing list, and one or more conference calls. The exact agenda for the event will be developed similarly, but will be largely devoted to coding time. At the event itself, participants will self-organize into small subgroups (of 2-5) focused on particular targets. The NeXML, CDAO, and PhyloWS standards are products of the Evolutionary Informatics working group (http://evoinfo.nescent.org), under the auspices of whom this event is being organized. CALL FOR PARTICIPATION We invite all individuals interested in attending to apply by responding to the questions below. We specifically encourage applications from members of underrepresented groups, specifically women and minorities, and from graduate students and postdocs. 1. Please indicate if you would be available for all or only for part of the March 9-13 time period. 2. All code and documentation produced at the event is to be made available immediately under an OSI-approved open-source license or a Creative Commons license. Please indicate if this would pose any difficulty for your participation. 3. Please briefly describe your qualifications (programming languages, metadata standards, experience with data schemas, web-service programming, mash-up programming, etc). 4. Please state what you would most like to accomplish at the hackathon, given your current understanding. If you would not be writing software at the event, please state how you would like to contribute and how you would expect to benefit. 5. Please indicate if you are a member of an underrepresented group (including women, persons with disabilities, and any of the following minorities: African American, Hispanic, American Indian, Alaska Native, Native Hawaiian, and Pacific Islander). To apply, please enter your personal information and your responses by February 5 into the online form at http://spreadsheets.google.com/viewform?key=p6ikV0To6fXpJ369ozyNSSw&hl=en In addition, if possible please email a CV to the organizers at hackathon3 at nescent.org by the same deadline. If you are interested in participating but are unable to respond in full by that deadline, please let us know as soon as possible. Please understand that the funds as well as the space for this event are limited. We also need to balance a critical mass of developers in certain areas of expertise with a broad participation of different data providers, and so not all qualified applicants can be guaranteed acceptance. Yours, The Organizing Committee Arlin Stoltzfus, Rutger Vos (Evolutionary Informatics Working Group) Hilmar Lapp, Todd Vision (NESCent) Katja Schulz (Tree of Life) From nir at rosettadesigngroup.com Tue Jan 27 07:59:29 2009 From: nir at rosettadesigngroup.com (Nir London) Date: Tue, 27 Jan 2009 14:59:29 +0200 Subject: [BiO BB] Rosetta Academic Training Workshop Message-ID: Due to public demand, ?Rosetta Design Group? is organizing a ?Rosetta? software training workshop, aimed for academic groups. The format of the workshop will be a ?webinar? - a web seminar, enabling more groups to attend while avoiding the annoying jet lag and accommodation troubles. Would you be interested in participating? If so please fill the form located at: http://rosettadesigngroup.com/blog/rosetta-academic-workshop/ and we will contact you when the details are finalized.* Nir London | Rosetta Design Group http://rosettadesigngroup.com/ * If you?re not from an academic group, don?t worry, write us anyway?