From marty.gollery at gmail.com Mon Dec 1 01:34:43 2008 From: marty.gollery at gmail.com (Martin Gollery) Date: Sun, 30 Nov 2008 22:34:43 -0800 Subject: [BiO BB] informatics opportunity: "Human genomes in minutes?" In-Reply-To: References: Message-ID: Yes, all the people that are now working on building and improving tools for short read sequencing systems may find that these programs need to be thrown out or revamped before long. Marty On Fri, Nov 28, 2008 at 5:15 AM, Mike Marchywka wrote: > > > This is a rather obvious thing to try, > > http://www.nature.com/news/2008/081120/full/news.2008.1245.html > > Erika Check Hayden > > A much-watched Silicon Valley company has published a proof of concept for its DNA-sequencing technology, which it hopes will one day be going through entire human genomes in minutes. > Pacific Biosciences of Menlo Park, California, reports today that it can generate continuous stretches of DNA sequence up to thousands of base pairs long. > > > > But it may be something to watch for non-obvious bio-informatics opps. > Is anyone aware of particularly interesting efforts related to the above? > > > > > Mike Marchywka > 586 Saint James Walk > Marietta GA 30067-7165 > 415-264-8477 (w)<- use this > 404-788-1216 (C)<- leave message > 989-348-4796 (P)<- emergency only > marchywka at hotmail.com > Note: If I am asking for free stuff, I normally use for hobby/non-profit > information but may use in investment forums, public and private. > Please indicate any concerns if applicable. > Note: hotmail is getting cumbersom, try also marchywka at yahoo.com > _________________________________________________________________ > Access your email online and on the go with Windows Live Hotmail. > http://windowslive.com/Explore/Hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_access_112008 > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- -- Martin Gollery Senior Bioinformatics Scientist From marchywka at hotmail.com Mon Dec 1 19:27:35 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Mon, 1 Dec 2008 19:27:35 -0500 Subject: [BiO BB] Save protein structure image as an adobe SVG format file In-Reply-To: <2849EC40-0DE9-49B1-9657-59350FDF1B41@utoronto.ca> References: <1226534454.491b6e36e7d14@webmail.upv.es> <1226946262.4921b6d6b14d5@webmail.upv.es> <1227118784.492458c03ec5a@webmail.upv.es> <3E951E84-BE5A-42AC-A31F-BB16E240D52F@utoronto.ca> <2849EC40-0DE9-49B1-9657-59350FDF1B41@utoronto.ca> Message-ID: > From: boris.steipe at utoronto.ca > Date: Wed, 26 Nov 2008 17:33:39 -0500 > To: bbb at bioinformatics.org > Subject: Re: [BiO BB] Save protein structure image as an adobe SVG format file > >> Spheres aren't that hard for z-sorting, > > > Yes, a collection of atoms can be well approximated with a Z-sorted > stack of circles in 2D. But *molecules* are represented by > intersecting spheres and the line of intersection is a circle at an > arbitrary orientation relative to the viewer. It projects as an > ellipse, and part of the ellipse is occluded. > > Think "methane". I guess when I wrote sphere and posted the bounding volume link, I meant this, http://en.wikipedia.org/wiki/Sphere The rest of that stuff is non-trivial but hardly prohibitive. The intersecting ones are easy to find, the intersection can be solved with vector manipulation, ( I think this is 3 lines if you write a vector expression for a triangle consrained by sphere radii and distance, find the normal and radius or intersection- if you use vectors the orientation is really not important http://en.wikipedia.org/wiki/Vector ). etc. You could probably write a plugin or modify source for your favorite viewer if you are sold on this approach. > > (And working with ball and stick models, or even cartoon or mesh > representations, you'll start recoding much of what the 3D-viewer is > there to do in the first place.) > > BKchem is 2D chemical structure editor. > > > Again: Molscript produces postscript output. Postscript can be > converted to svg. > Obviously this would capture more of the capabilities of the viewer and you wouldn't have to guess about the matricies. Even without a program, you could probably write a script to do this pretty easily too :) If you are just making a document and don't really have detail at many levels, there is always ctrl-alt-printscreen. I would strongly suggest the model based approach where practical but in a pdf document I don't think you can salvage much anyway :) > _________________________________________________________________ Windows Live Hotmail now works up to 70% faster. http://windowslive.com/Explore/Hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_faster_112008 From rtanishya at gmail.com Tue Dec 2 01:14:57 2008 From: rtanishya at gmail.com (Jaya Handa) Date: Tue, 2 Dec 2008 11:44:57 +0530 Subject: [BiO BB] Query Message-ID: <22b4d0a80812012214q5581cebcsa806862883d094bb@mail.gmail.com> Hello Sir I wish to know when we read bacterial genomes in ncbi how do you number. Suppose the + starand is 5'-3' and - strand is 3'-5'. now if we number + trand as [5'] 1,2,3,4 [3'] bases then will the - strand be like [3'] 4,3,2,1 [5']. Suppose we read this source 1..2256640 /organism="Bifidobacterium longum NCC2705" /mol_type="genomic DNA" /strain="NCC2705" /db_xref="taxon:206672 " gene 49..288 /gene="cspA" /locus_tag="BL0001" CDS 49..288 /gene="cspA" /locus_tag="BL0001" /note="CspA; COG family: cold shock proteins; PFAM_ID: CSD" /codon_start=1 /transl_table=11 /product="cold shock protein" /protein_id="AAN23868.1 " /db_xref="GI:23325186" gene 526..2151 /gene="groEL" /locus_tag="BL0002" CDS 526..2151 /gene="groEL" /locus_tag="BL0002" /note="GroEL; COG family: chaperonin GroEL (Hsp60 family); PFAM_ID: cpn60_TCP1" /codon_start=1 /transl_table=11 /product="chaperone" /protein_id="AAN23869.1 " /db_xref="GI:23325187" gene complement(2248..2538) /locus_tag="BL0003" CDS complement(2248..2538) /locus_tag="BL0003" /note="COG family: methyl-accepting chemotaxis protein" /codon_start=1 /transl_table=11 /product="hypothetical protein" /protein_id="AAN23870.1 " /db_xref="GI:23325188" Now the complement will be read as continuation of 2151 then we read same for both +/- strand irrespective of its orientation. Please clarify me on this Thank You and waiting for your reply Jaya Handa From pandey.gaurav at gmail.com Tue Dec 2 14:04:41 2008 From: pandey.gaurav at gmail.com (Gaurav Pandey) Date: Tue, 2 Dec 2008 13:04:41 -0600 Subject: [BiO BB] protein function prediction using protein interaction network In-Reply-To: References: Message-ID: <627ca1900812021104r5eb7f491sa2a24409d0ea22f2@mail.gmail.com> Hi Huang, There are several easy to implement computational approaches to predict gene/protein function from interaction networks. Take a look at Section 8 of a survey we have written on function prediction techniques ( http://www-users.cs.umn.edu/~kumar/papers/survey.php), which discusses several such approaches for protein interaction networks. Also, feel free to contact me at gaurav at cs.umn.edu, and I might be able to share with you an implementation of the FunctionalFlow algorithm (Nabieva et al, ISMB 2005), which is popular for this problem. Good luck, Gaurav On Fri, Nov 28, 2008 at 7:27 AM, Kie Kyon Huang wrote: > hi everyone, > > i would like to know if anyone knows of software that can infer function > for > uncharacterised gene using protein interaction network? > > thanks > > Huang > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Gaurav Pandey Email: gaurav at cs.umn.edu Computer Science Department Webpage: www.cs.umn.edu/~gaurav University of Minnesota Tel: 612-701-2494 From tejalonline at gmail.com Wed Dec 3 04:18:53 2008 From: tejalonline at gmail.com (T Joshi) Date: Wed, 3 Dec 2008 10:18:53 +0100 Subject: [BiO BB] sequence clustering Message-ID: <11417a880812030118r2068613cvaee694193637a121@mail.gmail.com> Hi, I would like to know if there are any tools/software for clustering DNA sequences. I searched for them, but mostly I ended up with those which work on protein sequences. If there is any bioconductor package which also could work with sequence data, it would be good to know. Thanks Josh From marty.gollery at gmail.com Wed Dec 3 15:33:54 2008 From: marty.gollery at gmail.com (Martin Gollery) Date: Wed, 3 Dec 2008 12:33:54 -0800 Subject: [BiO BB] sequence clustering In-Reply-To: <11417a880812030118r2068613cvaee694193637a121@mail.gmail.com> References: <11417a880812030118r2068613cvaee694193637a121@mail.gmail.com> Message-ID: There are many programs for clustering ESTs or other nucleic sequences. Try blastclust, D2 or Cap3 for starters. Martin Gollery On Wed, Dec 3, 2008 at 1:18 AM, T Joshi wrote: > Hi, > I would like to know if there are any tools/software for clustering > DNA sequences. I searched for them, but mostly I ended up with those > which work on protein sequences. If there is any bioconductor package > which also could work with sequence data, it would be good to know. > > Thanks > Josh > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- -- Martin Gollery Senior Bioinformatics Scientist From jprudhomme at healthtech.com Wed Dec 3 16:41:24 2008 From: jprudhomme at healthtech.com (Jim Prudhomme) Date: Wed, 3 Dec 2008 16:41:24 -0500 Subject: [BiO BB] Adopting Integrated R&D Informatics Systems Message-ID: <000601c9558f$e3a4ea50$aaeebef0$@com> Final Conference Details Posted for: CHI?s Adopting Integrated R&D Informatics Systems February 25-27, 2009 Moscone North Convention Center, San Francisco, CA http://www.tri-conference.com/09_ird.asp AGENDA-AT-A-GLANCE PRE-CONFERENCE SHORT COURSE* Tuesday, February 24 - 2:00 - 5:00 pm (SC6) Best Practices in Translational Medicine, Drug Discovery and Informatics 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. MAIN CONFERENCE February 25-27, 2009 INTEGRATED R&D - DRIVING PRODUCTIVITY, INNOVATION & MANAGING RESOURCES & COSTS PLENARY KEYNOTE: Using Molecular Medicine to do Therapeutic Development in the Network Age Jay M. Tenenbaum, Ph.D., Chairman and Chief Scientist, CollabRx, Inc. Scientific Workflows as Productivity Tools for Drug Discovery Juergen Hammer, Ph.D., M.Sc., M.B.A., Global Research Informatics Director, Group Research Information- Global Head in silico Sciences - Center Head - Liaison to Pharma Research, Hoffmann-La Roche Inc. 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. Sponsored by: Symyx 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 Ward, Ph.D.,Executive Advisor, Biotechnology & Pharma Panelists: All of the above speakers TRANSLATIONAL RESEARCH INFORMATICS 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 Nikolai Daraselia, Ph.D., Senior Director of Research, Ariadne Sponsored by 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 Sponsored by 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, Executive Editor, Bio-IT World Panelists: All of the above speakers Analysis of Genome-wide Genotyping Data for Copy Number Variation in Breast Cancer Aubree Hoover, Senior Product Manager, Rosetta Biosoftware Sponsored by Rosetta Biosoftware 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" DATA, INFORMATION AND KNOWLEDGE MANAGEMENT Tales from the Edge: Advanced Approaches to Knowledge Integration & Search David M. Hodgson, Site Head, Global Research Informatics & Global Head, Group Knowledge Exchange, Roche 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 Chris Waller, Ph.D., Senior Director, Chemistry Informations, Research and Development Informatics, Worldwide Technology, Pfizer, Inc. Integrating Public and Private Data Reece Hart, Ph.D., Scientific Manager, Research Computing & Informatics, Genentech Inc. INTEGRATING GENOMIC DATA 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 Sponsored by NextBio Panel: Meeting of the Minds Those who Generate the Data with Those who Store, Analyze and Integrate Data DATA INTEGRATION AND MANAGEMENT FOR EARLY AND LATE CHEMISTRY 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 *separate registration is required to attend pre-conference short course. http://www.tri-conference.com/09_ird.asp For more information, contact: Cambridge Healthtech Institute Tel: 781-972-5400 E-mail: jprudhomme at healthtech.com From nuin at genedrift.org Wed Dec 3 17:10:18 2008 From: nuin at genedrift.org (Paulo Nuin) Date: Wed, 03 Dec 2008 17:10:18 -0500 Subject: [BiO BB] sequence clustering In-Reply-To: References: <11417a880812030118r2068613cvaee694193637a121@mail.gmail.com> Message-ID: <493703CA.2070401@genedrift.org> You can also try CDHit-est. Paulo Martin Gollery wrote: > There are many programs for clustering ESTs or other nucleic > sequences. Try blastclust, D2 or Cap3 for starters. > > Martin Gollery > > On Wed, Dec 3, 2008 at 1:18 AM, T Joshi wrote: > >> Hi, >> I would like to know if there are any tools/software for clustering >> DNA sequences. I searched for them, but mostly I ended up with those >> which work on protein sequences. If there is any bioconductor package >> which also could work with sequence data, it would be good to know. >> >> Thanks >> Josh >> >> _______________________________________________ >> BBB mailing list >> BBB at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bbb >> >> > > > > From bsmagic at gmail.com Thu Dec 4 05:15:53 2008 From: bsmagic at gmail.com (Sheng Wang) Date: Thu, 4 Dec 2008 18:15:53 +0800 Subject: [BiO BB] sequence clustering In-Reply-To: <11417a880812030118r2068613cvaee694193637a121@mail.gmail.com> References: <11417a880812030118r2068613cvaee694193637a121@mail.gmail.com> Message-ID: <793f8aed0812040215y65f0ae63na23603645f6b795b@mail.gmail.com> NCBI Tools User's Manual. NAME. blastclust - BLAST score-based single-linkage clustering. SYNOPSIS *...* -- Regards, Sheng Wang On Wed, Dec 3, 2008 at 5:18 PM, T Joshi wrote: > Hi, > I would like to know if there are any tools/software for clustering > DNA sequences. I searched for them, but mostly I ended up with those > which work on protein sequences. If there is any bioconductor package > which also could work with sequence data, it would be good to know. > > Thanks > Josh > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From pmr at ebi.ac.uk Fri Dec 5 07:51:30 2008 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 05 Dec 2008 12:51:30 +0000 Subject: [BiO BB] Query In-Reply-To: <22b4d0a80812012214q5581cebcsa806862883d094bb@mail.gmail.com> References: <22b4d0a80812012214q5581cebcsa806862883d094bb@mail.gmail.com> Message-ID: <493923D2.8040704@ebi.ac.uk> Jaya Handa wrote: > Hello Sir > I wish to know when we read bacterial genomes in ncbi how do you number. > Suppose the + starand is 5'-3' and - strand is 3'-5'. > now if we number + trand as [5'] 1,2,3,4 [3'] bases then will the - strand > be like [3'] 4,3,2,1 [5']. Hmmm, '+' and '-' strands (and 'Watson' and 'Crick' strands) seem to have gone out of fashion. What we now have are sequences deposited in databases in the orientation of the genome map (for whole genomes) or their coding sequences (for individual genes) or their original sequence (3' ESTs for example will have coding sequence on the reverse strand). > Suppose we read this This gene is on the forward strand (the transcribed RNA matches the sequence in the database entry), numbers with 1 as the start of the sequence in the NCBI entry. > CDS 49..288 > /gene="cspA" > /locus_tag="BL0001" > /note="CspA; COG family: cold shock proteins; PFAM_ID: > CSD" > /codon_start=1 > /transl_table=11 > /product="cold shock protein" > /protein_id="AAN23868.1" > /db_xref="GI:23325186" This gene is on the reverse strand (the transcribed RNA is the reverse complement of the sequence in the database entry). Again we number from 1 at the start of the sequence but the complement() in the location tells us to reverse complement the sequence from 2248 to 2538. The coding sequence starts at base 2538 and reads back along the reverse strand to base 2248. For splicing, the feature locations are more complicated: joins of forward of complemented fragments, or joins of forward fragments that are then complemented (ugh!) but the numbering principles are the same. > CDS complement(2248..2538) > /locus_tag="BL0003" > /note="COG family: methyl-accepting chemotaxis protein" > /codon_start=1 > /transl_table=11 > /product="hypothetical protein" > /protein_id="AAN23870.1" > /db_xref="GI:23325188" In the early days (before we even called the field bioinformatics) there were complaints about numbering sequences from 1, and numbering promoters from -1 so there was no zero. My answer to those who complained was that I will do it differently when there is a year AD zero :-) However, writing early programs in Fortran had something to do with it. If we had been using C then sequences would start at zero. Hope this helps, Peter Rice From isbra-l at engr.uconn.edu Fri Dec 5 12:19:27 2008 From: isbra-l at engr.uconn.edu (ISBRA Symposium Announcements) Date: Fri, 5 Dec 2008 12:19:27 -0500 (EST) Subject: [BiO BB] [ISBRA-L] ODGEA'09 CFP Message-ID: 2nd International Workshop on Optimal Data Mining in Gene Expression Analysis held in conjunction with 5th International Symposium on Bioinformatics Research and Applications May 13-16, 2009 Nova Southeastern University, Ft. Lauderdale, Florida, USA The rapid development of several high-throughput gene expression monitoring technologies in the past decade has facilitated the generation of a huge amount of gene expression data. The data could either be rich or poor in the number of samples in a wide variety of experimental design setups. Aforementioned factors led to a need to develop suitable statistical procedures for optimal analysis, visualization and interpretation of the data. We are soliciting original research papers (including significant works in progress) involving gene expression analysis, including the following: A. Novel supervised and unsupervised analysis and visualization methodologies B. Novel experimental designs, problems and suitable procedures to solve them C. Optimal feature selection for tumor classification and patient-outcome prediction D. Integrative analysis of gene expression data obtained from different platforms and laboratories E. Interpretation of gene expression data with other datasets such as binding site data, copy number data and proteomics data F. Significance assessment of predictions SUBMISSION and PUBLICATION The workshop proceedings will be published along with the ISBRA proceedings in Springer-Verlag's Lecture Notes in Bioinformatics series. Papers must be submitted electronically by following the instructions at: http://www.cs.gsu.edu/isbra09/papers.html Submissions must be formatted using the Springer LNCS style and must not exceed 12 pages in length. Simultaneous submission to journals or other conferences with published proceedings is not allowed. Further, it is anticipated that a special issue of a major bioinformatics journal will be devoted to extended versions of best conference and workshop papers. IMPORTANT DATES 12 Jan 2009 Submission of papers 06 Feb 2009 Notification 20 Feb 2009 Camera Ready Papers 13 May 2009 Workshop Presentation WORKSHOP ORGANIZERS General Chair: Lonnie R. Welch, Stuckey Professor 322A Stocker Center School of Electrical Engineering and Computer Science Ohio University Athens, OH 45701-2979 welch at ohio.edu Program Chairs: R. Krishna Murthy Karuturi Sr Research Scientist Computational & Mathematical Biology Genome Institute of Singapore A*STAR (Agency for Science, Technology and Research) #02-01, Genome, 60 Biopolis ST Republic of Singapore 138672 karuturikm at gis.a-star.edu.sg Qihua Tan, Associate Professor Dept of Biochemistry, Pharmacology and Genetics Odense University Hospital Sdr. Boulevard 29 DK-5000, Odense C Denmark Qihua.Tan at ouh.regionsyddanmark.dk Jahangheer Shareef Shaik, Staff Scientist, Dept. of pathology and Immunology, Washington University, St. Louis, Missouri jahangeer.shaik at gmail.com Program Committee: Jing Hua Zhao, Medical Research Council in Cambridge, UK Xiaoli Li, Institute of Infocom Research, A-Star, Singapore Chengpeng Bi, University of Missouri - Kansas City, USA. Talamuthu Anbupalam, Genome Institute of Singapore, A-Star, Singapore Vladimir Kuznetsov, Bioinformatics Institute, A-Star, Singapore Meena Sakharkar, Nanyang Technological University, Singapore Zhengxin Chen, University of Nebraska, Omaha, USA Vinhthuy Phan, University of Memphis, USA Parvathi Chundi, University of Nebraska, Omaha, USA Lih Deng, University of Memphis, USA Sach Mukherjee, University of Warwick, UK Yuri Orlov, Genome Institute of Singapore, A-Star, Singapore Vinsensius Vega, Genome Institute of Singapore, A-Star, Singapore _______________________________________________ ISBRA-L mailing list ISBRA-L at dna.engr.uconn.edu http://dna.engr.uconn.edu/mailman/listinfo/isbra-l From isbra-l at engr.uconn.edu Fri Dec 5 12:18:25 2008 From: isbra-l at engr.uconn.edu (ISBRA Symposium Announcements) Date: Fri, 5 Dec 2008 12:18:25 -0500 (EST) Subject: [BiO BB] [ISBRA-L] CIGE'09 CFP Message-ID: 2nd Workshop on Computational Issues in Genetic Epidemiology May 13-16, 2009 Nova Southeastern University, Ft. Lauderdale, Florida, USA The Workshop on Computational Issues in Genetic Epidemiology (CIGE) provides a forum for computer scientists, geneticists, and statisticians aiming to address current computational challenges in gene mapping. The first edition of CIGE, held on August 21-22, 2008 at the DIMACS center of Rutgers University, enjoyed a great success. The second edition will be held in conjunction with the 5th International Symposium on Bioinformatics Research and Applications (ISBRA'09, http://www.cs.gsu.edu/isbra09/) on May 13-16, 2009 in Ft. Lauderdale, Florida. Topics of interest include but are not limited to: * Dealing with complex missing data patterns * Effects of structural genomic variation * Gene-gene and gene-environment interactions * Multiple hypotheses testing * Population substructure * Using biological networks in whole-genome studies We seek two categories of submissions: (1) papers for the proceedings volume and (2) abstracts for presentation. Submission implies the willingness of at least one of the authors to register and present the paper/abstract at the symposium. PROCEEDINGS PAPER SUBMISSION Papers of up to 12 pages in Springer LNCS format should be submitted electronically at http://www.easychair.org/conferences?conf=isbra09 by selecting the "Workshop on Computational Issues in Genetic Epidemiology -- Proceedings Papers" track. Accepted papers will be published as part of the ISBRA'09 proceedings in a volume of Springer-Verlag's Lecture Notes in Bioinformatics series. ABSTRACT SUBMISSION Abstracts of up to 4 pages in Springer LNCS format should be submitted electronically at http://www.easychair.org/conferences?conf=isbra09 by selecting the "Workshop on Computational Issues in Genetic Epidemiology -- Abstracts" track. The abstracts accepted for either oral or poster presentation will be distributed in electronic form on the ISBRA'08 website and on CD-ROM. TRAVEL SUPPORT Pending approval from NSF, we expect to have partial financial support for graduate students and postdocs attending the workshop. Preference will be given to students and postdocs presenting at the workshop. IMPORTANT DATES Papers for Proceedings Volume Submission deadline January 19, 2009 Notification of acceptance February 6, 2009 Final version due February 20, 2009 Abstracts for Presentation Submission deadline March 16, 2009 Notification of acceptance March 23, 2009 Final version due March 30, 2009 STEERING COMMITTEE Andrew Allen, Duke University Ion Mandoiu, University of Connecticut Dan Nicolae, University of Chicago Yi Pan, Georgia State University Alex Zelikovsky, Georgia State University PROGRAM COMMITTEE CHAIRS Andrew Allen, Duke University Itsik Pe'er, Columbia University _______________________________________________ ISBRA-L mailing list ISBRA-L at dna.engr.uconn.edu http://dna.engr.uconn.edu/mailman/listinfo/isbra-l From marchywka at hotmail.com Sat Dec 6 08:59:37 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Sat, 6 Dec 2008 08:59:37 -0500 Subject: [BiO BB] =?windows-1252?q?_RE=3A_=5BBiO_News=5D_Amazon_Web_Servic?= =?windows-1252?q?es_launches_=93Public_Data_Sets_on_AWS=94?= In-Reply-To: References: Message-ID: I'm not entirely sure what the commercial AWS service offers but similar issues come up in many areas. For example, this is about real estate ( and admittedly could use some editing in the NCBI discussion ), http://files.ots.treas.gov/comments/fddad554-1e0b-8562-eb37-34e416089fee.pdf ( RFC is here http://www.ots.treas.gov/?p=OpenComment&Topic_id=c0316a9e-1e0b-8562-ebd0-1ae5298909e2 ) but makes the case for free "API" based access to raw data for both personal usage and "valued added" interface providers, which "AWS" appears to offer. Or, maybe "weather.com" which presumably repackages data available at noaa.gov would be a good example too, http://forecast.weather.gov/MapClick.php?CityName=Marietta&state=GA&site=FFC&textField1=33.9509&textField2=-84.5411&e=0 For personal ad hoc analysis, I'd hate to be constrained by even token fees if the data can be reasonably made available for free I can write my own analysis locally and require no support from a commercial service. I've actually used the census data too and the flat download formats provided by the census is the perfect format, if you want to look see here for example, ( development tool, not assurance this will be stable), http://www.spottext.com/launcher/db/loc.cfm?action=find&longitude=-81.46277&latitude=33.4375&dimo=.2&dima=.2&lim=50 The tiger files are huge and I'm working on an API to present arbitrary SQL to a remote user ( no forms or html etc). > To: marchywka at hotmail.com > Subject: [BiO News] Amazon Web Services launches ?Public Data Sets on AWS? > From: news at bioinformatics.org > Date: Fri, 5 Dec 2008 20:26:19 -0500 > > Bioinformatics.Org News & Commentary > --------------------------------------------------------------------- > Amazon Web Services launches ?Public Data Sets on AWS? > Submitted by Mark Luo; posted on Saturday, December 06, 2008 > --------------------------------------------------------------------- > ``Public Data Sets on AWS provides a centralized repository of public data sets that can be seamlessly integrated into AWS cloud-based applications. AWS is hosting the public data sets at no charge for the community, and like all AWS services, users pay only for the compute and storage they use for their own applications. An initial list of data sets is already available, and more will be added soon. > > ``Previously, large data sets such as the mapping of the Human Genome and the US Census data required hours or days to locate, download, customize, and analyze. Now, anyone can access these data sets from their Amazon Elastic Compute Cloud (Amazon EC2) instances and start computing on the data within minutes. Users can also leverage the entire AWS ecosystem and easily collaborate with other AWS users. For example, users can produce or use prebuilt server images with tools and applications to analyze the data sets. By hosting this important and useful data with cost-efficient services such as Amazon EC2, AWS hopes to provide researchers across a variety of disciplines and industries with tools to enable more innovation, more quickly.'' > > FOR MORE INFORMATION: > http://aws.amazon.com/publicdatasets/ > _________________________________________________________________ Send e-mail anywhere. No map, no compass. http://windowslive.com/Explore/hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_anywhere_122008 From jalil.fallah at gmail.com Sat Dec 6 00:05:45 2008 From: jalil.fallah at gmail.com (jalil fallah) Date: Sat, 6 Dec 2008 08:35:45 +0330 Subject: [BiO BB] finding repeat sequences Message-ID: Dear all , I was wondering if you would mind answering my request. How could I access to a software or a database to find tandem repeat sequences in a prokaryotic gene ? Thank you in advance -- Jalil Fallah Ph.D Candidate of Medical Bacteriology Dep. of Bacteriology School of Medicine Tarbiat Modarres University Tehran - Iran P.O.Box 14115-331 Cell Phone +98- 912- 5093060 From reddy at i-asr.org Sat Dec 6 02:36:08 2008 From: reddy at i-asr.org (Institute of Advanced Scientific Reseach (IASR)) Date: Fri, 05 Dec 2008 23:36:08 -0800 Subject: [BiO BB] Call for Paper(JARB) Message-ID: <20081205233608.p4khmg9kaokkowko@secure29.inmotionhosting.com> ====================================================================== ?????????????????????????????????? Journal of Advanced Research in?Bioinformatics ?????????????????????????????????????????????????????????????????JARB ??????????????????????????????????????????????????? CALL FOR PAPERS ??????????????????????????????????????????? ? ???http://www.i-asr.org/jarb.html ??????????????????????????????????????? ???(ELECTRONIC ISSN: 1943-0213) ====================================================================== ? The Journal of Advanced Research in Bioinformatics (JARB) is an Open Access online journal which publishes original research articles in all areas of Bioinformatics and Computational Biology. JARB, a peer reviewed journal, aims to provide the most ?complete and reliable source of information on current developments in all areas of the field. The emphasis will be on publishing quality articles rapidly and freely available to researchers worldwide. ? For more information about this journal, please visit the following links: ???????????????????????????????????????? http://www.i-asr.org ? or ?????????????????????????????????????? www.i-asr.org/jarb.html Please do not hesitate to contact us if you have any questions regarding the journal. Sincerely yours, Sophia S. Reddy Executive manager reddy at i-asr.org From idoerg at gmail.com Mon Dec 8 12:55:11 2008 From: idoerg at gmail.com (Iddo Friedberg) Date: Mon, 8 Dec 2008 09:55:11 -0800 Subject: [BiO BB] finding repeat sequences In-Reply-To: References: Message-ID: http://tandem.bu.edu/trf/trf.html On Fri, Dec 5, 2008 at 9:05 PM, jalil fallah wrote: > Dear all , > > I was wondering if you would mind answering my request. > How could I access to a software or a database to find tandem repeat > sequences in a prokaryotic gene ? > > Thank you in advance > > > -- > Jalil Fallah > Ph.D Candidate of Medical Bacteriology > Dep. of Bacteriology > School of Medicine > Tarbiat Modarres University > Tehran - Iran > P.O.Box 14115-331 > Cell Phone +98- 912- 5093060 > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- 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 jeff at bioinformatics.org Mon Dec 8 13:09:29 2008 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Mon, 08 Dec 2008 13:09:29 -0500 Subject: [BiO BB] finding repeat sequences In-Reply-To: References: Message-ID: <493D62D9.9050602@bioinformatics.org> There is a nascent article on the topic here (mostly about nomenclature right now): http://wiki.bioinformatics.org/Repetitive_DNA_sequence If anyone would like to contribute to it, please do. There are a number of programs available for finding repetitive sequences. Since you're looking for tandem repeats, that narrows it down some. There are differences in scale as well: are you looking for short or long repeating units? The methods for finding repeats vary, too. Some use a library of known repeats (good for larger repeating units), while others take a de novo, "all possible combinations" approach. And gaps are an important consideration. Some programs don't consider them. Anyway, the article above lists a few programs. It's also possible to use regular expressions. Cheers, Jeff jalil fallah wrote: > Dear all , > > I was wondering if you would mind answering my request. > How could I access to a software or a database to find tandem repeat > sequences in a prokaryotic gene ? > > Thank you in advance > > -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 978 562 4800 -- From bsmagic at gmail.com Tue Dec 9 00:09:47 2008 From: bsmagic at gmail.com (Sheng Wang) Date: Tue, 9 Dec 2008 13:09:47 +0800 Subject: [BiO BB] finding repeat sequences In-Reply-To: References: Message-ID: <793f8aed0812082109q15a321a4jab244fb31165c92a@mail.gmail.com> try censor, http://www.girinst.org/censor/index.php -- Regards, Sheng Wang On Sat, Dec 6, 2008 at 1:05 PM, jalil fallah wrote: > Dear all , > > I was wondering if you would mind answering my request. > How could I access to a software or a database to find tandem repeat > sequences in a prokaryotic gene ? > > Thank you in advance > > > -- > Jalil Fallah > Ph.D Candidate of Medical Bacteriology > Dep. of Bacteriology > School of Medicine > Tarbiat Modarres University > Tehran - Iran > P.O.Box 14115-331 > Cell Phone +98- 912- 5093060 > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From tejalonline at gmail.com Tue Dec 9 10:58:04 2008 From: tejalonline at gmail.com (T Joshi) Date: Tue, 9 Dec 2008 16:58:04 +0100 Subject: [BiO BB] checking conservation of short sequences Message-ID: <11417a880812090758w9c8a825g5de3dc7e0ffa3ea@mail.gmail.com> Hi, I have some small short sequences of less than 40nt. I want to check if they are evolutionarily conserved across some species. One way I could do so is to download conservation track from UCSC in .aln format and use that with clustalw or clustalx for alignment with my query sequences. Blastn also doesn't have any database containing information on conservation. Could you suggest some other way by which I could do so without downloading the conservation track ? Thanks a lot.. From svtrived at hotmail.com Tue Dec 9 12:38:47 2008 From: svtrived at hotmail.com (Seema Trivedi) Date: Tue, 9 Dec 2008 23:08:47 +0530 Subject: [BiO BB] finding repeat sequences In-Reply-To: References: Message-ID: Hi One program is SPUTNIK at the following link http://espressosoftware.com/pages/sputnik.jsp but one will have to modify it a bit to take longer sequences as it analyzes only short seq. You can also use the online version of the same at http://cbi.labri.fr/outils/Pise/sputnik.html. The modified version of this program is available possibly with MORGANTE MICHELE michele.morgante at dpvta.uniud.it as indicated in the following link http://bioinf.dimi.uniud.it/software/software/sputnik. However, do not know the drawbacks of this modified version. Seema Trivedi > Date: Mon, 8 Dec 2008 09:55:11 -0800 > From: idoerg at gmail.com > To: bbb at bioinformatics.org > Subject: Re: [BiO BB] finding repeat sequences > > http://tandem.bu.edu/trf/trf.html > > > > On Fri, Dec 5, 2008 at 9:05 PM, jalil fallah wrote: > > > Dear all , > > > > I was wondering if you would mind answering my request. > > How could I access to a software or a database to find tandem repeat > > sequences in a prokaryotic gene ? > > > > Thank you in advance > > > > > > -- > > Jalil Fallah > > Ph.D Candidate of Medical Bacteriology > > Dep. of Bacteriology > > School of Medicine > > Tarbiat Modarres University > > Tehran - Iran > > P.O.Box 14115-331 > > Cell Phone +98- 912- 5093060 > > _______________________________________________ > > BBB mailing list > > BBB at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > -- > 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 > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ Search for videos of Bollywood, Hollywood, Mollywood and every other wood, only on Live.com http://www.live.com/?scope=video&form=MICOAL From dan.bolser at gmail.com Wed Dec 10 06:12:07 2008 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 10 Dec 2008 11:12:07 +0000 Subject: [BiO BB] Fwd: Free Vector NTI replacement? In-Reply-To: <2c8757af0812100306m323ca48cx50b5b505c101bb56@mail.gmail.com> References: <2c8757af0812100306m323ca48cx50b5b505c101bb56@mail.gmail.com> Message-ID: <2c8757af0812100312y572dfb29nae53bfe45097c1ee@mail.gmail.com> ---------- Forwarded message ---------- From: Dan Bolser Date: 2008/12/10 Subject: Free Vector NTI replacement? To: "General Forum at Bioinformatics.Org" I seem to remember that there were some projects on bioinformatics.org to develop a free replacement for the Vector NTI package? Since it seems like this package is shortly going to become very expensive, can anyone recommend a replacement? I searched the archives, and the best I could find was this (JellyFish): http://www.bioinformatics.org/pipermail/bio_bulletin_board/2001-October/000312.html But the link seems dead. Thanks for any help, Dan. From manojiids at gmail.com Wed Dec 10 03:24:40 2008 From: manojiids at gmail.com (manoj yadav) Date: Wed, 10 Dec 2008 13:54:40 +0530 Subject: [BiO BB] checking conservation of short sequences In-Reply-To: <11417a880812090758w9c8a825g5de3dc7e0ffa3ea@mail.gmail.com> References: <11417a880812090758w9c8a825g5de3dc7e0ffa3ea@mail.gmail.com> Message-ID: first u have to done multiple sequence alignment using any available software.In output u will get the evolutionary similar sequences according to the e-values. On 12/9/08, T Joshi wrote: > > Hi, > I have some small short sequences of less than 40nt. I want to check > if they are evolutionarily conserved across some species. > > One way I could do so is to download conservation track from UCSC in > .aln format and use that with clustalw or clustalx for alignment with > my query sequences. Blastn also doesn't have any database containing > information on conservation. > > Could you suggest some other way by which I could do so without > downloading the conservation track ? > > Thanks a lot.. > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Manoj Kumar Yadav Research Scholar, Center for Bioinformatics BHU,Varanasi +91 9838016500 From mgalle at irisa.fr Wed Dec 10 08:21:23 2008 From: mgalle at irisa.fr (=?ISO-8859-1?Q?Matthias_Gall=E9?=) Date: Wed, 10 Dec 2008 14:21:23 +0100 Subject: [BiO BB] finding repeat sequences In-Reply-To: References: Message-ID: <1d1653ef0812100521m54e73497tda3b05b857b1b60b@mail.gmail.com> Let me also recommend vmatch (http://www.vmatch.de/), that search for maximal repeats. It is not open source nor can it be downloaded immediately, but a free of charge licence can be obtained by sending an email to its developer (Stefan Kurtz) On Tue, Dec 9, 2008 at 18:38, Seema Trivedi wrote: > > Hi > One program is SPUTNIK at the following link http://espressosoftware.com/pages/sputnik.jsp > but one will have to modify it a bit to take longer sequences as it analyzes only short seq. You can also use the online version of the same at http://cbi.labri.fr/outils/Pise/sputnik.html. > The modified version of this program is available possibly with MORGANTE > MICHELE michele.morgante at dpvta.uniud.it as indicated in the following link http://bioinf.dimi.uniud.it/software/software/sputnik. However, do not know the drawbacks of this modified version. > > Seema Trivedi > > > > >> Date: Mon, 8 Dec 2008 09:55:11 -0800 >> From: idoerg at gmail.com >> To: bbb at bioinformatics.org >> Subject: Re: [BiO BB] finding repeat sequences >> >> http://tandem.bu.edu/trf/trf.html >> >> >> >> On Fri, Dec 5, 2008 at 9:05 PM, jalil fallah wrote: >> >> > Dear all , >> > >> > I was wondering if you would mind answering my request. >> > How could I access to a software or a database to find tandem repeat >> > sequences in a prokaryotic gene ? >> > >> > Thank you in advance >> > >> > >> > -- >> > Jalil Fallah >> > Ph.D Candidate of Medical Bacteriology >> > Dep. of Bacteriology >> > School of Medicine >> > Tarbiat Modarres University >> > Tehran - Iran >> > P.O.Box 14115-331 >> > Cell Phone +98- 912- 5093060 >> > _______________________________________________ >> > BBB mailing list >> > BBB at bioinformatics.org >> > http://www.bioinformatics.org/mailman/listinfo/bbb >> > >> >> >> >> -- >> 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 >> _______________________________________________ >> BBB mailing list >> BBB at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bbb > > _________________________________________________________________ > Search for videos of Bollywood, Hollywood, Mollywood and every other wood, only on Live.com > http://www.live.com/?scope=video&form=MICOAL > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Matthias Gall? Gaudeamus igitur From marty.gollery at gmail.com Wed Dec 10 09:50:51 2008 From: marty.gollery at gmail.com (Martin Gollery) Date: Wed, 10 Dec 2008 06:50:51 -0800 Subject: [BiO BB] Fwd: Free Vector NTI replacement? In-Reply-To: <2c8757af0812100312y572dfb29nae53bfe45097c1ee@mail.gmail.com> References: <2c8757af0812100306m323ca48cx50b5b505c101bb56@mail.gmail.com> <2c8757af0812100312y572dfb29nae53bfe45097c1ee@mail.gmail.com> Message-ID: Dan, You can find jellyfish software at www.jellyfishsoftware.com It is offered for $200/US per year. Also try Geneious at www.geneious.com and the CLC workbench at www.clcbio.com/ All of these have a free version or a free demo period. Best, Marty On Wed, Dec 10, 2008 at 3:12 AM, Dan Bolser wrote: > ---------- Forwarded message ---------- > From: Dan Bolser > Date: 2008/12/10 > Subject: Free Vector NTI replacement? > To: "General Forum at Bioinformatics.Org" > > > > I seem to remember that there were some projects on bioinformatics.org > to develop a free replacement for the Vector NTI package? > > Since it seems like this package is shortly going to become very > expensive, can anyone recommend a replacement? > > I searched the archives, and the best I could find was this (JellyFish): > > http://www.bioinformatics.org/pipermail/bio_bulletin_board/2001-October/000312.html > > > But the link seems dead. > > > Thanks for any help, > Dan. > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- -- Martin Gollery Senior Bioinformatics Scientist From dan.bolser at gmail.com Fri Dec 12 02:17:01 2008 From: dan.bolser at gmail.com (Dan Bolser) Date: Fri, 12 Dec 2008 07:17:01 +0000 Subject: [BiO BB] Fwd: Free Vector NTI replacement? In-Reply-To: References: <2c8757af0812100306m323ca48cx50b5b505c101bb56@mail.gmail.com> <2c8757af0812100312y572dfb29nae53bfe45097c1ee@mail.gmail.com> Message-ID: <2c8757af0812112317t1e928df4se7a1897d9cc55dd3@mail.gmail.com> 2008/12/10 Martin Gollery : > Dan, > You can find jellyfish software at > > www.jellyfishsoftware.com > > It is offered for $200/US per year. > > Also try Geneious at www.geneious.com > and the CLC workbench at www.clcbio.com/ > > > All of these have a free version or a free demo period. Cheers Marty, Seems like a good candidate for a 'free' alternative - is there any 'Top 10' type initiative on Bioinformatics.Org for development of open software? Dan. > Best, > Marty > > On Wed, Dec 10, 2008 at 3:12 AM, Dan Bolser wrote: >> ---------- Forwarded message ---------- >> From: Dan Bolser >> Date: 2008/12/10 >> Subject: Free Vector NTI replacement? >> To: "General Forum at Bioinformatics.Org" >> >> >> >> I seem to remember that there were some projects on bioinformatics.org >> to develop a free replacement for the Vector NTI package? >> >> Since it seems like this package is shortly going to become very >> expensive, can anyone recommend a replacement? >> >> I searched the archives, and the best I could find was this (JellyFish): >> >> http://www.bioinformatics.org/pipermail/bio_bulletin_board/2001-October/000312.html >> >> >> But the link seems dead. >> >> >> Thanks for any help, >> Dan. >> >> _______________________________________________ >> BBB mailing list >> BBB at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bbb >> > > > > -- > -- > Martin Gollery > Senior Bioinformatics Scientist > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From landman at scalableinformatics.com Sat Dec 13 22:06:35 2008 From: landman at scalableinformatics.com (Joe Landman) Date: Sat, 13 Dec 2008 22:06:35 -0500 Subject: [BiO BB] [Fwd: [Mpihmmer] Announcing GPU-HMMER] Message-ID: <4944783B.7010800@scalableinformatics.com> -------- Original Message -------- Subject: [Mpihmmer] Announcing GPU-HMMER Date: Sat, 13 Dec 2008 21:50:55 -0500 From: John Paul Walters To: mpihmmer at mpihmmer.org Hi Folks, We'd like to announce the availability of GPU-HMMER, a port of HMMER's hmmsearch utility to NVIDIA CUDA-enabled GPUs. Anyone who is interested is invited to visit www.mpihmmer.org to get the source. A brief user's guide and installation guide are provided at mpihmmer.org as well. This version has been tested on 8800 GTX Ultra and Tesla C1060 GPUs, though we expect that the code should work on a wider range of GPUs than has been tested. The current source code supports a single GPU with speedups that range from 20x-38x, depending on the size of the HMM. In the coming weeks we plan to release support for multiple GPUs within a single node. Current tests demonstrate speedups that exceed 100x using 3 Tesla GPUs, also depending on the size of the HMM. Thereafter we plan to integrate GPU support directly into MPI-HMMER to support multiple GPUs via MPI. As always we welcome any feedback or bug reports. We are especially interested in compatibility reports and will post compatibility updates to www.mpihmmer.org as necessary. best regards, JP Walters _______________________________________________ Mpihmmer mailing list Mpihmmer at mpihmmer.org http://lists.scalableinformatics.com/mailman/listinfo/mpihmmer -- Joseph Landman, Ph.D Founder and CEO Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://www.scalableinformatics.com http://jackrabbit.scalableinformatics.com phone: +1 734 786 8423 x121 fax : +1 866 888 3112 cell : +1 734 612 4615 From jeff at bioinformatics.org Wed Dec 17 15:17:36 2008 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 17 Dec 2008 15:17:36 -0500 Subject: [BiO BB] Course on dChip for Gene Expression and SNP Microarray Data Analysis Message-ID: <49495E60.5020200@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 harry.mangalam at uci.edu Mon Dec 22 13:39:40 2008 From: harry.mangalam at uci.edu (Harry Mangalam) Date: Mon, 22 Dec 2008 10:39:40 -0800 Subject: [BiO BB] gene expression software for mere biologists? Message-ID: <200812221039.40453.harry.mangalam@uci.edu> 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.] From idh at poulet.org Mon Dec 22 13:56:17 2008 From: idh at poulet.org (Yannick Wurm) Date: Mon, 22 Dec 2008 19:56:17 +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: Hi Harry, have you had a look at TIGR's MEV ? it's limited compared to command-line tools, but definitely worth a click.... also, some Bioconductor packages have GUIs: eg limmagui But I think the bottom line is that "pure molecular" who want to do genome-scale experiments need to - either learn how to get around a commandline - or collaborate with someone who knows how to. cheers yannick -------------------------------------------- yannick . wurm @ unil . ch Ant Genomics, Ecology & Evolution @ Lausanne http://www.unil.ch/dee/page28685_fr.html On 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 x.sole at iconcologia.net Mon Dec 22 14:51:05 2008 From: x.sole at iconcologia.net (Sole Acha, Xavi) Date: Mon, 22 Dec 2008 20:51:05 +0100 Subject: [BiO BB] gene expression software for mere biologists? In-Reply-To: <200812221039.40453.harry.mangalam@uci.edu> Message-ID: <50805D6FBD91904D86AF433349315E420170B073@ICOSRVCORREO01.ICO.SCS.local> This is a difficult problem to solve. Maybe you can have a look a these three suites, I believe they may be the most complete ones you can find elsewhere. - dChip, from Harvard (http://biosun1.harvard.edu/complab/dchip/) - TM4 Suite from TIGR (http://www.tm4.org/) - GEPAS (http://gepas.bioinfo.cipf.es/) Obviously there is a trade-off between versatility and ease-of-use. With R (and Bioconductor), you will always be able to write your own procedures and perform your own analyses. Maybe it should be worth trying to teach R (and a bit of basic algorithmics theory) to your biologists. But that depends on how eager they are to learn. Hope this helps a little. Xavier Sol? Acha Unitat de Bioestad?stica i Bioinform?tica // Biostatistics and Bioinformatics Unit Institut Catal? d'Oncologia // Catalan Institute of Oncology Av. Gran Via s/n km 2,7 08907 L'Hospitalet de Llobregat, Barcelona, Spain. Phone: +34 93 260 71 86 / +34 93 335 90 11 (ext. 3189) Fax: +34 93 260 71 88 E-mail: x.sole at iconcologia.net -----Mensaje original----- De: bbb-bounces at bioinformatics.org [mailto:bbb-bounces at bioinformatics.org] En nombre de Harry Mangalam Enviado el: dilluns, 22 / desembre / 2008 19:40 Para: BBB Asunto: [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 aledni at gmail.com Mon Dec 22 16:11:06 2008 From: aledni at gmail.com (Nicoline) Date: Tue, 23 Dec 2008 10:11:06 +1300 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: Hi, Try BRB-ARRAY, it is an very extensive Excell plug in with option to include R/Bioconductor packages. http://linus.nci.nih.gov/BRB-ArrayTools.html Nicoline van Loenen, PhD candidate Lincoln University C-fACS Centre for Advanced Computing Agricultural & Life Sciences Division http://www.lincoln.ac.nz/story28668.html On Tue, Dec 23, 2008 at 7:39 AM, 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 > > > -- Nicoline http://www.lincoln.ac.nz/story28668.html From ashwathy.bl at gmail.com Mon Dec 22 23:25:20 2008 From: ashwathy.bl at gmail.com (Ashwathy) Date: Tue, 23 Dec 2008 09:55:20 +0530 Subject: [BiO BB] Difference between Protein Interaction Network (PIN) and Protein-Protein Interaction Network (PPIN) Message-ID: <215bd4440812222025s375b949ft1e221feb3fb05ae8@mail.gmail.com> 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.. 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? Aswathi Centre for Bioinformatics Kerala University From veredcc at bgu.ac.il Tue Dec 23 02:39:25 2008 From: veredcc at bgu.ac.il (Vered Caspi) Date: Tue, 23 Dec 2008 09:39:25 +0200 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: <003201c964d1$949476f0$bdbd64d0$@ac.il> 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 paolo.romano at istge.it Tue Dec 23 09:23:09 2008 From: paolo.romano at istge.it (Paolo Romano) Date: Tue, 23 Dec 2008 15:23:09 +0100 Subject: [BiO BB] BITS '09: First announcement and preliminary Call for Papers Message-ID: <200812231436.mBNEa9i5016718@ibm43p.biotech.ist.unige.it> ================================= Apologies, if you're receiving multiple copies ================================= BITS 2009 Sixth Annual Meeting of the Italian Bioinformatics Society 18-20 March 2009, Genova http://bits09.istge.it/ First Announcement and Preliminary Call for Papers The Sixth Annual Meeting of the Bioinformatics Italian Society (BITS 2009) aims at presenting some of the hottest bioinformatics achievements, as well as a landscape of Italian bioinformatics research. It is also intended to allow young researchers to present their work in a collaborative and supporting atmosphere. BITS 2009 will include keynote lectures, oral communications, posters presentations and tutorials. Social activities will include a welcome reception, a guided tour of the historical city center of Genoa, one of the oldest towns in Italy, and the social dinner. Invited Speakers ? Alex Bateman, Sanger Institute, United Kingdom ? Peer Bork, EMBL, Heidelberg, Germany ? Rob Russel, EMBL, Heidelberg, Germany ? One more speaker to be confirmed Topics Submitted contributions should address novel bioinformatics methods, algorithms, databases, tools and applications for research and development in one or more of the following domains: - Genomics - Molecular Evolution - Protein structure and function - Proteomics - Transcriptomics - Gene expression - Biological Interaction Networks and Pathways - Systems Biology - In-silico drug design - Clinical Bioinformatics - Bio-ontologies This list is by no means exclusive of any further topics in the field of Bioinformatics. Deadlines - January 20, 2009: Oral communications submission - February 10, 2009: Posters submission - February 13, 2009: Early registration (reduced fee) Instructions Abstracts must be submitted through the BITS 2009 Abstracts submission form (soon available!). All abstracts must be written in English and structured in the following sections: Motivation, Methods, Results. Abstracts' length cannot be greater than 5,000 characters or 4,000 characters (spaces included) when a figure is also included. All accepted contributions will be published in the abstracts' book. Organizers are considering the possibility of identifying an internationally peer-reviewed journal to publish a Supplement including extended versions of best oral communications and posters as full papers. Scientific Committee + D. Bordo, National Cancer Research Institute of Genova + R. Casadio, University of Bologna + M.L. Chiusano, University of Naples + M. Helmer-Citterich, University of Rome "Tor Vergata" + F. Masulli, University of Genoa + L. Milanesi, ITB/CNR, Milan + M. Muselli, IEIIT/CNR, Genoa + E. Pizzi, National Institute of Health, Rome + G. Pesole, Univerity of Bari + P. Romano, National Cancer Research Institute of Genoa Organizing Committee + D. Bordo, National Cancer Research Institute of Genova + F. Masulli, University of Genoa + M. Muselli, IEIIT/CNR, Genoa + P. Romano, National Cancer Research Institute of Genoa Paolo Romano (paolo.romano at istge.it) Bioinformatics, National Cancer Research Institute (IST), Genova, Italy http://www.nettab.org/promano/ From harry.mangalam at uci.edu Tue Dec 23 17:22:49 2008 From: harry.mangalam at uci.edu (Harry Mangalam) Date: Tue, 23 Dec 2008 14:22:49 -0800 Subject: [BiO BB] gene expression software for mere biologists? In-Reply-To: <003201c964d1$949476f0$bdbd64d0$@ac.il> References: <200812221039.40453.harry.mangalam@uci.edu> <003201c964d1$949476f0$bdbd64d0$@ac.il> Message-ID: <200812231422.50130.harry.mangalam@uci.edu> 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.] From marchywka at hotmail.com Mon Dec 29 12:16:36 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Mon, 29 Dec 2008 12:16:36 -0500 Subject: [BiO BB] Save protein structure image as an adobe SVG file In-Reply-To: <2849EC40-0DE9-49B1-9657-59350FDF1B41@utoronto.ca> References: <1226534454.491b6e36e7d14@webmail.upv.es> <1226946262.4921b6d6b14d5@webmail.upv.es> <1227118784.492458c03ec5a@webmail.upv.es> <3E951E84-BE5A-42AC-A31F-BB16E240D52F@utoronto.ca> <2849EC40-0DE9-49B1-9657-59350FDF1B41@utoronto.ca> Message-ID: > >> From: boris.steipe at utoronto.ca >> Date: Wed, 26 Nov 2008 17:33:39 -0500 >> To: bbb at bioinformatics.org >> Subject: Re: [BiO BB] Save protein structure image as an adobe SVG format file >> >>> Spheres aren't that hard for z-sorting, >> >> >> Yes, a collection of atoms can be well approximated with a Z-sorted >> stack of circles in 2D. But *molecules* are represented by >> intersecting spheres and the line of intersection is a circle at an >> arbitrary orientation relative to the viewer. It projects as an >> ellipse, and part of the ellipse is occluded. >> IIRC, the OP asked a general question apparently not having any specific viewer or rendering model in mind so I assume that a ball model would be worth consideration. I haven't done much with graphics lately ( while I did write an openGL app, it hides most of the graphics stuff) and needed to review some trig/spherical eqns for location based services, so I thought I would give this a shot. It doesn't turn out to be that hard for most cases, [ I cleverly put a large bmp file on the page,along with links to generated svg, it may load slowly and I may go ahead and update or delete this ] http://www.spottext.com/marchywka/pdb2svg.cfm?src=biobb but could take some thought to make a clean application. I don't recall if there are a lot of analytical approaches to this as oppposed to more brute force/empirical and more general things like ray tracing but probably in CAD solid modelling this is well known. It wouldn't be hard to generalize to more simple object types like rods or fix some of the obvious problems with the current code. Note that your concern with arbitrary angles etc is easily handled with vector dot and cross products, expanded in Cartesian coordinates as the last step, to produce simple results. It took a while to figure out a few rules and how the SVG arc code works. >> Think "methane". The illustration uses this $ head cd25sulfenic.pdb HEADER Hydrolase, Cell Cycle 21-Jan-05 1YML COMPND Crystal Structure Of The Cdc25b Phosphatase Catalytic Domain COMPND 2 With The Active Site Cysteine In The Sulfenic Form SOURCE ORGANISM_SCIENTIFIC: Homo sapiens; ORGANISM_COMMON: human AUTHOR G.K.Buhrman, B.Parker, J.Sohn, J.Rudolph & C.Mattos _________________________________________________________________ It?s the same Hotmail?. If by ?same? you mean up to 70% faster. http://windowslive.com/online/hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_broad1_122008 From veredcc at bgu.ac.il Wed Dec 24 08:57:00 2008 From: veredcc at bgu.ac.il (Vered Caspi) Date: Wed, 24 Dec 2008 15:57:00 +0200 Subject: [BiO BB] gene expression software for mere biologists? In-Reply-To: <200812231422.50130.harry.mangalam@uci.edu> References: <200812221039.40453.harry.mangalam@uci.edu> <003201c964d1$949476f0$bdbd64d0$@ac.il> <200812231422.50130.harry.mangalam@uci.edu> Message-ID: <005d01c965cf$7e682580$7b387080$@ac.il> 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.] From school2009 at biocomp.unibo.it Mon Dec 29 09:56:18 2008 From: school2009 at biocomp.unibo.it (Bologna Winter School 2009) Date: Mon, 29 Dec 2008 15:56:18 +0100 Subject: [BiO BB] Announcement of the 10th Bologna Winter School Message-ID: <4958E512.9070400@biocomp.unibo.it> *10th Bologna Winter School* *MACHINE LEARNING AND COMPUTATIONAL BIOLOGY: * *New Paradigms for a new science* *Bologna - Italy* 2-6 February 2009 ------------------------------------------------------------------------ URL: http://www.biocomp.unibo.it/school *Description:* In the post-genome era the vast mass of biological data is growing more than ever before. The creation of automatic and "intelligent" tools that can help to organize, analyze and unravel the underlying information is one of the most wonted and less solved problems in biological 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. Moreover, great expectations have been generated in different fields by the increasing role and impact of computer science in processing and analyzing terabytes of data. Machine Learning methods are among the most successful computational tools that have been introduced so far in Computational Biology. The 10^th edition of the Bologna Winter School in Bioinformatics will provide comprehensive overview of different Machine Learning fields in the light of their common probabilistic framework. The programme starts with an introduction to Graphical Models that are the unifying formalism on which most of the current machine learning methods can be described. Dynamical Bayesian networks with specific application to the reconstruction of biological networks will be then discussed. An introduction to the hidden Markov models will explain the details of the these highly successful probabilistic models. Finally two days are devoted at the Statistical learning models such as Support Vector Machines and andvanced Neural Networks. These different one-morning tutorials will be followed by general lectures describing the most recent and successful applications in Computational Biology. *TEACHERS:* Florence d'Alch? -Buc University of Evry-Val-d'Essonne Evry, FR Paolo Frasconi Universityof Florence Florence, IT Dmitrij Frishman Technical University Munich, DE Roderic Guig? University "Pompeu Fabra" Barcelona, ES David T. Jones University College London, UK Anders Krogh University of Copenhagen Copenhagen, DK Arthur Lesk PennState University University Park, USA Gianluca Pollastri University College Dublin, IE Massimiliano Pontil University College London, UK Anna Tramontano University "La Sapienza" Roma, IT Alfonso Valencia Centro Nacional de Investigaciones Oncol?gicas Madrid, ES ------------------------------------------------------------------------------------------ *Contact:* school2009 at biocomp.unibo.it For Application send a short C.V. to school2009 at biocomp.unibo.it. You will be notified by e-mail of acceptance. Deadline for application: *January 20, 2009*