From nomijill at yahoo.com Mon Jan 4 11:58:27 2010 From: nomijill at yahoo.com (naomi Thomson) Date: Mon, 4 Jan 2010 08:58:27 -0800 (PST) Subject: [BiO BB] 454/Newbler assembly finishing software? Message-ID: <320345.16008.qm@web38301.mail.mud.yahoo.com> HI Dan, I just read your advice to Edith on the Bioinformatics Forum. Can you tell me about the assembly workshop you attended. Thanks, Naomi Thomson From dan.bolser at gmail.com Tue Jan 5 04:11:26 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 5 Jan 2010 09:11:26 +0000 Subject: [BiO BB] 454/Newbler assembly finishing software? In-Reply-To: <320345.16008.qm@web38301.mail.mud.yahoo.com> References: <320345.16008.qm@web38301.mail.mud.yahoo.com> Message-ID: <2c8757af1001050111s164e479bu6872997c9fd10dd4@mail.gmail.com> Hi Naomi, Hopefully you can find some more information under here: http://www.nesc.ac.uk/esi/events/1020/ Cheers, Dan. 2010/1/4 naomi Thomson : > HI Dan, > > I just read your advice to Edith on the Bioinformatics Forum. Can you tell me about the assembly workshop you attended. > > Thanks, > > Naomi Thomson > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From jprudhomme at healthtech.com Mon Jan 4 16:07:08 2010 From: jprudhomme at healthtech.com (Jim Prudhomme) Date: Mon, 4 Jan 2010 16:07:08 -0500 Subject: [BiO BB] Adopting R&D Informatics Systems Message-ID: <011101ca8d81$dff71510$9fe53f30$@com> This CHI conference is part of the 17th International Molecular Medicine Tri-Conference to be held on February 3-5, 2010, Moscone North Convention Center, San Francisco. This week is the advanced registration discount deadline. Register at https://chidb.com/register/2010/mmtc/reg.asp Here is a short summary of the program: Featured Presentations Recent Strategies with Cloud, Wikis, Ontologies and Open Source Data Standards Giles M. Day, Senior Director, BBC Informatics, Pfizer, Inc. Enterprise Scientific Workflow Environment Drives Innovation Juergen Hammer, Ph.D., M.B.A., Pharma Research Scientific Informatics; Global Head, In Silico Sciences; Center Head, Scientific Informatics, F. Hoffmann-La Roche, Inc. Integrated Informatics Systems for R&D John Reynders, Ph.D., CIO, Pharmaceutical Research & Development, Johnson & Johnson The Pistoia Alliance, Inc. - A Construct for Precompetitive Collaboration Chris Waller, Ph.D., Senior Director, Precompetitive Collaborations, Research, Development & Medical Informatics, Worldwide Technology, Pfizer, Inc. Executive Panel with Q&A Are We Integrating the Right Data: Extending Beyond Laboratory Data to Decisions Impacting Project Success Moderator: David M. Sedlock, Ph.D., Senior Director, Research & Development Systems, Millennium, The Takeda Oncology Company Thought-Leaders will Address - Executive Strategies - Integrated R&D Informatics - Data Information and Knowledge Management - Cloud, Wikis, Ontologies & Semantic Web - Translational Informatics - Integrated Genomic, Biology and Image Data Pre-Conference Short Courses* (SC1) Applying Next Generation Sequencing Technologies to Research Introduction to New Technologies and Application in Research (SC2) Best Practices in Translational & Personalized Medicine Link to PDF Brochure: http://www.tri-conference.com/dload2010_ird_brochure.asp Link to Speakers and Abstracts: http://www.tri-conference.com/ird.asp Link for Sponsorship & Exhibit Information: http://www.tri-conference.com/sponsorexhibit.asp Questions or to register by telephone, call +1 781-972-5400. Thanks, James Prudhomme Cambridge Healthtech Institute From divi.bioinfor88 at gmail.com Tue Jan 5 04:32:57 2010 From: divi.bioinfor88 at gmail.com (divya sree) Date: Tue, 5 Jan 2010 15:02:57 +0530 Subject: [BiO BB] HELP Message-ID: Would you able to say where we get the PKS gene sequence. From maximilianh at gmail.com Wed Jan 6 15:56:29 2010 From: maximilianh at gmail.com (Maximilian Haussler) Date: Wed, 6 Jan 2010 20:56:29 +0000 Subject: [BiO BB] HELP In-Reply-To: References: Message-ID: <76f031ae1001061256y3c7feaa0sa511e5023cc7327f@mail.gmail.com> Here: http://www.genome.ucsc.edu/cgi-bin/hgGene?hgg_gene=uc010nhs.1 Consider using Genecards.org. cheers Max On Tue, Jan 5, 2010 at 9:32 AM, divya sree wrote: > Would you able to say where we get the PKS gene sequence. > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From harry.mangalam at uci.edu Wed Jan 6 18:27:22 2010 From: harry.mangalam at uci.edu (Harry Mangalam) Date: Wed, 6 Jan 2010 15:27:22 -0800 Subject: [BiO BB] Search like Molecular Information Agent (MIA) [was at SDSC] Message-ID: <201001061527.22762.harry.mangalam@uci.edu> Is there a search tool like the cited MIA at SDSC? It seems to have gone ... MIA (sorry). It was at mia.sdsc.edu, but that link is 404 now. I'm looking for essentially a bio-oriented text-mining tool for filtering links between hits (as generated by a large-scale screen such as a micro-array) by searching thru a number of databases. thanks in advance.. hjm -- Harry Mangalam - Research Computing, NACS, Rm 225 MSTB, UC Irvine [ZOT 2225] / 92697 949 824-0084(o), 949 285-4487(c) MSTB=Bldg 415 (G-5 on --- I don't have a facebook page; I have a workshop. From cannataro at unicz.it Sun Jan 10 18:04:00 2010 From: cannataro at unicz.it (Mario Cannataro) Date: Mon, 11 Jan 2010 00:04:00 +0100 (CET) Subject: [BiO BB] Deadline Ext. Workshop on Biomedical and Bioinformatics' Challenges to Computer Science In-Reply-To: References: Message-ID: <9d3962a41f6d33fddd8fe0321fd67370.squirrel@email.unicz.it> INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE (ICCS 2010) http://www.iccs-meeting.org/ University of Amsterdam, The Netherlands May 31 - June 2, 2010 3rd Workshop on Biomedical and Bioinformatics Challenges to Computer Science http://staff.icar.cnr.it/cannataro/iccs2010/ Full papers submission (Extended Deadline): January 15, 2010 CALL FOR PAPERS Bioinformatics is providing the foundation for fast and reliable data analysis. Genomics, transcriptomics, proteomics, epidemiological, clinical and text mining applications have made essential progress through using bioinformatics tools. Standard tools are usually offered through the Web. This is no longer sufficient with more complex analysis and simulation tasks from emerging research fields like systems biology, image analysis, biomedical applications or data management. In recent years Grid and Web services based approaches have been developed to face the new challenges. Moreover, emerging life sciences applications need to use in a coordinated way both bioinformatics tools, biological data banks, and patient?s clinical data, that requires seamless integration, privacy preservation and controlled sharing. This 3rd Workshop on Biomedical and Bioinformatics Challenges to Computer Science will bring together scientists from computer and life sciences to discuss future directions of bioinformatics algorithms, applications, and data management. Questions to be looked at are whether wrapping existing algorithms as Grid or Web service will be sufficient to cope with the more complex applications and the increasing volume of data to be processed or which applications would profit from being redeveloped as native parallel or distributed application. Furthermore, the use of novel parallel architectures and dedicated hardware to implement bioinformatics and biomedical algorithms will be discussed. TOPICS OF INTEREST The workshop is seeking original research papers presenting innovative solutions from parallel, distributed and Grid computing applied to bioinformatics algorithms and life sciences applications. Specifically we are interested in the following topics: - sequence and structure bioinformatics - computational proteomics - systems biology - biomedical image analysis - biomedical simulation - data management - data integration - data visualization - workflow modelling - distributed biomedical applications - high performance computing - dedicated hardware and architectures - parallelisation techniques - service orientation - volunteer computing - peer-to-peer computing PAPER SUBMISSION AND PUBLICATION We invite original previously unpublished contributions that are not submitted concurrently to a journal or another conference. The submitted paper must be camera-ready and formatted according to the rules of Procedia Computer Science (for formatting information see for text/latex and for MSword. Click here for a Latex template plus instructions). Submission implies the willingness of at least one of the authors to register and present the paper. PostScript and source versions of your paper must be submitted electronically through the paper submission system. Please, note that papers must not exceed ten pages in length, when typeset using the Procedia format. Dates of deadlines for draft paper submission (full paper), notification of acceptance, deadline for camera-ready paper submission and registration may be found in the Important Dates section of the ICCS Web site. Papers must be based on unpublished, mature and original work and must be submitted to ICCS only. JOURNAL SPECIAL ISSUE At the end of the workshop, we plan to invite the best 4-6 papers of the workshop for a special section on an international journal. Selected papers (extended and revised version) accepted on the 1st edition of the workshop have been published on a special section of Future Generation Computer Systems, Elsevier. IMPORTANT DATES Full papers submission (Extended Deadline): January 15, 2010 Notification of acceptance: February 20, 2010 Camera ready papers: March 1, 2010 Early registration opens: February 15, 2010 Early registration closes: March 31, 2010 Conference sessions : May 31 - June 2, 2010 WORKSHOP CO-ORGANIZERS Mario Cannataro, University Magna Gr?cia of Catanzaro, Italy Joakim Sundnes, Simula Research Laboratory, Norway Rodrigo Weber dos Santos, Federal University of Juiz de Fora, Brazil PROGRAM COMMITTEE (TO BE CONFIRMED) 1. Dave Angulo, DePaul University, Chicago, USA 2. Rui Brito, University of Coimbra, Portugal 3. Tim Clark, Harvard Medical School, USA 4. Giuseppe Di Fatta, University of Reading, UK 5. Werner Dubitzky, University of Ulster, UK 6. Christine Froidevaux, LRI-Bioinformatics Group - University Paris XI, Orsay, France 7. Alan Garny, University of Oxford, Department of Physiology, Anatomy & Genetics 8. Concettina Guerra, University of Padova, Italy 9. Pietro Hiram Guzzi, University Magna Gr?cia of Catanzaro, Italy 10. Ulrich Hansmann, Research Centre Juelich, Germany 11. Vicente Hern?ndez, Univ. Polit?cnica de Valencia, Spain 12. Pilar Herrero, Universidad Polit?cnica de Madrid, Madrid, Spain 13. Ela Hunt, University of Strathclyde, Scotland 14. Glenn Terje Lines, Simula Research Laboratory, Norway 15. Marcelo Lobosco, Federal University of Juiz de Fora, Brazil 16. Uko Maran, University of Tartu, Estonia 17. Wagner Meira Jr., Federal University of Minas Gerais, Brazil 18. Maria Mirto, University of Salento, Italy 19. Hartmut Mix, University of Technology Dresden, Germany 20. Salvatore Orlando, University of Venezia, Italy 21. Mar?a S. P?rez, Universidad Polit?cnica de Madrid, Madrid, Spain 22. Gernot Plank, University of Graz, Austria 23. Omer F. Rana, Cardiff University, UK 24. Blanca Rodriguez, University of Oxford, UK 25. Luis Paulo da Silva Barra, Federal University of Juiz de Fora, Brazil 26. Fabrizio Silvestri, ISTI-CNR, Italy 27. Raymond Spiteri, University of Saskatchewan, Canada 28. Roberto Tagliaferri, University of Salerno, Italy 29. El-Ghazali Talbi, Universit? des Sciences et Technologies de Lille, France 30. Paolo Trunfio, University of Calabria, Italy 31. Pierangelo Veltri, University Magna Gr?cia of Catanzaro, Italy 32. Edward J. Vigmond, University of Calgary, Canada 33. Albert Zomaya, University of Sydney, Australia **************************************** New book release Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine, and Healthcare ISBN: 978-1-60566-374-6; 1,050 pp; May 2009 Published under Medical Information Science Reference an imprint of IGI Global http://www.igi-global.com/reference/details.asp?id=34292 Edited by: Mario Cannataro, University Magna Graecia of Catanzaro, Italy **************************************** Prof. Mario Cannataro, Informatics and Biomedical Engineering, University "Magna Gr?cia" of Catanzaro, Viale Europa (Localit? Germaneto), 88100 CATANZARO, ITALY, Tel: 0961-369 4100, Fax: 0961-369 4073/4090, Email: cannataro at unicz.it, Web: http://bioingegneria.unicz.it/~cannataro/ **************************************** From alessandra.bilardi at gmail.com Sun Jan 10 18:27:50 2010 From: alessandra.bilardi at gmail.com (Alessandra) Date: Mon, 11 Jan 2010 00:27:50 +0100 Subject: [BiO BB] GBrowse.org project In-Reply-To: References: Message-ID: Hi all, I'm Alessandra and I run GBrowse.org. GBrowse.org is a resource for using and setting up GBrowse genome browsers. The site provides one location where biologists and bioinformaticians can find: 1. Genome browser web sites for any organism that has them. If a species has a genome browser anywhere on the web, then we aim to link to it. 2. Links to sequence and annotation files that are available online. 3. Links to genome browser configuration files, when available 4. An FTP site containing genome annotation and configuration files for each annotated genome that does not have its own web site. GBrowse.org emphasizes the GBrowse genome browser in its organization, but also links to sites that use other browser packages such as UCSC, Ensembl, and JBrowse. Also, we are currently conducting a survey seeking input on future project direction. Please take a few minutes now to provide your feedback. Survey link: http://gbrowse.org/survey/index.php?sid=64264&lang=en GBrowse.org introdution link: http://gmod.org/wiki/August_2009_GMOD_Meeting#GBrowse.org Thank you for your help, Alessandra Bilardi. http://gbrowse.org/ CRIBI Genomics, University of Padua http://genomics.cribi.unipd.it/ From gigi at biocomp.unibo.it Mon Jan 11 06:01:23 2010 From: gigi at biocomp.unibo.it (Martelli Pier Luigi) Date: Mon, 11 Jan 2010 12:01:23 +0100 Subject: [BiO BB] Announcement: 11th Bologna Winter School Message-ID: <4B4B0503.8000709@biocomp.unibo.it> 11th Bologna Winter School Computational Methods for Systems Biology University of Bologna 8 Feb 2010 - 12 Feb 2010 ------------------------------------------------------------------------ URL: http://www.biocomp.unibo.it/~school2010/ Systems biology is a new interdisciplinary field that aims at describing the complex interactions between the elementary components of a biological system for understanding the mechanisms at the basis of the complex biological behaviour. To this goal, several experimental techniques have been developed for finding the full content of a cell in terms of expressed mRNAs (transcriptomics), transcribed proteins (proteomics) and metabolites (metabolomics). Furthermore, techniques are available for exploring the interactions between the expressed proteins (interactomics), and between proteins and DNA-sequences (regulomics). These huge amounts of data need to be analysed considering the different tissues, the different phases of the cell cycle and the different conditions that can influence the biological processes inside the cell. For these reasons Computational methods hold a central role in Systems Biology. The 11th edition of the Bologna Winter School will provide an introduction to different computational approaches developed for describing the structure of the interaction networks and for simulating the kinetic evolution of the underlying systems. In particular, the lecturers will present the theory of large networks useful for describing the structure of interactions, two alternative simulation techniques based on differential equations and on stochastic process calculus, and the predictive methods based on machine learning approaches. Issues related to the techniques for parametrizing the models starting from the experimental data will be discussed in detail. These topics will cover half- or one-day tutorials that will present both the theoretical and the applicative aspects, with the aim of highlighting the usefulness and the domain of application of the different approaches in the field of Systems Biology. TEACHERS Gilles Bernot University of Nice-Sophia Antipolis Nice, FR Jacques Chomilier University "Pierre et Marie Curie" Paris, FR Pierpaolo Degano University of Pisa Pisa, IT David T. Jones University College London, UK Arthur Lesk PennState University University Park, USA Mauno Vihinen University of Tampere Tampere, FI APPLICATION should be submitted by e-mail to: school2010 AT biocomp DOT unibo DOT it The School may provide 3 ECTS credits Maximum number of participants is limited to 30 students. For Application send a short C.V. to school2010 AT biocomp DOT unibo DOT it You will be notified by e-mail of acceptance. Deadline for application: *January 20, 2010* From dan.bolser at gmail.com Tue Jan 12 04:09:55 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 12 Jan 2010 09:09:55 +0000 Subject: [BiO BB] GBrowse.org project In-Reply-To: References: Message-ID: <2c8757af1001120109kb45364dsc8bd4f2a906fd23@mail.gmail.com> Cheers Alessandra, Its nice to see more sites using Semantic MediaWiki :-) One question, how do I register for an account on the site? There doesn't seem to be any way to register for an account. Cheers, Dan. 2010/1/10 Alessandra : > ?Hi all, > > ? I'm Alessandra and I run GBrowse.org. > GBrowse.org is a resource for using and setting up GBrowse genome > browsers. The site provides one location where biologists and > bioinformaticians can find: > > ?1. Genome browser web sites for any organism that has them. If a > species has a genome browser anywhere on the web, then we aim to link > to it. > ?2. Links to sequence and annotation files that are available online. > ?3. Links to genome browser configuration files, when available > ?4. An FTP site containing genome annotation and configuration files > for each annotated genome that does not have its own web site. > > GBrowse.org emphasizes the GBrowse genome browser in its organization, > but also links to sites that use other browser packages such as UCSC, > Ensembl, and JBrowse. > > Also, we are currently conducting a survey seeking input on future > project direction. Please take a few minutes now to provide your > feedback. > > ? Survey link: http://gbrowse.org/survey/index.php?sid=64264&lang=en > ? GBrowse.org introdution link: > http://gmod.org/wiki/August_2009_GMOD_Meeting#GBrowse.org > > ? Thank you for your help, > > ? Alessandra Bilardi. > ? http://gbrowse.org/ > ? CRIBI Genomics, University of Padua > ? http://genomics.cribi.unipd.it/ > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From alessandra.bilardi at gmail.com Tue Jan 12 07:47:32 2010 From: alessandra.bilardi at gmail.com (Alessandra) Date: Tue, 12 Jan 2010 13:47:32 +0100 Subject: [BiO BB] GBrowse.org project In-Reply-To: <2c8757af1001120109kb45364dsc8bd4f2a906fd23@mail.gmail.com> References: <2c8757af1001120109kb45364dsc8bd4f2a906fd23@mail.gmail.com> Message-ID: Dear Dan, I have got 1024 questions about semantic mediawiki.. well, at some other time.. I create GBrowse.org personal account if someone asks me. I would like to check all people would write into GBrowse.org .. :-P If you want GBrowse.org account, then send me your username and you'll receive wiki email.. well, I think that you know very well the rest.. :) Cheerio, Ale. On 1/12/10, Dan Bolser wrote: > Cheers Alessandra, > > Its nice to see more sites using Semantic MediaWiki :-) > > One question, how do I register for an account on the site? There > doesn't seem to be any way to register for an account. > > > Cheers, > Dan. > > 2010/1/10 Alessandra : >> Hi all, >> >> I'm Alessandra and I run GBrowse.org. >> GBrowse.org is a resource for using and setting up GBrowse genome >> browsers. The site provides one location where biologists and >> bioinformaticians can find: >> >> 1. Genome browser web sites for any organism that has them. If a >> species has a genome browser anywhere on the web, then we aim to link >> to it. >> 2. Links to sequence and annotation files that are available online. >> 3. Links to genome browser configuration files, when available >> 4. An FTP site containing genome annotation and configuration files >> for each annotated genome that does not have its own web site. >> >> GBrowse.org emphasizes the GBrowse genome browser in its organization, >> but also links to sites that use other browser packages such as UCSC, >> Ensembl, and JBrowse. >> >> Also, we are currently conducting a survey seeking input on future >> project direction. Please take a few minutes now to provide your >> feedback. >> >> Survey link: http://gbrowse.org/survey/index.php?sid=64264&lang=en >> GBrowse.org introdution link: >> http://gmod.org/wiki/August_2009_GMOD_Meeting#GBrowse.org >> >> Thank you for your help, >> >> Alessandra Bilardi. >> http://gbrowse.org/ >> CRIBI Genomics, University of Padua >> http://genomics.cribi.unipd.it/ >> >> _______________________________________________ >> BBB mailing list >> BBB at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bbb >> > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Alessandra Bilardi, Ph. D. ---- CRIBI, University of Padova, Italy Via Ugo Bassi, 58/B - 35121 Padova Tel +390498276165 Fax +390498276159 http://www.linkedin.com/in/bilardi ---- La semplicit? ? la pi? alta forma di perfezione (Leonardo Da Vinci) Keep simple, stupid (KISS, IT) ---- From dan.bolser at gmail.com Tue Jan 12 17:20:25 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 12 Jan 2010 22:20:25 +0000 Subject: [BiO BB] GBrowse.org project In-Reply-To: References: <2c8757af1001120109kb45364dsc8bd4f2a906fd23@mail.gmail.com> Message-ID: <2c8757af1001121420j3d32507bs4654523bc165a848@mail.gmail.com> Yeah, SMW can be tricky at first! There are several good resources (listed below). Please do sign me up to GBrowse.Org (as user 'Dan Bolser')... or better yet, can you do openID sign-ins? SMW resources: * The official site: http://semantic-mediawiki.org * The community site: http://smw.referata.com * The user mailing list: http://sourceforge.net/mailarchive/forum.php?forum_name=semediawiki-user * The IRC chat room: irc://irc.freenode.net/#semantic-mediawiki Which reminds me, there are always people ready to talk bioinformatics in the Bioinformatics chat room :-) irc://irc.freenode.net/#bioinformatics If you don't want to install a chat client, try http://java.freenode.net/ Cheers, Dan. 2010/1/12 Alessandra : > Dear Dan, > > I have got 1024 questions about semantic mediawiki.. well, ?at some other time.. > I create GBrowse.org personal account if someone asks me. > I would like to check all people would write into GBrowse.org .. :-P > If you want GBrowse.org account, then send me your username and you'll > receive wiki email.. well, I think that you know very well the rest.. > :) > > Cheerio, > Ale. > > On 1/12/10, Dan Bolser wrote: >> Cheers Alessandra, >> >> Its nice to see more sites using Semantic MediaWiki :-) >> >> One question, how do I register for an account on the site? There >> doesn't seem to be any way to register for an account. >> >> >> Cheers, >> Dan. >> >> 2010/1/10 Alessandra : >>> ?Hi all, >>> >>> ? I'm Alessandra and I run GBrowse.org. >>> GBrowse.org is a resource for using and setting up GBrowse genome >>> browsers. The site provides one location where biologists and >>> bioinformaticians can find: >>> >>> ?1. Genome browser web sites for any organism that has them. If a >>> species has a genome browser anywhere on the web, then we aim to link >>> to it. >>> ?2. Links to sequence and annotation files that are available online. >>> ?3. Links to genome browser configuration files, when available >>> ?4. An FTP site containing genome annotation and configuration files >>> for each annotated genome that does not have its own web site. >>> >>> GBrowse.org emphasizes the GBrowse genome browser in its organization, >>> but also links to sites that use other browser packages such as UCSC, >>> Ensembl, and JBrowse. >>> >>> Also, we are currently conducting a survey seeking input on future >>> project direction. Please take a few minutes now to provide your >>> feedback. >>> >>> ? Survey link: http://gbrowse.org/survey/index.php?sid=64264&lang=en >>> ? GBrowse.org introdution link: >>> http://gmod.org/wiki/August_2009_GMOD_Meeting#GBrowse.org >>> >>> ? Thank you for your help, >>> >>> ? Alessandra Bilardi. >>> ? http://gbrowse.org/ >>> ? CRIBI Genomics, University of Padua >>> ? http://genomics.cribi.unipd.it/ >>> >>> _______________________________________________ >>> BBB mailing list >>> BBB at bioinformatics.org >>> http://www.bioinformatics.org/mailman/listinfo/bbb >>> >> >> _______________________________________________ >> BBB mailing list >> BBB at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bbb >> > > > -- > ?Alessandra Bilardi, Ph. D. > ---- > ?CRIBI, University of Padova, Italy > ?Via Ugo Bassi, 58/B - 35121 Padova > ?Tel +390498276165 Fax +390498276159 > ?http://www.linkedin.com/in/bilardi > ---- > La semplicit? ? la pi? alta forma di perfezione (Leonardo Da Vinci) > Keep simple, stupid (KISS, IT) > ---- > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From nikpreb at mail.ntua.gr Tue Jan 12 19:10:53 2010 From: nikpreb at mail.ntua.gr (Nikolaos Preve) Date: Wed, 13 Jan 2010 02:10:53 +0200 Subject: [BiO BB] Final Call for Chapters - Computational and Data Grids: Principles, Designs, and Applications Message-ID: <4B4D0F8D.6090807@mail.ntua.gr> Apologies for cross-postings. Please send it to interested colleagues and students. Thanks! Best regards, Nikolaos --------------------------------------------------------------------------- FINAL CALL FOR CHAPTERS Proposal Submission Deadline: January 30, 2010 Computational and Data Grids: Principles, Designs, and Applications A book edited by Dr. Nikolaos Preve National Technical University of Athens, Greece To be published by IGI Global: http://www.igi-global.com/requests/details.asp?ID=748 Introduction Grid computing is the next generation information technology infrastructure that promises to transform the way organizations and individuals compute, communicate and collaborate. Grid computing is an evolution of distributed computing and it refers to a large-scale high-performance computing which combines distributed heterogeneous computing resources and the result is a unique large virtual supercomputer with a vast amount of shared processing power and data storage. Considering the enormous amount of these underutilized computing resources, the necessity of a grid infrastructure is compulsory. A computational grid provides access to users who want to utilize the shared processing resources in order to efficiently apply high throughput applications on distributed machines. The second most common shared resource used in a grid is data storage and it is known as data grid. This type of grid provides distributed storage capacity such as attached memory to the processor, hard disk drives or other types of permanent storage. Grid computing can assist grid users in order to utilize to the maximum computing resources by applying tasks and solving a scientific or technical problem that requires a great number of computer processing cycles or the need to process large amounts of data. Objective of the Book This book aims to provide relevant theoretical frameworks and will cover the latest empirical research findings in the area of grid computing. The goal of this book is to represent theoretical frameworks, methodologies, implementations, and cutting edge research findings with a critical perspective bridging the gap between academia and the latest achievements of the computer industry. It will be written for professionals, as well as students, who are involved or interested in the study, use, design, and development of grid computing and want to improve and empower their understanding of it. Also, this book aims to help researchers and developers understand the basics of the field, to highlight the various developments over the years in the field by giving an in depth analysis of grid networks. Target Audience The target audience of this book will be composed of professionals, engineers, researchers and students who are interested and working in the field of grid computing. Moreover, the book will provide insights and can serve as both literature at an undergraduate level and as an overview of the area. Recommended topics include, but are not limited to, the following: 1.Theories, definitions, methodologies, models, applications, simulations, and architectures relevantto grid computing 2.Implementations of computational grids, data grids, sensor and mobile grids 3.Grid data storage, grid databases, data management, and data mining 4.Indexing and query optimization over grid databases 5.Grid middleware 6.Web services 7.Security, cryptography, and cryptanalysis 8.Artificial intelligence 9.Algorithms 10.Scheduling, resource management, and optimization 11.Workflow and fault tolerance 12.Programming in grid computing 13.Cloud computing and grids 14.Grid computing in scientific areas (i.e. astrophysics, biology, chemistry, economy and finance, e-health, electromagnetics, geophysics, meteorology, numerical analysis, statistics) Submission Procedure Researchers and practitioners are invited to submit on or before January 30, 2010, a 1-2 page chapter clearly explaining the mission and concerns of the proposed chapter. We also highly encourage early full chapter submissions. Please include the title of the book in the subject line of your e-mail. Authors will be notified by February 15, 2010 about the status of their proposals and will be sent chapter guidelines. Full chapters are expected to be submitted by March 31, 2010 or earlier. All submitted chapters must not have been published elsewhere and will undergo a double-blind peer review by at least two referees. Contributors may also be requested to serve as reviewers for this project. Publisher This book is scheduled to be published by IGI Global (formerly Idea Group Inc.), publisher of the Information Science Reference (formerly Idea Group Reference), Medical Information Science Reference,Business Science Reference, and Engineering Science Reference imprints. For additional information regarding the publisher, please visit www.igi-global.com. This publication is anticipated to be released in 2010. Important Dates January 30, 2010: Proposal Submission Deadline February 15, 2010: Notification of Acceptance March 31, 2010: Full Chapter Submission June 15, 2010: Review Results Returned August 15, 2010: Final Chapter Submission September 15, 2010: Final Deadline Inquiries and submissions can be forwarded electronically (Word document) or by mail to: Dr. Nikolaos Preve School of Electrical and Computer Engineering National Technical University of Athens, 15773 Zographou, Greece Tel.: +30 211 770 8053 - GSM: +30 697 750 4197 E-mail: nikpreb at mail.ntua.gr with cc to: Editorial Board E-mail: editorialt at gmail.com From mal503 at ohm.york.ac.uk Wed Jan 13 07:41:40 2010 From: mal503 at ohm.york.ac.uk (Michael Lones) Date: Wed, 13 Jan 2010 12:41:40 +0000 Subject: [BiO BB] CfP: Special Session on Computational Intelligence for Bioinformatics (CIB), WCCI 2010 Message-ID: Dear Colleagues, The 2010 IEEE World Congress on Computational Intelligence will be held on July 18-23, 2010, in Barcelona, Spain. The special session "Computational Intelligence for Bioinformatics" (CIB) is intended to bring together top researchers, practitioners, and students from around the world. CIB will serve as a platform to discuss applications of Computational Intelligence in the fields of Bioinformatics, Computational Biology, Bioengineering, and Pharmacy, for solving problems in the life sciences, biology, health and medicine. The CIB special session is sponsored and co-organised by the IEEE BBTC, the IEEE DMTF and the INNS SIGs on Bioinformatics and Biopatterns. CIB consists of four tracks, namely: 1. CIBCBB: Computational Intelligence in Bioinformatics, Computational Biology, and Bioengineering. 2. CIBDA: Computational Intelligence for BioPattern Data Analysis. 3. CIPI: Computational Intelligence for the Pharmaceutical Industry 4. CIBSDF : Computational Intelligence in Biomedical Sciences and DNA Forensics We cordially invite you to submit research articles in this special session of WCCI 2010. We also encourage you to forward this Call for Papers to your colleagues. *** The submission deadline is January 31st, 2010 *** For more information about the CIB special session, please visit http://www.neuronelab.dmi.unisa.it/wcci2010 . We hope to see you in Barcelona. With Best Regards, Michael Lones, On behalf of the WCCI 2010 CIB co-organisers. Dr. Michael Lones Intelligent Systems Research Group Department of Electronics University of York, UK http://www-users.york.ac.uk/~mal503/ From steps.dev at gmail.com Thu Jan 14 22:55:25 2010 From: steps.dev at gmail.com (STEPS Development Team) Date: Fri, 15 Jan 2010 12:55:25 +0900 Subject: [BiO BB] STochastic Engine for Pathway Simulation release Message-ID: We are pleased to announce the release of STochastic Engine for Pathway Simulation (STEPS) version 1.0. STEPS is a package for exact stochastic reaction-diffusion simulation in complex 3D geometries. Our core algorithm is an implementation of Gillespie's SSA extended for membrane reactions and diffusive fluxes between elements in a tetrahedral mesh. STEPS was developed for simulation of neuronal signaling pathways in dendritic spines and around synapses, however it is a general tool that may be used for studying spatial gradients and morphology in any biochemical pathway. STEPS supports a number of free and research-licensed powerful mesh- generation packages that can produce structured 3D tetrahedral meshes representing the required morphology. STEPS provides further functionality to retrieve all spatial information from the imported mesh necessary to initialize and run a simulation. The user-interface to STEPS is in Python, with core computations carried out in C++ for maximal speed of execution. The user creates Python scripts to build a model and control a simulation, optionally taking advantage of the many powerful scientific computing tools available for Python to process and visualize data. STEPS can be downloaded from the sourceforge website (http://steps.sourceforge.net/ ) where pre-compiled binaries are available for Mac OS X 10.5-10.6 and Windows, along with source-code, documentation and support. Best regards, The STEPS Development Team Website: http://steps.sourceforge.net/ Mailing List: http://lists.sourceforge.net/lists/listinfo/steps-users Email: steps.dev at gmail.com Computational Neuroscience Unit Okinawa Institute of Science and Technology http://www.irp.oist.jp/cns/ From jeedward at yahoo.com Sun Jan 17 13:39:11 2010 From: jeedward at yahoo.com (John Edward) Date: Sun, 17 Jan 2010 10:39:11 -0800 (PST) Subject: [BiO BB] BCBGC-10 Call for papers Message-ID: <554139.12529.qm@web45912.mail.sp1.yahoo.com> BCBGC-10 Call for papers The 2010 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) (website: http://www.PromoteResearch.org) will be held during 12-14 of July 2010 in Orlando, FL, USA. BCBGC is an important event in the areas of bioinformatics, computational biology, genomics and chemoinformatics and focuses on all areas related to the conference. The conference will be held at the same time and location where several other major international conferences will be taking place. The conference will be held as part of 2010 multi-conference (MULTICONF-10). MULTICONF-10 will be held during July 12-14, 2010 in Orlando, Florida, USA. The primary goal of MULTICONF is to promote research and developmental activities in computer science, information technology, control engineering, and related fields. Another goal is to promote the dissemination of research to a multidisciplinary audience and to facilitate communication among researchers, developers, practitioners in different fields.The following conferences are planned to be organized as part of MULTICONF-10. * International Conference on Artificial Intelligence and Pattern Recognition (AIPR-10) * International Conference on Automation, Robotics and Control Systems (ARCS-10) * International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) * International Conference on Computer Networks (CN-10) * International Conference on Enterprise Information Systems and Web Technologies (EISWT-10) * International Conference on High Performance Computing Systems (HPCS-10) * International Conference on Information Security and Privacy (ISP-10) * International Conference on Image and Video Processing and Computer Vision (IVPCV-10) * International Conference on Software Engineering Theory and Practice (SETP-10) * International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-10) We invite draft paper submissions. Please see the website http://www.PromoteResearch.org for more details. Sincerely James Heralds Publicity committee From natemsutton at yahoo.com Sun Jan 24 17:24:53 2010 From: natemsutton at yahoo.com (Nate Sutton) Date: Sun, 24 Jan 2010 14:24:53 -0800 (PST) Subject: [BiO BB] Student searching for Bioinformatics research ideas to explore Message-ID: <968299.4704.qm@web37308.mail.mud.yahoo.com> Hello everyone, My name is Nate and I am a Biomedical Informatics master's student.? I am currently searching for Bioinformatics research ideas to pursue.? I am interested in a variety of Bioinformatics topics.? Some of those topics are genome wide association studies, sequence annotations, and integrating genetic data into EHRs.? What are some interesting types of research or novel research ideas that I can explore in Bioinformatics?? I appreciate your help! Thanks, Nate From longdang_98 at yahoo.com Sun Jan 24 18:32:08 2010 From: longdang_98 at yahoo.com (Long Dang) Date: Sun, 24 Jan 2010 15:32:08 -0800 (PST) Subject: [BiO BB] Need help in building a high throughtput genotyping lab Message-ID: <477397.46902.qm@web50005.mail.re2.yahoo.com> Hi all, I am involved in a project to build a high throughput human genotyping lab for a developing country. If anyone has experience in buidling and/or running a genotyping lab and is willing to share it, I would be very grateful to hear from him/her. I am als interested to know any good reference source about that kind of experience. Thank you very much, Dang Long ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dang Long, Ph.D. Divison of Genetics Wadsworth Center NYS Department of Health Center for Medical Science 150 New Scotland Avenue, rm 2021 Albany, New York 12208 Phone 518 408-2141 FAX 518 402-4623 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From kanzure at gmail.com Sun Jan 24 21:43:23 2010 From: kanzure at gmail.com (Bryan Bishop) Date: Sun, 24 Jan 2010 20:43:23 -0600 Subject: [BiO BB] Need help in building a high throughtput genotyping lab In-Reply-To: <477397.46902.qm@web50005.mail.re2.yahoo.com> References: <477397.46902.qm@web50005.mail.re2.yahoo.com> Message-ID: <55ad6af71001241843g3a019e01v2979f62db2c48f0d@mail.gmail.com> On Sun, Jan 24, 2010 at 5:32 PM, Long Dang wrote: > I am involved in a project to build a high throughput human genotyping lab for a developing country. If anyone has experience in buidling and/or running a genotyping lab and is willing to share it, I would be very grateful to hear from him/her. I am als interested to know any good reference source about that kind of experience. Hi there. I do not have any direct experience, but I may know people who can help you out. In fact, many of us on this mailing list can probably help you in different ways. Please keep us updated with specific needs and I'm sure we can help :-). - Bryan http://heybryan.org/ 1 512 203 0507 From daniele.gianni at gmail.com Wed Jan 27 15:42:30 2010 From: daniele.gianni at gmail.com (Daniele Gianni) Date: Wed, 27 Jan 2010 21:42:30 +0100 Subject: [BiO BB] CfP: Workshop on Collaborative Modeling and Simulation (CoMetS) In-Reply-To: References: Message-ID: <7fc6c6431001271242s793f5561i3ebc5c5238077f5a@mail.gmail.com> ################################################################# IEEE WETICE 2010 1st International Workshop on Collaborative Modeling and Simulation CALL FOR PAPERS ################################################################# June 28 - June 30, 2010, Larissa (Greece) * **http://www.sel.uniroma2.it/CoMetS10* ################################################################# # Papers Due: *** March 2, 2010 *** # Accepted papers will be published in the conference proceedings # by the IEEE Computer Society Press and indexed by EI. ################################################################# Modeling and Simulation (M&S) is increasingly becoming a central activity in the design of new systems and in the analysis of existing systems because it enables designers and researchers to investigate systems behavior through virtual representations. For this reason, M&S is gaining a primary role in many industrial and research fields, such as space, critical infrastructures, manufacturing, emergency management, biomedical systems and sustainable future. However, as the complexity of the investigated systems increases and the types of investigations widens, the cost of M&S activities increases because of the more complex models and of the communications among a wider number and variety of M&S stakeholders (e.g., sub-domain experts, simulator users, simulator engineers, and final system users). To address the increasing costs of M&S activities, collaborative technologies must be introduced to support these activities by fostering the sharing and reuse of models, by facilitating the communications among M&S stakeholders, and more generally by integrating processes, tools and platforms. Aside from seeking applications of collaborative technologies to M&S activities, the workshop seeks innovative contributions that deal with the application of M&S practices to the design of collaborative environments. These environments are continuously becoming more complex and therefore their design requires systematic approaches to meet the required quality of collaboration. This is important for two reasons: to reduce rework activities on the actual collaborative environment, and to maximize the productivity and the quality of the process the collaborative environment supports. M&S offers the methodologies and tools for such investigations and therefore it can be used to improve the quality of collaborative environments. A non-exhaustive list of hi-level topics includes: * collaborative environments for M&S * agent-based M&S * collaborative distributed simulation * net-centric M&S * web-based M&S * model sharing and reuse * model building and evaluation * modeling and simulation of business processes * modeling for collaboration * simulation-based performance evaluation of collaborative networks * model-driven simulation engineering * domain specific languages for the simulation of collaborative environments * domain specific languages for collaborative M&S To stimulate creativity, however, the workshop maintains a wider scope and invites interested researchers to present contributions that offer original perspectives on collaboration and M&S. +++++++++++++++++++++++++++++++++++ On-Line Submissions and Publication +++++++++++++++++++++++++++++++++++ CoMetS'10 intends to bring together researchers and practitioners to discuss key issues, approaches, open problems, innovative applications and trends in the workshop research area. Papers should contain original contributions not published or submitted elsewhere. Papers up to six pages (including figures, tables and references) can be submitted. Papers should follow the IEEE format, which is single spaced, two columns, 10 pt Times/Roman font. All submissions should be electronic (in PDF) and will be peer-reviewed by at least three program committee members. Full papers accepted for the workshop will be included in the proceedings, published by the IEEE Computer Society Press (IEEE approval pending). Note that at least one author from each accepted paper should register to attend WETICE 2010 to get the paper published in the proceedings. Authors may contact the organizers for expression of interests and content appropriateness at any time. Papers can be submitted in PDF format at the submission site (*http://www.easychair.org/conferences/?conf=comets10*), which is supported by the EasyChair conference management system. Please contact the workshop chairs (*comets10 at easychair.org*) if you experience problems with the EasyChair Web site. +++++++++++++++ Important Dates +++++++++++++++ * Submission Deadline: March 2, 2010 * Decision to paper authors: April 2, 2010 * Final version of accepted papers due to IEEE: April 14, 2010 * Conference dates: June 28 - June 30, 2010 ++++++++++++++++++++ Organizing Committee ++++++++++++++++++++ * Andrea D'Ambrogio, University of Roma TorVergata, Italy * Daniele Gianni, European Space Agency, Netherlands * Joachim Fuchs, European Space Agency, Netherlands * Giuseppe Iazeolla, University of Roma TorVergata, Italy +++++++++++++++++ Program Committee +++++++++++++++++ * Michele Angelaccio, University of Roma TorVergata, Italy * Olivier Dalle, University of Nice Sophia Antipolis, CNRS & INRIA, France * Steve McKeever, University of Oxford, UK * Alessandra Pieroni, University of Roma TorVergata, Italy * Andrew Rice, University of Cambridge, UK * Jos? L. Risco-Martin, Universidad Complutense de Madrid, Spain * Helena Szczerbicka, University of Hannover, Germany * Hans Vangheluwe, McGill University, Canada * Gabriel Wainer, Carleton University, Canada * J.Chris White, ViaSim Solutions, USA * Quirien Wijnands, European Space Agency, Netherlands * Heming Zhang, Tsinghua University, China *** Contact Information *** Andrea D'Ambrogio (workshop co-chair) Email: *dambro at info.uniroma2.it* From clements at nescent.org Fri Jan 29 17:30:23 2010 From: clements at nescent.org (Dave Clements) Date: Fri, 29 Jan 2010 14:30:23 -0800 Subject: [BiO BB] 2010 GMOD Summer School - Americas In-Reply-To: References: <71ee57c71001291351q47994b82w10dffb390dbf2837@mail.gmail.com> <71ee57c71001291357h67112e2fkcf835687e59f66ae@mail.gmail.com> <71ee57c71001291358k74781b08n232534d8895c5ec1@mail.gmail.com> <71ee57c71001291400y28e40eb6i112ea91df977dc67@mail.gmail.com> <71ee57c71001291400n6133982eh3a02293ff741900b@mail.gmail.com> <71ee57c71001291401y505b56baic61c11754d88a444@mail.gmail.com> <71ee57c71001291402s23e3f2e9w2562d6acf85bd4ae@mail.gmail.com> <71ee57c71001291402h2ec67300r4fc7a3b2375f4080@mail.gmail.com> <71ee57c71001291403s19be18f3s3a1d5a314c74def@mail.gmail.com> Message-ID: Hello all, I am pleased to announce that we are now accepting applications for: ? 2010 GMOD Summer School - Americas ? ? 6-9 May 2010 ? ? NESCent, Durham, NC, USA ? ? http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas This will be a hands-on multi-day course aimed at teaching new GMOD users/administrators how to get GMOD Components up and running. The course will introduce participants to the GMOD project and then focus on installation, configuration and integration of popular GMOD Components. GMOD (http://gmod.org/) is a collection of open-source and interoperable software components for visualizing, annotating, and managing biological, especially genomic, data.? GMOD is also a community of users and developers addressing common challenges with their data. The course will be held May 6-9, at NESCent in Durham, NC, and these GMOD components will be covered: ? ?* Apollo - genome annotation editor ? ?* Chado - a modular and extensible database schema ? ?* Galaxy - workflow system ? ?* GBrowse - the Generic Genome Browser ? ?* GBrowse_syn - A generic synteny browser ? ?* JBrowse - genome browser ? ?* MAKER - genome annotation pipeline ? ?* Tripal - web front end for Chado The deadline for applying is the end of Friday, February 22. Admission is competitive and is based on the strength of the application (especially the statement of interest). In 2009 there were over 50 applications for the 25 slots. Any applications received after the deadline will be placed on the waiting list. See the course page for details and an application link: ?http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas Thanks, Dave Clements GMOD Help Desk PS: We are also investigating holding a GMOD course in the Asia/Pacific region, sometime this fall. Watch the GMOD mailing lists and the GMOD News page/RSS feed for updates. -- http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas http://gmod.org/wiki/GMOD_News