From apico at gladstone.ucsf.edu Sun Apr 1 22:26:12 2012 From: apico at gladstone.ucsf.edu (Alexander Pico) Date: Sun, 01 Apr 2012 19:26:12 -0700 Subject: [BiO BB] Call for Abstracts: NetBio SIG at ISMB 2012: DUE APRIL 16TH In-Reply-To: Message-ID: Network Biology SIG at ISMB 2012 in Long Beach, CA, July 13th The Network Biology SIG will focus on two major areas: (1) the development of network-related tools and resources, and (2) the application of network analysis and visualization in the study of biology, synthetic biology and medicine. The meeting will provide a unique interface between tool developers and users in the field of network biology. Through these complementary lenses, the SIG will bring into focus the current state of the field, its future promise and how to get there. http://nrnb.org/netbiosig Call for Abstracts We invite abstracts for talks and posters We are seeking a diversity of submissions to represent the breadth and depth of the Network Biology field. Find guidelines at http://nrnb.org/netbiosig Keynote Speakers * Chris Evelo?- Head of Department of Bioinformatics, BiGCaT at Maastricht University, NL * Hiroaki Kitano?- Director of Systems Biology Institute in Tokyo * Chris Sander - Chair of Computational Biology at Sloan-Kettering Institute * Josh Stuart - Assoc. Professor of Biomedical Engineering at UC Santa Cruz Important Dates April 16: Abstract submission deadline May 21: Notification of accepted abstracts June 1: Early registration deadline July 13: NetBio SIG 2012 July 15-17: ISMB 2012 See you there! NetBio SIG Organizing Committee Alexander Pico (apico at gladstone.ucsf.edu), Scooter Morris, Allan Kuchinsky, Gary Bader, Mario Albrecht, Ian Donaldson, Natasa Przulj, Esti Yeger-Lotem From Robin.Haw at oicr.on.ca Tue Apr 3 10:22:19 2012 From: Robin.Haw at oicr.on.ca (Robin Haw) Date: Tue, 3 Apr 2012 14:22:19 +0000 Subject: [BiO BB] Google Summer of Code - Genome Informatics Message-ID: The Genome Informatics group, is taking part in the Google Summer of Code (GSoC) program. This year, the Genome Informatics group, will be organizing the joint efforts of Galaxy, GBrowse, Generic Model Organism Database (GMOD), JBrowse, Reactome, Wormbase, and PortEco. GSoC is a global program that funds student programmers around the world to write code for open source projects. More information about our project ideas and the GSoC program is available on the GMOD website. If you are a student interested in coding for our open source projects, then check out the links above and submit your project proposal as soon as possible. The application deadline is 6th April 2012. Robin Haw Genome Informatics Group Admin http://gmod.org/wiki/GSoC From huwenhuo at gmail.com Fri Apr 6 22:32:36 2012 From: huwenhuo at gmail.com (wenhuo hu) Date: Fri, 6 Apr 2012 22:32:36 -0400 Subject: [BiO BB] GSEA analysis, phenotype labels Message-ID: Hi all, I have a question about GSEA analysis. There is an parameter about phenotype label (Java version GSEA), it is about the .cls data, with an extension, e.g. "WT~KO", or "KO~"WT". I tried both way, the results are quite different. The way described in the original paper on how GSEA works does not seem give an excuse how this parameter affect the results, and why this happened. Please help! Wenhuo Hu mskcc From idoerg at gmail.com Mon Apr 9 18:22:17 2012 From: idoerg at gmail.com (Iddo Friedberg) Date: Mon, 9 Apr 2012 18:22:17 -0400 Subject: [BiO BB] Reminder: AFP SIG abstracts due April 18, 2012 Message-ID: Locale: Long Beach, California USA Date: July 14, 2012 (Just before ISMB 2012) URL: http://biofunctionprediction.org Important dates: April 18, 2012: Deadline for submitting abstracts. May 9, 2012: Notifications for accepted abstracts e-mailed to corresponding authors May 16, 2012: Deadline for presenters to confirm acceptance of invitation to speak. July 14, 2012: AFP SIG preceding ISMB 2012 An ISMB Special Interest Group Meeting Automated Protein Function Prediction Sequence and structure genomics have generated a wealth of data, but extracting meaningful information from genomic information is becoming an increasingly difficult challenge. Both the number and the diversity of discovered sequences are increasing, while the fraction of genes whose function is known is decreasing.In addition, there is a need for annotation which is standardized so that it could be incorporated into function annotation on a large scale. Finally, there is a need to assess the quality of the function prediction software which is out there. For these reasons and many more, automated protein function prediction is rapidly gaining interest among computational biologists in academia and industry. The AFP SIG has been part of ISMB since 2005. We call upon all researchers involved in gene and protein function prediction to submit an abstract to the AFP meeting. Authors of select abstracts will be invited to give a talk and/or present a poster. This year, AFP is delighted to have Jonathan Eisen from the University of California, Davis as its keynote speaker. >From his lab page: http://bobcat.genomecenter.ucdavis.edu/mediawiki/index.php/Main_Page "Dr. Eisen has published more than 200 scientific papers and is a co-author of a relatively recently published Evolution Textbook. Dr. Eisen is also a strong proponent of the Open Access movement in scientific publishing and is Academic Editor in Chief of PLoS Biology. For recent news see http://twitter.com/phylogenomics" For further instructions on how to submit abstracts to AFP 2012, please go here: http://biofunctionprediction.org/node/415 We are looking forward to seeing you in Long Beach, California! Iddo Friedberg on behalf of the AFP organizing committee -- Iddo Friedberg http://iddo-friedberg.net/contact.html ++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.> ++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----. .>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>> >>----.<--.>++++++.<<<<------------------------------------. From german.terrazas at nottingham.ac.uk Wed Apr 18 07:48:00 2012 From: german.terrazas at nottingham.ac.uk (German Terrazas Angulo) Date: Wed, 18 Apr 2012 12:48:00 +0100 Subject: [BiO BB] CfP ICARIS 2012 - Extended Deadlines: May 14th, 2012 & June 15th, 2012 Message-ID: <4F8EA9F0.4050202@nottingham.ac.uk> CALL FOR PAPERS, ORAL PRESENTATIONS & POSTERS *Apologies for cross-posting* The 11th International Conference on Artificial Immune Systems 28-31 August 2012 Taormina, Italy http://www.artificial-immune-systems.org/icaris/2012/ https://www.easychair.org/conferences/?conf=icaris2012 http://www.artificial-immune-systems.org/icaris/2012/callForPapers.php IMPORTANT DATES: * Paper Submission deadline: May 14th, 2012 * Paper Notification of acceptance: June 14th, 2012 ** Abstract/Poster/Short Presentation Submission deadline: June 15th, 2012 ** Notification deadline: June 20th, 2012 *** Proceedings will be published in Lecture Notes in Computer Science - Springer **** Three special issues on the following journals: Immunomics Research journal Evolutionary Intelligence Natural Computing ***** Plenary Speakers: - Piero Mastroeni, University of Cambridge, UK - Stephanie Forrest, University of New Mexico, USA ****** Tutorial Speaker: - Christian Blum, Universitat Politecnica de Catalunya, Spain - Luca Zammataro, Italian Institute of Technology - Center of Genomic Science, Italy ******************************************************************************** ICARIS 2012 is divided into two main tracks: * 28 and 29 August 2012: Computational Immunology, Immunoinformatics & Systems Immunology http://www.artificial-immune-systems.org/icaris/2012/callForPapers.php (for Oral Presentations & Posters submission) * 30 and 31 August 2012: Immunological Computation, Immune-inspired Engineering, Immune-inspired Heuristics https://www.easychair.org/conferences/?conf=icaris2012 (for Full papers submission) http://www.artificial-immune-systems.org/icaris/2012/callForPapers.php (for Oral Presentations & Posters submission) ******************************************************************************** We look forward to welcoming you to Taormina in August 2012. C. Coello Coello, J. Greensmith, N. Krasnogor, P. Lio', G. Nicosia, M. Pavone. Publicity Chairs: German Terrazas Angulo, Nareli Cruz Cortes, Renato Umeton -- German Terrazas, Ph.D. Research Fellow Interdisciplinary Computing and Complex Systems (ICOS) School of Computer Science Jubilee Campus, University of Nottingham Nottingham NG8 1BB United Kingdom website: http://www.cs.nott.ac.uk/~gzt This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. From hlapp at gmx.net Tue Apr 24 13:50:45 2012 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 24 Apr 2012 13:50:45 -0400 Subject: [BiO BB] Call for Software Bazaar entries open for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) Message-ID: The Call for Software Bazaar entries is now open for the 2012 conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), at http://ievobio.org/ocs2/index.php/ievobio/2012. See below for instructions. The Software Bazaar features presenters demonstrating their software live on a laptop. At iEvoBio, this session takes the place of a poster session, and will be approximately 2.0 hours in duration. Conference attendees will be able to walk from one demonstration to the next and talk with the presenters. Please also see our FAQ (http://ievobio.org/faq.html). Entries should be software aimed at advancing research in phylogenetics, evolution, and biodiversity, and can include interactive visualizations that have been pre-computed (such as SVGs, or Google Earth-compatible KML files). Note that commercial marketing activities are not permitted - presenters wishing to promote commercial or proprietary services or products should contact the Evolution conference about exhibitor space (http://www.confersense.ca/Evolution2012). Submissions consist of a title, which will typically be the name of the software (or visualization method) being presented, the URL of a website where more information can be obtained, and the license under which the source code is available. The website must contain a link to where the source code (and possibly binaries) can be downloaded. If it is not obvious from the website, the submission must describe what the software does. Reviewers will judge whether a submission is within scope of the conference (see above), and need to be able to verify whether the open-source requirement(*) is met. Presenters are expected to bring their own laptops for presentation, and any auxiliary devices necessary (such as a mouse). Power will be available at the presentation tables (110V/60Hz, US-style plugs; international presenters need to bring a suitable adaptor). Please let the organizing committee know as much in advance as possible if you expect to have unusually high demands for wireless network bandwidth, a large display, or other hardware. Review and acceptance of Software Bazaar submissions will be on a rolling basis. The deadline for submission is the morning of the first day of the conference (July 10), but, because space for Software Bazaar presentations is finite, we cannot guarantee the availability of slots for late submissions. We cannot accept submissions until the open-source requirements are met. Software Bazaar demonstrations are only 1 of 5 kinds of contributed content that iEvoBio will feature. The other 4 are: 1) Full talks (closed), 2) Lightning talks, 3) Challenge entries, and 4) Birds-of-a-Feather gatherings. The Calls for Challenge entries (http://ievobio.org/challenge.html) and Lightning Talks (same submission URL as above) remain open, and the Birds-of-a-Feather call is forthcoming. More details about the conference and program are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/iEvoBio and Google+ page, or subscribe to the low-traffic iEvoBio announcements mailing list at http://groups.google.com/group/ievobio-announce. iEvoBio 2012 is sponsored by the US National Evolutionary Synthesis Center (NESCent) and by Biomatters Ltd., in partnership with the Society for the Study of Evolution (SSE) and the Systematic Biologists (SSB). The iEvoBio 2012 Organizing Committee: Hilmar Lapp, US National Evolutionary Synthesis Center (chair) Robert Beiko, Dalhousie University Nico Cellinese, University of Florida and Florida Museum of Natural History Robert Guralnick, University of Colorado at Boulder Rebecca Kao, Denver Botanic Gardens Ellinor Michel, Natural History Museum, London Nadia Talent, Royal Ontario Museum Andrea Thomer, University of Illinois at Urbana-Champaign (*) iEvoBio and its sponsors are dedicated to promoting the practice and philosophy of Open Source software development (see http://www.opensource.org/docs/definition.php) and reuse within the research community. For this reason, software to be demonstrated to conference attendees must be licensed with a recognized Open Source License (see http://www.opensource.org/licenses/), and be available for download, including source code, by a tar/zip file accessed through ftp/http or through a widely used version control system like cvs, Subversion, git, Bazaar, or Mercurial. Authors are advised that non-compliant submissions must be revised to meet the requirement by July 8 at the latest, and in the event that presentation slots run out, precedence is established by the date they are first found in compliance, not the date of submission. From jprudhomme at healthtech.com Tue Apr 24 13:50:28 2012 From: jprudhomme at healthtech.com (James Prudhomme) Date: Tue, 24 Apr 2012 13:50:28 -0400 Subject: [BiO BB] Structure-Based Drug Design: Discount Deadline Week to Register Message-ID: <010b01cd2242$bc446fc0$34cd4f40$@com> *** Please distribute this message to your colleagues. Thank you. *** Advanced Registration Discount Ends Friday, April 27 CHI and Bio-IT World Present the Twelfth Annual Structure-Based Drug Design: Predicting Biological and Kinetic Profiles from Structure June 6-8, 2012 Royal Sonesta Hotel Boston, Cambridge, MA http://www.healthtech.com/sbd About the event: Structure-based drug design took nearly two decades of multiple, parallel technological improvements to arrive at its current mainstream position in medicinal chemistry. Developments in computer graphics, high-power radiation sources, computational processing power, refinement protocols, virtual screening and crystallography were all necessary to create the environment for rapid, iterative structure-based drug discovery. Given the crisis facing the pharmaceutical industry in the translation of early stage drug discovery results, a different set of tools, concerned with algorithms and methods for developing best in class drugs that engage biological targets with kinetically optimized potency and selectivity will need to be refined. In this conference, we bring to focus recent advancements in this field from an experienced faculty. Keynote Address: Binding Kinetics in Drug Discovery David Swinney, Ph.D., CEO, Institute for Rare and Neglected Diseases Drug Discovery (iRND3) Themed Sessions: - Structure to Function - Free Energy Calculation and Molecular Dynamics Simulation - GPCR - Fragment-Based Design - Druggability and Kinetics-Based Drug Design - Trends and Advances Download a PDF brochure at http://www.healthtech.com/Conferences_Overview.aspx?ekfrm=111573&libID=11152 8 Advance registration discounts end on April 27. Register at https://chidb.com/register/2012/sbd/reg.asp or call 781-972-5400. To inquire about sponsoring and/or exhibiting, contact Jon Stroup at 781-972-5483, jstroup at healthtech.com Please contact me with any questions. James Prudhomme Cambridge Healthtech Institute 250 First Avenue, Suite 300 Needham, MA 02494 jprudhomme at healthtech.com From arockia_babu at imu.edu.my Fri Apr 27 00:14:51 2012 From: arockia_babu at imu.edu.my (Arockia Babu) Date: Fri, 27 Apr 2012 04:14:51 +0000 Subject: [BiO BB] Regarding the molecular modeling hands on training workshop Message-ID: <7F0B1AFE7497B74691B0A77D7D2EF2A81760A6A4@IMUBKJEXH03.imu.dir> Dear sir/madam, International Medical University will be organising three workshops on "Computational Chemistry Techniques in Drug Design" from 12th to 14th June 2012 at Bukit Jalil, Kuala Lumpur, Malaysia. More details can be found in the brochure attached. If you are willing to undertake these hands on training, kindly send us the dully filled registration form by email or fax along with your bank remittance copy. Further, I am pleased to inform you that these hands on training workshops have been awarded CPD points by Malaysian Medical Association (MMA) and Malaysian Pharmaceutical Society (MPS). The CPD points awarded by Malaysian Medical Association (MMA) as below, One day workshop-3 points Two days workshop-6 points Three days workshop-9 points The CPD points awarded by Malaysian Pharmaceutical Society (MPS) as below, One day workshop - 6 points Two days' workshop - 10 points 3 days' workshop - 15 points To know more about the speakers, kindly visit this link in Facebook http://www.facebook.com/pages/Computational-Chemistry-Techniques-in-Drug-Design-2012/105888072877921 Please don't hesitate to contact me for further information Regards, Dr. M. Arockia Babu Organising Chairman "The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. 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