From jeff at bioinformatics.org Fri May 3 06:23:55 2013 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri, 03 May 2013 06:23:55 -0400 Subject: [BiO BB] Free online conference today Message-ID: <5183903B.1060408@bioinformatics.org> Hi All, We're running a conference via WebEx today, and you're welcome to join us! Here's the URL for the conference website: http://www.bioinformatics.org/edu/BIFX13 And here's the WebEx meeting URL (password: Bioinformatics): https://bioinformaticsorg.webex.com/bioinformaticsorg/j.php?ED=214133457&UID=491603942&PW=NNzNhNWY1MTU0&RT=MiMxMQ%3D%3D Schedule: 12:00-12:45 GMT (8:00-8:45 AM EDT) GPS Raghava, PhD Institute of Microbial Technology, Chandigarh, India Designing therapeutic peptides and proteins using Open Source Software 12:45-13:30 GMT Prasad Siddavatam, PhD Senior Bioinformatics Scientist, Seralogix, LLC, Austin, TX, USA Trends in Next Generation Sequencing (NGS) Technologies - Advances and Applications 13:30-14:15 GMT Vincent VanBuren, PhD Texas A & M University, USA Big Data in Biomedical Research: Inference of Transcriptional Regulation in Mouse Cardiac Development 14:30-16:00 GMT Special Track on Bioinformatics in Developing Countries Talks on career building in bioinformatics, review writing, virtual entrepreneurship in bioinformatics, women in biology and bioinformatics for industry, followed by a group dialogue Speakers: Mohana Latha on "Women in Biology" Rajdeep Poddar and Partha Das on "Bioinformatics for Industry" Prash Suravajhala, PhD on "Virtual Entrepreneurship and Review Writing" Poster Huy Vuong, PhD NIH Post Doctoral Fellow, Vanderbilt University in Nashville, USA Detection of somatic mutations: A data mining and a computational approach Videos and slides will also be available on the conference website for later viewing. Cheers, Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1-978-621-8258 -- From volunteers at iscbsc.org Fri May 3 04:57:14 2013 From: volunteers at iscbsc.org (Umesh Nandal) Date: Fri, 3 May 2013 10:57:14 +0200 Subject: [BiO BB] PLOS Computational Biology T-shirt competition Message-ID: *PLOS Computational Biology T-shirt competition* For the fourth year in a row, PLOS Computational Biology is calling on scientists and designers to send eye-catching designs that appeal to the computational biology community and encapsulate a recent advance or innovation in the field. The creator(s) of the winning design will receive a free t-shirt and a write-up of their design and research on PLOS Biologue. This year?s PLOS Computational Biology t-shirt will debut at *July?s ISMB/ECCB 2013 meeting in Berlin*. To enter the competition, send your design to ploscompbiol[at]plos.org by *Tuesday May 14th 2013*. For more details and design requirements for the competition go the following link: http://blogs.plos.org/biologue/2013/04/12/we-want-you-to-design-the-2013-plos-computational-biology-t-shirt/ Regards, ISCB Student Council for PLOS Computational Biology From jprudhomme at healthtech.com Tue May 7 12:57:32 2013 From: jprudhomme at healthtech.com (James Prudhomme) Date: Tue, 7 May 2013 12:57:32 -0400 Subject: [BiO BB] Structure-Based Drug Design: Genome to Drug Lead with Big Data Approach Message-ID: <00ea01ce4b43$f7749db0$e65dd910$@com> ******** Register by Friday, May 10 at the Advance Discount Rate******** ************************************************************************** CHI/Bio-IT World's 13th Annual Structure-Based Drug Design: Genome to Drug Lead with Big Data June 19-21, 2013- The Revere Hotel - Boston, MA http://www.healthtech.com/sbd ************************************************************************** At CHI/Bio-IT World's thirteenth annual Structure-Based Drug Design conference, you will hear about developments in insilico technology, as well as experimental approaches useful for accurately predicting and modeling the structures of proteins in structure-based drug design efforts. In addition, examples of successful applications of such technology approaches to genome-to-drug lead investigations will be addressed. Keynote Presentation: Drugging the Undruggable: Transforming Nature's ?-Helix into Breakthrough Medicines Tomi Sawyer, Ph.D., CSO, Aileron Therapeutics Sessions: * Structure-Based Drug Design for Kinase * Drug Resistance * Force Field Calculation * GPCR * Water & Solvation in Drug Design * Fragment-Based Drug Design * Protein-Protein Interaction * Epigenetic Targeting Scientific Advisory Board: Dr. Don Jacobs, University of North Carolina Charlotte Dr. Jon Mason, Heptares Therapeutics Ltd. Dr. Stephan Schurer, University of Miami Dr. Xiayang Qiu, Pfizer, Inc. Dr. David Dalgarno, ARIAD Pharmaceuticals, Inc. Dr. Gergely Toth, University of Cambridge Dr. Scot Mente, Pfizer Global R&D Groton Labs CALL FOR POSTERS: CHI invites researchers to present a poster to expose their research to its delegates. Accepted posters will be included in the conference proceedings. http://www.healthtech.com/Conferences_Overview.aspx?id=88586 DOWNLOAD PDF BROCHURE: http://www.healthtech.com/Conferences_Content.aspx?ekfrm=122075 HOW TO REGISTER: Web: https://chidb.com/register/2013/sbd/reg.asp Call: 781-972-5400 Email: reg at healthtech.com From amelia.ireland at gmod.org Thu May 23 13:51:06 2013 From: amelia.ireland at gmod.org (Amelia Ireland) Date: Thu, 23 May 2013 10:51:06 -0700 Subject: [BiO BB] GMOD Summer School Message-ID: Learn how to get started with GMOD's toolkit for genetics and genomics, GMOD in the Cloud! July 19-23, 2013; NESCent, Durham, North Carolina http://gmod.org/wiki/2013_GMOD_Summer_School The 2013 GMOD Summer School is the best way to get to grips with GMOD in the Cloud, GMOD's suite of genomic and genetic software. Over five days, attendees will learn how to install, configure, and run popular GMOD software for visualization, storage, and dissemination of genetic and genomic data. The following software is covered: - Chado, a species-independent database schema covering many areas of genetic and genomic data; - GBrowse, the ubiquitous genome browser; - GBrowse syn, a synteny browser built on GBrowse; - Galaxy, analysis and computation pipeline; - JBrowse, genome browsing evolved; - MAKER, automated annotation pipeline; - Tripal, a slick web interface for displaying and editing data from Chado; and - WebApollo, distributed community genome annotation tool (built on JBrowse). There are additional sessions on setting up a GMOD in the Cloud virtual machine in the Amazon cloud, and common file formats. Courses are taught by members of the software development teams, and there are work sessions in the evenings for participants to talk to the developers or apply what they have been taught to their own data. For more information and to apply, visit http://gmod.org/wiki/2013_GMOD_Summer_School. There are some scholarship funds available for those from underrepresented minorities. All applications should be in by June 10th. If you have any questions, please contact the GMOD help desk at help at gmod.org. Hope to see you there! Thanks, Amelia Ireland GMOD Community Support http://gmod.org || @gmodproject From cannataro at unicz.it Tue May 28 13:55:19 2013 From: cannataro at unicz.it (Mario Cannataro) Date: Tue, 28 May 2013 19:55:19 +0200 (CEST) Subject: [BiO BB] Euro-Par 2013 (Deadline Extended) - High Performance Bioinformatics and Biomedicine (HiBB) In-Reply-To: <5841aa156eb8a359174b4b409bd82f18.squirrel@email.unicz.it> References: <49488aa30fce78e7e8b644f2b6443229.squirrel@email.unicz.it> <0b90f151c841a8029f34aa95146d4a02.squirrel@email.unicz.it> <637f7d51898906671cc8ef02e2be2ccc.squirrel@email.unicz.it> <2bfa571d2421ca5842919c2d8038f74e.squirrel@email.unicz.it> <057ca61063d2df86dbfedb3f33fe06f8.squirrel@email.unicz.it> <29b4f0ef371de5adb52505f83a1d153a.squirrel@email.unicz.it> <8a9b80c485a3eac1ad09c3134eb1841d.squirrel@email.unicz.it> <5ef1e4bd7aebe7bd69da47a45ee9d058.squirrel@email.unicz.it> <8e6a0eaa020399bfb82507040c017757.squirrel@email.unicz.it> <5841aa156eb8a359174b4b409bd82f18.squirrel@email.unicz.it> Message-ID: <32aeb4557cb3495b03c4411723800615.squirrel@email.unicz.it> I apologize for any cross-posting of this announcement. ===================================================================== 4th International Workshop on High Performance Bioinformatics and Biomedicine (HiBB) http://staff.icar.cnr.it/cannataro/hibb2013/ held in conjunction with Euro-Par 2013 Aachen, Germany August 26-30, 2013 http://www.europar2013.org ===================================================================== DEADLINE EXTENDED TO: JUNE 10, 2013 ===================================================================== * * * CALL FOR PAPERS * * * ===================================================================== High-throughput technologies (e.g. microarray and mass spectrometry) and clinical diagnostic tools (e.g. medical imaging) are producing an increasing amount of experimental and clinical data. In such a scenario, large-scale databases and bioinformatics tools are key tools for organizing and exploring biological and biomedical data with the aim to discover new knowledge in biology and medicine. High-performance computing may play an important role in many phases of life sciences research, from raw data management and processing, to data analysis and integration, till data exploration and visualization. In particular, at the raw data layer, Grid infrastructures may offer the huge data storage needed to store experimental and biomedical data, while parallel computing can be used for basic pre-processing (e.g. parallel BLAST) and for more advanced analysis (e.g. parallel data mining). In such a scenario, novel parallel architectures (e.g. e.g. CELL processors, GPUs, FPGA, hybrid CPU/FPGA) coupled with emerging programming models may overcome the limits posed by conventional computers to the mining and exploration of large amounts of data. At an higher layer, emerging biomedical applications need to use in a coordinated way both bioinformatics tools, biological data banks and patient?s clinical data, that require seamless integration, privacy preservation and controlled sharing. Service Oriented Architectures and semantic technologies, such as ontologies, may allow the building and deployment of the so-called ?collaboratories? where remote scientists may conduct experimental research in a collaborative way. The goal of HiBB is to bring together scientists in the fields of high performance computing, computational biology and medicine to discuss, among the others, the organization of large-scale biological and biomedical databases and the parallel implementation of bioinformatics algorithms and biomedical applications. 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 applications of parallel and high performance computing to biology and medicine. Topics of interest include, but are not limited to: - Large scale biological and biomedical databases - Data integration and ontologies in biology and medicine - Parallel bioinformatics algorithms - Parallel visualization and exploration of biomedical data - Parallel visualization and analysis of biomedical images - Computing environments for large scale collaboration - Scientific workflows in bioinformatics and biomedicine - (Web) Services for bioinformatics and biomedicine - Grid Computing for bioinformatics and biomedicine - Peer-To-Peer Computing for bioinformatics and biomedicine - Emerging architectures and programming models (e.g. Cell, GPUs) for bioinformatics and biomedicine - Parallel processing of bio-signals - Modeling and simulation of complex biological processes PROGRAM The workshop will take place on August 26 or 27, 2013 (To Be Announced). It is scheduled as half-day. The program is not available yet. PAPER SUBMISSION, REGISTRATION AND PUBLICATION We invite original previously unpublished contributions. Submission implies that at least one author will register for the workshops at Euro-Par 2013 and present the paper in the workshop session, if accepted. Full papers should not exceed 10 pages in the Springer LNCS style (http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0). Download LNCS Latex style here (ftp://ftp.springer.de/pub/tex/latex/llncs/latex2e/llncs2e.zip). Springer's author guidelines are available here. Paper submission has to be performed by using the HiBB-2013 EasyChair submission server (https://www.easychair.org/conferences/?conf=hibb2013). In case of problems, authors may send their manuscript in PDF to the workshop chair: cannataro AT unicz.it. Papers accepted for publication must also be supplied in source form (Latex or Word). All accepted and presented papers will be included in the Workshops proceedings that will be published in a separate Springer LNCS Euro-Par 2013 Workshop volume after the conference. Authors of accepted papers will be required to sign up a Springer copyright form. 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. IMPORTANT DATES Workshop papers due: June 10, 2013 (Deadline Extended) Workshop author notification: July 8, 2013 Revised papers to be distributed at the workshop due: July 29, 2013 Workshop session: August 26 or 27, 2013 Important dates for EuroPar Workshop Proceedings preparation Workshop camera-ready papers for Euro-Par Workshop Proceedings due: October 3, 2013 WORKSHOP ORGANIZER Mario Cannataro, University Magna Gr?cia of Catanzaro, Italy PROGRAM COMMITTEE (TO BE CONFIRMED) 1. Pratul K. Agarwal, Oak Ridge National Laboratory, USA 2. David A. Bader, College of Computing, Georgia University of Technology, USA 3. Ignacio Blanquer; Universidad Polit?cnica de Valencia, Valencia, Spain 4. Daniela Calvetti, Case Western Reserve University, USA 5. Werner Dubitzky, University of Ulster, UK 6. Ananth Y. Grama, Purdue University, USA 7. Concettina Guerra, University of Padova, Italy 8. Vicente Hern?ndez, Univ. Polit?cnica de Valencia, Spain 9. Salvatore Orlando, University of Venezia, Italy 10. Horacio Perez-Sanchez, University of Murcia, Spain 11. Omer F. Rana, Cardiff University, UK 12. Richard Sinnott; National e-Science Centre, University of Glasgow, Glasgow, United Kingdom 13. Fabrizio Silvestri, ISTI-CNR, Italy 14. Erkki Somersalo, Case Western Reserve University, USA 15. Paolo Trunfio, University of Calabria, Italy 16. Albert Zomaya, University of Sydney, Australia From patrick at bioplanet.com Thu May 30 17:25:44 2013 From: patrick at bioplanet.com (Patrick Miller) Date: Thu, 30 May 2013 16:25:44 -0500 Subject: [BiO BB] We need your input! Message-ID: Bioinformatics.org Members, My name is Patrick Miller, with BioPlanet.com. Our goal at bioplanet is to engage the NGS informatics community with information, tools, and discussion, while building transparency amongst the field. BioPlanet is the same site that brought you the GCAT tool for comparing different alignment and variant calling algorithms (check it out at http://www.bioplanet.com/gcat). Anyway, we are currently trying to gather some very interesting information and put together really cool infographics about the NGS informatics space. To do so, we need as many survey respondents as possible, so please fill out our survey!!!!!! *Plus, each survey respondent gets a free $25 gift card to restaurant.com, so that's worth it right?! * The link to the survey is: http://fluidsurveys.com/s/bioplanetNGS/ Again, just looking to get as many people involved as possible. If you have any questions or want more info, just email me at patrick at bioplanet.com. Thanks, Patrick & The BioPlanet Team