From hlapp at gmx.net Sat Mar 3 15:19:20 2012 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 3 Mar 2012 15:19:20 -0500 Subject: [BiO BB] Call for Abstracts open for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) Message-ID: The Call for Abstracts for full talks 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. Accepted talks will be 15 minutes in length and will be presented during the full talk session of the conference. Because the number of program slots for full talks is limited, some talks may be moved to the Lightning Talk session (5 minutes in length). Submitted talks should be in the area of informatics aimed at advancing research in phylogenetics, evolution, and biodiversity, including new tools, cyberinfrastructure development, large-scale data analysis, and visualization. Submissions should be 1 page long at most and include a title, a list of contributors, and an abstract. The abstract should provide an overview of the talk's subject, and give enough detail to allow reviewers to decide whether the submission merits a full talk, or whether it should be moved to a Lightning Talk session. If the subject of the talk is a specific software component for use by the research community, the abstract must state the license and give the URL where the source code is available so reviewers can verify that the open-source requirement(*) is met. The deadline for submission is April 2, 2012. We intend to notify authors of accepted talks before early registration for iEvoBio (and Evolution) ends. Further instructions for submission are at the following URL: http://ievobio.org/ocs2/index.php/ievobio/2012/schedConf/cfp Full talks are one of the five kinds of contributed content that feature in iEvoBio. The other four are: 1) Lightning talks (5 mins long), 2) Challenge entries, 3) Software bazaar demonstrations, and 4) Birds-of-a-Feather gatherings. The Call for Challenge entries is already open (see http://ievobio.org/challenge.html). The calls for contribution to the other three sessions will open later, and will remain open until shortly before the conference or until the respective track fills up. In addition, 2012 iEvoBio sponsor Biomatters Ltd will be running the Geneious Challenge alongside this year?s iEvoBio Challenge, see http://ievobio.org/geneious_challenge.html for more information. 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, if a submitted talk concerns a specific software system for use by the research community, that software 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 of full talks who cannot meet this requirement at the time of submission should state their intentions, and are advised that the requirement must be met by July 9, 2012, at the latest. From djwild at indiana.edu Sun Mar 4 12:43:01 2012 From: djwild at indiana.edu (David Wild) Date: Sun, 4 Mar 2012 12:43:01 -0500 Subject: [BiO BB] New Introductory Cheminformatics eBook available Message-ID: All, I'm pleased to announce the availability of a new eBook called Introducing Cheminformatics. The eBook is derived from learning materials used at Indiana University, and gives an intensive introduction to cheminformatics, including the history of the field, representing 2D and 3D chemical structures on computer, storing and using databases of chemical and related biological information, handling chemical information on the web and in the scholarly literature, and giving an overview of some advanced topics such as use of cheminformatics in chemistry libraries, clustering and diversity, QSAR and predictive modeling, 3D alignment and docking, and software toolkits cheminformatics software. The eBook is provided in PDF format, and is split into 12 lessons, each focusing on a particular area of cheminformatics. The first six are focused on the foundational aspects of the field, such as representing 2D structures, and the remaining six cover more advanced applications in the field. Each lesson details learning objectives and concludes with a set of questions that are designed to be thought provoking, with responses and answers in a final chapter. The text is hyperlinked to current resources on the web, with references to pertinent external articles where appropriate. The eBook is designed for chemistry, library science and other students needing an introduction to the field, and also would be suitable for professional life science or computing practitioners who need a rapid, flexible introduction to this field. The eBook is available on LuLu for $29 at http://www.lulu.com/product/ebook/introducing-cheminformatics/18934281 (a preview is also available at the site). Please feel free to forward this to anyone who might be interested David ____________________________________________________ Dr. David J. Wild, djwild at indiana.edu, http://djwild.info Assistant Professor of Informatics & Computing Director, Cheminformatics & Chemogenomics Research Group Indiana University School of Informatics and Computing 150 S. Woodlawn Rm 330B, Bloomington, IN 47405 Tel. +1 812 856 1848 From jprudhomme at healthtech.com Wed Mar 7 12:41:43 2012 From: jprudhomme at healthtech.com (James Prudhomme) Date: Wed, 7 Mar 2012 12:41:43 -0500 Subject: [BiO BB] Structure-Based Drug Design: March 9 Deadline Message-ID: <060801ccfc89$8fc36c50$af4a44f0$@com> *** Please distribute this message to your colleagues. Thank you. *** 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 Early registration rate ends on March 9, 2012. 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 Early registration discounts end on March 9. 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 ngadewal at yahoo.com Tue Mar 6 23:30:49 2012 From: ngadewal at yahoo.com (nikhil gadewal) Date: Tue, 6 Mar 2012 20:30:49 -0800 (PST) Subject: [BiO BB] MSA on webserver Message-ID: <1331094649.20143.YahooMailNeo@web39404.mail.mud.yahoo.com> Dear?all, We are?developing a database, where?the sequences has to be aligned using multiple sequence alignment and the output to be displayed. My query is that, a readymade script, tool or package available (installed on or webserver) where, the?sequences to be aligned in a given as input in fasta format in text file. The?MSA?will only be performed using default parameter and output will be displayed on our server. Any example (demo) if provided will be helpful. The other option, is any server (online tool) available which can take our sequences as input and send a output to our server which we can displayed. Please let me know any other possibility or other way to solve this problem. Thanking you in advance. Thanks & regards, Nikhil Gadewal From dan.bolser at gmail.com Fri Mar 9 08:38:05 2012 From: dan.bolser at gmail.com (Dan Bolser) Date: Fri, 9 Mar 2012 13:38:05 +0000 Subject: [BiO BB] MSA on webserver In-Reply-To: <1331094649.20143.YahooMailNeo@web39404.mail.mud.yahoo.com> References: <1331094649.20143.YahooMailNeo@web39404.mail.mud.yahoo.com> Message-ID: You can have a look a JalView, which, I think, does all this. On 7 March 2012 04:30, nikhil gadewal wrote: > Dear?all, > > We are?developing a database, where?the sequences has to be aligned using multiple sequence alignment and the output to be displayed. > > My query is that, a readymade script, tool or package available (installed on or webserver) where, the?sequences to be aligned in a given as input in fasta format in text file. The?MSA?will only be performed using default parameter and output will be displayed on our server. Any example (demo) if provided will be helpful. > > The other option, is any server (online tool) available which can take our sequences as input and send a output to our server which we can displayed. > > Please let me know any other possibility or other way to solve this problem. > > Thanking you in advance. > > Thanks & regards, > Nikhil Gadewal > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb From hlapp at gmx.net Tue Mar 13 21:23:02 2012 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 13 Mar 2012 21:23:02 -0400 Subject: [BiO BB] Call for Lightning Talks now open for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) Message-ID: <22298399-7E0D-47B0-B603-9DF5773AA56E@gmx.net> The Call for Lightning Talks 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. Lightning talks are short presentations of 5 minutes. They are ideal for drawing the attention of the audience to new developments, tools, and resources, or to subsequent events where more in-depth information can be obtained. Please also see our FAQ for more information (http://ievobio.org/faq.html#lightning). Lightning talks will be part of the more interactive program elements on both conference days. Submitted talks should be in the area of informatics aimed at advancing research in phylogenetics, evolution, and biodiversity, including new tools, cyberinfrastructure development, large-scale data analysis, and visualization. Submissions should be 1 page long at most and include a title, a list of contributors, and an abstract. The abstract should provide an overview of the talk's subject. Reviewers will judge whether a submission is within scope of the conference (see above). If applicable, the abstract must also state the license and give the URL where the source code is available so reviewers can verify that the open-source requirement(*) is met. Review and acceptance of lightning talks will be on a rolling basis. The deadline for submission is the morning of the first day of the conference (July 10), but see below. Further instructions for submission are at the following URL: http://ievobio.org/ocs2/index.php/ievobio/2012/schedConf/cfp Please make sure to choose the Lightning Talks track for your submission. Note that the number of lightning talk slots is finite and that therefore the track may fill up early. We cannot accept lightning talks until the open-source requirements are met, and so waiting with that until the deadline risks that the track is full by that time. We ask all submitters of lightning talks to be willing to also serve as reviewers of such, as described above. Lightning talks are only 1 of 5 kinds of contributed content that iEvoBio will feature. The other 4 are: 1) Full talks (open until April 2), 2) Challenge entries, 3) Software bazaar demonstrations, and 4) Birds-of- a-Feather gatherings. The Call for Challenge entries remains open (see http://ievobio.org/challenge.html). The calls for contribution to the other two sessions will open later, and will remain open until shortly before the conference or until the respective track fills up. In addition, 2012 iEvoBio sponsor Biomatters Ltd will be running the Geneious Challenge alongside this year?s iEvoBio Challenge, see http://ievobio.org/geneious_challenge.html for more information. 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, if a submitted talk concerns a specific software system for use by the research community, that software 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. From bsdsig2012 at gmail.com Thu Mar 15 10:05:08 2012 From: bsdsig2012 at gmail.com (BSD SIG) Date: Thu, 15 Mar 2012 10:05:08 -0400 Subject: [BiO BB] [Call for Submissions] Biological Systems Design 2012 - BSD-SIG @ ISMB 2012 - July 13, 2012, Long Beach, CA Message-ID: --------------------------------------------------------------------------------------------------- Apologies for cross-posting --------------------------------------------------------------------------------------------------- CALL FOR SUBMISSIONS SPECIAL INTEREST GROUP ON BIOLOGICAL SYSTEMS DESIGN (BSD-SIG 2012) Intelligent Systems for Molecular Biology (ISMB 2012) July 13, 2012 - Long Beach, CA USA Homepage: http://bsd2012.bme.jhu.edu/ Submission site: https://www.easychair.org/conferences/?conf=bsdsig2012 Email: bsd2012 at jhu.edu --------------------------------------------------------------------------------------------------- Important Dates: Paper submission: April 20, 2012 Author notification: May 4, 2012 Workshop: July 13, 2012 --------------------------------------------------------------------------------------------------- **General Information** The complexity of the genomic structure and our limited understanding of biological processes require new computational methods to investigate the huge number of possible designs for circuits, pathways, and entire genomes, with the ideal being the ability to model, simulate and redesign a biological system in-silicon prior to fabrication, similar to CAD/CAM for physical devices. Synthetic Biology aims to establish a standard and effective biological design flow, where biological systems are designed and verified computationally, before in vitro synthesis and in vivo experiments. Each phase of this process has multiple challenges ranging from managing high-throughput laboratory operations to developing new software and defining accurate and interoperable computational models. The Special Interest Group in Biological Systems Design (BSD-SIG 2012) aims to provide a broad view of the current state-of-the-art for scientists from biology, chemistry, computer science, mathematics and engineering. --------------------------------------------------------------------------------------------------- **Keynote Speakers** - Jef D. Boeke, Johns Hopkins University - Christodoulos A. Floudas, Princeton - Dan Gusfield, UC Davis - Nathan J. Hillson, Joint BioEnergy Institute **Invited Speakers** - Jake Beal, BBN Technologies - Michal Galdzicki, University of Washington School of Medicine - Sarah Richardson, Joint Genome Institute --------------------------------------------------------------------------------------------------- **Sessions** BSD-SIG is structured in four sessions: * Genome Design * Protein Design * Computer Aided Design Tools * Data management & standards **Genome Design** The availability of high-fidelity techniques for the synthesis of long DNA strands constitutes the starting point for effective pathway engineering. The aim of this session is to present state-of-the-art methods for genome design, focusing, but not limited to, on the following topics: oligo-nucleotides design, Probe and watermark design, High-throughput techniques, theoretical aspects of DNA design. **Protein Design** An important purpose of synthetic DNA is to express non-native or human-designed proteins. Protein expression and design introduce additional complexities. This session provides a forum to discuss the recent advances in this field, with particular emphasis on the design of therapeutic peptides and proteins. **Computer Aided Design Tools** The design of biological systems is often characterized by ad hoc, human-centric procedures, which limit applications to small-scale problems. While Computer-Aided-Design (CAD) tools are standard in many engineering fields, CAD capabilities for synthetic biology are at a very early stage. This session gives a broad view of some emerging approaches in Biological Design Automation (BDA), with the aim of finding and discussing new areas where CAD tools can improve and accelerate the synthesis of living matter. **Data management & standards** The enormous amount of data generated by high-throughput techniques and synthesis processes requires the introduction of new and specific representation schemes, along with efficient and open standards for interfacing different data sources. New systems are also required to collect information and performing on-line data analysis. The aim of this session is twofold: first, exploring data structures and representations for synthetic biology; second, promoting and discussing use-case scenarios for the Synthetic Biology Open Language (SBOL). --------------------------------------------------------------------------------------------------- **Submissions** We encourage submissions in the form of oral and poster presentation; authors must submit a 1 page abstract specifying the track and the form of the contribution. Two blind reviewers will review each submission, and suggest the most appropriate form for presentation. All the accepted abstracts will be published on the hands-out materials of BSD-SIG. Contributions must be submitted through EasyChair: https://www.easychair.org/conferences/?conf=bsdsig2012 --------------------------------------------------------------------------------------------------- We are looking forward to see you in Long Beach: Joel Bader, Doug Densmore, Swapnil Bathia and Giovanni Stracquadanio From cfp at cscjournals.org Thu Mar 15 15:14:32 2012 From: cfp at cscjournals.org (J. Stewart) Date: Thu, 15 Mar 2012 11:14:32 -0800 Subject: [BiO BB] CFP - INTERNATIONAL JOURNAL OF BIOMETRICS AND BIOINFORMATICS (IJBB) Message-ID: <001901cd02df$e18dedb0$2705a8c0@iss> CALL FOR PAPERS - INTERNATIONAL JOURNAL OF BIOMETRICS AND BIOINFORMATICS (IJBB) ISSN: 1985-2347 Volume 6, Issue 3 Info. at http://www.cscjournals.org/csc/journals/IJBB/journal_cfp.php?JCode=IJBB Computer Science Journals (CSC Journals) invites researchers, editors, scientists & scholars to publish their scientific research papers in an International Journal of Biometrics and Bioinformatics (IJBB) Volume 6, Issue 3. The International Journal of Biometric and Bioinformatics (IJBB) brings together both of these aspects of biology and creates a platform for exploration and progress of these, relatively new disciplines by facilitating the exchange of information in the fields of computational molecular biology and post-genome bioinformatics and the role of statistics and mathematics in the biological sciences. Bioinformatics and Biometrics are expected to have a substantial impact on the scientific, engineering and economic development of the world. Together they are a comprehensive application of mathematics, statistics, science and computer science with an aim to understand living systems. We invite specialists, researchers and scientists from the fields of biology, computer science, mathematics, statistics, physics and such related sciences to share their understanding and contributions towards scientific applications that set scientific or policy objectives, motivate method development and demonstrate the operation of new methods in the fields of Biometrics and Bioinformatics. CSC Journals anticipate and invite papers on any of the following topics: Bio-grid Data visualization Bio-ontology and data mining DNA assembly, clustering, and mapping Bioinformatics databases E-health Biomedical image processing (fusion) Fuzzy logic, Neural networks Biomedical image processing (registration) Gene expression and microarrays Biomedical image processing (segmentation) Gene identification and annotation Biomedical modeling and computer simulation Genetic algorithms Computational genomics & intelligence Hidden Markov models Computational proteomics High performance computing Computational structural biology Molecular evolution and phylogeny Molecular modeling and simulation Molecular sequence analysis Important Dates - IJBB CFP - Volume 6, Issue 3. Paper Submission: March 31, 2012 Author Notification: May 15, 2012 Issue Publication: June 2012 For complete details about IJBB archives publications, abstracting/indexing, editorial board and other important information, please refer to IJBB homepage. We look forward to receive your valuable papers. If you have further questions please do not hesitate to contact us at cscpress at cscjournals.org. Our team is committed to provide a quick and supportive service throughout the publication process. A complete list of journals can be found at http://www.cscjournals.org/csc/bysubject.php Sincerely, J. Stewart Computer Science Journals (CSC Journals) B-5-8 Plaza Mont Kiara, Mont Kiara 50480, Kuala Lumpur, Malaysia Tel: + 603 6207 1607, + 603 2782 6991 Fax:+ 603 6207 1697 Url: http://www.cscjournals.org From jmsallen12 at gmail.com Thu Mar 15 14:07:52 2012 From: jmsallen12 at gmail.com (James Allen) Date: Thu, 15 Mar 2012 14:07:52 -0400 Subject: [BiO BB] World's biggest fake conference in computer sci Message-ID: --- Better not to have a publication than to publish in WORLDCOMP and spoil the resume forever --- If you didn't know already, WORLDCOMP is the World's biggest fake conference in computer science http://sites.google.com/site/worlddump1 The next WORLDCOMP (consists of more than twenty different conferences) will be during July 16-19, 2012, USA. Hamid Arabnia (a professor in computer science from University of Georgia, USA) has been running this fake (bogus or junk or scam) conference business to collect registration fee for over a decade. He accepts almost all submitted papers but cheating that there is a review by "two experts". He accumulated millions of dollars by this business. If the above link didn't work, you may try http://copy-shake-paste.blogspot.com/2012/02/fake-conference-worldcomp.html If none of these links work, search internet using worldcomp bogus If you have a paper in WORLDCOMP 2011 or earlier, you may file a lawsuit against Hamid Arabnia because he cheated you about reviews, reviewers, acceptance policies and acceptance rates. Sincerely, James Allen LATEST NEWS (as of March 11, 2012): Hamid Arabnia removed his name and address (ie, University of Georgia, where he is working as a professor) from WORLDCOMP website. If the conference is not fake, why he removed them suddenly? Who is the chair/coordinator of this bogus conference now? There are no committee members, keynote speeches and sponsors. The draft paper submission date is quietly extended. Why is Hamid Arabnia still running the fake conference anonymously and for whose benefit? We ask him to answer all these questions. This is the first time (in the entire world) a conference is running without the chair/coordinator name listed. Hamid Arabnia may soon bring another person (just for name sake) as the chair of WORLDCOMP and still Hamdid Arabnia run it from behind the scenes forever. From s.gugushvili at vu.nl Thu Mar 15 11:15:13 2012 From: s.gugushvili at vu.nl (Gugushvili, S.) Date: Thu, 15 Mar 2012 15:15:13 +0000 Subject: [BiO BB] Workshop on Parameter Estimation for Dynamical Systems Message-ID: ***ANNOUNCEMENT*** Workshop on Parameter Estimation for Dynamical Systems (PEDS-II) Date: 4-6 June 2012 Location: Eurandom, Eindhoven, The Netherlands Summary: Differential equations (deterministic or stochastic) play a fundamental role in modelling dynamic phenomena in fields as diverse as physics, biology, finance, engineering, chemistry, biochemistry, neuroscience, ecology, meteorology, pharmacology and others. Models defined via differential equations (or systems of differential equations) usually depend on finite- or possibly infinite-dimensional parameters. In order to obtain a model that is useful in practice, it is critical to know these parameters, or to estimate them in case they are unknown. The workshop aims at providing a meeting place for researchers and practitioners in the area of parameter estimation for deterministic and stochastic differential equations, who will review different methods used to tackle the problems arising in these fields, assess the achieved progress and identify future research directions. It is hoped that by bringing together experts in statistical estimation for differential equations, a fertile ground for exchange of mutually beneficial ideas will be created. The emphasis of the workshop is on presentation of new methodological work with a good balance from applications. Importantly, appropriateness of either deterministic or stochastic models in various contexts will be discussed and due attention to both the frequentist and the Bayesian approaches to parameter estimation of differential equations will be paid. The workshop is a follow-up on the Workshop on Parameter Estimation for Dynamical Systems (PEDS-I) held on 8-10 June 2009 at Eurandom. Invited speakers: Florence d'Alch?-Buc (Universit? d'Evry-Val d'Essonne), Lorenz Biegler (Carnegie Mellon University), Mark Girolami (University College London), Rikkert Hindriks (Universiteit Twente), Stefano Iacus (Universit? degli Studi di Milano), Lennart Ljung (Link?pings universitet), Markus Rei? (Humboldt-Universit?t zu Berlin), Michael S?rensen (University of Copenhagen), Eberhard Voit (Georgia Institute of Technology), Darren Wilkinson (Newcastle University), Harry van Zanten (Eindhoven University of Technology). Registration: Registration is mandatory for participation in the workshop and can be done through the workshop website. The registration fee is ?100. There is no closing date for registration, but the number of places is limited. Participants will be given an opportunity to present talks and posters on their research. Organisers: Chris Klaassen (Universiteit van Amsterdam & Eurandom), Aad van der Vaart (Vrije Universiteit & Eurandom), Shota Gugushvili (Vrije Universiteit) and Bart Bakker (Philips Research). For additional information please visit the workshop website: http://www.few.vu.nl/~shota/peds2.php From jigar.halani at wipro.com Fri Mar 16 03:10:26 2012 From: jigar.halani at wipro.com (jigar.halani at wipro.com) Date: Fri, 16 Mar 2012 07:10:26 +0000 Subject: [BiO BB] 19th IEEE International Conference on HPC (HiPC 2012) Message-ID: <570CCE1B70440E41AC71CE961741809542912EAA@BLR-EC-MBX3.wipro.com> ********************************************************************* C A L L F O R P A P E R S 19th IEEE International Conference on High Performance Computing (HiPC 2012) December 18-21, 2012 Pune, INDIA http://www.hipc.org Paper Submission Deadline: May 16, 2012 ********************************************************************* IMPORTANT DATES April 02, 2012 Conference Paper Submission Begins May 16, 2012 Conference Paper Submission Ends Mar1, 2012 Workshop Proposals Due July 31, 2012 Notification of Acceptance/Rejection Aug 18, 2012 Camera-Ready Paper Submission Sep 16, 2012 Student Symposium Submissions Due Oct 21, 2012 Student Symposium Accept/Reject Decisions Nov 14, 2012 Early Registration Deadline ------------------------------------------------------------------- The 19th annual IEEE International Conference on High Performance Computing (HiPC 2012) will be held at the Le Meridian hotel in Pune, India, during December 18-21, 2012. It will serve as a forum for researchers from around the world to present their current research efforts and findings, and will act as a venue for stimulating discussions and highlighting high performance computing (HPC) related activities in Asia. The conference has a history of attracting participation from reputed researchers from all over the world. HiPC 2012 will focus on the design and analysis of high performance computing and networking systems and their scientific, engineering, and commercial applications. In addition to technical sessions consisting of contributed papers, the conference will include invited presentations, a student research symposium, tutorials, and vendor presentations in the industry, user and research symposium. The 18th meeting, held in Bengaluru in December 2011, had 40 contributed papers chosen from 206 submissions from 22 countries, and more than 450 attendees. The 17th meeting, held in Goa in December 2010, had 40 contributed papers chosen from 208 submissions from 22 countries, and more than 280 attendees. The 16th meeting, held in Kochi, India in December 2009, had 49 contributed papers that were selected from 261 submissions from 20 countries, and about 225 participants attended the meeting. Further information about HiPC 2012 and the HiPC series of meetings is available on the conference website at http://www.hipc.org. -------------------------------------------------------------------- CO-SPONSORED BY: * IEEE Computer Society Technical Committee on Parallel Processing (TCPP) - Pending * HiPC Education Trust IN COOPERATION WITH: * ACM Special Interest Group on Computer Architecture (SIGARCH) - Pending * European Association for Theoretical Computer Science - Pending * IFIP Working Group on Concurrent Systems - Pending * National Association of Software and Service Companies (NASSCOM) - Pending * Manufacturers' Association for Information Technology (MAIT) - Pending ------------------------------------------------------------------- VENUE AND MEETING INFORMATION HiPC will be held at Pune, India. The advance program will be available in early August 2012. Please check the conference website at http://www.hipc.org for updated information. -------------------------------------------------------------------- ======================= HiPC 2012 CALL FOR PAPERS ======================= Authors are invited to submit original unpublished research manuscripts that demonstrate current research in all areas of high performance computing including design and analysis of parallel and distributed systems, embedded systems, and their applications in scientific, engineering, and commercial areas. Topics of interest include but are not limited to: > High-Performance Computing > Parallel and Distributed Algorithms/Systems > Parallel Languages and Programming Environments > Hybrid Parallel Programming with GPUs and Accelerators > Load Balancing, Scheduling and Resource Management > Resilient/Fault-Tolerant Algorithms and Systems > Scientific/Engineering/Commercial Applications and Workloads > Emerging Applications such as Biotechnology and Nanotechnology > Cluster, Cloud, and Grid Computing > Heterogeneous Computing > Interconnection Networks and Architectures > Scalable Servers and Systems > High Performance/Scalable Storage Systems > Power-Efficient and Reconfigurable Architectures > Compiler Technologies for High-Performance Computing > Software Support and Advanced Micro-architecture Techniques > Operating Systems for Scalable High-Performance Computing One or more best paper awards will be given for outstanding contributed papers. Further details about call for student research symposium, workshops, tutorials, and exhibits, as well as submission guidelines are available at the conference website http://www.hipc.org. --------------------------------------------------------------------- MANUSCRIPT GUIDELINES Submitted manuscripts should be structured as technical papers and may not exceed 10 letter size (8.5 x 11) pages including figures, tables and references using the IEEE format for conference proceedings (print area of 6-1/2 inches (16.51 cm) wide by 8-7/8 inches (22.51 cm) high, two-column format with columns 3-1/16 inches (7.85 cm) wide with a 3/8 inch (0.81 cm) space between them, single-spaced 10-point Times fully justified text). Submissions not conforming to these guidelines may be returned without review. Authors should submit the manuscript in PDF format and make sure that the file will print on a printer that uses letter size (8.5 x 11) paper. The official language of the meeting is English. Manuscript submission will start on April 02, 2012. Manuscript submission procedures will then be available over the Web at http://www.hipc.org. Electronic submissions must be in the form of a readable PDF file. Manuscripts must be received by May 16, 2012. Manuscripts should demonstrate current research in any area of high performance computing. All manuscripts will be reviewed and will be judged on correctness, originality, technical strength, significance, quality of presentation, and interest and relevance to the conference attendees. Submitted papers must represent original unpublished research that is not currently under review for any other conference or journal. Papers not following these guidelines will be rejected without review and further action may be taken, including (but not limited to) notifications sent to the heads of the institutions of the authors and sponsors of the conference. Submissions received after the due date, exceeding length limit, or not appropriately structured may also not be considered. Authors may contact the Program Chair at the address below for further information or clarification. Notification of review decisions will be mailed by July 31, 2012. Camera-ready papers are due by August 18, 2012. A published proceedings will be available at the conference. Program Chair: Dhabaleswar K. (DK) Panda Ohio State University, USA Email: panda at cse.ohio-state.edu --------------------------------------------------------------------- WORKSHOPS Proposals are solicited for workshops to be held in conjunction with the main conference. Interested individuals should submit a proposal by March1, 2012 to the Workshops Chair. Additional details and submission guidelines will be available at the conference website. Workshops Co-Chairs: Pavan Balaji Argonne National Laboratory, USA Email: balaji at mcs.anl.gov Manimaran Govindarasu Iowa State University, USA Email: gmani at iastate dot edu Chiranjib Sur IBM, India Email: chiranjib.sur at in dot ibm dot com --------------------------------------------------------------------- STUDENT RESEARCH SYMPOSIUM HiPC 2012 will feature the FifthStudent Research Symposium (SRS) on High Performance Computing (HPC) aimed at stimulating and fostering student research, and providing an international forum to highlight student research accomplishments. The symposium will also expose students to the best practices in HPC in academia and industry. The one-day symposium will feature brief presentations by student authors on their research, followed by a poster exhibit. Short invited talks by leading HPC researchers/practitioners will be part of the program. The HiPC Conference Reception and Student Symposium Poster Exhibits will provide an opportunity for students to interact with HPC researchers, practitioners and recruiters from academia and industry. To be considered, students should submit a 5 page extended abstract of their research. Submissions will be reviewed and evaluated by the program committee for technical quality, innovative contributions, and presentation. Submission instructions will be available at the Student Symposium web site, accessible from http://www.hipc.org after August 15, 2012. For additional details, please visit the conference web site or contact the Symposium Co-Chairs. Symposium Co-Chairs: Ashok Srinivasan Florida State University Email: ashokpriya at yahoo dot com Yogesh Simmhan University of Southern California Email: simmhan at usc dot edu Symposium Coordinator: Kishore Kothappalli IIIT Hyderabad Email: kkishore at iiit dot ac dot in --------------------------------------------------------------------- INDUSTRY, RESEARCH AND USER SYMPOSIUM (IRUS) The HiPC Industry/User Symposium aims at bringing together the users / practitioners of HPC including both commercial and non-commercial users, and giving them a platform to share their challenges and successes, as well as to discuss relevant technology issues. Symposium IRUSCo-Chairs: Jigar Halani Wipro, India Email: jigar.halani at hipc dot org VipinChaudhary CRL, India Email: vipinc at gmail dot com --------------------------------------------------------------------- ============================== HiPC 2012 ORGANIZATION ============================== GENERAL CO-CHAIRS Ramamurthy Badrinath, HP, India Rama Govindaraju, Google, USA VICE GENERAL CO-CHAIRS Rajeev Muralidhar, Intel, India Manish Parashar, Rutgers University, USA PROGRAM CHAIR Dhabaleswar K. (DK) Panda, Ohio State University, USA PROGRAM VICE CHAIRS Algorithms: Yves Robert, ENS Lyon, France Applications: AdolfyHoisie, Pacific Northwest National Laboratory, USA Architecture: Ron Brightwell, Sandia National Laboratories, USA Software: Alan Sussman, University of Maryland, USA STEERING CHAIR Viktor K. Prasanna, University of Southern California, USA WORKSHOPS CO-CHAIRS Pavan Balaji, Argonne National Laboratory, USA Manimaran Govindarasu, Iowa State University, USA Chiranjib Sur, IBM, India STUDENT RESEARCH SYMPOSIUM CHAIR Ashok Srinivasan, Florida State University, USA Yogesh Simmhan, University of Southern California, USA INDUSTRY, RESEARCH, USER SYMPOSIUM CO-CHAIRS VipinChaudhary, CRL, India Jigar Halani, Wipro, India LOCAL COORDINATION CO-CHAIRS Seetharam Krishna, CRL, India Santhosh Daivajna, 8KMiles, India INDUSTRY EXHIBITS COORDINATOR Kalyana Krishna, NCSA, USA PUBLICATIONS CO-CHAIRS Hoang Le, Irvine Sensors Corporation, USA Ananth S. Narayan, Intel India Sushil K. Prasad, Georgia State University, USA PRODUCTION CHAIR Animesh Pathak, INRIA, France CYBER CHAIR Alok Kumbhare, University of Southern California, USA FINANCE CO-CHAIRS Ajay Gupta, Western Michigan University, USA ThondiyilVenugopalan, India PUBLICITY CO-CHAIRS Manisha Gajbe, NCSA, USA Neelima Bayyapu, NMAMIT, Nitte, India. Yinglong Xia, IBM, USA REGISTRATION CO-CHAIRS Sally Jelinek, Electronic Design Associates, USA JyothsnaKasturirengan, Fiberlink, India STEERING COMMITTEE Srinivas Aluru, Iowa State University, USA, IIT Bombay, India P. Anandan, Microsoft Research, India David A. Bader, Georgia Institute of Technology, USA Ramamurthy Badrinath, HP, India Frank Baetke, HP, USA Manish Bali, NVIDIA, India Luc Boug?, ENS Cachan, Brittany extension, France R. Govindarajan, Indian Institute of Science, India Rama Govindaraju, Google Inc., USA Manish Gupta, India Systems and Technology Lab, IBM, India Stefan Heinzel, Garching Computing Centre (RZG), Max Planck Society, Germany Victor Malyshkin, Russian Academy of Sciences, Russia Ashwini K. Nanda, HPC Research Inc. Siddhartha Nandi, NetApp, India Manish Parashar, Rutgers University, USA IshwarParulkar, Cisco, India Viktor K. Prasanna, University of Southern California, USA (Chair) Ramesh Rajagopalan, Dell India R&D, Bangalore, India VenkatRamana, Cray-Hinditron, India SartajSahni, University of Florida, USA LokendraShastri, Infosys, India Sunil Sherlekar, Intel, India SantoshSreenivasan, Talentain Technologies, India V. Sridhar, SRM Research Institute, India Harrick M. Vin, Tata Research, Development and Design Center (TRDDC), Pune, India Steering Committee 2012 membership also includes the general co-chairs, program chairs and vice general co-chairs from 2011, 2012 and 2013. From dan.bolser at gmail.com Tue Mar 20 19:33:44 2012 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 20 Mar 2012 23:33:44 +0000 Subject: [BiO BB] New online Machine Learning course from Caltech In-Reply-To: References: Message-ID: Here is the link: http://work.caltech.edu/telecourse.html From clements at galaxyproject.org Tue Mar 20 16:39:32 2012 From: clements at galaxyproject.org (Dave Clements) Date: Tue, 20 Mar 2012 13:39:32 -0700 Subject: [BiO BB] 2012 Galaxy Community Conference (GCC2012) Early Registration is Now Open In-Reply-To: References: Message-ID: Hello all, We are pleased to announce that early registration for the 2012 Galaxy Community Conference (GCC2012, http://galaxyproject.org/GCC2012) is now open. GCC2012 will be held July 25-27, at the UIC Forum, in Chicago, Illinois. The conference will feature two full days of presentations, discussions, lightning talks, and breakouts. We have also added a new full day of training this year, featuring 3 parallel tracks with four workshops each, covering seven different topics. The Galaxy Community Conference is for: * Sequencing core facility staff * Bioinformatics core staff * Bioinformatics tool and workflow developers * Bioinformatics focused principal investigators and researchers * Data producers * Power bioinformatics users This event is about integrating, analyzing, and sharing the diverse and very large datasets that are now typical in biomedical research. GCC2012 is an opportunity to share best practices with, and learn from, a large community of researchers and support staff who are facing the challenges of data-intensive biology. Galaxy is an open web-based platform for data intensive biomedical research (http://galaxyproject.org) that is widely used and deployed at research organizations of all sizes and around the world. Registration is very affordable, especially for post-docs and students. You can can save an additional 40% by registering on or before June 11. Conference lodging can also be booked. Low-cost rooms have been reserved on the UIC campus. You can also stay at the official conference hotel, at a substantial discount arranged for conference attendees. There are a limited rooms available in both, and you are encouraged to register early, if you would like to take advantage of these. Abstract submission is also open, from now through April 16. Abstract submissions on any topic of interest to the Galaxy community are strongly encouraged. See the Abstracts page for details. Dave Clements, on behalf of the GCC2012 Organizing Committee PS: Please help get the word out.? A flyer and graphics are at http://wiki.g2.bx.psu.edu/Events/GCC2012/Promotion. -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ From isbra-l at dna.engr.uconn.edu Tue Mar 20 20:31:43 2012 From: isbra-l at dna.engr.uconn.edu (ISBRA Mailing List) Date: Tue, 20 Mar 2012 20:31:43 -0400 Subject: [BiO BB] [ISBRA-L] ISBRA'12 -- short abstract submission deadline April 9, 2012 Message-ID: CALL FOR SHORT ABSTRACTS 8th International Symposium on Bioinformatics Research and Applications May 21-23, 2012, Dallas, Texas http://www.cs.gsu.edu/isbra/ The International Symposium on Bioinformatics Research and Applications (ISBRA) provides a forum for the exchange of ideas and results among researchers, developers, and practitioners working on all aspects of bioinformatics and computational biology and their applications. Submissions presenting original research are solicited in all areas of bioinformatics and computational biology, including the development of experimental or commercial systems. Topics of interest include but are not limited to: * Biomedical databases and data integration * Biomolecular imaging * Bio-ontologies * Comparative genomics * Computational genetic epidemiology * Computational proteomics * Data mining and visualization * Gene expression analysis * Genome analysis * High-performance bio-computing * High-throughput sequencing data analysis * Molecular evolution * Molecular modeling and simulation * Pattern discovery and classification * Population genetics * Software tools and applications * Structural biology * Systems biology Authors are invited to submit electronically short abstracts of up to 4 pages (in Springer LNCS format) by following the instructions at http://www.easychair.org/conferences/?conf=isbra2012 Accepted short abstracts will be published online and on CD-ROM and selected for either oral or poster presentation. As in previous years, authors of selected short abstracts will be invited to submit full versions to a peer-reviewed supplement to be published after the symposium in BMC Bioinformatics. KEY DATES FOR SHORT ABSTRACTS Submission deadline April 9, 2012 Notification of acceptance April 16, 2012 Final version due April 23, 2012 CONFIRMED KEYNOTE SPEAKERS Bhaskar Dasgupta (UIC) Cynthia Gibas (UNC Charlotte) Ambuj Singh (UCSB) Dong Xu (U. of Missouri) Michael Zhang (UT Dallas) STEERING COMMITTEE Dan Gusfield (UC Davis) Ion Mandoiu (UConn) Yi Pan (GSU), Chair Marie-France Sagot (INRIA) Alexander Zelikovsky (GSU) GENERAL CHAIRS Ovidiu Daescu (UT Dallas) Raj Sunderraman (GSU) PROGRAM CHAIRS Leonidas Bleris (UT Dallas) Ion Mandoiu (UConn) Russell Schwartz (Carnegie Mellon) Jianxin Wang (Central South Univ.) _______________________________________________ To modify subscription preferences or unsubscribe from the ISBRA-L mailing list visit http://dna.engr.uconn.edu/cgi-bin/mailman/options/isbra-l/bbb%40bioinformatics.org From m.francescatto at vumc.nl Tue Mar 20 08:35:49 2012 From: m.francescatto at vumc.nl (Francescatto, M.) Date: Tue, 20 Mar 2012 12:35:49 +0000 Subject: [BiO BB] 8th ISCB Student Council Symposium 2012 - last call for abstracts Message-ID: <8890C124EDA3C04189F7F22B2039EE4001A447@SP-MX-MBX3.vumc.nl> The 8th Symposium of ISCB Student Council 2012 will be held July 13 in Long Beach, California, as a satellite meeting of the ISMB conference. The opportunity to submit an abstract eligible for oral presentation is closing soon! As the central part of the symposium, 10 students will be selected for an oral presentation from the submitted abstracts. This is your chance to present your work to an international audience of young scientists. We welcome abstracts covering both scientific studies as well as novel tools and applications in the field of computational biology and bioinformatics. All abstracts accepted for oral presentation will be published in a special issue of BMC Bioinformatics journal. As in previous years, awards will be given to outstanding posters and presentations. Travel Fellowships are also available; all candidates are encouraged to apply. Abstract Deadline: April 2 Travel Fellowships Deadline: April 13 Submission information: http://symposium.iscbsc.org/content/submissions Travel Fellowship information: http://symposium.iscbsc.org/content/travel-fellowships Symposium website: http://symposium.iscbsc.org/ Please help spread the word by sharing this mail with your colleagues and collaborators. We look forward to receiving your abstract! Alexander Goncearenco Chair, SCS2012 Olga Botvinnik Co-Chair, SCS2012 From hlapp at gmx.net Wed Mar 21 11:39:51 2012 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 21 Mar 2012 11:39:51 -0400 Subject: [BiO BB] Call for Challenge entries for conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) Message-ID: <78DCBF56-D22D-466B-B7D5-2930B93BECF1@gmx.net> Many trees enter. Fresh analysis ensues. New insights emerge. The conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) is again holding a Challenge competition in 2012, on the theme "Synthesizing Phylogenies". Somewhere, buried in large sets of trees, lies a stunning new revelation, a baffling discovery, the answer to a longstanding controversy, or simply something not obvious to the naked eye. The mission of the 2012 iEvoBio challenge is to find those revelations, discoveries and answers within your own data and/or within one of the datasets provided by the challenge. What new scientifically interesting results can you pull from these trees, using any combination of techniques at your disposal? Further information on the nature of challenge entries and how to submit them can be found on the iEvoBio website at http://ievobio.org/challenge.html. Submissions are due by June 25, 2012. Selected candidates will make short oral presentations to demonstrate their work in a "Challenge session" at the conference, and if suitable will automatically be entered into the Software Bazaar track of the conference. Cash prizes will be awarded for first place (USD 1,500) and runner-up entries. The winning entries will be selected by a vote of the iEvoBio meeting participants. Alongside the iEvoBio Challenge, 2012 iEvoBio sponsor Biomatters Ltd is running the Geneious Challenge. The goal of this challenge is to develop a new plugin to Geneious Pro, using the public API, that enables a new and exciting visualization or analysis. The winning entry will receive a $1000 cash prize, and all entrants who submit by the deadline will receive a 12-month subscription license. The Geneious Challenge has the same open and closing dates as the iEvoBio Challenge. See http://ievobio.org/geneious_challenge.html for more information. Separate from iEvoBio, the Encyclopedia of Life (EOL) is leading a Phylogenetic Tree challenge to encourage not only the development of large phylogenies, but their practical use. Together with the Global Names project they will choose two winning entries: one for the best large tree and one for the most promising but not necessarily large tree -- both in Darwin Core Archive format suitable for use in major biodiversity websites such as EOL. The two winners will receive paid trips to the 2012 iEvoBio conference. See http://eol.org/info/tree_challenge for more information. More details about the iEvoBio 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 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 From 3dsig12 at gmail.com Thu Mar 22 11:24:18 2012 From: 3dsig12 at gmail.com (3Dsig12) Date: Thu, 22 Mar 2012 17:24:18 +0200 Subject: [BiO BB] 3DSIG 2012 Compuational Biophysics & Structural Bioinformatics: Call for Contributions Message-ID: We are happy to announce the eighth 3DSIG meeting in Long Beach, California on July 13 and 14, 2012. *Deadline for Submissions is April 13!* http://bcb.med.usherbrooke.ca/3dsig12 Please visit our site for submissions and complete information and help us make 3DSIG 2012 a success as in previous years by distributing this email and the attached poster with your colleagues as well as Facebook, Twitter, etc. Q: What is 3DSIG? A: '3DSIG: Structural Bioinformatics and Computational Biophysics' is the main event in the field of structural bioinformatics and computational biophysics since 2004. It is organized as a satellite meeting linked to the Intelligent Systems for Molecular Biology (ISMB) conference. Q: How is 3DSIG organized? A: Two very full days with a balance of invited talks, short oral presentations, two laptop/poster sessions, and critical, topic-focused discussions. A truly unique event bringing together in one place the structural computational biology community. Q: Who are the 2012 keynotes? A: Currenty confirmed: Ada Yonath (WIS, Nobel Laureate Chemistry 2008) Adam Godzik (SBMRI) Arthur Olson (Scripps) David Goodsell (Scripps) Fran?ois Major (U. Montreal) Olivier Lichtarge (Baylor) Chris Sander (Memorial Sloan-Kettering Cancer Center) Keith Dunker (Indiana University) Looking fwd to seeing you at 3Dsig, Organizing Committee 3DSIG 2012: Structural Bioinformatics and Computational Biophysics An ISMB 2012 satellite meeting Long Beach California July 13-14, 2012 http://bcb.med.usherbrooke.ca/3dsig12 3dsig12 at gmail.com From hlapp at gmx.net Sat Mar 24 13:03:02 2012 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 24 Mar 2012 13:03:02 -0400 Subject: [BiO BB] Call for student applications: PhyloSoC 2012 Message-ID: <21E748D0-DF03-477B-83EF-3B444675D511@gmx.net> *** Please disseminate widely at your local institutions, including *** *** posting to message and job boards, so that we reach as many *** *** students as possible *** Are you a student interested in evolutionary biology and open-source software development? PHYLOINFORMATICS SUMMER OF CODE 2012 http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2012 The Phyloinformatics Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for evolutionary informatics under the mentorship of experienced developers from around the world. The program is the participation of the US National Evolutionary Synthesis Center (NESCent) as a mentoring organization in the Google Summer of Code(tm) (http://code.google.com/soc/ ). Students in the program receive a stipend from Google (and the coveted T-shirt upon completion!), and work from their home, or home institution, for the duration of the 3 month program. You will have the opportunity to collaborate with our enthusiastic mentor community, and will have at least one dedicated mentor to help you complete your project. We are particularly targeting students interested in both evolutionary biology and software development. Our website, above, lists potential projects. Projects include many programming languages (e.g. C/C++, Java, Perl, R) and cover subjects ranging from visualization to algorithm implementation to data interoperability. You don't need to be an expert in either evolutionary biology or software development - find a project idea that interests you, and we can work with you to develop a proposal that fits your skills. We also welcome novel project ideas apart from those already on the list. INTERESTED? Contact us phylosoc {at} nescent {dot} org. We strongly encourage all interested students to get in touch with us with their ideas as early on as possible. Admission is competitive, and we want plenty of time to work with you to develop a great project proposal. TO APPLY: Apply online at the Google Summer of Code website: http://www.google-melange.com/gsoc/homepage/google/gsoc2012 where you will also find GSoC program rules and eligibility requirements. The 14-day application period for students opens on Monday March 26th and runs through Friday, April 6th, 2012. Google Summer of Code FAQ: http://www.google-melange.com/gsoc/document/show/gsoc_program/google/gsoc2012/faqs Karen Cranston and Jim Proctor National Evolutionary Synthesis Center http://nescent.org From arockia_babu at imu.edu.my Thu Mar 29 00:16:35 2012 From: arockia_babu at imu.edu.my (Arockia Babu) Date: Thu, 29 Mar 2012 04:16:35 +0000 Subject: [BiO BB] Regarding the hands on training on QSAR analysis, Homology Modelling of Proteins and Protein-Ligand Docking Studies in International Medical University, Kuala Lumpur, Malaysia Message-ID: <7F0B1AFE7497B74691B0A77D7D2EF2A8175CBA28@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. Under each workshop, there will be 2 lectures in the morning session and the entire afternoon session will be allocated to hands-on training via computational exercises. The details of titles and key note speakers of these workshops are given below, 12-6-2012: WORKSHOP ON LIGAND BASED DRUG DESIGN Lecture-1: Title: QSAR and molecular modelling in drug discovery research Speaker: Dr A.K. Saxena, Medicinal & Process Chemistry Division, Central Drug Research Institute (CDRI), Lucknow, India Website: http://www.anilkumarsaxena.com/ or http://www.cdriindia.org/anilkumarsaxena.htm Lecture 2: Title: Quantitative structure-activity relationships and its application for lead optimisation Speaker: Prof Sudhir A. Kulkarni, Vlife Sciences Technologies Private Limited, Pune, India Website: http://www.vlifesciences.com/ 13-6-2012: WORKSHOP ON HOMOLOGY MODELLING Lecture-1: Title: Comparative modelling of protein structures and protein-protein complexes Speaker: Prof N. Srinivasan, Molecular Biophysics Unit (MBU), Indian Institute of Sciences (IISc), Bangalore, India Website: http://pauling.mbu.iisc.ernet.in/ Lecture 2: Title: Homology modelling and protein analysis Speaker: Dr Kundan Ingale, Vlife Sciences Technologies Private Limited, Pune, India Website: http://www.vlifesciences.com/ 14-6-2012: WORKSHOP ON STRUCTURE BASED DRUG DESIGN Lecture 1: Title: Scoring function for Molecular docking Speaker: Prof R. Sowdhamini, National Centre for Biological Sciences (NCBS), Bangalore, India Website: http://caps.ncbs.res.in/ Lecture 2: Title: Protein-ligand docking and its application in novel lead optimisation technique Speaker: Prof Sami Mukhopadhyay, Vlife Sciences Technologies Private Limited, Pune, India Website: http://www.vlifesciences.com/ Kindly find enclosed herewith a copy of flyer for your ready reference and further action. Registration is on a first- come-first-serve-basis as we have limited seats. If you know any of your colleagues/friends who might be interested, please forward the workshop flyer to them. I request the research supervisors to encourage their research students to participate and take the advantage of this hand-on training. Furthermore, I humbly request you to display enclosed flyer on your notice board of your organisation. For new aspirants, it would be a benefit to acquire knowledge and skills on drug discovery and development research. If you have any further queries, please don't hesitate to contact me Regards Dr. M. Arockia Babu Organizing Chairman International Medical University Workshop website: http://www.imu.edu.my/about_events.asp?pageid=1&browseeventsid=162 "The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you have received this e-mail in error, please notify us immediately by return e-mail or telephone +603 8656 7228 and destroy the original message without delay."