From clements at nescent.org Sun Aug 1 13:19:55 2010 From: clements at nescent.org (Dave Clements) Date: Sun, 1 Aug 2010 10:19:55 -0700 Subject: [BiO BB] GMOD Evo Hackathon Open Call for Participation In-Reply-To: References: Message-ID: We are seeking participants for the GMOD Tools for Evolutionary Biology Hackathon, held November 8-12, 2010 at the US National Evolutionary Synthesis Center (NESCent) in Durham, NC. This hackathon targets three critical gaps in the capabilities of the GMOD toolbox that currently limit its utility for evolutionary research: 1. Visualization of comparative genomics data 2. Visualization of phylogenetic data and trees 3. Support for population diversity and phenotype data If you are interested in these areas and have relevant expertise, you are strongly encouraged to apply. Relevant areas of expertise include more than just software development: if you are a GMOD power user, visualization guru, domain expert (comparative, phylogenetics, population, ...), or documentation wizard, then your skills are needed! How To Apply: Fill out the online application form at http://bit.ly/gmodevohack. Applications are due August 25. About GMOD: GMOD is an intercompatible suite of open-source software components for storing, managing, analyzing, and visualizing genome-scale data. GMOD includes many widely-used software components: GBrowse and JBrowse, both genome viewers; GBrowse_syn, a comparative genomics viewer; Chado, a generic and modular database schema; CMap, a comparative map viewer; as well as many other components including Apollo, MAKER, BioMart, InterMine, and Galaxy. We hope to extend the functionality of existing GMOD components, and integrate new components as well. About Hackathons: A hackathon is an intense event at which a group of programmers with different backgrounds and skills collaborate hands-on and face-to-face to develop working code that is of utility to the community as a whole. The mix of people will include domain experts and computer-savvy end-users. More details about the event, its motivation, organization, procedures, and attendees, as well as URLs to the hackathon and related websites are included below. Sincerely, The GMOD EvoHack Organizing Committee (and project affiliations as relevant): Nicole Washington, Chair (LBNL, modENCODE, Phenote) Robert Buels (SGN, Chado NatDiv) Scott Cain (OICR, GMOD) Dave Clements (NESCent, GMOD) Hilmar Lapp (NESCent, Phenoscape, Chado NatDiv) Sheldon McKay (University of Arizona, iPlant, GBrowse_syn) ----------------------------- About the GMOD Evo Hackathon OverviewWe are organizing a hackathon to fill critical gaps in the capabilities of the Generic Model Organism Database (GMOD) toolbox that currently limit its utility for evolutionary research. Specifically, we will focus on tools for 1) viewing comparative genomics data; 2) visualizing phylogenomic data; and 3) supporting population diversity data and phenotype annotation.The event will be hosted at NESCent and bring together a group of about 20+ software developers, end-user representatives, and documentation experts who would otherwise not meet. The participants will include key developers of GMOD components that currently lack features critical for emerging evolutionary biology research, developers of informatics tools in evolutionary research that lack GMOD integration, and informatics-savvy biologists who can represent end-user requirements. The event will provide a unique opportunity to infuse the GMOD developer community with a heightened awareness of unmet needs in evolutionary biology that GMOD components have the potential to fill, and for tool developers in evolutionary biology to better understand how best to extend or integrate with already existing GMOD components. Before the Event Discussion of ideas and sometimes even design actually starts well before the hackathon, on mailing lists, wiki pages, and conference calls set up among accepted attendees. This advance work lays the foundation for participants to be productive from the very first day. This also means that participants should be willing to contribute some time in advance of the hackathon itself to participate in this preparatory discussion.During the Event Typically, hackathon participants use the morning of the first day of the event to organize themselves into working groups of between 3 and 6 people, each with a focused implementation objective. Ideas and objectives are discussed, and attendees coalesce around the projects in which they have the most experience or interest.Deliverables / Event Results The meeting?s attendance, working groups, and outcomes will be fully logged and documented on the GMOD wiki (http://gmod.org). Each working group during the event will typically have its own wiki page, linked from the main EvoHack page, where it documents its minutes and design notes, and provides links to the code and documentation it produces. Also, since GMOD and NESCent are both committed to open source principles, all code and documentation produced by participants during the hackathon must be published under an OSI-approved open source license. As contributions to existing GMOD tools, all hackathon products will most likely satisfy this requirement automatically.NESCent This event is sponsored by the US National Evolutionary Synthesis Center (NESCent, http://www.nescent.org) through its Informatics Whitepapers program ( http://www.nescent.org/informatics/whitepapers.php). NESCent promotes the synthesis of information, concepts and knowledge to address significant, emerging, or novel questions in evolutionary science and its applications. NESCent achieves this by supporting research and education across disciplinary, institutional, geographic, and demographic boundaries (see http://www.nescent.org/science/proposals.php). Links Main GMOD EvoHack page, and full proposal: http://gmod.org/wiki/GMOD_Evo_Hackathon NESCent: http://www.nescent.org/ GMOD: http://gmod.org Similar past NESCent events, see: http://hackathon.nescent.org/ GMOD hackathon application: http://bit.ly/gmodevohack -- http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/GMOD_Europe_2010 http://gmod.org/wiki/Help_Desk_Feedback From clements at nescent.org Thu Aug 5 13:14:26 2010 From: clements at nescent.org (Dave Clements) Date: Thu, 5 Aug 2010 10:14:26 -0700 Subject: [BiO BB] GMOD Europe 2010, 13-16 Sept, Cambridge, UK Message-ID: GMOD Europe 2010 ================ 13-16 September 2010 Cambridge, UK http://gmod.org/wiki/GMOD_Europe_2010 We are pleased to announce GMOD Europe 2010, four days of GMOD events being held 13-16 September 2010, at the University of Cambridge. GMOD Europe 2010 includes: 1) GMOD Community Meeting, Monday & Tuesday: Project updates, developer and user presentations and best practices, project direction. 2) GMOD Satellite Meetings, Wednesday: Special interest groups where GMOD community members meet to discuss specific topics of interest. 3) InterMine Workshop, Wednesday: A one day workshop on installing, configuring and using the InterMine biological data warehouse system. 4) BioMart Workshop, Thursday: A one day workshop on using the BioMart biological data warehouse system, including accessing data through APIs. Registration is now open for these events. There is a ?50 registration fee for the GMOD Meeting to cover catered lunches and other expenses. Registration for all other events is free, but required, as space is limited. These events are open to all: GMOD users, developers, prospective users, biologists, and computer scientists. See http://gmod.org/wiki/January_2010_GMOD_Meeting for an idea of what goes on at GMOD meetings, GMOD is a collection of interoperable open source software components for managing, visualizing and annotating biological data. GMOD incorporates many widely used tools, including GBrowse and JBrowse for genome browsing, InterMine and BioMart for data mining, Galaxy and Ergatis for workflow, Chado for data management, GBrowse_syn and CMap for comparative genomics, plus many other tools (Apollo, MAKER, Pathway Tools, Textpresso, ...). GMOD is also an active community of researchers and developers addressing common challenges in exploiting their data. If you are struggling to fully exploit your data then please consider attending GMOD Europe 2010. Please let us know if you have any questions, and we hope to see you in Cambridge. Thanks, Scott Cain and Dave Clements -- http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/GMOD_Evo_Hackathon http://gmod.org/wiki/GMOD_Europe_2010 http://gmod.org/wiki/Help_Desk_Feedback From somnathtagore at yahoo.co.in Wed Aug 18 08:13:07 2010 From: somnathtagore at yahoo.co.in (somnath tagore) Date: Wed, 18 Aug 2010 17:43:07 +0530 (IST) Subject: [BiO BB] One Day Workshop on Sequence Analysis Message-ID: <266871.1977.qm@web95516.mail.in.yahoo.com> ?Januganak?- the Bioinformatics Community of Department of Biotechnology and Bioinformatics of?Padmashree Dr. D.Y. Patil University, is pleased to inform you that a One Day workshop on ?Sequence Analysis? in being organized. This workshop is the first of a series of workshops which are aimed at giving complete hands-on experience in various tools and techniques used in the field of Life Science and Bioinformatics. ?Sequence Analysis? Session is aimed at giving practical experience on the basic methods of handling biological sequences using bioinformatics tools. Both under-graduate and post-graduate students can participate in this workshop. Interested candidates from Research Fraternity as well as faculties from various areas of Life Sciences are also welcome. We hope that this workshop will provide fairly good amount of knowledge about handling of biological databases and analysis of the sequences which is essential in all fields of Life?Sciences today. Kindly inform to your friends From hanbing at ittc.ku.edu Wed Aug 18 17:03:59 2010 From: hanbing at ittc.ku.edu (hanbing at ittc.ku.edu) Date: Wed, 18 Aug 2010 16:03:59 -0500 (CDT) Subject: [BiO BB] Call for Participation: 1st ACM International Health Informatics Symposium (IHI) Message-ID: <1380.129.237.120.82.1282165439.squirrel@webmail.ittc.ku.edu> Call for Participation IHI 2010 1st ACM International Health Informatics Symposium Arlington, VA November 11-12, 2010 http://ihi2010.sighi.org IHI 2010 is the inaugural symposium on health informatics promoted by the Association for Computing Machinery (ACM). IHI is designed to run as an annual showcase for exciting and innovative research on techniques and technologies developed in universities, hospitals, research labs, and companies all over the world. IHI 2010 will feature about 120 contributions from more than 30 countries, including regular 10-page papers, short 5-page papers, and demonstrations. Selected regular papers will be presented in oral plenary sessions. Other papers and demos will be presented by the authors in an open setting, specifically designed to encourage conversation and discussion. The symposium will cover the breadth of problems faced by the community: health informatics education, telemedicine, systems for decision support, human-centered design, information retrieval techniques for health applications, accessibility to personalized predictive modeling techniques, and so on. A highlight of the conference is that we will give awards for the best regular paper and the best short paper. IHI 2010 reflects a collective community effort including reviewers as well as corporate sponsors, who gave generously of their time and who provided funds to specific areas of the symposium. The following companies and institutions generously provided financial support: Pacific Northwest National Laboratory, IBM, Indiana University, Google, Hidola, and Siemens. Arlington, VA is in the Washington, DC metropolitan area. The conference hotel, Hilton Crystal City, is conveniently located near the Washington Red Line Metro and the Reagan National Airport. Within a few subway stops it is possible to reach many of the Washington area museums, monuments, and other attractions. Online registration is now available at the conference website (http://ihi2010.sighi.org). We also encourage you to stay at the conference hotel at the pre-negotiated conference rates. A direct link to the Hilton hotel reservation system is conveniently available at the conference website. The conference co-organizers are looking forward to your visit!