Computational Tools for Next-generation Sequencing Applications
at PSB 2008
Jun 08, 2007
Next generation, rapid, low-cost genome sequencing has the potential to address a broad range of genetic analysis applications. As the promise of several of these next generation sequencing technologies becomes reality, computational methods for analyzing and managing the massive numbers of the short reads produced by these platforms, are urgently needed. This session of PSB 2008 will be focused on the computational methods, tools, and algorithms required for utilizing the staggering volumes of short-read data produced by NGS. The session will similarly consider application-specific algorithms, analysis methods, or study planning and design tools with emphasis in the new types of biology that these technologies enable. For more information see the official PSB 2008 Web page: http://psb.stanford.edu
CNRS ATIP PROGRAMMES: Call for Team Leaders
Jun 05, 2007
The "Département des Sciences du Vivant" (Life Sciences Division) of the CNRS, offers an opportunity to scientists at the end of their postdoctoral training for developing an innovative independent research project while setting up their own group within a CNRS laboratory. Successful applicants will receive a three year grant (150K € for equipment and consumables), the possibility of hiring a postdoctoral fellow for two years, at least 50 m2 of lab space and, whenever possible, technical assistance. At the end of the three years, the ATIP team leaders may compete for a two year extension through the "ATIP Plus" programme. Eight programmes concern specific research areas (Biodiversity and ecosystem dynamics, Cell biology and Immunology, Developmental biology, Genetics, Microbiology, Systems biology, Neurobiology: from molecular to cognitive neurosciences, Structure-function relationships, Dynamics of biomolecules and their assemblies), and one (ATIP "Blanche") is open to any project of high scientific quality related to Life Sciences. Applications from scientists presently working in a foreign country are particularly encouraged. Applicants must be less than 40 years old, or have defended their PhD thesis within the last ten years (exception may be made for women with children). Application forms and more detailed information are available either directly or through the web site of the CNRS: http://www.cnrs.fr/infoslabos/atip/lifeatip.htm. Applications must be written in English and addressed before October 1st, 2007 to: Jean HOUMARD - Chargé de Mission CNRS - Département des Sciences de la Vie 3, rue Michel Ange - F-75794 Paris Cedex 16. E-mail: sdv-atipe@cnrs-dir.fr
First Issue of HFSP Journal Now Available
May 25, 2007
HFSP Publishing is proud to announce the publication of the first issue of the HFSP Journal, Frontiers of Interdisciplinary Research in the Life Sciences, which is available online free of charge at http://hfspj.aip.org. The HFSP Journal is a new journal which aims to foster communication between scientists publishing high quality, innovative interdisciplinary research at the interface between biology and the physical sciences. The first issue features Editorials, Commentaries, Perspectives, and Research Articles from top scientists on the cutting edge of research. The Editorial Board of the HFSP Journal represents 5 distinguished scientists from different disciplines but each with a strong focus on living systems: • Arturo Falaschi (International Centre for Genetic Engineering and Biotechnology, Trieste and Scuola Normale Superiore of Pisa, Italy). • Marcelo Magnasco (Department of Physics, Rockefeller University), • Peter Seeberger (Department of Chemistry, ETH Zurich, Switzerland), • Dan Kiehart (Department of Biology, Duke University) and • Mitsuo Kawato (ATR Computational Neuroscience Laboratories, Kyoto University, Japan). The HFSP Journal offers its authors the fee option of Open Access immediately upon publication, or access limited to subscribers for the first 6 months, and free thereafter. The HFSP Journal is operated by HFSP Publishing, the not-for-profit publisher of the leading international funding agency the Human Frontier Science Program Organization (HFSPO). This international funding agency has been supporting innovative research at the frontier of biology since its establishment in 1989. Contact: Dr. Valerie Ferrier Managing Editor Tel + 33 (0) 3 88 21 52 83 info@hfsp-publishing.org http://hfspj.aip.org
wwPDB Announcement: Release of Remediated PDB Data
May 05, 2007
The wwPDB has collaborated on a project to remediate the PDB archive and create a new set of corrected files. The entire archive has been reviewed and remediated with the objectives of improving the detailed chemical description of non-polymer and monomer chemical components; standardizing atom nomenclature; updating sequence database references and taxonomies; resolving any remaining differences between chemical and macromolecular sequences; improving the representation of viruses; and verifying primary citation assignments. In addition, the atom nomenclature for amino acids and nucleotides now conforms with IUPAC standards. A new FTP server containing the remediated data has been set up for testing. The access details for this site are provided at http://www.wwpdb.org/remediation-downloads.html. The new ftp site will be updated weekly in concert with the current production site at ftp://ftp.rcsb.org. Both sites share the same directory structure. The remediated data is served using gzip compression. Your input is very important to us. The details of the final transition will be announced on the wwPDB website (http://www.wwpdb.org). Detailed information about the wwPDB remediation project can be found at http://remediation.wwpdb.org. Comments about the files should be sent to info@wwpdb.org. Major announcements will be made at the wwPDB website (http://www.wwpdb.org) as well as on the individual member websites.
Discover the Bay Area’s Newest State of the Art Core Analytics Lab
Apr 11, 2007
The San Jose BioCenter is a state of the art facility equipped with common lab areas including a cold room, tissue culture rooms, service alcoves, equipment rooms, a Biology Lab and a Chemistry Analytics Lab, and a full suite of business development services, individual wet and dry labs and office space for emerging technology companies in a variety of convergence technology areas. Our brand new core Chemistry Analytics Lab, includes valuable pieces such as a NMR, a LC/MS, and an HPLC. Our goal is to support early stage ventures to move quickly from concept to commercialization, which will in turn support the industry overall. Therefore, the SJBC Chemistry Analytics Lab is open to all emerging technology companies. Contact Jennifer at Jennifer@sjbiocenter.com or at 408.960.3807, or visit our Core Labs webpage [www.sjbiocenter.com/corelabs.html]to open a BioCenter Chemistry Analytics Lab account.
Invitation to Submit to Source Code for Biology and Medicine
Jan 08, 2007
Dear Colleague, We are pleased to announce that Source Code for Biology and Medicine has now been launched and is freely available online http://www.scfbm.org/. Source Code for Biology and Medicine is an open access http://www.biomedcentral.com/info/about/charter, peer-reviewed online journal that publishes articles on source code employed over a wide range of applications in biology and medicine. Several articles that might be interesting to you have already been published: Editorial Welcome to Source Code for Biology and Medicine http://www.scfbm.org/content/1/1/1 Leif E Peterson and Emmanuel C Ifeachor Source Code for Biology and Medicine 2006, 1:1 (12 October 2006) Research A traveling salesman approach for predicting protein functions http://www.scfbm.org/content/1/1/3 Olin Johnson and Jing Liu Source Code for Biology and Medicine 2006, 1:3 (12 October 2006) Methodology DADOS-Prospective: an open source application for Web-based prospective data collection http://www.scfbm.org/content/1/1/7 Lam Nguyen, Anand Shah, Matthew Harker, Henrique Martins, Mariana McCready, Andreia Menezes, Danny O Jacobs and Ricardo Pietrobon Source Code for Biology and Medicine 2006, 1:7 (13 November 2006) To keep up to date with the latest articles from Source Code for Biology and Medicine, why not register to receive article alerts http://www.scfbm.org/alerts/ when new research is published?
