From isbra-l at dna.engr.uconn.edu Mon Nov 1 10:22:23 2010 From: isbra-l at dna.engr.uconn.edu (International Symposium on Bioinformatics Research and Applications) Date: Mon, 1 Nov 2010 10:22:23 -0400 Subject: [BiO BB] [ISBRA-L] ISBRA 2011 First Call for Papers Message-ID: 7TH INTERNATIONAL SYMPOSIUM ON BIOINFORMATICS RESEARCH AND APPLICATIONS May 27-29, 2011 Central South University, Changsha, China 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 We seek two categories of submissions: extended abstracts of up to 12 pages in Springer LNCS format, and short abstracts of up to 4 pages. Both types of submissions must be made electronically by following the instructions at http://www.easychair.org/conferences/?conf=isbra2011i. Submission implies willingness of at least one author to register and present at the symposium. Accepted extended abstracts will be published prior to the symposium in Springer-Verlag's Lecture Notes in Bioinformatics series and presented orally at the symposium. Accepted short abstracts will be published online and on CD-ROM and selected for either oral or poster presentation. As in previous years, full versions of selected extended abstracts presented at the symposium will be invited to a peer-reviewed special issue of IEEE/ACM Transactions on Computational Biology and Bioinformatics. The authors of remaining extended and short abstracts will be invited to submit full versions to a peer-reviewed volume to be published after the symposium in BMC Bioinformatics. IMPORTANT DATES Extended Abstracts Short Abstracts (12 pages) (4 pages) Submission deadline February 11, 2011 April 8, 2011 Notification of acceptance March 11, 2011 April 22, 2011 Final version due March 18, 2011 April 29, 2011 STEERING CHAIRS Dan Gusfield (UC Davis) Yi Pan (Georgia State) Marie-France Sagot (INRIA) GENERAL CHAIRS Mona Singh (Princeton) Lijian Tao (Central South University) Albert Y. Zomaya (University of Sydney) PROGRAM CHAIRS Jianer Chen (Texas A&M) Jianxin Wang (Central South University) Alexander Zelikovsky (Georgia State) -------------- next part -------------- _______________________________________________ ISBRA-L mailing list ISBRA-L at dna.engr.uconn.edu http://dna.engr.uconn.edu/mailman/listinfo/isbra-l From Robin.Haw at oicr.on.ca Wed Nov 3 14:38:58 2010 From: Robin.Haw at oicr.on.ca (Robin Haw) Date: Wed, 3 Nov 2010 14:38:58 -0400 Subject: [BiO BB] Reactome releases New Website and Pathway Analysis Platform Message-ID: Browsing, searching, analyzing and visualizing pathway data are easier with the new and updated Reactome. Reactome has released a new web interface for its open-source curated database of pathways and reactions. New features include: * A newly designed website with an intuitive user interface for exploring pathway knowledge and a new suite of data analysis tools * Pathway Browser, an SBGN-based visualization system of pathway diagrams with advanced navigation features, including zooming, scrolling and event highlighting. * PSIQUIC web services to overlay our curated pathway diagrams with molecular interaction data from the Reactome Functional Interaction Network and external interaction databases such as IntAct, BioGRID, ChEMBL, iRefIndex, MINT, and STRING. * Pathway and Expression Analysis tools, which allow researchers to analyze experimental datasets by providing ID mapping, pathway assignment and over-representation analysis. * Reactome Functional Interaction Network Cytoscape plugin that is useful in the discovery of network patterns related to cancer and other types of disease. * Improved tools for display and analysis of Ensembl Compara ortholog-based pathway predictions in 20 non-human species, including the 12 species of the GO Reference Genome Annotation project. * A species Comparison tool, which allow users to compare pathways from another species with human data by providing an overlap indicating the degree of orthology between the two species. A full description of the new features offered by Reactome is available on the new Reactome website at http://www.reactome.org. Reactome is a collaboration between groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University Medical Center, and The European Bioinformatics Institute. Freely available to academic, clinical, and commercial researchers and scientists worldwide, the Reactome database offers pathway data encapsulating areas of human biology ranging from basic pathways of metabolism to complex events such as GPCR signaling and apoptosis, extracted from the published literature by Reactome curatorial staff and cross-referenced to a wide range of standard biological databases. Reactome data and software are distributed under the terms of the Creative Commons Attribution 3.0 Unported License. For more information contact: Robin Haw Email: help at reactome.org Tel: 647-260-7985 Robin Haw, PhD Scientific Associate Manager of Reactome Outreach Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Tel: 647-260-7985 Toll-free: 1-866-678-6427 http://www.oicr.on.ca http://www.reactome.org This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. From dan.bolser at gmail.com Thu Nov 4 09:21:27 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 4 Nov 2010 13:21:27 +0000 Subject: [BiO BB] List of 'BioWIkis'? Message-ID: Hi, I'm building a list of 'BioWikis' here: http://nettab.referata.com/wiki/BioWiki Using SMW it *should* be easy to syndicate that list. Please feel free to contribute with 'your favourite wiki' :-) Dan. From siehnel at uw.edu Thu Nov 11 17:12:44 2010 From: siehnel at uw.edu (Richard Siehnel) Date: Thu, 11 Nov 2010 22:12:44 +0000 (UTC) Subject: [BiO BB] PDB files on Cn3D References: <1226534454.491b6e36e7d14@webmail.upv.es> Message-ID: Javier Forment Millet ibmcp.upv.es> writes: > > Hi, all... Does anyone know any way to open custom .pdb files with the Cn3D > tool? > Go to: http://www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html Choose your .pdf file & "Submit". On next page that opens Choose "Save File" option of the "All Atom Model" & Click "View 3D structure" The file downlaoded (to your downloads folder) can be opened with Cn3D (Optional: Start the VAST calcualtion) From mahef111 at link.net Mon Nov 29 13:48:26 2010 From: mahef111 at link.net (Mahmoud ElHefnawi) Date: Mon, 29 Nov 2010 20:48:26 +0200 Subject: [BiO BB] Program for exploring known interactions ( direct or indirect) between genes / their products In-Reply-To: Message-ID: Hi all, Happy Thanks giving. Does anyone know of a program that explores known/ predicts relationships ( direct or indirect interactions) between genes / their products in a genome ( humans)? For example, I am trying to find any links between BFGF and TGGF Beta. Many thanks, Mahmoud ElHefnawi