Sun Computational Biology SIG Newsletter - 8 June 2005
Presentations From "Webservices in Computational Biology and Bioinformatics" at VBI Now Online https://www.vbi.vt.edu/article/articleview/503/1/125/ There were 75 attendees at this interesting Sun Sponsored conference, with presentations on bioMOBY and semantic MOBY, myGRID, caCORE/caBIG, BioGraphNet, BioExtract Server, PathPort/ToolBus, G-BLAST, G2C and many other topics. Genome Canada Bioinformatics Course, 8-12 August 2005, Halifax http://www.gcbioinformatics.ca Creating and managing a bioinformatics system for a lab, institute, or university presents a host of problems. While there are an enormous number of software tools, databases and hardware choices, integrating these into a coherent, reliable and easy-to-use system is difficult to do well. This course will guide participants through the steps needed to install and tailor a system to the needs of the local user community, whether a single research lab or a campus or company-wide system. Sun HPC Consortium CB-SIG Agenda, 21 June 2005, Heidelberg http://www.sun-registration.com/hpc/ You may attend the CB-SIG for free, but we think the entire HPCC meeting is well worth the extra day!
Sun CB-SIG 21 June 2005 Note: the Agenda may be slightly revised to accomodate an additional speaker. Sun Enhancements to NAB Permit New Biomolecular Simulation Capabilities http://www.scripps.edu/mb/case/ Nucleic Acid Builder (NAB) is open-source software available from Scripps Institute (www.scripps.edu/case/nab-5.0.tar.gz). NAB was originally designed to construct models for non-helical and helical nucleic acids, but now permits in addition the construction of models for proteins. As NAB developed, an implementation of the AMBER force field was added, including the AMBER implementation of the generalized Born model for solvation effects. Sun's Dr Russell Brown has contributed to Scripps Institute an enhancement to NAB that calculates the analytic second derivatives of the AMBER force field, including the generalized Born model. These second derivatives allow for Newton-Raphson minimization of the energy of a biomolecule in aqueous solution. Another use for these derivatives is the calculation of normal modes of vibration, as well as the estimation of the entropy, of the solvated molecule. Calculation of the analytic first and second derivatives of the generalized Born model can be computationally intensive. For this reason, Sun has used OpenMP to parallelize the computation of these derivatives. This parallelized code has been contributed to Scripps Institute and is available as part of the NAB version 5.0 download.
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