July 2012 - compbio-allhands@cgl.ucsf.edu

[Compbio-allhands] Seminar - Dr. Juergen Haas, University of Basel - Friday, Aug. 10, 2012 - 11:00am - 12:00pm - Byers Hall 212
by Hilary Mahon 31 Jul '12

31 Jul '12

Please see attached for information about Dr. Haas's seminar, "New developments in the Continuous Automated Model EvaluatiOn (CAMEO) system". Thank you. --- Hilary Mahon Assistant to Dr. Sali University of California, San Francisco MC 2552 Byers Hall Room 503 1700 4th Street San Francisco, CA 94158-2330 Phone +1 (415) 514 4228 Fax +1 (415) 514 4231 Email hilary(a)salilab.org

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[Compbio-allhands] Giovanni Bussi Seminar - July 27
by Hilary Mahon 23 Jul '12

23 Jul '12

Please see information about Dr. Bussi's seminar. Thank you, Hilary --- Hilary Mahon Assistant to Dr. Sali University of California, San Francisco MC 2552 Byers Hall Room 503 1700 4th Street San Francisco, CA 94158-2330 Phone +1 (415) 514 4228 Fax +1 (415) 514 4231 Email hilary(a)salilab.org

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[Compbio-allhands] Fwd: Rapid Molecular Dynamics Prototyping and Simulations on GPU Workshop with Dr. Vijay Pande
by Andrej Sali 10 Jul '12

10 Jul '12

Begin forwarded message: > From: "Joy P. Ku" <joyku(a)stanford.edu> > Subject: Rapid Molecular Dynamics Prototyping and Simulations on GPU Workshop with Dr. Vijay Pande > Date: July 9, 2012 9:43:06 PM PDT > To: <sali(a)salilab.org> > > Hi Dr. Sali, > > I’m the Director of Simbios, an NIH National Center for Biomedical Computing focused on physics-based simulations of biological structures based at Stanford University. Based on your research activities, I thought you would be interested in our upcoming workshop on rapid prototyping and simulations of molecular dynamics on GPUs that we are hosting with Dr. Vijay Pande. Please see the announcement below for the details. > > We invite you to attend and would appreciate you forwarding the announcement to colleagues and those in your lab that may be interested. > > Thank you. > > Regards, > Joy Ku > On behalf of Vijay Pande and the OpenMM team > --------------------------------------------------------------------------------------------------------- > Simbios invites you to join us at its next Open Molecular Mechanics (OpenMM) workshop. > OpenMM is open-source software that enables molecular dynamics (MD) simulations to be accelerated on high performance computer architectures. It has demonstrated speed ups for both implicit solvent[1] and explicit solvent simulations[2] on graphics processing units (GPUs) [see benchmarks]. > And with the new application layer in its recent release, OpenMM will allow non-programmers to easily and quickly run MD simulations and develop custom algorithms on GPUs, while continuing to enable programmers to integrate OpenMM into their own programs. > > ***WORKSHOP: RAPID MOLECULAR DYNAMICS PROTOTYPING AND SIMULATIONS ON GPUS *** > > Where: Stanford University > When: September 6-7, 2012 > Description: > > During the workshop, you will gain hands-on experience using OpenMM’s new application layer and application programming interface (API). Learn to: > > * Set up and run an MD simulation on your GPU using both PDB and AMBER files > > * Create a custom force to apply to your simulations > > * Customize the simulation through Python scripting > > You will also have time to work with the OpenMM development team on your own research project. > > This workshop is designed for those interested in accelerating MD simulations on GPUs and/or developing new MD algorithms that can automatically be implemented and accelerated on GPUs. No programming background is required, thoughprogramming topics will also be covered for those who are interested in them. > Registration: > > Registration is free but required and spaces are limited. To register or for more information, visithttp://simbios.stanford.edu/MDWorkshop.htm. > > OpenMM is supported by Simbios, an NIH National Center for Physics-Based Simulation of Biological Structures. To learn more about Simbios and its research and software tools, visit http://simbios.stanford.edu. > > [1] OpenMM accelerated code running on NVIDIA GeForce GTX 280 GPU vs. conventional code with Amber9 running on Intel Xenon 2.66 GHz CPU. MS Friedrichs, et al., "Accelerating Molecular Dynamic Simulation on Graphics Processing Units," J. Comp. Chem., 2009, 30(6):864-872. > [2]Eastman, P. and Pande, V.S., “Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit,” J. Comp. Chem., 2010, 31(6):1268-1272. > > > > > > -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] Fwd: [Simbiosnews] Job Opening for Software Engineer with Molecular Dynamics Expertise
by Tom Ferrin 03 Jul '12

03 Jul '12

-------- Original Message -------- Subject: [Simbiosnews] Job Opening for Software Engineer with Molecular Dynamics Expertise Date: Mon, 2 Jul 2012 13:14:05 -0700 (PDT) From: Joy P. Ku <joyku(a)stanford.edu> To: <dissemination-simbiosnews(a)simtk.org>, <openmm-news(a)simtk.org>, <simbios_postdocs(a)mailman.stanford.edu>, <simbios_all(a)mailman.stanford.edu> Dear Simbios friends: We have an opening for a software engineer with expertise in molecular dynamics simulations and high performance scientific computing. Details about the position are given below. To learn more or to apply, please visit http://bit.ly/ypYq8w. Please forward this to others who may be interested. Thank you, Joy *Software Engineer, Exempt, 4P3, 2 Year Fixed Term * Simbios, the Center for Physics-based Simulation of Biological Structures, is one of eight national centers funded by the National Institutes of Health to build a biomedical-computing infrastructure to speed progress in biomedical research. We are looking for a software engineer with expertise in molecular dynamics simulations and high performance scientific computing to support and extend the functionality of our OpenMM and Folding@Home software projects. OpenMM (http://simtk.org/home/openmm) is an open-source molecular dynamics prototyping and simulation software package that runs accelerated calculations on GPUs. Folding@home (http://folding.stanford.edu) is a distributed computing project that uses the power of hundreds of thousands of CPUs and GPUs around the world to study protein folding. This position is a fixed term position that will be conterminous with our grant funding from NIH. Our NIH grant is scheduled to end on August 31, 2014. Should our funding continue beyond this date, this position would likely be extended. *JOB DETAILS* You will be responsible for the entire software pipeline, including but not limited to: * Develop new algorithms and improve the performance of OpenMM, * Test and validate OpenMM * Migrate OpenMM code into the Folding@home framework * Coordinate the release of new Folding@home GPU cores * Act as liaison to GPU manufacturers NVIDIA and AMD * Actively participate in both the OpenMM and Folding@home support forums * Contribute to user documentation *QUALIFICATIONS* */Minimum Requirements /* * Experience in scientific algorithm development, high performance computing applications, and molecular dynamics simulations * Requires a minimum of five years programming experience * Four year college degree or equivalent years of applicable experience. * Experience and comfort with professional software development practices * Excellent communication skills, both written and oral * Possess an understanding of the underlying biology */Desired Requirements /* * MS or PhD in physics, biochemistry, bioinformatics, computer science, engineering, or life sciences or an equivalent combination of education and experience * Experience programming in C++, Python, and OpenCL * Experience programming graphics processing units (GPUs) * Experience with Windows, Unix, Linux, Mac platform cross-development * Has experience working in an interdisciplinary environment Resume & Cover Letter are mandatory for consideration. *The final candidate will need to successfully pass a background check to be considered for this position.* /Stanford University values diversity and is committed to equal opportunity in employment./ To learn more or to apply, please visit http://bit.ly/ypYq8w / / / / / / /_______________________________________________/ / / /Joy P. Ku, PhD/ /Director, Simbios/ /http://simbios.stanford.edu/ / / /Director of Communications & Training,/ /National Center for Simulation in Rehabilitation Research/ /http://opensim.stanford.edu/ / / /(W) 650.736.8434, (F) 650.723.7461/ /Email: joyku(a)stanford.edu <mailto:joyku@stanford.edu>/

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compbio-allhands July 2012