Grid Application Developer Position Open

Apply at UCSD Jobs Bulletin, Position open till Apr 26, 2011.

http://jobs.ucsd.edu/bulletin/job.aspx?cat=search&sortby=rank&jobnum_in=57192&search=57192

What’s Up Doc(k)? Development and applications of virtual protein/ligand docking

What’s Up Doc(k)? Development and applications of virtual protein/ligand docking
Speaker: Jerome Baudry, Ph.D.,
Assistant Professor, University of Tennessee
Oak Ridge National Laboratory

Time: 11am -12 pm
Date: March 24, 2011
Location: Room 4004, Atkinson Hall, Calit2, UCSD

Hosts: Rommie Amaro, Ph.D., and Wilfred W. Li, Ph.D.,
UCI, UCSD, California, USA
Abstract: We describe our development of the AutoDock docking program for High Performance Computing and Cloud architectures. We also present applications of protein/ligand virtual docking to identify environmental estrogenic pollutants in multiple proteins of a biochemical pathway.

Speaker bio: Dr. Baudry obtained his Ph.D. in Molecular Biophysics from the University of Paris, France and the French Atomic Energy Commission, under the direction of Prof. Jeremy Smith. As a postdoc he worked with Prof. Klaus Schulten at the University of Illinois in Urbana-Champaign (UIUC). After working at a pharmaceutical company in North Carolina for 2 years, Dr. Baudry returned to UIUC, first as a staff scientist, and then as a non-tenure track research faculty. He is currently an Assistant Professor at the University of Tennessee, with appointments in the department of Biochemistry & Cellular and Molecular Biology, the UT/ORNL center for molecular biophysics, and the UT/ORNL Joint Center for Computational Sciences.

Hands-on Workshop on Computational Biophysics

“Hands-on” Workshop on Computational Biophysics, July 12-16, 2010, at San Diego

The Theoretical and Computational Biophysics Group, NIH Resource for
Macromolecular Modeling and Bioinformatics (www.ks.uiuc.edu) at the
University of Illinois at Urbana-Champaign (www.uiuc.edu), presents a

“Hands-On” Workshop on Computational Biophysics

http://www.ks.uiuc.edu/Training/Workshop/SanDiego/

to be held July 12-16, 2010 at the National Resource for Automated
Molecular Microscopy on the Scripps Research Institute campus in San Diego, California, USA. Application, selection, and notification of participants is on-going through July 2, 2010.

The workshop will explore physical models and computational approaches used for the simulation of biological systems and the investigation of their function at an atomic level. The course will be based on case studies including the properties of membranes and membrane proteins, mechanisms of molecular motors, trafficking in the living cell through water and ion channels, and signaling pathways. Relevant physical concepts, mathematical techniques, and computational methods will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers and steered molecular dynamics simulations.

The workshop is designed for graduate students and postdoctoral researchers in computational and/or biophysical fields who seek to extend their research skills to include computational and theoretical expertise, as well as other researchers interested in theoretical and computational biophysics. Theory sessions in the morning will be followed by hands-on computer labs in the afternoon in which students will be able to set up and run simulations. Enrollment limited to 35 participants. The workshop will be held July 12-16, 2010. All participants are required to bring their own laptop, prepared for
use in workshop tutorial sessions. Course materials will be provided.

The workshop is sponsored by the Nationaal Biomedical Computation Resource (www.nbcr.net), the National Resource for Automated Molecular Microscopy (nramm.scripps.edu), and the NIH National Center for Research Resources (www.ncrr.nih.gov).

We look forward to receiving your application.

TCBG Workshop Organizers
Email: workshop+sandiego@ks.uiuc.edu

Biological Diffusion and Brownian Dynamics Brainstorm 2

Biological Diffusion and Brownian Dynamics Brainstorm 2

October 11-13, 2010

Following a very successful workshop on the simulation and experimental study of biomolecular diffusional processes in Heidelberg in 2007, a second workshop will take place this coming fall. The principal site will again be in Heidelberg, but there will be live video teleconferencing (VTC) of key lectures and discussions with a secondary site at UCSD in La Jolla, California.

Information on the original workshop can be found here:

http://projects.eml.org/mcm/BDBDB/index.html

Information on the 2010 workshop can be found here:

http://projects.villa-bosch.de/mcm/BDBDB2/

Because participants at the UCSD site will primarily be from the San Diego area, no special provisions for housing or meals are planned, and no registration charges will be levied. Contributions of posters and a limited number of lectures at the UCSD site are invited. If you wish to attend at the UCSD site, please email your abstract(s) for posters and/or lectures to Prof. Andy McCammon at jmccammon@ucsd.edu; please also submit your abstract and
complete the registration form at http://projects.eml.org/mcm/BDBDB2/registration.htm

Due to the time zone difference between Heidelberg and San Diego, the joint sessions between the two sites through VTC are scheduled to occur 9AM – noon at UCSD, and 6PM – 9PM in Heidelberg on the same day. Even though only a subset of talks will be possible during the joint VTC sessions, we hope to arrange for copies of all talks and posters to be shared between the two sites.

The 5th NBCR Summer Institute (SI 2010)

The 5th NBCR Summer Institute (SI 2010)
2 – 6 August 2010

The National Biomedical Computation Resource (NBCR) will hold its 5th Summer Institute (SI) the week of August 2 – 6 2010, in La Jolla, California, on the campuses of the University of California San Diego (UCSD) and The Scripps Research Institute (TSRI).

The goal of this fifth NBCR SI is to provide significant training opportunities for members of the biomedical research community in targeted areas of computational multiscale biomedical research: computer aided drug discovery; mesoscale modeling; and computational cardiac electrophysiology and mechanics. Training will include hands-on use of key NBCR tools that are freely available to the academic community. For NBCR a positive outcome of the workshop will be the creation of new users of these tools. In particular, there will be opportunities for participants to work with their own data and analyses in extended sessions.

In addition to training, students will be able to hear talks in a Computational Science Seminar Series (CS3) on new directions under the theme of Challenges in Multiscale Computational Modeling, from cutting edge research undertaken by users and collaborators of the NBCR resource.

This year’s workshop will have four major activities
• In-depth, Hands-on Training sessions in key areas of multiscale biomedical research (see list of “tracks” below).
• Plenary CS3 Talks on Challenges in Multiscale Computational Modeling
• Special Topics on Emerging Technologies in Multiscale Modeling, including special mini-talks or tutorials for innovative software and algorithms for Multiscale Modeling to be available in the near future.
• Poster session by participants, to allow NBCR instructors and researchers to interact with the participants and to explore new opportunities for collaboration or user needs.

For further information, please send an e-mail to nbcrsi2010@googlegroups.com, or go to the website http://si.nbcr.net for more information.

Overview of SI 2010 Program, Monday – Friday, 2 – 6 August 2010*

Tutorial Tracks (morning)
• Computational Cardiac Electrophysiology and Mechanics. Tutorials on use of Continuity 6.3 by NBCR (http://www.continuity.ucsd.edu/Continuity). Chair: Prof. Andrew McCulloch, UCSD.
• Molecular Electrostatics and Diffusions. Tutorials on use of Adaptive Poisson Boltzmann Solvers (APBS, http://www.poissonboltzmann.org/apbs/) and BrownDye (http://browndye.ucsd.edu/browndye/doc/manual.html). Chair: Prof. J. Andrew McCammon, UCSD.
• Programming Scalable Scientific Workflows. Tutorials on Vision (https://www.nbcr.net/pub/wiki/index.php?title=MGLTools). Application of the Vision Workflow environment. Chair: Prof. Michel Sanner, TSRI.

Tutorial Tracks (afternoon*)
• Virtual Screening and Computer Aided Drug Discovery (CADD). Tutorials on use of AutoDock and AutoDock Tools (http://mgltools.scripps.edu/) and a cloud computing based virtual screening pipeline for CADD Pipeline. Chair: Prof. Arthur Olson, TSRI.
• From Cluster to Cloud Computing. Tutorials on Opal (http://www.nbcr.net/software/opal/), Rocks (http://www.rocksclusters.org/wordpress/), along with virtualization and running inside Amazon’s EC2 platform. Chair: Peter W. Arzberger, Ph.D., UCSD.
• Special Topics on Emerging Technologies in Multiscale Modeling. Minitalks and/or Tutorials on emerging software and novel algorithms in multiscale modeling. Chair: Prof. Michael Holst, UCSD.

CS3: Challenges in Multiscale Computational Modeling (noon-time)
• Invited speakers to discuss cutting edge research and how to address Challenges in multiscale computational modeling, with an emphasis in bridging scales and on the mesoscale.

Special Sessions (afternoon*)
• Each morning track may schedule labs to allow the students to gain additional experience with specific tools or to work on their own problems.

Posters Session
• There will be a poster session offered for participants, to allow greater interaction with NBCR researchers and networking with other Summer Institute participants. The best poster prizes will be selected by the SI 2010 program committee members.

* There will be afternoon sessions only on Monday – Thursday. There will be no afternoon session on Friday 6 August.

Key Information on the NBCR SI

Who should attend: The workshop is aimed at graduate students, postdocs and researchers interested in learning how to use specific tools covered by this summer institute or who are interested in understanding specific examples of computational approaches to multiscale biomedical research.

Costs: For individuals who do not need housing, the costs are $400. For individuals who require housing and meals, the costs are $700 for 5 nights (Sunday-Thursday), with included cost for the tutorials.

Posters: Participants may wish to present a poster. Submission of abstracts for posters is required. More information on posters will be forthcoming.

Scholarships: There will be a limited number of scholarships available for students, post-doctoral fellows or junior investigators to defray the costs of attending the meeting. Applicants should submit a poster abstract and a letter of support from a senior mentor to Dr. Wilfred Li, wilfred@ucsd.edu. Those who wish to present mini-talks (15 min) during the Special Topics Sessions should also send in their slides for consideration.

Venue: The Institute will be held in La Jolla California on the University of California San Diego and The Scripps Research Institute campuses.

Important Dates:
Registration opens: May 15, 2010
Registration closes: July 26, 2010
Scholarship application deadline: June 21, 2010
Scholarship awards announced: July 5, 2010.
Campus housing and meals deadline: July 19, 2010.

For more information on the workshop, visit our website http://si.nbcr.net or contact nbcrsi2010@googlegroups.com. We strongly encourage individuals to register early.

About NBCR: NBCR is a resource for the biomedical community. Our mission is to conduct, catalyze, and enable biomedical research by harnessing forefront computational and information technologies, focusing on targeted translational and multiscale challenges. We consist of researchers from the University of California, San Diego, including the San Diego Supercomputer Center (SDSC), the California Institute of Telecommunications and Information Technology (Calit2), The Center for Research in Biological Structure (CRBS), The Scripps Research Institute (TSRI), and Washington University in St. Louis and the University of Wisconsin in Milwaukee. We are supported by the National Institutes of Health’s National Center for Research Resources (P41 RR08605). More information about NBCR is found at http://nbcr.net.

2010 San Diego Science Festival

Leading science, technology, engineering, and mathematical organizations throughout the San Diego area join forces each spring to host the annual San Diego Science Festival (SDSF). The Whole Brain CatalogTM, the Community Cyberinfrastructure for Advanced MarineMicrobial Ecology Research and Analysis (CAMERA), the National Biomedical Computation Resource (NBCR), and the Neuroscience Information Framework (NIF), recently represented the Center for Research in Biological Systems (CRBS) at the Science Festival’s 2010 Expo Day at PetcoPark. The all-day event included presentations and an assortment of interactive demonstrations aimed to inspire the next generation of possible scientists.

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The first San Diego Science Festival took place in 2009 when local scientific community leaders joined up with the University of California, San Diego to organize this countywide event. The festival has partnered with many San Diego school districts to encourage students to take an interest in modern science. “Festival Week,” held March 20-27, 2010, was packed with events across the county and culminated in the Expo Day on March 27 at Petco Park. This event was free to the public and featured over 150 hands-on activities to get young students involved and interested in science and technology.

The Whole Brain CatalogTM booth featured a large plasma screen running an animation of neural structures and events that attracted and maintained a steady crowd throughout the day. The children were encouraged to use the computer to explore the brain by zooming in and out of brain images on brain maps. Sarah Maynard and Christopher Aprea engaged the festival-goers and fielded questions about the brain and the Whole Brain CatalogTM. Wilfred Li, Teri Simas, Guy Perkins, and Shulei Shu also participated in Expo Day as representative researchers of CRBS.

With perfect weather and over 30,000 San Diegans in attendance, Expo Day 2010 was a great success.

source: The Whole Brain Catalog Project Blog.

AutoDock Workshop

The MGL lab at the Scripps Research Institute is holding a free AutoDock
workshop April 29.

Using AutoDock with AutoDockTools April 29, 2010 1:30pm to 4:30pm

Please email Ruth Huey at rhuey@scripps.edu for workshop registration
and/or more information.

AutoDockTools development is supported in part by NBCR.

Dynamical View of Energy Coupling Mechanisms in Active Membrane Transporters

Event: NBCR Computational Science Seminar Series
Date: Thursday, March 11, 2010
Time: 4:00pm – 5:00pm
Location: Fung Auditorium, PFBH Hall, UCSD

Title: Dynamical View of Energy Coupling Mechanisms in Active Membrane Transporters

Speaker: Emad Tajkhorshid, PhD
Affiliation: Department of Biochemistry, Center for Biophysics and Computational Biology, and Beckman Institute, University of Illinois at Urbana Champaign

Abstract: Membrane transporters constitute the principal players in active exchange of materials across the cellular membrane in an energy-dependent manner. These complex proteins constitute highly sophisticated, fine-tuned molecular pumps that efficiently couple various sources of energy in the cell to the transport of a wide range of molecules across the membrane against their chemical gradient. Substrate binding and translocation along the transport pathway in membrane transporters are closely coupled to numerous stepwise protein conformational changes of various magnitudes that are induced by and/or coordinated with the energy-providing mechanisms. A detailed description of the mechanism of membrane transporters, therefore, relies on high-resolution methodologies that can describe the dynamics of the process at an atomic level. In this talk, latest results of molecular dynamics simulations performed on a number of atomic structures of membrane transporters and the molecular events involved in their function revealed by these simulations will be presented.

Host: Andy McCammon, Ph.D., Wilfred W. Li, Ph.D.

2010 NBCR Summer Institute to be Held Aug 2-6, 2010 at UCSD

The National Biomedical Computation Resource (NBCR) is pleased to present its fifth annual Summer Institute to be held Aug 2-6, 2010.
This training program will provide an overview of cyberinfrastructure and multiscale modeling approaches, and will include a mini-symposium and hands-on training sessions using the tools essential for cutting edge biomedical research. NBCR’s goal in offering this Summer Institute is to broaden the impact of these tools and work closely with the biomedical community in future developments, while offering significant opportunities for networking among researchers and participants.

More details will be available soon.

CSSS: Modeling and simulation of actin polymerization in cells

NBCR Computational Science Seminar Series (CSSS) 2010

Speaker: Leslie M. Loew, Ph.D.
Time: 4-5 pm
Date: Jan 12, 2010
Location: Fung Auditorium, PFBH Hall, UCSD

Abstract: We have built a quantitative model based on the dendritic nucleation scheme for actin assembly. The model explicitly incorporates the major mechanisms for actin polymerization starting with activation of Arp2/3 at the cell membrane by NWASP. We first used this model to establish the steady state properties of the actin system in the absence of nucleation by Arp2/3. The model reproduces all the experimental behaviors derived from in vitro studies of sub-systems of the component molecules. We then constructed 3D spatial models of cells with thin lamellipodia and thick cell bodies. Activation of Arp2/3 in a small segment of lamellipodium membrane causes rapid localized actin nucleation and a buildup of F-actin to the 1mM level. The model provides an explanation for speckle microscopy experiments showing a remarkably sharp transition from filament assembly at the leading edge of cells and filament disassembly just 1µm away from the leading edge. We also applied the model to experimental data on signaling aggregates propelled by actin comet tails. Simulation results are in quantitative agreement with the observed profiles of actin distribution in the comets. Because this model and the simulation results are “open source”, in the sense that they are publicly available and editable through the Virtual Cell database (http://vcell.org), they can be accessed, analyzed, modified and extended.

Biography: Leslie M. Loew is Professor of Cell Biology, Director of the Richard D. Berlin Center for Cell Analysis and Modeling (CCAM) and holds the Boehringer Ingelheim Chair in Cell Sciences at the University of Connecticut Health Center. He is also Professor of Computer Science and Engineering within the School of Engineering on the UCONN Storrs campus. Loew came to Farmington in 1984 after 10 years on the faculty of SUNY at Binghamton in the Department of Chemistry. He received his Ph.D. in Chemistry from Cornell University and was a post-doctoral fellow in the laboratory of F. H. Westheimer at Harvard University. His research focuses on the chemical and physical mechanisms underlying cell biological processes. As a key part of this research he has been involved in the design and synthesis of fluorescent dyes to probe cell physiology and the development of quantitative high resolution microscopic methods for mapping cell structure and function. His laboratory is credited with being the first to apply the non-linear optical effect known as second harmonic generation to high resolution microscope imaging. He established CCAM in 1994 with the aim of developing new optical, photonic, image processing and computational techniques for the investigation of the behavior of living cells. The largest CCAM project, Virtual Cell, aims to develop a computational environment for modeling the complex events underlying cell function. It is the core technology development project of a NIH/NCRR “National Biomedical Technology Research Resource” and has over 12,000 registered users worldwide. Most recently, the computational and biophotonics research that is housed within CCAM has led to the establishment of a “National Technology Center for Networks and Pathways” at UCHC with a $12.3M five year NIH Roadmap grant, of which Loew is the Principal Investigator. CCAM has also become a regional resource for the biomedical research community with over $7 million of state of the art instrumentation used by approximately 50 academic and industrial laboratories. Loew is the author of over 150 research publications, including 3 patents and 1 book; he lectures widely, traveling to scientific meetings and universities about once each month to deliver invited seminars. Over 40 Ph.D. and post-doctoral students have need trained in Loew’s laboratory. He is the founding and continuing organizer of the international symposium on Computational Cell Biology, is on several Editorial Boards for scientific journals and has served as Chair of the Modeling and Analysis of Biological Systems NIH Study Section.

Host: Andrew McCulloch, Ph.D., Wilfred W. Li, Ph.D.