- compbio-allhands@cgl.ucsf.edu - RBVI Mailing Lists

[Compbio-allhands] NO BBC Journal Club 3/20/12
by Nicole Takesono Flowers 19 Mar '12

19 Mar '12

Hi all, Just a reminder that there the BBC Journal Club will NOT be held tomorrow, Tuesday, March 20. Thank you, Nicole Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Time/Room Change - March 13, Adrian Elcock Seminar
by Hilary Mahon 12 Mar '12

12 Mar '12

Please see attached for updated time and room. 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: [Simbiosnews] Job Opening for Software Engineer with Molecular Dynamics Expertise
by Tom Ferrin 09 Mar '12

09 Mar '12

-------- Original Message -------- Subject: [Simbiosnews] Job Opening for Software Engineer with Molecular Dynamics Expertise Date: Fri, 9 Mar 2012 13:00:36 -0800 (PST) From: Joy P. Ku <joyku(a)stanford.edu> To: <dissemination-simbiosnews(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./ /_______________________________________________/ / / /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] Fwd: Opening for Professor in Spatiotemporal Modeling of Biological Processes
by Andrej Sali 08 Mar '12

08 Mar '12

-- 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 Begin forwarded message: > From: Torsten Schwede <torsten.schwede(a)unibas.ch> > Subject: Opening for Professor in Spatiotemporal Modeling of Biological Processes > Date: March 8, 2012 1:46:20 PM PST > To: Torsten Schwede <Torsten.Schwede(a)unibas.ch> > > Dear colleagues, > > there is an opening for a professorship in computational biology at the Biozentrum in Basel. If you know somebody working in the field of Spatiotemporal Modeling of Biological Processes who might be interested, could you please forward the announcement? > > Thanks a lot for your help, > > Torsten > > > ========================== > Professor in Spatiotemporal Modeling of Biological Processes > > Job Specification > The Biozentrum of the University of Basel in Switzerland invites applications for a professorship in modeling of spatiotemporal processes in biology. The position can be filled at the Assistant (Tenure-track), Associate or Full Professor level depending on the qualifications of the applicant. > > We are searching for applicants that are at the forefront of research and methods development in the field of spatiotemporal modeling in biology including multiscale modeling. The ideal candidate should combine her/his activity in the development of novel computational modeling and analysis methods with a deep understanding of biology and focus on concrete biological questions from a well-defined area of molecular or cell biology in which spatiotemporal processes play an important role. Areas of interest include, but are not limited to, spatiotemporal patterns of gene expression, morphogenesis, and the dynamics of the cell cycle, of membranes, and of chromatin organization. Applications from candidates that combine cutting-edge computational modeling with wet lab approaches are encouraged. The successful candidate will have a strong research record and communication skills, should complement the research portfolio of the Biozentrum, have a desire to engage in local collaborations, and will actively participate in teaching at the undergraduate and postgraduate level. > > The Biozentrum offers an outstanding scientific environment and an attractive research endowment. Basel is the home of a vibrant international life science community and provides a high standard of living and a superb cultural atmosphere. > > Applications, including CV, list of publications and a short research summary, should be sent by e-mail (pdf or zip) to Prof. Dr. Martin Spiess, Dean, Faculty of Science, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland, to dekanat-philnat-at-unibas.ch. For informal inquiries please contact Prof. Dr. Erich A. Nigg (erich.nigg-at-unibas.ch, phone: +41-61-267 16 56). > > The deadline for receipt of applications is March 19, 2012. The University of Basel is an equal opportunity employer and encourages applications from female candidates. > > Contact > > Universität Basel > Philosophisch-Naturwissenschaftliche Fakultät Dekanat > Klingelbergstrase 50 > 4056 Basel > Switzerland > > http://www.biozentrum.unibas.ch/open-positions/ > >

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[Compbio-allhands] 3/15/12 Seminar with Harmit Malik
by Nicole Takesono Flowers 07 Mar '12

07 Mar '12

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Harmit Malik FHCRC Genetic conflicts: the usual suspects and beyond March 15, 2012 John Gross, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Announcing the 'Frontiers in Systems Biology' Symposium on Monday, March 19th, 2012
by Lee, Connie 07 Mar '12

07 Mar '12

FRONTIERS IN SYSTEMS BIOLOGY SYMPOSIUM featuring young scientists in an emerging field MONDAY, MARCH 19th, 2012 Genentech Hall (Byers) Auditorium 9:30 - 10:00 am Light Breakfast in atrium 10:00 - 10:40 am Joshua Weinstein | Stanford University 'From zebrafish to humans: what snapshots of antibody repertoires can tell us about immune dynamics' 10:40 - 11:20 am Sean Summers | ETH 'Systems, biology, and control: from cell function discovery to cyborg cells' 11:20 - 12:00 pm Moran Yassour | Hebrew University / Broad Institute 'Characterizing transcriptomes from high throughput sequencing data: from yeast to mammals and back' 12:00 - 12:45 pm Lunch on your own 12:45 - 1:25 pm Marisa Eisenberg | Ohio State University 'Identifiability and parameter estimation for modeling human disease' 1:25 - 2:05 pm Mohammed AlQuraishi | Stanford University 'Predicting protein-DNA interactions from first principles' 2:05 - 2:45 pm Sean Stromberg | Emory University 'Dynamics of chronic infections and passive demethylation' 3:00 - 5:00 pm Poster session & reception in atrium All are welcome to attend | no registration required Sponsored by the UCSF Center for Systems & Synthetic Biology ------------------------------------------ Connie M. Lee, Ph.D. Associate Director Center for Systems & Synthetic Biology University of California, San Francisco 1700 4th Street, Byers Hall 408A, Box 2540 San Francisco, CA 94158 +1 (415) 514-1290 connie.lee2(a)ucsf.edu<mailto:connie.lee2@ucsf.edu> http://systemsbiology.ucsf.edu/ http://www.facebook.com/pages/UCSF-Center-for-Systems-Synthetic-Biology/231… ------------------------------------------

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[Compbio-allhands] QBC Journal Club, Tuesday, March 13- 10:45AM, GH Aud
by Nicole Takesono Flowers 07 Mar '12

07 Mar '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, March 13 10:45 am, GH Auditorium Nicole Olson, CCB Widespread Genetic Switches and Toxicity Resistance Proteins for Fluoride. JL Baker, N Sudarsan, Z Weinberg, A Roth, RB Stockbridge, RR Breaker. Science, 13 January 2012, 335 (6065): 233-235. Greg Fedewa, iPQB Flavor network and the principles of food pairing. YY Ahn, SE Ahnert, JP Bagro, AL Barabasi. Scientific Reports Vol 1. 2011 bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Postdoctoral Research Fellowship Opportunities-- Stanford Molecular Imaging Scholars Program
by Tom Ferrin 06 Mar '12

06 Mar '12

-------- Original Message -------- Subject: Postdoctoral Research Fellowship Opportunities-- Stanford Molecular Imaging Scholars Program Date: Fri, 02 Mar 2012 09:53:12 -0800 From: Sofia Gonzales <sofias(a)stanford.edu> To: tef(a)cgl.ucsf.edu CC: jmolla(a)cgl.ucsf.edu, nicole(a)picasso.ucsf.edu Dear Dr. Ferrin, The Stanford Molecular Imaging Scholars (SMIS) Program is currently recruiting 3 postdoctoral fellows (flyer attached). We would appreciate it if you could forward this information on to your graduate students or postdocs. More information can be found at: http://mips.stanford.edu/grants/smis/ Thank you, Sofia ~~~~~ Sofia Gonzales Program Coordinator Stanford Molecular Imaging Scholars (SMIS) Program Stanford University Tel: (650) 724-9139; Fax: (650) 721-6619 Email: sofias(a)stanford.edu SMIS web site: http://mips.stanford.edu/grants/smis/

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[Compbio-allhands] Fwd:
by Brian Shoichet 06 Mar '12

06 Mar '12

FYI. ---------- Forwarded message ---------- From: Shahriar Mobashery <mobashery(a)nd.edu> Date: Tue, Mar 6, 2012 at 11:27 AM Subject: To: shoichet <shoichet(a)cgl.ucsf.edu> Dear Brian: I have a computational postdoctoral position open in my lab (description enclosed), which I hope that you would bring to the attention of suitable candidates. Best regards, S. -- Shahriar Mobashery Navari Family Professor of Life Sciences Department of Chemistry and Biochemistry 423 Nieuwland Science Center University of Notre Dame Notre Dame, IN 46556 USA phone: (574) 631-2933 fax: (574) 631-6652 email: mobashery(a)nd.edu Web site: http://chemistry.nd.edu/**faculty/detail/smobashe/<http://chemistry.nd.edu/faculty/detail/smobashe/> THIS MESSAGE IS INTENDED FOR THE USE OF THE PERSON TO WHOM IT IS ADDRESSED. IT MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE UNDER APPLICABLE LAW. If you are not the intended recipient, your use of this message for any purpose is strictly prohibited. If you have received this communication in error, please delete the message and notify the sender so that we may correct our records. -- Brian Shoichet Professor University of California, San Francisco Dept. of Pharmaceutical Chemistry phone: 415-514-4126; fax: 415-514-4260 http://shoichetlab.compbio.ucsf.edu

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[Compbio-allhands] QBC Journal Club, Tuesday, March 6- 10:45AM, ROCK HALL Aud
by Nicole Takesono Flowers 29 Feb '12

29 Feb '12

Please note the location change. Please also be advised that this date must start on time, and end promptly at 11:45 as there is another group coming in directly after. BMI ~ BP ~ CCB ~ PSPG Tuesday, March 6 10:45 am, ROCK HALL Auditorium Adrian Stecula, PSPG Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development. Stephens, Philip J, Chris D Greenman, Beiyuan Fu, Fengtang Yang, Graham R Bignell, Laura J Mudie, Erin D Pleasance, et al. Cell 144 (1) pp. 27-40. January 7, 2011. Javona White Bear, iPQB TBA bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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