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

[Compbio-allhands] Fwd: CIBM postdoctoral fellowship
by Jacobson, Matt 11 Feb '12

11 Feb '12

-- Matt Sent from my iPad Begin forwarded message: From: Qiang Cui <cui(a)chem.wisc.edu<mailto:cui@chem.wisc.edu>> Date: February 11, 2012 3:05:00 PM PST To: Tanja Kortemme <kortemme(a)cgl.ucsf.edu<mailto:kortemme@cgl.ucsf.edu>> Cc: <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Subject: Fwd: CIBM postdoctoral fellowship Hi, Tanja and Matt - We have a project on developing mathematical/continuum mechanics models for coiled coils - the ultimate aim is to construct molecular models for myosin rods, which are fascinating assembly of coiled coils. The work is in collaboration with my colleague in the biochemistry department, Prof. Ivan Rayment, a renowned crystallographer, especially in the area of myosin related proteins. If you have a student interested in pursing this line of research for postdoc, please ask him/her to contact me. The support for CIBM postdocs is quite generous... Thanks! Best regards QC --------------- To: CIBM (Computation and Informatics in Biology and Medicine) Faculty Re: Nominations for a CIBM Postdoctoral Traineeship We are calling for nominations for several postdoctoral traineeships in the Computation and Informatics in Biology and Medicine (CIBM) Training Program, funded by the NLM Grant 5T15LM007359, to begin July, 2012 or later. We are attaching a form you can use to nominate outstanding candidates for the CIBM Training Program. The postdoctoral traineeship is for a one- to two-year period, and the traineeship award is contingent on the awarding of the renewal of the NLM Grant supporting the CIBM Training Program. These traineeships are designed for cross-disciplinary training - thus we are asking that the candidate have a secondary mentor in addition to the primary mentor (one from computational / informatics areas, and the other from biological areas). A list of the CIBM trainers is available on the CIBM website (<http://www.cibm.wisc.edu/>www.cibm.wisc.edu<http://www.cibm.wisc.edu> <<http://www.cibm.wisc.edu/>http://www.cibm.wisc.edu> ). The National Library of Medicine has changed its focus for its informatics training programs in the next five-year period to emphasize translational bioinformatics in addition to its current focuses on clinical research informatics and health/clinical informatics. Translational bioinformatics is defined to be bioinformatics research that has a clear linkage to health. The CIBM Training Program is interested in research in all three areas. All nominations should reflect one (or more) of these focuses. The due date for the nominations is Monday, March 19th, 2012 (by 3 p.m. in the CIBM Office, Rm. 3420 Biotechnology Center Addition). If you have questions, please contact myself (<mailto:lpape@wisc.edu>lpape(a)wisc.edu<mailto:lpape@wisc.edu>), Karen Nafzger (<mailto:nafzger@biotech.wisc.edu>nafzger(a)biotech.wisc.edu<mailto:nafzger@biotech.wisc.edu>), or a member of the CIBM Management Committee. They include: -Amit Acharya (<mailto:acharya.amit@mcrf.mfldclin.edu>acharya.amit(a)mcrf.mfldclin.edu<mailto:acharya.amit@mcrf.mfldclin.edu>) -Patricia Brennan (<mailto:pbrennan@engr.wisc.edu>pbrennan(a)engr.wisc.edu<mailto:pbrennan@engr.wisc.edu>) -Mark Craven (<mailto:craven@biostat.wisc.edu>craven(a)biostat.wisc.edu<mailto:craven@biostat.wisc.edu> -Eneida Mendonca (<mailto:emendonca@biostat.wisc.edu>emendonca(a)biostat.wisc.edu<mailto:emendonca@biostat.wisc.edu>) -C. David Page (<mailto:page@biostat.wisc.edu>page(a)biostat.wisc.edu<mailto:page@biostat.wisc.edu>) -George Phillips (<mailto:phillips@biochem.wisc.edu>phillips(a)biochem.wisc.edu<mailto:phillips@biochem.wisc.edu>) -Jude Shavlik (<mailto:shavlik@cs.wisc.edu>shavlik(a)cs.wisc.edu<mailto:shavlik@cs.wisc.edu>) Regards, Louise Louise Pape, PhD Coordinator Computation and Informatics in Biology and Medicine (CIBM) Training Program University of Wisconsin-Madison 3445 Biotechnology Center 425 Henry Mall Madison WI 53706 608-265-7935 Best Regards QC Qiang Cui ------------------------------------------------------------ Professor of Chemistry Department of Chemistry and Theoretical Chemistry Institute, Rm8305I University of Wisconsin, Madison 1101 University Avenue Madison, WI 53706 ------------------------------------------------------------ Phone: (+1)-608-262-9801 Fax: (+1)-608-262-9918 Email: <mailto:cui@chem.wisc.edu> cui(a)chem.wisc.edu<mailto:cui@chem.wisc.edu> Web: <http://www.chem.wisc.edu/users/cui> http://www.chem.wisc.edu/users/cui Group: <http://www.chem.wisc.edu/~cui> http://www.chem.wisc.edu/~cui

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[Compbio-allhands] 2/16/12 Seminar with Minna Bissell
by Nicole Takesono Flowers 10 Feb '12

10 Feb '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 Minna Bissell LBNL Why don't we get more cancer? The proposed role of the microenvironment in tissue specificity and breast cancer. February 16, 2012 C. Nyitray, 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] Fwd: [ISBRA-L] Full Professor in Bioinformatics
by Andrej Sali 10 Feb '12

10 Feb '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: ISBRA Mailing List <isbra-l(a)dna.engr.uconn.edu> > Subject: [ISBRA-L] Full Professor in Bioinformatics > Date: February 10, 2012 9:12:30 AM PST > To: <sali(a)salilab.org> > Reply-To: <isbrainfo(a)gmail.com> > > > The Department of Computer Science at Georgia State University invites applications for an anticipated position of Full Professor in the bioinformatics area beginning Fall Semester 2012, pending budgetary approval. Earned Ph.D. in Computer Science or a related discipline is required. An offer of employment will be conditional on background verification. > > Prospective candidates should demonstrate ability to bring national and international recognition to the department as a center of excellence for bioinformatics research and education. The hired scholar is expected to bring in major extramural funding, mentor junior faculty, recruit top-quality Ph.D. students, and foster interdisciplinary collaborations among faculty in various departments in GSU. > > This position is part of a university-wide initiative <http://www.gsu.edu/secondcentury> that is seeking to hire excellent faculty in several interdisciplinary areas. Prospective candidates should demonstrate ability to bring national and international recognition to the department. The hired applicant is expected to foster interdisciplinary research collaborations among faculty in various departments in GSU. > > Georgia State University, founded in 1913, is a Carnegie Doctoral/Research Extensive university. Located in the heart of downtown Atlanta, this major research university has an enrollment of more than 30,000 undergraduate and graduate students in six colleges. Georgia State is the second-largest university in the state, with students coming from every county in Georgia, every state in the nation, and from over 145 countries. Georgia State University is currently embarking on a record $1 billion campus expansion. The Computer Science Department offers programs leading to the B.S., M.S., and Ph.D. degrees in computer science. Currently, 20 out of more than 60 Ph.D. students are involved in bioinformatics research. They are supervised by 10 faculty members fully or substantially involved in bioinformatics research through collaboration with Computer Science and Biology faculty. Departmental computing facilities for research and instruction include a departmental network of PCs, Unix/Linux workstations, two interconnected Beowulf clusters, and a 24-processor supercomputer. The department's faculty attracts substantial funding from many federal agencies, including five NSF CAREER Awards. > > Applicants should send letter of interest, C.V., and three letters of recommendation to: > > Dr. Yi Pan, Chair > Department of Computer Science > Georgia State University > 34 Peachtree Street, Suite 1450 > Atlanta, Georgia 30303 > > > _______________________________________________ > To modify subscription preferences or unsubscribe from the ISBRA-L mailing list visit http://dna.engr.uconn.edu/cgi-bin/mailman/options/isbra-l/sali%40salilab.org

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[Compbio-allhands] QBC Journal Club, Tuesday, February 14- 10:45AM, GH Aud
by Nicole Takesono Flowers 08 Feb '12

08 Feb '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, February 14 10:45 am, GH Auditorium Juan Perez Bermejo, iPQB Love in the Time of Chagas Costales JA, Daily JP, Burleigh BA. Cytokine-dependent and –independent gene expression changes and cell cycle block revealed in Trypanosoma cruzi-infected host cells by comparative mRNA profiling. BMC Genomics 10:252, 2009. Rose Citron, iPQB The Ribosome Modulates Nascent Protein Folding. Christian M. Kaiser, et al. Science 334, 1723, 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: Open positions in Computational Structural Biology in Barcelona (Spain)
by Andrej Sali 08 Feb '12

08 Feb '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: "Marc A. Marti-Renom" <mmarti(a)pcb.ub.cat> > Subject: Open positions in Computational Structural Biology in Barcelona (Spain) > Date: February 8, 2012 8:38:41 AM PST > To: "Marc A. Marti-Renom" <mmarti(a)pcb.ub.cat> > > Dear Friends and Colleagues, > > We have an opening in our group for a Postdoc on chromatin biophysics. The successful candidate will team with other members of our group in our efforts towards elucidating the 3D structure of genomic domains and genomes. Recent publication from the group in this field include: > > - Umbarger, M. A., Toro, E., Wright, M. A., Porreca, G. J., Baù, D., Hong, S.-H., Fero, M. J., et al. (2011). Molecular Cell, 44(2), 252–264 > - Marti-Renom, M. A., & Mirny, L. A. (2011). PLoS Computational Biology, 7(7), e1002125 > - Sanyal, A., Baù, D., Martí-Renom, M. A., & Dekker, J. (2011). Current Opinion in Cell Biology. doi:10.1016/j.ceb.2011.03.009 > - Baù, D., Sanyal, A., Lajoie, B. R., Capriotti, E., Byron, M., Lawrence, J. B., Dekker, J., et al. (2011). Nature Structural & Molecular Biology, 18(1), 107–114. > > More details are included in the attached PDF file. > > I would appreciate if you could forward this announcement to whom may be interested. > > Many thanks in advance! > Marc > ------- > Marc A. Marti-Renom, Group Leader > Structural Genomics Group, National Center for Genomic Analysis (CNAG) > Parc Cientific de Barcelona - Torre I - Baldiri Reixac, 4 - 2a.p - 08028 - Barcelona > Tel +34 934 033 743 Fax +34 934 037 279 > email mmarti(a)pcb.ub.cat web http://marciuslab.org & http://cnag.cat > > *** Consider the environment. Print responsibly. *** >

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[Compbio-allhands] Fwd: Merck Summer Internships for Computational Chemists
by Andrej Sali 03 Feb '12

03 Feb '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: "Voigt, Johannes" <johannes.voigt(a)merck.com> > Subject: Merck Summer Internships for Computational Chemists > Date: February 3, 2012 3:08:38 PM PST > To: "sali(a)salilab.org" <sali(a)salilab.org> > > Dear Professor Sali, > > I am writing to inform you that Merck Research Labs will be offering 2012 summer internships in the Chemistry Modeling and Informatics groups at the Rahway, NJ, Boston, MA, or West Point, PA research facilities. Internships will begin in early June 2012, and will run for 10-12 weeks. > Qualified graduate students in computational chemistry or a related life sciences field who are selected for these positions will have the opportunity to conduct research on a project relevant to drug discovery. > They will gain firsthand experience in modern drug discovery, and will also make valuable contacts within industry. > > Interested candidates can apply online at > https://merck.taleo.net/careersection/merck_university_recruiting_career_se… > > To complete the application, candidates must upload a cover letter, CV, and transcript. Please note that the application deadline is February 13, 2012. > > Sincerely, > > Johannes H. Voigt Ph. D. on behalf of Global Structural Chemistry, Merck Research Laboratories > Head – Chemistry Modeling & Informatics Rahway > Merck & Co., Inc. > 126 East Lincoln Ave > RY50SW-100 > Rahway, NJ 07065 > phone: (732) 594-3938 > fax: (732) 594-0670 > > Notice: This e-mail message, together with any attachments, contains > information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, > New Jersey, USA 08889), and/or its affiliates Direct contact information > for affiliates is available at > http://www.merck.com/contact/contacts.html) that may be confidential, > proprietary copyrighted and/or legally privileged. It is intended solely > for the use of the individual or entity named on this message. If you are > not the intended recipient, and have received this message in error, > please notify us immediately by reply e-mail and then delete it from > your system.

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[Compbio-allhands] Fwd: Rapid MD Prototyping and Simulations on GPU Workshop with Dr. Vijay Pande
by Andrej Sali 03 Feb '12

03 Feb '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: "Joy P. Ku" <joyku(a)stanford.edu> > Subject: Rapid MD Prototyping and Simulations on GPU Workshop with Dr. Vijay Pande > Date: February 3, 2012 1:19:41 PM PST > 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) [seebenchmarks]. > 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: Mar. 12-13, 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, though programming 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/MDWorkshops.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, visithttp://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. > > > > > >

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[Compbio-allhands] QBC Journal Club, Tuesday, February 7- 10:45AM, GH Aud
by Nicole Takesono Flowers 02 Feb '12

02 Feb '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, February 7 10:45 am, GH Auditorium Rahel Woldeyes, CCB HIV-1 restriction factor SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase. Goldstone, D. C., Ennis-Adeniran, V., Hedden, J. J., Groom, H. C. T., Rice, G. I., Christodoulou, E., et al. (2011). Nature, 480, 379-382. Sara Calhoun, iPQB Hot Spots for Allosteric Regulation on Protein Surfaces. Reynolds, K.A., McLaughlin, R.N., and Ranganathan, R. (2011) Cell, 147:1564-1575 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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