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

[Compbio-allhands] Fwd: Hiring at the Friedberg lab
by Alexandra Schnoes 30 Mar '12

30 Mar '12

---------- Forwarded message ---------- From: Iddo Friedberg <idoerg(a)gmail.com> Date: Wed, Mar 28, 2012 at 8:26 AM Subject: Hiring at the Friedberg lab To: Dear Friends, Apologies for the mass email. Please pass this on to interested parties. PDF version attached. Location: Miami University, Oxford OH, USA Department: Microbiology Start date: as soon as possible Salary: competitive and commensurate with experience and qualifications The Friedberg Lab is looking to hire a Scientific Programmer/ Bioinfromatics Specialist to implement and maintain a genomic database web site; implement data management tools including relational database management applications for efficient storage and retrieval of genomic data; perform other duties as related to the position such as data and project management to ensure data are being processed in an efficient and timely manner; contribute to writing scientific manuscripts. Three year position renewed annually depending on funding and performance. *Required qualifications*: BS or BA in Computer Science, bioinformatics, or a related discipline; demonstrated programming experience, particularly in Python and SQL databases; demonstrated web programming experience; knowledge of Linux/Unix; excellent spoken and written communication and documentation skills. *Preferred qualifications*: Advanced degree (M.Sc. or Ph.D) or equivalent in Computer Science, Bioinformatics, Molecular Biology or a related discipline; experience in development of bioinformatic algorithms; knowledge of R programming; experience in development of or contribution to open source projects; experience in collaborative software development such as the use of version control software, writing and following software specifications, participation in code review; knowledge of basic molecular biology; experience with genomic browser programming, such as GMOD or equivalent. Candidates should send a CV or resume and have three letters of reference sent separately to Dr. Iddo Friedberg at friedberg.lab.jobs(a)gmail.comScreening of applications begins April 14, 2012 and will continue until the position is filled. Miami University is an affirmative action/equal opportunity employer with smoke-free campuses. Consumer Information http://www.miami.muohio.edu/about-miami/publications-and-policies/student-c…. Hard copy upon request. -- Iddo Friedberg http://iddo-friedberg.net/contact.html ++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.> ++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----. .>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>> >>----.<--.>++++++.<<<<------------------------------------.

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[Compbio-allhands] QBC Journal Club, Tuesday, April 3- 10:45AM, GH Aud
by Nicole Takesono Flowers 27 Mar '12

27 Mar '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, April 3 10:45 am, GH Auditorium Aishjay Jayagopal, PSPG First-in-Human Testing of a Wirelessly Controlled Drug Delivery Microchip. R. Farra et al, Science Translational Medicine, Feb 2012. Tara Friedrich, iPQB Multiple Epigenetic Modifiers Induce Aggressive Viral Extinction in Extraembryonic Endoderm Stem Cells. M.C. Golding, L. Zhang, M.R.W. Mann. Cell Stem Cell, Volume 6, Issue 5, 457-467, 7 May 2010. 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] David Sivak Seminar - Monday, April 2 - 11am - 12pm, Byers Hall 212
by Hilary Mahon 26 Mar '12

26 Mar '12

Please see attached for Dr. Sivak of the Lawrence Berkeley Lab. --- 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] QBC Journal Club, Tuesday, March 27- 10:45AM, GH Aud
by Nicole Takesono Flowers 21 Mar '12

21 Mar '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, March 27 10:45 am, GH Auditorium Amy Jacobson, CCB Antiparallel EmrE exports drugs by exchanging between asymmetric structures. Moarrison E.A., et al. Nature 481, 45-50 (2012). Kale Kundert, iPQB Identification of oxadiazoles as new drug leads for the control of schistosomiasis. A. Sayed, A. Simeonov, C. Thomas, J. Inglese, C. Austin and D. Williams. Nature Medicine 14, 407-412 (2008). 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] 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 March 2012