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

[Compbio-allhands] 5/17/12 Seminar with Jennifer Lippincott-Schwartz
by Nicole Takesono Flowers 11 May '12

11 May '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 Jennifer Lippincott-Schwartz NIH Mitochondria, metabolism and cell cycle control: an imaging perspective May 17, 2012 Amanda Silber & Si-Han Chen, Hosts 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] QBC Journal Club, Tuesday, May 15- 10:45AM, GH Aud
by Nicole Takesono Flowers 10 May '12

10 May '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, May 15 10:45 am, GH Auditorium Russell Goodman, iPQB Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy. Soranno A. et al., Proc Natl Acad Sci. 2012 Apr 6. James Webber, iPQB DNA breaks and chromosome pulverization from errors in mitosis. Crasta K et al, Nature. 2012 Feb 2; 482(7383):53-8. 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] QBC Journal Club, Tuesday, May 8- 10:45AM, GH Aud
by Nicole Takesono Flowers 02 May '12

02 May '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, May 8 10:45 am, GH Auditorium Xiaoming Liang, PSPG A PGC1-α-dependent myokine that drives brown-fat-like development of white fat and thermogenesis. Bostrom P. et al. Nature. Jan 11;481(7382):463-8. 2012 Stephen Nayfach-Battilana, iPQB Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota. Iverson, V et al. Science Vol. 335 no. 6068 pp. 587-590. 2012. 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] 5/3/12 Seminar with Russ Altman
by Nicole Takesono Flowers 27 Apr '12

27 Apr '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 Russ Altman Stanford The emerging network of data for linking genes and drugs May 3, 2012 Chris Wen, 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: Position in structural biology available at Lilly Biotechnology Center in San Diego
by Andrej Sali 26 Apr '12

26 Apr '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences 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: "J. Michael Sauder" <sauder_j_michael(a)lilly.com> > Subject: Position in structural biology available at Lilly Biotechnology Center in San Diego > Date: April 26, 2012 11:06:01 AM PDT > To: "J. Michael Sauder" <sauder_j_michael(a)lilly.com> > > A position is opening for a person with significant experience in structural biology and broad knowledge of several therapeutic areas. It is an opportunity to work in an industrial, drug-discovery setting and make significant contributions to a world class structural biology team. > > Details are available on the lilly.com website (Careers, job id 50448492), or by following this link: > https://careers.peopleclick.com/careerscp/client_lilly/external/jobDetails.… > > Please feel free to forward this message to anyone you think might be interested. > > Mike > > J. Michael Sauder, Ph.D. > Research Advisor, Structural Biology > Lilly Biotechnology Center > 10300 Campus Point Dr, San Diego, CA 92121 > michael.sauder(a)lilly.com > office: 858-638-8802 main: 858-597-4990 >

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[Compbio-allhands] Fwd: Intern Positions at Janssen Pharmaceutical R&D
by Andrej Sali 25 Apr '12

25 Apr '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences 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: "Stephens, Susan [JRDUS]" <sstephens1(a)ITS.JNJ.COM> > Subject: Intern Positions at Janssen Pharmaceutical R&D > Date: April 25, 2012 5:14:59 PM PDT > To: "Stephens, Susan [JRDUS]" <sstephens1(a)ITS.JNJ.COM> > > The In Silico Immunology team in Janssen Pharmaceutical Research & Development L.L.C., a member of Johnson and Johnson's family of companies, is recruiting for two Research Scientists for 2012 Pharmaceutical R&D internships, located in Radnor, PA. > > Please share information about the positions with any candidates that may be interested. Formal applications should be made on the J&J Career Web site (http://careers.jnj.com) > > Kind regards, > > Susie > > > 2012 PHARMACEUTICAL R&D INTERNSHIPS in In Silico Immunology - 000004FN > > 1. Network Pharmacology > > Janssen Pharmaceutical Research & Development is seeking a graduate student with strong computational skills interested in an internship position in the Network Pharmacology group. The candidate’s current research area should be Systems Biology, Bioinformatics, Computer Science or Engineering, have a solid understanding of network analysis methods and biology as well as programming experience and ability to write R, Matlab and/or Perl script. Experience with large-scale genomics data and a solid understanding of bioinformatics tools and databases is a plus. The successful candidate will focus on the development of bioinformatics approaches to integrate and analyze data from various cutting-edge projects in the Immunology Therapeutic Area. > > The candidate will develop and investigate methods to understand dysregulated mechanisms in disease using Network Pharmacology approaches. They will conduct network analysis and inference on large-scale data that provides a global view of the disease that would help determining its representation in the relevant in-vivo and in-vitro models. > > · Construct biological networks from molecular profiling data and from molecular interaction data stored in databases > > · Conduct research on topological analysis to find key regulatory genes/proteins via biological network and genomic data > > · Identify robust sub-networks using different data modalities (mRNA, proteins, DNA, etc.) > > · Reconstruct network modules from the identified key regulators to discover affected biological processes and disease-related genes > > > 2. Lifecycle Management > > Janssen Pharmaceutical Research & Development is seeking a graduate student with strong computational skills interested in an internship position in focused on Lifecycle Management. The candidate’s current research area should be Systems Biology, Bioinformatics, Computer Science or Engineering. The intern will be responsible for developing algorithms and workflows that will facilitate the analysis of preclinical and clinical data. Through the implementation of these workflows, the intern will explore potential new disease indications for marketed and late stage development clinical compounds across the large and small molecule Immunology Therapeutic Area portfolio. The successful intern will work with the In Silico Immunology team to develop computational methodologies that will enable the combination of data outputs from different software platforms to build in silico networks of autoimmune and pulmonary diseases. > > Experience in computational algorithms and mathematical modeling, preferably of biological or disease networks, is required for this position. Analysis of large datasets, especially microarray data, is preferred. Expertise in computer software such as R, Matlab, Ingenuity Pathways, and Cytoscape is also desirable. > > > > >

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[Compbio-allhands] QBC Journal Club, Tuesday, May 1- 10:45AM, GH Aud
by Nicole Takesono Flowers 24 Apr '12

24 Apr '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, May 1 10:45 am, GH Auditorium Katherine Southard, CCB Small-molecule-induced DNA damage identifies alternative DNA structures in human genes. R. Rodriguez et al. Nature chemical biology 8 (3) p. 301-10. 2012. Graham Heimberg, iPQB The most expensive cold diagnosis ever Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes Rui Chen et al. Cell 148, 1293-1307. March 16, 2012. 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] 4/26/12 Seminar with Howard Hang
by Nicole Takesono Flowers 20 Apr '12

20 Apr '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 Howard Hang Harvard Chemical Reporters for Protein S-Palmitoylation in Cell Biology and Innate Immunity April 26, 2012 Danica Galonic Fujimori, 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] QBC Journal Club, Tuesday, April 24- 10:45AM, GH Aud
by Nicole Takesono Flowers 18 Apr '12

18 Apr '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, April 24 10:45 am, GH Auditorium Alex Pankov, iPQB Detecting novel associations in large datasets. D. N. Reshef, Y. A. Reshef, H. K. Finucane, S. R. Grossman, G. McVean, P. J. Turnbaugh,E. S. Lander, M. Mitzenmacher, P. C. Sabeti. Science, 334: 1518-1524, (2011). Christina Fitzsimmons, CCB To Knot or Not? Knot formation in newly translated proteins is spontaneous and accelerated by chaperonins. A.L. Mallam & S.E. Jackson. Nature Chemical Biology, 2012, 8, 147-153. doi: 10.1038/nchembio.742. 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: Automated Function Prediction: and ISMB Special Interest Group Meeting
by Alexandra Schnoes 17 Apr '12

17 Apr '12

---------- Forwarded message ---------- From: Iddo Friedberg <idoerg(a)gmail.com> Date: Tue, Apr 17, 2012 at 8:27 AM Subject: Automated Function Prediction: and ISMB Special Interest Group Meeting To: ISB(a)listserv.it.northwestern.edu Locale: Long Beach, California USA Date: July 14, 2012 (Just before ISMB 2012) URL: http://biofunctionprediction.org Important dates: April 25, 2012: Deadline for submitting abstracts. (extended!) May 9, 2011: Notifications for accepted abstracts e-mailed to corresponding authors May 16, 2011: Deadline for presenters to confirm acceptance of invitation to speak. July 14, 2011: AFP SIG preceding ISMB 2012 An ISMB Special Interest Group Meeting Automated Protein Function Prediction Sequence and structure genomics have generated a wealth of data, but extracting meaningful information from genomic information is becoming an increasingly difficult challenge. Both the number and the diversity of discovered sequences are increasing, while the fraction of genes whose function is known is decreasing.In addition, there is a need for annotation which is standardized so that it could be incorporated into function annotation on a large scale. Finally, there is a need to assess the quality of the function prediction software which is out there. For these reasons and many more, automated protein function prediction is rapidly gaining interest among computational biologists in academia and industry. The AFP SIG has been part of ISMB since 2005. We call upon all researchers involved in gene and protein function prediction to submit an abstract to the AFP meeting. Authors of select abstracts will be invited to give a talk and/or present a poster. This year, AFP is delighted to have Jonathan Eisen from the University of California, Davis as its keynote speaker. Prof. Eisen is a pioneer in the field of function prediction. >From his lab page: http://bobcat.genomecenter.ucdavis.edu/mediawiki/index.php/Main_Page "Dr. Eisen has published more than 200 scientific papers and is a co-author of a relatively recently published Evolution Textbook. Dr. Eisen is also a strong proponent of the Open Access movement in scientific publishing and is Academic Editor in Chief of PLoS Biology. For recent news see http://twitter.com/phylogenomics" For further instructions on how to submit abstracts to AFP 2012, please go here: http://biofunctionprediction.org/node/415 We are looking forward to seeing you in Long Beach, California! Iddo Friedberg on behalf of the AFP organizing committee -- Iddo Friedberg http://iddo-friedberg.net/contact.html -- Alexandra Schnoes, Ph.D. Scientist, Babbitt Laboratory Program Coordinator, Graduate Student Internships for Career Exploration University of California San Francisco Tel: 415-502-1248 Fax: 415-514-9656 Email: schnoes(a)gmail.com

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[Compbio-allhands] 4/19/12 Seminar with Alan Engelman
by Nicole Takesono Flowers 13 Apr '12

13 Apr '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 Alan Engelman Harvard Retroviral integrase function and drug resistance mechanisms April 19, 2012 Bob Stroud, 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] 5/31/12 Seminar with Greg Verdine- CANCELLED
by Nicole Takesono Flowers 12 Apr '12

12 Apr '12

Due to unforeseen circumstances, the seminar scheduled on 5/31/12 has been cancelled. Please stay tuned for a new speaker announcement. 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] QBC Journal Club, Tuesday, April 17- 10:45AM, GH Aud
by Nicole Takesono Flowers 11 Apr '12

11 Apr '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, April 17 10:45 am, GH Auditorium Marian Deuker, CCB The molecular basis of acid insensitivity in the African naked mole-rat. Smith ES, Omerbasic 263; D, Lechner SG, Anirudhan G, Lapatsina L, Lewin GR. Science. 2011 Dec 16;334(6062):1557-60. Liz Howe, BMI Host Cell Invasion by Apicomplexan Parasites: Insights from the Co-Structure of AMA1 with a RON2 peptide ML Tonkin, M Roques, MH Lamarque, M Pugniere, D Douguet, J Crawford, M Lebrun, MJ Boulanger. Science 22 July 2011: Vol. 333 no. 6041 pp. 463-467. 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] 4/12/12 Seminar with Michelle Chang
by Nicole Takesono Flowers 05 Apr '12

05 Apr '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 Michelle Chang UC Berkeley Building new chemical function in living organisms April 12, 2012 Kevan Shokat & Jack Taunton, Hosts 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] QBC Journal Club, Tuesday, April 10- 10:45AM, GH Aud
by Nicole Takesono Flowers 04 Apr '12

04 Apr '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, April 10 10:45 am, GH Auditorium Sarah Woldemariam, CCB Critical Role of Amyloid-like Oligomers of Drosophila Orb2 in the Persistence of Memory Cell, Volume 148, Pages 515-529, Published February 3, 2011 Kyle Barlow, iPQB Of mice and men: an Alzheimer's cure for our murine brethren ApoE-Directed Therapeutics Rapidly Clear Β-Amyloid and Reverse Deficits in AD Mouse Models Cramer, Paige E, John R Cirrito, Daniel W Wesson, C. Y. Daniel Lee, J. Colleen Karlo, Adriana E Zinn, Brad T Casali, et al. Science 335, no. 6075 (March 23, 2012): 1503-1506. 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] 4/5/12 Seminar with Ian Wilson
by Nicole Takesono Flowers 02 Apr '12

02 Apr '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 Ian Wilson Scripps Broad neutralization of HIV and influenza viruses April 5, 2012 Bob Stroud, 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: 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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