March 2020 - compbio-allhands@cgl.ucsf.edu

[Compbio-allhands] Fwd: URGENT: White House Announces New Partnership to Unleash U.S. Supercomputing Resources to Fight COVID-19
by Andrej Sali 22 Mar '20

22 Mar '20

fyi > Begin forwarded message: > > From: "Guglielmo, B Joseph" <BJoseph.Guglielmo(a)ucsf.edu> > Subject: Fwd: URGENT: White House Announces New Partnership to Unleash U.S. Supercomputing Resources to Fight COVID-19 > Date: March 22, 2020 at 6:52:10 PM PDT > To: "SALI, ANDREJ" <sali(a)salilab.org>, "Krogan, Nevan" <Nevan.Krogan(a)ucsf.edu>, Matthew Jacobson <matthewpjacobson(a)gmail.com>, "Desai, Tejal" <Tejal.Desai(a)ucsf.edu> > > > > Sent from my iPad > > Begin forwarded message: > >> From: "Kiser, Gretchen" <Gretchen.Kiser(a)ucsf.edu> >> Date: March 22, 2020 at 6:38:33 PM PDT >> To: "FUNDING_OPPS(a)LISTSRV.UCSF.EDU" <FUNDING_OPPS(a)LISTSRV.UCSF.EDU> >> Subject: URGENT: White House Announces New Partnership to Unleash U.S. Supercomputing Resources to Fight COVID-19 >> Reply-To: "Kiser, Gretchen" <Gretchen.Kiser(a)UCSF.EDU> >> >> >> >> >> THE WHITE HOUSE >> Office of Science and Technology Policy >> >> FOR IMMEDIATE RELEASE >> March 22, 2020 >> >> White House Announces New Partnership to Unleash U.S. Supercomputing Resources to Fight COVID-19 >> >> Today, The White House announced the launch of the COVID-19 High Performance Computing Consortium <https://urldefense.proofpoint.com/v2/url?u=http-3A__covid19-2Dhpc-2Dconsort…> to provide COVID-19 researchers worldwide with access to the world’s most powerful high performance computing resources that can significantly advance the pace of scientific discovery in the fight to stop the virus. >> >> This unique public-private consortium, spearheaded by The White House Office of Science and Technology Policy, IBM, the U.S. Department of Energy, and the National Science Foundation, includes the following government, industry, and academic leaders who have volunteered free compute time and resources on their machines: >> >> Industry >> IBM >> Amazon Web Services >> Google Cloud >> Microsoft >> Hewlett Packard Enterprise >> Academia >> Massachusetts Institute of Technology >> Rensselaer Polytechnic Institute >> U.S. Department of Energy National Laboratories >> Argonne National Laboratory >> Lawrence Livermore National Laboratory >> Los Alamos National Laboratory >> Oak Ridge National Laboratory >> Sandia National Laboratories >> Federal Agencies >> National Science Foundation >> NASA >> >> Researchers are invited to submit COVID-19 related research proposals to the consortium via the online portal <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.xsede.org_covid19-…> which will then be reviewed and matched with computing resources from one of the partner institutions. An expert panel of top scientists and computing researchers will work with proposers to quickly assess the public health benefit of the work and coordinate the allocation of the group’s powerful computing assets. >> >> The COVID-19 High Performance Computing Consortium currently pools 16 systems that together offer over 330 petaflops of supercomputing capacity. Additional capacity, including cloud computing resources, will be added through present and future partners. >> >> The sophisticated computing systems available through this Consortium can process massive numbers of calculations related to bioinformatics, epidemiology, molecular modeling, and healthcare system response, helping scientists develop answers to complex scientific questions about COVID-19 in hours or days versus weeks or months. >> >> “America is coming together to fight COVID-19, and that means unleashing the full capacity of our world-class supercomputers to rapidly advance scientific research for treatments and a vaccine. We thank the private sector and academic leaders who are joining the federal government as part of the Trump Administration’s whole-of-America response,” said Michael Kratsios, U.S. Chief Technology Officer. >> >> FEDERAL AGENCY PARTNERS >> >> “Under the Trump Administration, the United States has regained its position as the dominant global force in Supercomputing technology. The Department of Energy is home to the world’s fastest and most powerful supercomputers, and we are excited to partner with leaders across the scientific community who will use our world class innovation and technology to combat COVID-19,” said U.S. Energy Secretary Dan Brouillette. >> >> “The Department of Energy’s National Labs have made profound advancements towards combatting COVID-19,” said U.S. Department of Energy (DOE) Under Secretary for Science Paul Dabbar. “By providing researchers access to world leading technology here in our own backyard, we take an additional leap towards ending this pandemic. We look forward to collaborating with scientists and researchers to bring an end to COVID-19.” >> >> “The National Nuclear Security Administration is eagerly lending its world-class supercomputing resources to combat COVID-19 in collaboration with OSTP and other agencies,” said Lisa E. Gordon-Hagerty, DOE Under Secretary for Nuclear Security and NNSA Administrator. “Ten NNSA supercomputers will be available, empowering researchers to understand the COVID-19 virus, develop treatments and vaccines, and ultimately bring an end to this pandemic.” >> >> “The National Science Foundation is pleased to join the COVID-19 HPC Consortium to enhance access to the Nation’s leading HPC resources, including the NSF-funded Frontera supercomputer, the world’s most powerful HPC system deployed on an US academic campus,” said France Cordova, Director of the National Science Foundation. “Frontera and other NSF-funded advanced computing resources will enable the Nation’s science and engineering community to pursue data science, computational modeling, and artificial intelligence approaches to help us accelerate our understanding of COVID-19 and strategies for responding to the pandemic.” >> >> “We are pleased to lend NASA’s supercomputing expertise to assist in the global fight against this pandemic. For more than six decades the agency has used its expertise to take on challenges that have benefited people worldwide in unexpected ways,” said Jim Bridenstine, NASA Administrator. >> >> INDUSTRY PARTNERS >> >> “Accelerating the process of discovery to unlock treatments and a cure for COVID-19 is of vital importance to us all. By bringing together the world's most advanced supercomputers and matching them with the best ideas and expertise, this consortium can drive real progress in this global fight. IBM is proud to have helped kick-start this important effort," said Dario Gil, Director of IBM Research. >> >> “We know that high performance computing can reduce the time it takes to process massive data sets and perform complex simulations from days to hours,” said Mike Daniels, Vice President, Global Public Sector at Google Cloud. “We look forward to participating in this initiative alongside leaders in technology, academia, and the public sector to make more resources available to COVID-19 researchers and to apply Google Cloud computing capabilities toward the development of potential treatments and vaccines.” >> >> “We want to make sure researchers working to combat COVID-19 have access to the tools they need. Through our AI for Health program we’ve seen first-hand the impact of empowering talented researchers with powerful technology. We hope that by expanding access to the Azure cloud and High Performance Computing capabilities, and by creating more opportunities to collaborate with our own data scientists, we can help accelerate this important work,” said John Kahan, Microsoft Global Head, AI for Health Program. >> >> “We’re proud to support this critical work and stand ready with the compute power of AWS to help accelerate research and development efforts,” said Teresa Carlson, Vice President, Worldwide Public Sector at AWS. “Working together, government, business, and academic leaders can utilize the power of the cloud to advance the pace of scientific discovery and innovation, and help combat the COVID-19 virus.” >> >> ACADEMIC PARTNERS >> >> “In order to combat the devastating effects of this pandemic, we must be able to fully grasp the complexities and interconnectedness of biological systems and epidemiological data, as researchers work to develop therapeutic interventions and address gaps in our knowledge,” said Rensselaer President Shirley Ann Jackson. “This effort requires expertise, collaboration, and the ability to process incredible amounts of data, and Rensselaer is offering all three at this critical time. In particular, the ability to model at very large scales requires the unique capabilities of AiMOS.” >> >> "Computing and AI have a major role to play in bringing Covid-19 under control," said Christopher Hill, head of MIT’s research computing infrastructure. "We want to do our part by making MIT's two most powerful machines, Satori and TX-GAIA, available to researchers who are racing to understand the virus, model the outbreak, and accelerate drug discovery and design. This will be a team effort, and we hope our actions will inspire others to throw their computing power and brain power at the virus." >> >> >> >> Use this link to unsubscribe <http://listsrv.ucsf.edu/cgi-bin/wa?SUBED1=FUNDING_OPPS&A=1> from this mailing list. >>

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[Compbio-allhands] Fwd: Summer Internship in Computer-Aided Drug Design at Genentech
by Michael Keiser 17 Mar '20

17 Mar '20

FYI ---------- Forwarded message --------- From: Paul Beroza <beroza.paul(a)gene.com> Date: Tue, Mar 17, 2020 at 9:10 AM Subject: Summer Internship in Computer-Aided Drug Design at Genentech To: Paul Beroza <berozap(a)gene.com> I hope this email finds you well, in spite of all the corona-craziness going on. I could use your help. I have a summer intern position I'm trying to fill and am looking for candidates. The position would involve developing methods and workflows for virtual library screening. Brief description here: 2020 Comp Chem Internship at Genentech <https://www.gene.com/careers/detail/202002-105348/Intern-Research-and-Early…> We are focusing on undergraduates but are considering all student levels. If you could recommend someone or pass the link on to those who might be interested, I'd appreciate it. I need to identify a candidate before the end of the month (yes, this month...), so we need to move quickly. Thanks for the help and best regards! Paul <https://www.gene.com/careers/detail/202002-105348/Intern-Research-and-Early…> <https://www.gene.com/careers/detail/202002-105348/Intern-Research-and-Early…> -- Paul Beroza, Ph.D. Computational Drug Discovery, Genentech -- Michael J Keiser, PhD Assistant Professor, UCSF Chan Zuckerberg Initiative Ben Barres Investigator Paul G. Allen Frontiers Group Distinguished Investigator Dept Pharmaceutical Chemistry Dept Bioengineering & Therapeutic Sciences Bakar Computational Health Sciences Institute Kavli Institute for Fundamental Neuroscience Institute for Neurodegenerative Diseases p/1-415-886-7651 keiserlab.org <http://www.keiserlab.org> calendly.com/mjke

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[Compbio-allhands] Fwd: FW: Please help us spread the word on the Innovation Fellowship
by Brian Shoichet 12 Mar '20

12 Mar '20

FYI. These postdoctoral fellowships pay well, expose people to a drug discovery environment, and have a good reputation for training. ---------- Forwarded message --------- From: Urban, Laszlo <laszlo.urban(a)novartis.com> Date: Thu, Mar 12, 2020 at 7:39 AM Subject: FW: Please help us spread the word on the Innovation Fellowship To: Brian Shoichet (bshoichet(a)gmail.com) <bshoichet(a)gmail.com>, bryan_roth(a)med.unc.edu <bryan_roth(a)med.unc.edu>, Amanda Chen <axchen(a)mit.edu>, Robert Ietswaart <robertietswaart(a)gmail.com>, Seda Arat <seda8arat(a)gmail.com>, BUMJUN KIM <bumjunebjkim(a)gmail.com>, Saman Farahmand < saman.farahmand001(a)umb.edu> Dear All, I am asking for a favor. We have Innovation Fellow applications open until April 14th in Cambridge, MA and April 24th in Basel and looking for talented people who would consider this opportunity. In case you know people who would be interested, please send them the links below. “The Novartis Innovation Postdoctoral Fellowship offers aspiring drug hunters a unique opportunity to join our teams at the Novartis Institutes for BioMedical Research (NIBR), the innovation engine of Novartis. Mentored by experienced NIBR scientists, Innovation Fellows will gain first-hand experience in the design and development of breakthrough therapies and innovative technologies. We are looking for Innovation Fellows who will harness their scientific creativity and natural curiosity to help bring transformative treatments to patients. Join us as we reimagine medicine together. Program duration: 2-3 years.” Here are a few links: LinkedIn (Cambridge application): https://www.linkedin.com/jobs/search/?currentJobId=1738923966&geoId=1036442… ) LinkedIn (Basel application): https://www.linkedin.com/jobs/search/?geoId=106693272&keywords=novartis%20i… ) Brassring: *Apply - Cambridge* <https://www.novartis.com/careers/career-search/job-details/288900BR> *Apply - Basel* <https://www.novartis.com/careers/career-search/job-details/289991BR> External postdoc program website, which includes details on the program and links to the BrassRing ads: https://www.novartis.com/our-science/postdoc-program/novartis-innovation-po… Thanks in advance for your help! All the best, Laszlo -- Brian Shoichet, Professor, UCSF latest science from the lab: *http://www.bkslab.org/ <http://www.bkslab.org/contact.php>*

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[Compbio-allhands] CANCELLED! Re: 3/12/2020 BBC Seminar with Mikhail Shapiro, PhD **MH 1401/1402**
by Flowers, Nicole 06 Mar '20

06 Mar '20

Unfortunately, this talk has been cancelled. We’re hoping to reschedule Dr. Shapiro for a later date. Nicole Takesono Flowers Biophysics Graduate Program Manager UCSF MC 2240 600 16th St. Genentech Hall Room N474D San Francisco, CA 94143 P: 415.502.6518 From: "Flowers, Nicole" <Nicole.Flowers(a)ucsf.edu> Date: Friday, March 6, 2020 at 9:01 AM To: "bpstudents(a)listserv.ucsf.edu" <bpstudents(a)listserv.ucsf.edu>, BMI Students List <BMI_STUDENTS(a)LISTSRV.UCSF.EDU>, CCB Student List <CCB_STUDENTS(a)LISTSRV.UCSF.EDU>, "bbcfaculty(a)listserv.ucsf.edu" <bbcfaculty(a)listserv.ucsf.edu> Subject: 3/12/2020 BBC Seminar with Mikhail Shapiro, PhD **MH 1401/1402** BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, Noon Mission Hall 1401/1402 Livestream: http://tiny.ucsf.edu/WgjNou Zoom: https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.zoom.us_j_8590630… Mikhail Shapiro, Ph.D. CalTech Biomolecular Ultrasound for Non-Invasive Imaging and Control of Cellular Function March 12, 2020 J. Fraser, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Gladstone Center for Cell Circuitry. Nicole Takesono Flowers Biophysics Graduate Program Manager UCSF MC 2240 600 16th St. Genentech Hall Room N474D San Francisco, CA 94143 P: 415.502.6518

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[Compbio-allhands] 3/12/2020 BBC Seminar with Mikhail Shapiro, PhD **MH 1401/1402**
by Flowers, Nicole 05 Mar '20

05 Mar '20

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, Noon Mission Hall 1401/1402 Livestream: http://tiny.ucsf.edu/WgjNou Zoom: https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.zoom.us_j_8590630… Mikhail Shapiro, Ph.D. CalTech Biomolecular Ultrasound for Non-Invasive Imaging and Control of Cellular Function March 12, 2020 J. Fraser, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Gladstone Center for Cell Circuitry. Nicole Takesono Flowers Biophysics Graduate Program Manager UCSF MC 2240 600 16th St. Genentech Hall Room N474D San Francisco, CA 94143 P: 415.502.6518

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[Compbio-allhands] 3/5/2020 BBC Seminar with Demet Araç
by Flowers, Nicole 02 Mar '20

02 Mar '20

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, Noon Genentech Hall Auditorium Livestream: http://tiny.ucsf.edu/WgjNou Zoom: https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.zoom.us_j_8590630… Demet Araç, Ph.D. University of Chicago Cellular Communication via Adhesion in the Nervous System October 5, 2020 A. Manglik, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Gladstone Center for Cell Circuitry. Nicole Takesono Flowers Biophysics Graduate Program Manager UCSF MC 2240 600 16th St. Genentech Hall Room N474D San Francisco, CA 94143 P: 415.502.6518

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[Compbio-allhands] Fwd: Any Ph.D. student looking for a postdoc in CA?
by Brian Shoichet 01 Mar '20

01 Mar '20

FYI. brian ---------- Forwarded message --------- From: Vsevolod Katritch <katritch(a)usc.edu> Date: Sun, Mar 1, 2020 at 5:36 PM Subject: Any Ph.D. student looking for a postdoc in CA? To: shoichet(a)cgl.ucsf.edu <shoichet(a)cgl.ucsf.edu> Dear Brian, How are you doing? May I ask you for a favor? I am looking for a computational postdoc now (see attached), and was wondering if you know any bright PhD student graduating soon and applying for a position? If you do, please send them my way, I know your students are good! BTW, very proud of my alumni postdoc placements last year – two got tenure track faculty positions, one scientist in Genentech, one in Schoedinger… Thank you, Seva -------------------------------------------------- Vsevolod “Seva” Katritch, Ph.D. Asst. Professor of Biological Sciences and Chemistry University of Southern California Dana and David Dornsife College of Letters, Arts and Sciences Michelson Center for Convergent Bioscience The Bridge Institute 1002 West Childs Way, MCB-317 Los Angeles, CA 90089 Tel: 213-821-1488 http://katritch.usc.edu katritch(a)usc.edu -- Brian Shoichet, Professor, UCSF *http://www.bkslab.org/contact.php <http://www.bkslab.org/contact.php>*

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