prof. d. petkovic, director, ccls; chair, cs department sfsu 1 sfsu center for computing for life...

Prof. D. Petkovic, Director, CCLS; Chair, CS Department SFSU

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SFSU Center for Computing for Life Sciences – CCLS

Advisory Board Meeting April 08Summary

Prof. D. PetkovicDirector, CCLS

[email protected]

CCLS WWW site http://cs.sfsu.edu/ccls/index.html

04/23/08

mailto:[email protected]

http://cs.sfsu.edu/ccls/index.html


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CCLS Advisory Board meeting summary

• CCLS Advisory Board Meeting has been held 04/21/08 at SFSU

• This set of slides contains CCLS overview slides as presented by D. Petkovic (Part I) and summary of the discussion we had at the end of the meeting (Part II)


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Attendance – External Board Members

Russ Altman, MD, Ph.D.,Department of Genetics,Stanford University Medical

Center

W. Ekkehard Blanz, Ph.D.Vice President,Siemens Medical Solutions, Ultrasound

Division

Ljubomir Buturovic Pathwork Diagnostics, Inc.

Bill Cody, PhDSenior Manager, Healthcare Informatics IBM Almaden Research Center

Daniel Gusfield, Ph.D.Department of Computer Science, UC Davis

Regis Kelly, Ph.D.California Institute for Quantitative

Biomedical Research(QB3), San Francisco

Chung-Sheng Li, Senior ManagerIBM Thomas J. Research Center

De Witt Sumners, Ph.D.Florida State UniversityDepartment of Mathematics

Thomas D. Wu, M.D., Ph.D.Senior Scientist, Dept. of BioinformaticsGenentech, Inc.,


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Attendance – Internal Board members and others (SFSU)

• Axler, Sheldon - Dean, College of Science abd Ebgineeriung

• Petkovic, Dragutin - Director, CCLS• Mike Goldman - Chair, CCLS

Advisory Board• Abraham, Wendy - SFSU

Development • DeWitt, Jane - Chair, Chemistry and

Biochemustry• Hafernik, John - Biology

Department• Macher, Bruce - Chemiustry and

Biochemustry• Chris Smith - Biology Department

• Mike Wong, CCLS Research Scientist

• Niki Jorgensen, CCLS Staff

• Lannie Nguyen-Tang , SFSU, Events management

• Michelle Gagnon, ORSP

• Sung Hu, Associate Dean, COSE


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Part I – CCLS overview

• As presented by D. Petkovic


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Welcome and thanks for coming!


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What do we hope to get today?

• Introduce you to CCLS – who we are, what we have done so far

• Create a community of “CCLS supporters” to help us move CCLS to the next level:– Feedback on type of projects we should do– Ideas for collaborative partnerships with academia, industry– How to better educate our students– Help in placing our students in relevant internships and jobs– Help and ideas for funding: joint proposals/grants, industry

partnerships– Resources we need: skill needs, facilities, administrative support

• Get feedback and develop concrete plans for next 3 years


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Agenda

• Introductions, Overview of CCLS

• Collaborative projects in CCLS• Student Internships and Placements• Training for the Computing in Life Science field and jobs

Break

• Fundraising and Grants• Life Sciences, Biotechnology and Genomics – Prof. C. Smith, Biology• Closing perspective – recommendations and plans

• Dinner and Reception


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CCLS Mission• The CCLS provides an environment (e.g. space, IT

support, services, funding) for faculty and students to collaborate on multidisciplinary projects at the intersection of Computing and Life Sciences

• It involves faculty, researchers, and students from the SFSU departments of Biology, Chemistry and Biochemistry, Computer Science, Mathematics, Physics and Astronomy, and other SFSU Schools and Departments


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Our uniqueness• Addresses very broad areas and type of work

– From conceptual to applied research– Research projects, theses, grant writing, visitors, industry and academic

collaboration– Offers space, IT support, cluster computing, SW design help, support and

maintenance– Fulltime staff (1 person)– Funds seed grants, travel, SW tools

• Promotes true multidisciplinary projects and theses (mixed teams, mixed thesis committees)

• Involves underrepresented students• Leverages its strategic location (proximity to biotech, top universities)

• No faculty hired into CCLS, no curricular activities (but complements classes)


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Areas addressed by CCLS projects – they are broad by design

• Bioinformatics• Use of Machine Learning or analysis and classifications of genotypes• Data management for biology and drug development• Data visualization• Mathematical modeling of genetic structures• Advanced WWW applications and user interfaces• Serious games in health education• Sensor networks for biological and environmental applications• Data mining of biological data• High performance clusters and SW tools for computing for life

sciences• ……and whatever is next…


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A bit on history …

• Formal entity, approved by SFSU President in 2005• Funded by SFSU President, with funding and space from

SFSU. Committed to a review after three years (this year)• There was no collaborative activity of this type before at

SFSU• Governance: CCLS Director, CCLS Associate Director,

CCLS Advisory Board

• SFSU just renewed 3 year commitment


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Budget for the last three years

• 2 new faculty positions (hired by CS and Biology departments and doing research in CCLS)

• 1 full-time staff position (SW development, support and maintenance) – unique to CSU

• $ 45 K equipment• Yearly:

– $ 20 K in grant seed money– $ 25 K travel and conference support– $ 12 K equipment money


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Strategy Phase I (2005 to present – first three year cycle)

Strategy Phase I: Establish, educate, promote, seed..– Hire faculty to individual department who would do

CCLS type of research and theses and collaborate– Hire research staff to help develop and maintain SW

and provide cluster support– Provide and organize collaborative space– Provide IT and Cluster Computing and cooled IT space– Involve students in CCLS projects– “Seed many small projects in a wide field” give

number of smaller grants to as many faculty as possible to educate, promote, encourage AND learn see what works and build from that


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CCLS External WWW page http://cs.sfsu.edu/ccls/index.html


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CCLS Internal WWW site (polices, access, cluster)


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CCS Mini-grants• Objective in Phase I was to seed as many activities and

widely promote CCLS among COSE faculty, and to help faculty prepare for larger external grants

• Each year funded about 8-10 projects with about $ 50 K/year

• Process: Call for proposals, CCLS Internal Advisory Board (COSE Chairs) evaluates. Preference given to proposals with multidisciplinary teams

• Grants limited to $ 7 K (can buy one course release and some student funding)

• Some grants resulted in bigger external grants (NSF, CSUPERB)


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CCLS ClusterComputing Program

• Purpose:– To support computational biology education

and computationally expensive biology research by developing and teaching skills and procuring equipment necessary for high-performance cluster computing (HPCC)

• CCLS HPCC DELLTechnical Specifications:– 40 CPUs Intel Xeon 2.0 GHz– 80 GB RAM (being upgraded)– 4.0 Terabytes storage– Gigabit Ethernet– Dell PowerEdge and Apple XServe technology

Open source system mng. SW

• Access and allocation policies in place


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CCLS Cluster is a Complete Solution for Users

• Online documentation– Cluster specifications– Acceptable use policy– Access request web form– Software installation policy– Software installation request web form

• Staff assistance available via e-mail, phone, or by appointment– Training on developing software for parallel computing– CCLS staff can deliver custom software, at the discretion of staff

• Top Google search hit for phylogeny research with PAUP on Dell hardware [search: paup dell]

Users can request access via a web form


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CCLS Accomplishment Summary since founding 2005

• Over 20 faculty involved from various departments such as COSE (CS, Math, Biology, Chemistry and Biochemistry), but also Health and Human Services, Industrial Design

• Over 20 MS theses in CCLS area since 2004, with thesis committees from multiple departments (one from CS, others usually from Biology)

• Over 35 refereed publications in CCLS area since 2003. One best paper award, one second best paper award, one poster award

• NSF Career Grant to Prof. R. Singh for proposed research in CCLS area (data management and search for chemical data)


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CCLS Accomplishment Summary since founding 2005 (2)

• Grants: NSF, CSUPERB, Microsoft, Sun/Agilent• Collaborations (external): UCSF, UC Davis, SUN/Agilent,

Microsoft• Several top awards at COSE science fairs• Three rounds of mini grant and travel grants funded by

CCLS: over 30 faculty and students funded (about $ 150 K in three years)

• High performance cluster computer purchased and launched (40 node DELL HPC). Being used heavily by 14 projects from 4 Departments

• 5 students accepted to Ph. D. programs: U. of Washington, Seattle; 2 at UCSF; UCSD, Washington university in St. Louis


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Strategy Phase II – future, starting Fall 08

• SFSU just committed to next there years:– Staff support funded - 1 full-time staff position for SW

development, support and maintenance– $ 30 K/year

• Moving to next level - ideas– Fewer but bigger projects?– Bigger grants– Bigger collaborations (industry, universities)– Increased IT and cluster support– Increased admin and staff support– Host prominent external visitors

Need your help and advice to make it happen!


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Part II

• Summary of discussion points and action items discussed during “Closing Perspective” session


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CCLS projects – breadth, depth, new opportunities…

• Generally, it was agreed that broad scope of CCLS projects is valuable and should be continued.

• Low entry cost (process, paperwork, topics) and ease of applying and being included in CCLS activities were deemed very valuable strategy to be continued

• Discussion was held on whether some of the topics can be “directed” I.e. whether topic selection should be more “top-down”. There were pros and cons. It is hard to “predict” and direct research, so bottom up topic definition by faculty was deemed as very valuable way to do this.

• Some of the more specific topics mentioned:– Health informatics– Synthetic biology With aging population, senior health care will gain in

importance– Data mining and computer vision for analyzing clinical data– SW systems work, IT, QA with emphasis on clinical applications is a good

skills set to have


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CCLS ways of funding projects – is current way (many mini grants of up to $ 7 K)

adequate• Discussion was held as to whether to continue giving out large number of

small mini grants or do fewer but bigger ones. There were pros and cons. Again, bottom up approach of having larger number of smaller mini grants was deemed very valuable.

• We thought that one way to go forward was to keep number of smaller mini grants and add few bigger grants

• It was pointed that in current extremely competitive government funding climate it is hard to set expectations that external grants must be obtained, but we agreed they have to be applied for

• We agreed to start requesting mini grant recipients to submit respectable grants as a result of the mini-grant funding. Again, the danger was in making faculty to “just submit mediocre proposals” to satisfy the requirements vs. do a real grant preparation

• Teaming with Ph. D. granting schools in joint grants was mentioned and we need help from our Advisory Board members on this


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Starting new projects

• It was suggested to better organize inter SFSU communication and for example host meetings of faculty from multiple disciplines and brainstorm for joint projects

• Advisory Board members are encouraged to “think of CCLS” when applying for grants, in industry-university cooperation, and in identifying potential projects and to let us know about the opportunities

• CCLS advantages, in addition to some of the world-class research, are:– Ability and wiliness of students to do applied research, experimentation and

SW development which well complements some of the conceptual and early SW development work from other Ph.D granting schools and industry

– Involvement of underrepresented student groups– Involvement of some specialized Schools like Public health, Health Equity,

College of Health and Human Services (for experiments, data, surveys)


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Communication, outreach, connections

• Involve students from other SFSU colleges

• Organize more meetings where professors from life science area can present projects of interest to CS and Math students

• Organize some Bay Are meeting of people involved in similar activities to CCLS

• Visit local top schools and industry and have CCLS members talk

• Talk to schools, companies and research institutions in life sciences that do not have enough access to CS resources

• Develop a summary of projects done so far and a description of what CCLS students can do.Use it for communication and for project salutations. Post on the WWW site, make a brochure

• Offer CCLS consulting services where CS students can help others (for money, units etc.)


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Student Internships and Placements, Student training

• For CS students going into biotech and related IT: We confirmed that some (any) exposure to life sciences (courses, projects, lab work) gives them advantage when applying to IT/CS jobs in biotech

• For biology students, it was pointed out that they need courses where they learn basics of computers and SW in biology/life sciences context.

• Some good experiences for CCLS CS and math students: lab experience (any), use of clinical equipment, use of Perl and SQL

• It was pointed that number of pure bioinformatics jobs might be limited, while number of jobs in health care and health informatics as well s IT for health and biotech is much larger

• We would like Advisory Board (industrial members) help in establishing more long term connections and ongoing programs for placing our students in biotech industry


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Student Internships and Placements, Student training

(2)• It was pointed out that “guaranteeing” student internship placements is

hard. UC Davis for example has staff devoted to that, SFSU does not.

• We will encourage internships (and we do now) but we can not guarantee placements for now. Some more “permanent and organized” connections with local industry would greatly help.

• Estimate of students with CCLS background needing jobs/internships (yearly) is 10 from CS, 10 Biology and 10 Chemistry and Math

• It might help to send list of students from underrepresented groups to our industry contacts (e.g. Cody)

• As said before: create documents and WWW material with samples of projects CCLS students can do and have done. Use this to solicit new projects


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Fundraising and Grants• Our needs:

– Faculty release time for research in biotechnology– Competitive fellowships and tuition wavers for students– Travel funds for students and faculty – Hosting distinguished visitors– A CSU seminar series in biotechnology– Updates to various facilities related to CCLS – Increased admin support

• Possible sources – need Advisory Board help:– Individuals– Corporations– Foundations– Joint grants with other universities – complementary collaboration– Paid projects with local industry


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Other ideas and suggestions• Add to the “CCLS success measurement metrics” number of open

source developments and external postings (we have 2 so far)

• Hosting of outstanding visitors and speakers is very encouraged. Advisory Board Members should be invited to speak.

• On Cluster: think of how effective it will be in the future, HW gets old fast. Budget for maintenance in the future

• John Hafernick (SFSU) to help is with local Bio workshop

• Good local conf. for our students to attend Stanford Computational Systems Bioinformatics conferences (usually in August)

prof. d. petkovic, director, ccls; chair, cs department sfsu 1 sfsu center for computing for life...

Documents

ccls chair

cs department sfsu

petkovic director

petkovic slide

ccls overview slides

ccls mike goldman chair

sfsu center

ccls student internships