About Computational Biology

Computational Biology Core, UCSF

Core Members:

>Ritu Roy
>Henrik Bengtsson
>Adam Olshen, Director

The goal of the Computational Biology Core is to provide appropriate computational biology support for cancer-related research at UCSF through a recognized and accessible central resource. The intent is to support research of Cancer Center members. As time permits, consultation is available to non-Cancer-Center members through a recharge mechanism.

Core members have expertise in genetics, microarray analysis of all types, second-generation sequencing, pathway analysis and systems biology.

Core activities include but are not limited to: scientific consultation, grant development, study design, and data analysis.

Contacts:

Users are encouraged to contact the Core early in the project development process. If you have worked with a member on previous projects, feel free to contact that person again. Otherwise, contact the Director, Adam Olshen.

Services:

Microarray Analysis

Microarray analysis consultation up to one hour per project are provided at no cost. Consultation beyond one hour, and all data analyses, are handled through a recharge mechanism. The appropriate form is available for download here.

Pathway Analysis and Systems Biology

Services include downstream analysis of -omics experiments (e.g. microarray, aCGH, MS/MS, GWAS, DNA methylation, sequencing) via gene set/pathway enrichment statistics (e.g. GSEA) and identification of significantly affected protein-protein interaction modules (e.g. Ingenuity IPA).  The EGAN software developed by the BCB Core can be used by biologists to perform many of these analyses independently.  One hour of EGAN training is provided at no cost; subsequent training hours are handled through a recharge mechanism.  EGAN is available for free download at http://akt.ucsf.edu/EGAN/.

Second-Generation Sequencing

We have experience analyzing second-generation sequencing data for copy number, gene expression, methylation, mutation, and translational efficiency.  Consultation of up to one hour per project is provided at no cost.  Consultation beyond one hour and all data analyses are handled through a recharge mechanism or through grant support.

Education:

Faculty and staff are available to give short presentations on topics such as:

  • Determining quality of your microarray data
  • Finding differentially expressed genes
  • What clustering can and can not do for you
  • Building a predictor
  • Introduction to R statistical package

Recharge Rates:

> Rates effective July 1, 2009 (PDF)

Assistance to Cancer Center members in developing grant proposals and writing clinical research protocols is covered by Cancer Center Support Grant funds. Additional assistance is offered to members as time permits. A large portion of Core activities, however, is funded from grants that include data analysts as part of their budget. The Core encourages this practice for grants that will require substantial assistance; in such cases, recharges are on a percentage-effort basis.

In addition we provide microarray analysis consultation beyond one hour per project through a recharge mechanism. The appropriate form is available for download here.

* Internal users are funded by UCSF sources (or other UC campus sources) and provide a valid fund-DPA for payment.  Affiliate users are funded by non-UC sources and pay by check, but the funding is provided by a recognized UCSF affiliate (SFGH, SFVAMC, NCIRE, Gallo, Gladstone, HHMI, or LBNL). External users are funded by non-UC sources and pay by check.

Other Resources:

Dept. of Epidemiology & Biostatistics

http://www.biostat.ucsf.edu/courses_index.html
http://www.biostat.ucsf.edu/cbmb/bmi209/

Please contact the Biostatistics Core for assistance with requests concerning clinical biostatistics.

Additional Resources
A searchable database of core facilities at all UCSF campus locations, provided by the Clinical and Translational Science Institute at UCSF, is available here.

This core is supported by a National Cancer Institute Cancer Center Support Grant (5P30CA082103-15). Any publications related to work done by this core, should reference grant number 5P30CA082103-15 and must include a PMCID as required by the NIH. For more information on how to obtain a PMCID, please see http://publicaccess.nih.gov/submit_process.htm.

For more information on the CCSG, please contact Kate Shumate at shumatek@cc.ucsf.edu.