ImmunoX Computational Biology Initiative
A joint effort between the Data Science CoLab and ImmunoX

The ImmunoX Computational Biology Initiative seeks to promote data science participation and innovation in the biological space. Made possible by generous philanthropic support, funding will be invested into bridging biology and data science through the computer scientist sabbatical program, support for the UCSF Data Library platform, and investment in researchers at the post-baccalaureate and PhD level.  The overarching goal of the program is to leverage data collected by the entire UCSF ImmunoX research community, taken from a cross-section of health and disease, to discover treatments for human disease.

Visiting Computer Science Fellows Program

UCSF is at the forefront of biological data generation. Through combinations of high-dimensional cytometric, imaging and genomic datasets, collected across normal and diseased tissues, the community is rich with the data needed to understand the patterns of biological systems. This is enhanced by our ImmunoX- and campus-wide library initiative that both produces and curates data taken from UCSF labs. Because we are a medical campus, we realize that some of the most innovative data mining and visualization tools may be developed outside of our walls. To address this deficit and maximize our progress towards understanding and subsequently treating disease, we announce the ImmunoX Computational Biology Initiative sabbatical program at UCSF. The program is intended to give data scientists, computer scientists and software developers at parallel academic or industry institutions the opportunity to live and work with our teams and our data library.  The program will cover a salary and/or living/housing allowance and associated research support of up to $80,000 for up to a 9-month term.  Applicants will be solicited from across the globe and vetted by the DSCoLab Principal Investigator together with the ImmunoX Research Committee. Application coming soon Announcements will be made in March for earliest start date of August this year.

Studentship

Four incoming PhD students at UCSF will be funded as ImmunoX Computational Biology Initiative Fellows. The selected students will become part of the Data Science CoLab community through an initial meeting with the director, data science advising, set-down space in the DSCoLab and an invitation to lab meetings and workshops. In addition to support for their first year of training, an additional stipend may be applied to a fully loaded computer and related software/hardware to facilitate rapid entry into data science.

Post-Baccalaureate Research Program

Recent college graduates may apply to the ImmunoX Computational Biology Initiative Postbac Fellowship program, a 2-year research position through the Data Science CoLab. Fellows will contribute to research projects by analyzing complex data, such as CyTOF and single-cell RNAseq from UCSF patient cohorts, toward an understanding of molecular signatures of health and disease. Fellows will receive hands-on training in biological data science research, as well as some formal instruction in special topics in computing, data modeling, and next-generation biological data. Fellows will be additionally be members of the CoLabs postbac research program. Fellows are expected to come in with some programming experience and an interest in building their skills in biological data science. Two fellows have been selected for 2020. 

Principal Investigator Support for the Data Science CoLab

The Principal Investigator of the DSCoLab runs the data library project and jointly leads CoProjects with collaborating PIs. The combined support of the ImmunoX Computational Biology Initiative and additional grant funding will enable her to further pursue her lab’s research program that will focus on cross-project analysis of immune state and microbiome-immune interactions in humans. These projects will capitalize on the standardization of data generation and processing across CoProject cohorts as well as the curation of the Data Library to be able to truly realize meta-analyses of immune state that has not been done to date. They will use data collected from healthy individuals, and from conditions ranging from cancer, to chronic infection, to autoimmunity, in order explore the variation and extremes of immune state in the population.

Long-Term Systems Administrator Support and Hardware for the UCSF Data Library

The UCSF data library project aims to capture, curate, and share data generated on campus, enabling data search, exploration, and cross-project analyses through a series of applications in the browser. The library engineering team in the DSCoLab is building these tools with close collaboration and input from the other CoLabs and participating CoProject labs.  The ImmunoX Computational Biology Initiative is providing support for a systems administrator to build, maintain, and support the servers on which the data library runs, as well as provides funding for this hardware. Funding in the first year will also go toward a library engineer to help build out and secure the system architecture. Funds will be reserved for scaling solutions including expanding storage and compute needs and a possible transition to the cloud at a later date.