While CoProjects are investigator-driven, the day-to-day operations must be managed and run through the cutting-edge CoLabs. CoLabs are a collection of integrated laboratories specializing in infrastructure or technologies. It seeks to revitalize the model for core resources by capitalizing on critical personnel and cutting-edge technologies, and driving collaboration across disciplines. The model will house all CoLabs in a contiguous space and create a set of common pipelines and workflows in one centralized locale. It will recruit and retain world-class staff through project engagement, backstopped tenure, and annual operational funds. And it will develop and invest in transformative methods and technologies.
Conceived by ImmunoX in 2016, CoLabs are now a collection of integrated laboratories specializing in infrastructure or technologies. They are initially based on teams developed for the UCSF Immunoprofiler Consortium and the already-stellar Parnassus Flow Cytometry Core (PFCC), Biological Imaging Development Center, and Functional Genomics Core. The five primary CoLabs seeks to evolve the model for core resources by capitalizing on critical personnel and cutting-edge technologies, and driving collaboration across disciplines. CoLabs is now supported in partnership between the Provost and as a campus-wide collection of these linked collaborative resources.
Overseen by a campus administrative group that will help integrate science in them, four of these five initial CoLabs are slated to have semi-contiguous space in the spring of 2020 in a format designed to link expertise of many traditional PI labs at UCSF, providing key technology platforms and a highly collaborative environment. They are setup to have a front-end link with the Biospecimen Resource Program that helps bring important clinical samples to the Disease-to-Biology CoLab. The design of CoLabs are steeped in high-dimensional analysis of data through a shared Data Science CoLab which also houses a data library for community data storage and mining. In addition to providing backstop support for the Data Science CoLab operations, ImmunoX also supports a Computational Biology Initiative within this lab. The vision for these, linking technologies, expertise and data is below:
- Disease-to-Biology CoLab
A new CoLab that specializes in consistent and high-quality human specimen processing. Technicians associated with ImmunoX CoProjects are housed here and are responsible for coordinating specimen processing and data analysis workflows with other CoLabs.
- Flow Cytometry CoLab
A CoLab that integrates the existing Parnassus Flow Cytometry Core and specializes in counting, sorting, and analyzing suspensions of cells using advanced cell sorting and cytometric analyses technologies.
- Biological Imaging Development CoLab
A CoLab that integrates the existing Biological Imaging Development Center and specializes in assembling, testing, and applying emerging light microscopy techniques and technologies.
- Genomics CoLab
A CoLab that integrates existing but fragmented units at UCSF. It specializes in performing single-cell gene transcript sequencing and developing and deploying innovative methods for analyzing and modifying gene function.
- Data Science CoLab
A CoLab to develop bioinformatic frameworks for curating, storing, analyzing, and sharing access to data produced through the CoLabs pipeline. It will also house bioinformaticians and computational biologists to drive ImmunoX CoProjects.
CoLabs emphasizes the value of people and their active participation in the use of technology, whether instrumentation or computational-based. An important innovation is that the CoLab Directors have some protected salary support and security. CoLabs will have space for many traditional PI-labs to "embed" graduate students and postdoctoral fellows into the space with desk or bench space for a period ranging from days to years. Permanent CoLabs personnel are expected to be considered integral collaborators and to be included in project planning and as authors for publications. Each laboratory serves the community as a hub for its specific expertise, but has a vibrant energy of its own due to small and large projects that are ongoing in the lab. Well-funded, large multi-investigator team science projects and traditional recharge-style (e.g. hourly fee-for-service) mechanisms of support both provide the backbone and raison d’etre for the ongoing work.
As time develops, we model that we will house all CoLabs in a contiguous space and create a set of common pipelines and workflows in one centralized locale. We will recruit and retain world-class staff through project engagement, backstopped tenure, and annual operational funds. And we will develop and invest in transformative methods and technologies. To this end, with help from philanthropic support, ImmunoX has provided seed funding for five Junior CoLabs. These include:
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Gnotobiotics Junior CoLab (Peter Turnbaugh, PhD)
The mission of the Gnotobiotics Junior CoLab will be to lower the activation energy for researchers across departments to study the impact of the microbiome and pathogenic microorganisms on host pathophysiology and behavior. Mice will routinely be bred and maintained in a germ-free (sterile) state.
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Microbiome Junior CoLab (Susan Lynch, PhD)
Microbiome Junior CoLab will offer existing standardized microbiome genomics assays (i.e. DNA-based biomarker and shotgun metagenomics) and drives innovation through the development of the next generation of microbiome genomics tools.
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Metabolomics Junior CoLab (Jason Cyster, PhD, Peter Turnbaugh, PhD, Andrei Goga, PhD)
The Metabolomics Junior CoLab will create a strong cross-campus link to the robust protein mass spectrometry capabilities at the Mission Bay campus, putting UCSF at the forefront of protein and small molecule mass spectrometry.
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Microsurgery Junior CoLab (Mark Looney, MD)
The Microsurgery Junior CoLab will offer advanced surgical techniques to create chimeric animals using the organ transplantation technique to deplete cells, fate map cells during development, and track cellular migration.
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BSL3-Supported Junior CoLab (Anita Sil, MD, PhD)
The BSL3/ABSL3 facility for COVID-19 and other infectious disease research is a R&D BSL3/ABSL3 facility located at MS791 on the Parnassus campus of UCSF.
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CenTRe Junior CoLab (Alyssa Ward, PhD)
The CenTRe Junior CoLab is a collaborative enabler of clinical-translational research and works closely with clinical teams and other CoLabs to streamline processes and enable every team to accomplish their goals. We serve as a repository of expertise in the discipline of clinical-translational research. This CoLab offers guidance and expertise in clinical-translational project establishment and project management including assistance with IRB applications, developing protocols (in consultation with clinical and biological teams), consulting on project plans and timelines, and developing project-specific databases, pipelines, and resources as needed.
The goal of these Junior CoLabs support are to help obtain critical instrumentation and backstop salaries for key personnel, and to pre-purchase capacity in those CoLabs for studies undertaken in conjunction with ImmunoX labs. It is anticipated that many of these, once functional, will become valuable components of the ImmunoX- and Provost-sponsored CoLabs. Contact the listed lead PI or ImmunoX@ucsf.edu to inquire about use of these resources.