Rationale – Background and training in bioinformatics tools is required for the research community at UCSF to remain at the forefront of biomedical research and successfully compete for funding. Bioinformatics tools help translate our collective molecular understanding of disease into actionable insights and life-improving patient care innovations. Application of bioinformatics knowledge can minimize persistent barriers to progress in the translational research workflow by providing a bridge between the domain expertise of the experimentalist and the world of computationally driven, information-based research methods (see Appendix Fig 1).
Currently at UCSF, training on bioinformatics tools is decentralized. Services, databases, and courses are hosted by Core Labs, the UCSF Library, and other departments. Centers of data generation are not always integrated with the tools needed to gain insight from the data or place data in a disease-context. Navigating lists of bioinformatics tools can be a daunting task for researchers with no background in bioinformatics (see Appendix for current lists).
This arrangement carries numerous risks:
- Insufficient information about the best tools and platforms to address a particular research question.
- Inability to accurately gauge the true investment needed in both time and money to gain full value from an experiment.
- Poor return on investment from expensive experiments, and missed opportunities due to lack of awareness about tools available to translate raw data into findings and testable hypotheses.
In keeping with the UCSF Library’s commitment to support the continuing educational needs of information resource users, and extend services to a wider audience of researchers, we propose a pilot project to evaluate web-based methods for bioinformatics training. The UCSF Library will provide access to a centralized, web-based resource for training on well-adopted, authoritative bioinformatics resources by hosting the OpenHelix collection of bioinformatics tutorials on its website. This new service would cross-reference with related services (Core Labs, Cores Search, MyCORES etc.) to provide centralized and coordinated access to bioinformatics tools training at UCSF.
We are aware that there are a number of different groups at UCSF with expertise and interest in bioinformatics training and our aim with this proposal is to work with these groups to identify needs and develop solutions for translational medicine researchers.
Successful implementation of this new bioinformatics training service can:
- Provide researchers with the skills needed to locate, learn about, and apply the information housed in bioinformatics databases.
- Enable them to identify the right tool for their particular research question.
- Improve collaborations between experimentalists and bioinformatics experts at UCSF.
- Reduce time between data generation and insight by making bioinformatics training and tools available to those who generate data at the time it is generated.
- Reduce the current burden on Core Labs that may not have time for basic bioinformatics training requests from researchers.
- Establish an engaged user base through which the UCSF Library and Research Resource Program can continually evaluate services, identify unmet needs for training and resources, and design new services.
- Collaborate with the UCSF Institute for Computational Health Sciences, leveraging their expertise in bioinformatics to identify researchers' training needs and develop solutions to meet those needs.
- Form a Bioinformatics Tools User Group (user base for this pilot)
- Survey user group to identify bioinformatics tools and training needs
- Evaluate OpenHelix as an inexpensive, out of the box solution for bioinformatics training
- Make Go/No Go decision on value of OpenHelix
- Design and implement library-based home for resources such as OpenHelix: Bioinformatics @UCSF Library
- Collaborate with CTSI to create Marketing and Outreach plan for successful adoption of new service
- Ongoing evaluation of web-based bioinformatics training service and development of a business model for continued support of the service.
Criteria and Metrics for Success:
- Pilot user base includes bioinformatics subject matter experts as well as end users.
- Good response rates on User-Needs and OpenHelix evaluation surveys
- Steady increase in hits to library-based bioinformatics website 6 months after launch
- Steady increase in utilization of OpenHelix tutorials 6 months after launch
- Good response rate on User Satisfaction survey 1 year after launch of new service. Metrics identifying most/least utilized bioinformatics tools.
- Increase in User Satisfaction rating 2 years after launch of new service
Julie Auger, Executive Director of UCSF Research Resource Program (RRP)
Budget includes funding for:
- 2-year license to OpenHelix
- Programming resources to integrate with existing web infrastructure (UCSF Library, Core Labs and Cores Search)
- Minimal in-kind CTSI support for survey development, marketing and outreach plan
- External trainers for on-site training on most highly valued bioinformatics tools.
1. Hyperlinks to current lists of bioinformatics tools
2. Examples of Medical Libraries that host or are evaluating OpenHelix as part of their library-based bioinformatics services
- Mt. Sinai School of Medicine Levy Library –successful implementation with 5-year renewal and fully booked on-site training classes
- Becker Medical Library – Wash U
- University of Illinois
- Emory – Woodruff Health Sciences
- University of Pittsburg
- Weill Cornell Medical Library
3. Figure 1. Awareness and training in bioinformatics tools can eliminate persistent roadblocks in the translational research workflow.
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