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Open Access Publications from the University of California

UCSF Library

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About

The UCSF Library is one of the preeminent health sciences libraries in the world, containing an expansive digital and analog collection of the world’s health sciences knowledge base. Offering a diverse range of services and resources to the UCSF community and public visitors, the Library is a vital resource for learning, engagement and creativity within UCSF and beyond.

Our Mission

Through exemplary services and resources, the UCSF Library cultivates environments that advance science, promote health, and innovate in teaching and learning.

Our Vision

To be a catalyst for discovery, learning, connection, and innovation at UCSF in support of health worldwide.

Our Values

  • Facilitate CONNECTION
  • Inspire LEARNING
  • Deliver human-centered SERVICE
  • Apply INTEGRITY to everything we do
  • Embrace COLLABORATIVE approaches
  • Remain RESPONSIVE to our community

UCSF Library

There are 414 publications in this collection, published between 2012 and 2021.
UCSF Open Access Publishing Fund (388)
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Open Access Policy Deposits (25)

What’s behind OA2020? Accelerating the transition to open access with introspection and repurposing funds

In 2017, four University of California (UC) campuses took a public stance on accelerating the transition to open access (OA) by endorsing the Open Access 2020 (OA2020) initiative’s Expression of Interest (EOI). OA2020 is an international effort to convert the existing corpus of scholarly journals from subscription-based access to OA. In March 2017, when the first three UC campuses—UC-Berkeley, UC-Davis, and UC-San Francisco—endorsed,1,2 there had been only one U.S. signatory institution (California State University-Northridge, having endorsed in July 2016). Six months later in September 2017, another UC campus, Merced, added its affirmation. As of this writing, these five California universities remain the only OA2020 EOI signatories from the United States.3

Elevator Pitch Exercise Template and Examples

Use this elevator pitch template for exercises to create a concise and compelling job position or project description. Examples of the template are included describing two librarian positions as well as an open access policy. The template can be modified to describe a product, organization, or idea.

Assessing the impact of programming workshops on biomedical research reproducibility

Objective: Given the growing need for computational reproducibility in the biomedical sciences many libraries have started teaching programming workshops. However, little is known about the extent to which researchers are able to translate their new coding skills into more reproducible workflows. The goal of this study was to assess the impact of programming workshops on the computational reproducibility of biomedical workflows.

Methods: This mixed-methods study consisted of semi-structured in-depth interviews with 14 University of California, San Francisco researchers at two points in time: before they participated in a UCSF Library-led introductory R and Python programming workshop, and three months after they completed the workshop. During the interviews the author collected qualitative data on the tools, methods, and processes researchers used in their work, and quantitative data from a questionnaire that measured evidence of computationally reproducible behaviors. The author analyzed the quantitative data to see if there was a statistically significant difference in reproducible behaviors before and after the workshop, and used a thematic analysis approach on the qualitative data to extract the common characteristics of the research workflows before and after, and explore what enabled or prevented researchers from making changes in their workflows.

Results: Pre and post scores on a checklist of reproducible behaviors did not change in a statistically significant manner. The qualitative interviews revealed that several participants had made small changes to their workflows including switching to open source programming languages for their data cleaning, analysis, and visualization. Overall many of the participants indicated higher levels of programming literacy, and an interest in further training. Factors that enabled change included supportive environments and an immediate research need, while barriers included collaborators that were resistant to new tools, and a lack of time.

Conclusions: While none of the workshop participants completely changed their workflows, many of them did incorporate new practices, tools, or methods that helped make their work more reproducible and transparent to other researchers. This indicates that programming workshops now offered by libraries and other organizations contribute to computational reproducibility training for researchers.

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Presentations (4)

Elevator Pitch Exercise Template and Examples

Use this elevator pitch template for exercises to create a concise and compelling job position or project description. Examples of the template are included describing two librarian positions as well as an open access policy. The template can be modified to describe a product, organization, or idea.

Increasing Results to Federal Funded Research Results

Presented at the 2015 American Library Association Annual Meeting

Ethics and Open Science

Open science, the movement to open up the products of scientific research, has the potential to make biomedical research more transparent, reproducible, and equitable. However, as research practices and requirements evolve we are faced with new ethical questions around data ownership, participant consent, and paywalls. This talk will give an overview of the current state of open science in biomedical research and hopefully spark a dialogue about the ethics of practicing science in the open.

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