How Open Source Software Contributors Are Accelerating Biomedicine

“Each day, hundreds of thousands of scientists use open source software to advance biology and medicine, from studying cells in a microscope image to understanding how genes behave in healthy cells. Open source software underpins much of modern scientific research — providing reproducibility, transparency, and opportunities for collaboration. The impact of these tools is on par with some of the most cited papers in science in terms of reuse and adoption, yet even the most widely-used research software often lacks dedicated funding.

Our Essential Open Source Software for Science (EOSS) program was created to support these efforts — from software maintenance to growth, development, and community engagement for open source tools that are critical to science. We asked nine grantees from the first cycle of the EOSS program what drives them to create tools and how their commitment to open source moves science forward….”

Job Application for Science Program Manager, Open Science at Chan Zuckerberg Initiative

“Our mission is to support science and technology that will help make it possible to cure, prevent, or manage all diseases by the end of the century. Interdisciplinary teams of physicians, biologists, computational scientists, and engineers can expand our understanding of the human body and illness — the very science behind medicine. CZI fosters collaboration between scientists and engineers, develops tools and technologies, and builds support for basic scientific research. 

Open science—the practice of sharing data, methods, software, and results in the open in a timely and effective manner, so that other scientists have the ability to learn and build on them—is core to our vision. We believe open science is key to empowering more people to engage in research and accelerate the pace, robustness, and reproducibility of science. In order to achieve this goal, we will invest in platforms and initiatives that can shift incentives and culture in scientific communities towards early, open sharing and collaboration. 

We are supporting the scientific open source software ecosystem through a dedicated grant program (EOSS), as well as in-house software development through our software engineering and computational biology teams. We are supporting large-scale open data initiatives like the Human Cell Atlas, a global project to create a complete reference map of all the cells in the human body. We have invested in platforms like bioRxiv and to accelerate sharing and linking of research outputs and we are building Meta, a biomedical research discovery service.

As a Science Program Manager for Open Science, you will drive the execution of open science initiatives in the scientific communities CZI serves. You will manage and assist the development and operations of grant programs to support open science, including programs in progress, planned, or future programs to be developed. You will coordinate closely with the rest of the CZI Science team and the external community. You will be a public advocate of CZI’s mission and our priorities in open science and you will contribute to shaping our strategic directions in this area. The ideal candidate will have a strong understanding of open science practices, how open source software, open data, and collaborative platforms are used in science, and how open communities function….”

Meta and Kopernio partner to provide easy access to full-text scientific articles | Research Information

“Millions of full-text scientific articles will soon be available through an easy copyright-compliant one-click process, thanks to a new partnership between Kopernio, part of the Web of Science Group and Meta, a free biomedical discovery tool from the Chan Zuckerberg Initiative.

Meta users will have faster, easier access to millions of full-text scientific articles through Kopernio’s free web browser plug-in, giving scientists one-click access to complete versions of the latest relevant research delivered directly in their Meta feed.

Meta users will have the option to install the Kopernio plugin for one-click retrieval of full-text articles that are accessible to them, either by integrating with institutional subscriptions or by offering a copyright-compliant open access alternative. When the version of record is available via institutional subscriptions, librarians and institutions will receive full usage reporting via the original publisher, as Kopernio usage is COUNTER compliant….”

Kopernio and Meta Combine Expertise to Support Accelerated Scientific Discovery – Clarivate

Millions of full-text scientific articles will soon be available through an easy copyright-compliant one-click process, thanks to a new partnership between Kopernio, part of the Web of Science Group (a Clarivate Analytics plc company NYSE: CCC; CCC.WS) and Meta, a free biomedical discovery tool from the Chan Zuckerberg Initiative.

Meta users will have faster, easier access to millions of full-text scientific articles through Kopernio’s free web browser plug-in, giving scientists one-click access to complete versions of the latest relevant research delivered directly in their Meta feed….

Sam Molyneux, co-founder of Meta said: “Meta’s goal is to ensure you never miss an important paper. We have partnered with Kopernio to ensure that once you have found the paper you need, you know you can access the best version of that paper, copyright-compliant and for free, without changing your research habits. Kopernio prioritises the use of the version of record from publishers.” …”

Essential Open Source Software for Science – Chan Zuckerberg Science Initiative – Medium

We followed two guiding principles in creating this opportunity:

  • First, we didn’t want to limit funding to pure software development. Open source is more than just writing code. It includes improving documentation, addressing usability, managing the project, and building community. We want to provide opportunities in whatever form will help make the computational foundations of biological research more usable and robust….
  • Second, we wanted to be inclusive in defining the scope of what counts as essential software for biomedical research. The proposed work does not need to be tied to novel research. Additionally, both domain-specific software and foundational tools and infrastructure used across several domains of science will be eligible to apply, so long as they have some impact in biomedical science. Such foundational tools can range from data structures to numerical computation libraries to toolkits for workflow execution and reproducibility. These tools play a critical role, often acting as dependencies for more domain-specific tools….”

Coming Soon: Essential Open Source Software for Science – Chan Zuckerberg Initiative

The Chan Zuckerberg Initiative will soon invite applications for open source software projects that are essential to biomedical research. Applicants can request funding between $50k and $250k for one year. This RFA is the first of a series. CZI will invite applications during three distinct cycles, with rounds beginning June 18, 2019; mid-December 2019; and mid-June 2020. Read our Medium post to learn more….”

Power to the Protocols! – Chan Zuckerberg Science Initiative – Medium

“We require our grantees to contribute to open science in several ways, including:

  • Depositing software code to an open repository such as GitHub;
  • Submitting results to open-access preprint servers like bioRxiv upon submission to a peer-reviewed journal, if not earlier;
  • Making experimental protocols openly accessible….”

These challenges helped us identify a new technology platform for developing and sharing protocols. is an open access resource that allows researchers to discover and share up-to-date science methods, similar to the way code can be shared on GitHub. …”

Plan U: A proposal to achieve universal access to scientific and medical research via funder preprint mandates

“If all research funders required their grantees to post their manuscripts first on preprint servers — an approach we refer to as “Plan U” — the widespread desire to provide immediate free access to the world’s scientific output would be achieved with minimal effort and expense. As noted above, mathematicians, physicists and computer scientists have been relying on arXiv as their primary means of communication for decades. The biomedical sciences were slower to adopt preprinting, but bioRxiv is undergoing exponential growth and several million readers access articles on bioRxiv every month. Depositing preprints is thus increasingly common among scientists, and mandating it would simply accelerate adoption of a process many predict will become universal in the near future.

There is a precedent for mandating preprint deposition: since 2017, the Chan Zuckerberg Initiative (CZI) has mandated that all grantees deposit preprints prior to or at submission for formal publication. This requirement has been accepted by CZI-funded investigators, many of whom were already routinely depositing manuscripts on bioRxiv….”

Mark Zuckerberg’s man in the lab: ‘I want science to happen faster’ | Science | The Guardian

An interview with neuroscientist Jeremy Freeman, manager of computational biology at the Chan Zuckerberg Initiative (CZI). Quoting Freeman: “We [at CZI] are absolutely committed to open dissemination of data and code and knowledge; that’s something I have been committed to all the time I’ve been a scientist.”