How Open Source Software Contributors Are Accelerating Biomedicine

Hear from 9 People Working on Key Open Source Software Projects for Science

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.

Olga Vitek, MSstats and Cardinal

Olga Vitek of Northeastern University works on the open source software tools MSstats and Cardinal.

“As a graduate student, I benefited enormously from open source software, both as a learning experience and as a tool that enhanced my own research. Back then I made a commitment to pay it forward.” — Olga Vitek, Northeastern University.

MSstats and Cardinal provide statistical software for mass spectrometry-based experiments, which allow scientists to measure the weight of different molecules in a sample.

Why is open source software important to advancing science?

What do you hope your projects will allow researchers to do?

Kevin Eliceiri, MicroManager and ImageJ

Kevin Eliceiri of the University of Wisconsin, Madison, aligns a laser-scanning microscope controllable by the open source software tool μManager. Lab-built microscopes like this one help researchers answer important scientific questions, such as how cancer progresses.

What are you working on?

“I’ve always believed that science is best done by building on the work of others and openly sharing what you have done. Open source software not only saves time and resources, but can directly lead to new innovation and discovery.” — Kevin Eliceiri, University of Wisconsin, Madison.

Why is open source software important to advancing science?

Mark Musen, Protege

The Protégé team, which includes Mark Musen of Stanford University, regularly holds short courses to train users in the technology.

What do you hope your project will allow researchers to do?

“It’s very exciting for us to be developing software that has achieved such widespread use and that is helping to advance science in so many ways.” — Mark Musen, Stanford University.

What are you most excited about in the open source software field?

DeepLabCut allows researchers to track and label the body parts of moving animals such as this cheetah.

Mackenzie Mathis, DeepLabCut

“We wanted to create a tool that was easy to use without computer vision expertise. We hope to continue to enable scientists to do research in more real-world contexts.” — Mackenzie Mathis, Harvard University and the Swiss Federal Institute of Technology Lausanne.

Several areas of research, including neuroscience, medicine, and biomechanics, use data from tracking movement. Scientists are already using DeepLabCut to study octopuses, electric fish, and even the movements of robots that assist doctors in performing surgery.

Antonin Delpeuch, OpenRefine

Antonin Delpeuch of OpenRefine and Code for Science and Society.

Antonin Delpeuch works on OpenRefine, a tool for analyzing messy and large datasets. OpenRefine helps researchers quickly identify and fix issues in spreadsheet or tabular data. Its automated functions handle problems such as splitting cells that contain multiple data values, detecting duplicates, standardizing date formats, trimming extra spaces from cells, and combining multiple datasets into a single spreadsheet.

Why is open source software important to advancing science?

“Research software has to be open source if we want to take reproducibility seriously.” — Antonin Delpeuch, Code for Science and Society.

Why did you decide to become involved with open source software?

What are you most excited about in the open source software field?

Hannes Rost, OpenMS

OpenMS analyzes thousands of data slices like the one depicted here to piece together how human proteins affect health and disease.

“We are working on a technology that allows us to perform thousands of clinical tests in less than one hour — for a fraction of the cost.” — Hannes Rost, University of Toronto.

What are you working on?

What do you hope your projects will allow researchers to do?

A better understanding of human disease will hopefully also lead to the identification of novel drugs targeting proteins that are involved in the disease process, potentially improving the quality of life for patients or curing diseases.

Emmanuelle Gouillart, scikit-image and Dash

Emmanuelle Gouillart of Plotly Technologies, Inc.

Imaging of molecules, cells and tissues is central to biomedical research and clinical practice, allowing scientists to understand and identify disease. A single image of a tissue sample can contain millions of different cell types, and scientists need faster, better ways to analyze that data. Emmanuelle Gouillart develops tools to do just that.

What are you working on?

“I love empowering users with great tools that are not only designed brick-by-brick by large and diverse communities, but are also freely available for anyone to use and improve upon.” — Emmanuelle Gouillart, Plotly Technologies, Inc.

Why is open source software important to advancing science?

Gordon Smyth, limma, edgeR and Glimma

Developer Gordon Smyth, with Charity Law and Yunshun Chen stand by an image of chromosomal interactions detected with tools edgeR and diffHic. Interactions like these pinpoint how the 3D structure of DNA allows genes to be turned on and off as needed.

Gordon Smyth creates software tools that allow scientists to interpret genomic data in powerful and flexible ways, helping to make biomedical discoveries. His bioinformatics lab collaborates with other researchers at the Walter and Eliza Hall Institute in Melbourne, Australia, to understand the biology and treatment of breast cancer. A key success that depended on their software was the discovery of the cell of origin for the most invasive form of breast cancer.

What are you working on?

Why is open source software important to advancing science?

Greg Caporaso, QIIME 2

Greg Caporaso of Northern Arizona University (NAU). Photo courtesy of NAU.

The QIIME 2 software has already helped researchers discover a potential new avenue of treatment for autism, which will be explored in further clinical trials. Thanks to a grant from CZI, the community is hosting its first-ever co-convened user and developer workshop and networking event.

Why is open source software important to advancing science?

As part of this project, my lab developed novel algorithms to track engraftment, or the time period when transplanted cells start to make new blood cells, of a donor microbiome into a recipient. After treatment, the microbiomes of the children with autism resembled those of the children without autism more than they did at the beginning of the study.

We observed no adverse effects, and while this early stage trial was designed primarily to evaluate the safety of the treatment, we saw that many of the children experienced a reduction in the severity of their symptoms during the following two years.

Check out the full list of open source projects we’re supporting and apply for funding via the second cycle of our EOSS request for applications (closing February 4, 2020).

Chan Zuckerberg Science Initiative

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Supporting the science and technology that will make it possible to cure, prevent, or manage all diseases by the end of the century.

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