Building a foundation for open-source software and hardware with Kevin Eliceiri

Kevin Eliceiri, a professor at the University of Wisconsin-Madison in the Department of Biomedical Engineering and the Department of Medical Physics, is helping advance efforts in implementing open-source tools for medical research. With his research focusing on understanding cellular roles in disease and how to quantitate them, Eliceiri is a strong advocate for utilizing preexisting open-source tools to avoid continual reinvention, especially hardware. Alongside this, he is a director for the UW-Madison Center for Quantum Cell Imaging of the Morgridge Institute’s FabLab.

“We are allowed to build things, and so anything we build, we want to share. The same way that people have been for years sharing transgenic organisms or gene sequences,” Eliceiri said. “We’re just doing the same thing with hardware and software.”

Sharing newly built hardware and software can help create a foundation for others to build upon. Creating these projects to be open source can foster collaboration, while also ensuring that projects are not constantly being rebuilt.

“Open source can be about being free, but it’s beyond that. It’s really about transparency and being able to innovate with the work of others,” Eliceiri said.

One of the contributors of ImageJ, MicroManager and Bio-Formats, Eliceiri has been able to add onto these well-known packages. But while these packages have gained traction with their downloads, Eliceiri favors the community aspect that yields from these softwares. With this, open source is able to foster community collaboration, something Eliceiri believes is a key aspect to open source. Without it, open source would not have one of the essential aspects that makes it what it is. The code also needs to be available and free to use. Repositories and codes that are closed and only given to when contacting the contributor do not exactly fall under the open source category, according to Eliceiri.

“The community we built around it is probably most important to me, and the mentees and collaborators,” Eliceiri said.

In addition to open-source software, Eliceiri has been an advocate for open-source hardware. The less-common of the two, open-source hardware can instruct those in the community how to build things to progress work and research.

“People will share protocols, people will share software, but if you build something novel, we usually don’t share anything beyond maybe the parts list,” Eliceiri said. “True open source means that it’s documented beyond the parts list, that the build is documented.”

In an analogy of a cooking show, Eliceiri illustrated how someone can describe how to create something with a list of ingredients – or parts in terms of hardware – but there is no real way of following without a main set of instructions, or documentation.

Maintaining these hardware projects requires good documentation, but also funding. One of the main challenges with open source can be a lack of funding. With this lack of maintenance can propose the risks of security risks, or even runs the risk of the project to stop running certain operating systems.

“Maintenance of open-source software is a major issue and the idea that people are much more likely to contribute code to your program than maintain it for you, so maintaining it loosely is on the person that created it,” Eliceiri said.

While this may pose a challenge, there are still ways to be able to keep an open-source project afloat. Finding ways to generate more funding — as well as continuing to make an open-source project look more attractive to ensure people will want and choose to maintain — it can help ensure a project will continue long term. Using funding early on to ensure projects are maintained can help people continue to focus on maintenance throughout the project, according to Eliceiri.

“At the end of the day, it’s better to document and release it, period. Even if you can’t maintain it. But if you have the energy and the interest, it’s wonderful if you can,” Eliceiri said.

Despite these challenges, Eliceiri has received the byproduct of his projects: gratitude. While projects and their impact can be quantified with downloads and citations, any form of usage — whether praise or complaint — is all good with Eliceiri.

“I also get complaints, which is also a form of thanking you because if they take the time to complain, it means that they’re trying to use it,” Eliceiri said. “To me, one of the more satisfying things is people actually using it in their research.”

Many on campus can have access to these different open-source projects that are constantly being created on campus. But while the university itself may not have as large of a structured open-source community across all of campus yet, Eliceiri goes on to mention how broad the international community is.

“The community is way ahead of us, and UW is very prominent in that community with certain labs,” Eliceiri said. “But for the most part, every university is behind the game. UW gets some credit along with the other ones that they were able to get funding to do this, which is great. We’re very thankful that Sloan took a chance on UW.”

The university has a variety of established open-source labs that can mentor others throughout the community, according to Eliceiri. This mentorship can allow the open-source community to flourish in advancing academic research with support from the Alfred P. Sloan Foundation. Elevating the open-source community on campus can bring other labs or researchers into the conversation, especially those who may already be doing open-source work and not realize it.

Continuing to educate the UW-Madison community on what open source is can generate a stronger presence of open-source software and hardware on campus. With this, it can bring further innovation and discovery into many pockets of the community and in more academic areas.

“Reuse and sharing lead to innovation. What most people don’t realize is it’s not just convenient. It’s not just sharing resources,” Eliceiri said. “Very often because you gave someone the foundation to build on, they go farther and innovate based on your work. They may come up with ideas or uses you never thought of, and so a big key thing that’s often lost is innovation.”