From coding on paper to a computer - How Cécile Ane educates the community in open source

A young girl without a computer of her own, begged her grandma to buy her a book on coding. She had hopes of learning how to code, even if it had to be on paper. Today, that girl is Cécile Ane, an eminent professor at the University of Wisconsin-Madison in the Botany and Statistics departments. Her research currently focuses on developing statistical methods for evolutionary biology.

Ane is a strong advocate for open source, that the codes can benefit users, especially when modifying them to better help their own agendas and research needs. The best part – it’s easily accessible.

One of her most significant software contributions so far has been her package phylom. The 10-year-old R package has not only been impactful in terms of thousands of downloads and many citations in publications, but is still currently being maintained. The open-source software has garnered many contributors continuing to add features to the package.

Ane’s latest software is a Julia package, PhyloNetworks. The software is host to one core package and multiple companion packages. With this package, the users are able to add on whichever companion packages in addition to the core to help further their own projects and research with those additional features.

“The big advantage of having different features live in different packages is that it makes the system more modular,” Ane said. “It makes the dependency between different pieces of a code more easy to manage.”

While this open-source software makes it more accessible for users and contributors to collaborate on, there can be a lack of client support that comes with it. Software maintenance is time consuming and expensive – and with a lack of academic reward – it can be challenging.

In spite of the challenges that maintaining open-source projects can present, developing open-source software can have a large impact on those in the community who use these packages to further their studies.

“I see it as a lived experience when I go to conferences, for example, and I cross people I’ve never met and they say, ‘You’re Cécile, I’ve used your software.’ It’s so cool,” Ane said. “I get to meet lots of people who I’ve never met, and they really know me through packages that I’ve developed. That’s very rewarding.”

Open source can be an extremely rewarding tool for continuous research endeavors. While the open source community is growing at UW-Madison, there is still plenty to be accomplished to help foster a space for it on campus, where those contributing can feel more support.

“There are fantastic people who contribute to open-source software here at UW Madison, but as an institution, I don’t know of any support,” Ane said.

Providing resources and tools on campus can help make educating the community on open source far more accessible. Short workshops offered multiple times throughout the year can be effective for students and the community to learn small amounts of what open source has to offer and how to use it can aid those interested in using it in their research, according to Ane.

Ane has also developed a course ‘Computing Tools for Data Analytics’ here at UW-Madison. Though it was only taught three times, the course offered valuable skills in open source and collaborative research using code.

“It will have an impact at many levels, so in individual labs, you can use open source just to share primarily with your lab members, not necessarily with the whole world,” Ane said. “Even just that will have a huge impact so that a new graduate student can easily reuse code from another student who graduated two years before.”

Being able to reuse open-source code can be beneficial for those working on projects. If there is already a foundation to add to when contributing to a project, it can help those in the community be more efficient with their work.

“You don’t have to reinvent the wheel to have all the other stuff that you want the software to do,” Ane said. “You just need to add your piece, not reinvent everything from scratch.”

Educating and uplifting students and those in the community on open source can help drive research at the university and continue to grow a community surrounding open source. While it can be daunting to share code or ideas, it is important to note that everyone in the community starts somewhere.

“When I look at code that I wrote ten years ago, I’m like, ‘Oh no, that was bad code.’ But we’re all like this. It’s actually super stimulating because we’re learning all the time, and it means that I’m coding better now than I did ten years ago,” Ane said. “That’s the bright part, everybody’s that way. So just start sharing your code. Everybody’s in the same boat.”