Developer Tale

SBGrid Assumes Ownership of PyMOLWiki

Published September 15, 2016

After ten years of work developing and managing the PyMOLWiki, Jason Vertrees is turning over the helm to SBGrid. “They’re getting the whole site,” he says.

To Vertrees, that site represents more than helpful information and guidance for PyMOL users. It’s a mantle of sorts, a duty he took on to fill a need and kept working on to carry out the original vision of PyMOL as open source software. Open source software benefits from the verification and improvement that comes when code is shared, tested and fixed by a community of developers. It also speeds development and, under open source licensing schemes, widens the number of people who have access to it. “I’ve always been an advocate of open source and really jumped in when I started working on PyMOL,” says Vertrees.

Vertrees was first introduced to PyMOL in 2005 as a graduate student in biophysics at the University of Texas Medical Branch at Galveston during a class on macromolecular modeling. His interest went beyond that of a student learning structural biology. Vertrees had studied computer science as an undergraduate and appreciated PyMOL from the perspective of a developer—so much so that he joined the PyMOL user community and started supporting the software.

Over time, Vertrees noticed that the questions he was fielding were repetitive, so he launched a wiki for users to refer to for answers. He authored hundreds of pages describing PyMOL’s commands and settings. He has made over 4000 edits. Over time, the site gained a critical mass. “It was valuable enough that people found value in contributing themselves,” he says. “It took off and became this growing living thing.”

In 2009, after Vertrees finished his PhD, he decided to work on PyMOL full time. He joined Delano Scientific, a company founded by Warren Delano, the original author of PyMOL. Delano was committed to open source software and had worked to ensure that scientists and students had access to the software and the ability to contribute ideas and fixes. But just a few months after Vertrees joined the company, Delano passed away unexpectedly. Soon after, Schrödinger acquired the software and brought on Vertrees to continue supporting it.

Vertrees also continued his work supporting the PyMOLWiki. In the past year, the site has served over half a million sessions for over 200,000 unique users. Visitors to the site have come from 187 countries. “You can tell by the numbers that the site is still valuable to users,” says Vertrees.

In 2014, Vertrees left Schrödinger and took on the role of Chief Technology Officer at a startup in Austin, TX, called RealMassive. The company, similar to Zillow but for commercial rather than residential real estate, is taking up so much of his time that he needed to find a new way to support PyMOLWiki.

SBGrid has elected to purchase the wiki and continue to maintain and expand it. “Taking over PyMOLWiki makes sense for SBGrid and it’s mission to provide access to valuable resources to the computational structural biology community,” says SBGrid founder Piotr Sliz.

*-Elizabeth Dougherty