March OHBM Open Science Demo Call

By Elizabeth DuPre and Kirstie Whitaker

This month we continued our Open Science Demo Call series by speaking to Tim van Mourik Eleftherios Garyfallidis and Malin Sandström about the communities they’re building and supporting to make everyone’s lives easier through better open source software tools.

Tim van Mourik

After a few technical difficulties (Kirstie’s laptop inexplicably deleted the “broadcast” button so we were all chatting to each other without being able to include our viewers in the conversation!) Tim introduced Porcupine. Porcupine is a tool to visually program your analysis. By dragging and dropping modules that represent functions in your analysis, you can quickly build an insightful analysis and then Porcupine will provide the code that you or others need to run on your own data. All code and documentation is openly available at the project’s GitHub repository, and this is where you can also give any feedback or suggestions. Alternatively you can find Tim in the BrainHack Slack team (click here if you need an invitation to join) or via email at t.vanmourik@donders.ru.nl.

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Eleftherios Garyfallidis

Eleftherios told us about DIPY, a global, community-supported, software project for computational neuroanatomy, focusing mainly on structural and diffusion MRI. DIPY implements a broad range of algorithms for denoising, registration, reconstruction, microstructure, tracking, clustering, visualization, and statistical analysis of MRI data. You can get involved and help the DIPY team in many different ways, but Eleftherios particularly encouraged OHBM members to test their data with the DIPY algorithms and provide feedback on any challenges they have running the code. You can ask questions in the team’s live chatroom or send an e-mail to neuroimaging@python.org.
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INCF's GSoC org admins Malin Sandström (right) and Chris Fitzpatrick (middle) with 2016 GSoC student Devin Bayly, after a demo of Devin's project in the INCF booth at the SfN (Society For Neuroscience) annual meeting. Photo by Ylva Lillberg.

Linking very nicely to Eleftherios’ call for student applicants to work on the DIPY team’s suggested projects was Malin Sandström, INCF’s community manager who manages the organization’s Google Summer of Code (GSoC) program. GSoC allows students to be financed with stipends for their work on open source software over the summer. Open source organizations in the project contribute project ideas and mentors. INCF is participating as a GSoC mentoring organization for the 8th year in a row, with mentors from the worldwide INCF community and a wide range of neuro-tool projects.

You can browse the INCF project list to learn more about the summer plans. If you were too late to take part this year, we encourage you to keep an eye on the INCF GSoC projects page for updates on future rounds. If you have a project idea you would like to mentor with INCF for next year, get in touch at gsoc@incf.org by 1st December 2018.

Our next call will be on Thursday April 26th at 7pm BST (check your local time zone). If you’d like to nominate yourself or someone else to be featured on these monthly calls, please add their information at this github issue, or email the host of the calls Kirstie Whitaker at kw401@cam.ac.uk. You can also join the OSSIG google group to receive reminders each month.
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