Episode 187: Karthik Ram on Research Software Sustainability

Guest Karthik Ram Panelists Richard Littauer | Abby Cabunoc Mayes
Show Notes Hello and welcome to Sustain! The podcast where we talk
about sustaining open source for the long haul. In this episode,
Richard and Abby are joined by guest Karthik Ram, a research
scientist at UC Berkeley’s Institute for Data Science and Berkeley
Initiative for Global Change Biology, as well as co-founder and
director of the rOpenSci Project, and lead at URSSI. Karthik’s
journey from field ecologist to data scientist has propelled him
into roles that advocate for sustainable scientific software and
open science. He currently manages projects, fundraises, and
mentors while also overseeing initiatives aimed at developing best
practices in software development, advocating for supporting
policy, building user and developer communities. He emphasizes the
significance of reproducibility and sustainability in research
software and offers an empowering approach to maintaining academic
software. Hit download to hear much more! [00:02:00] Karthik
explains what he does as a senior data scientist, and he tells us
that he views himself as an “engineering manager” rather than an
individual contributor. [00:03:01] His transition from a field
ecologist to a data scientist was triggered by handling large
amounts of data and developing software to work with it. [00:06:21]
The conversation turns to the JOSS, the Journal of Open Source
Science, and Karthik shares the origin story for the software
review process. [00:09:03] Karthik dives into the UC Berkeley’s
Science Institute, he tells us how it started, and what his role
was there. [00:11:11] Karthik’s involved with the URSSI, where they
aim to collect and disseminate best practices in software
development, advocate for supporting policy at a national level,
and grow user and develop communities around their projects.
[00:12:55] One of the projects coming up in the fall for URSSI is
they’re going to run a school for research software engineering.
[00:15:16] Karthik and Kyle assembled a course focusing on the best
practices for developing sustainable research software by drawing
on topics from past workshops and classes they’ve conducted.
[00:17:12] We hear about the commonalities between scientific
software sustainability versus normal open source software
sustainability, and Karthik explains that scientific software
sustainability is unique because it caters to niche groups, making
it expensive to build and maintain. [00:20:20] Karthik tells us
about a project he’s working on with Patrice Lopez and James
Howison, to identify what tools researchers use in various domains,
how their usage evolves over time, and which clusters of tools
drive research in certain areas. [00:23:34] As part of this
project, Karthik and his team are using a tool called, GROBID, to
process structured documents to XML, extract entities, and analyze
the usage of software mentioned in scientific papers. [00:28:23]
Karthik highlights the difficulties researchers face in keeping
with best practices for code hosting and archival copies and
discusses the misconceptions about GitHub being a permanent archive
and the need for a safer, more reliable repository like Zenodo.
[00:31:31] Richard brings up the issue of measuring the impact of
code repositories and whether a similar system to academic journal
impact factors could arise. [00:33:02] Karthik details an approach
for maintaining academic software. [00:38:02] Find out where you
can learn more about Karthik and his work on the web. Quotes
[00:07:43] “They would bring their puppy and ask us to adopt it.”
[00:15:45] “Even today, we do not have a good appreciation for
research software and the role that it plays in driving research on
all the things that we care about.” [00:16:21] “Another pet peeve
that I have is that people think money is the solution to
everything.” [00:16:38] “If we teach more projects about best
practices, it’s very likely that software that integrates those
best practices will actually continue to exist.” [00:17:51] “The
challenge with research software is there’s a lot of software that
sits on the long tail.” [00:28:39] “I think the challenge is that
we don’t really need to invent anything new.” [00:36:14] “Part of
the work we want people to do is invest community early on.”
Spotlight [00:38:47] Abby’s spotlight is Governing Open by Shauna
Gordon-McKeon. [00:39:15] Richard’s spotlight is Bertram Ludäscher
and William Michener. [00:39:43] Karthik’s spotlight is Patrice
Lopez. Links SustainOSS (https://sustainoss.org/) SustainOSS
Twitter
(https://twitter.com/SustainOSS?ref_src=twsrc%5Egoogle%7Ctwcamp%5Eserp%7Ctwgr%5Eauthor)
SustainOSS Discourse (https://discourse.sustainoss.org/)
podcast@sustainoss.org (mailto:podcast@sustainoss.org) SustainOSS
Mastodon (https://mastodon.social/tags/sustainoss) Open
Collective-SustainOSS (Contribute)
(https://opencollective.com/sustainoss) Richard Littauer Twitter
(https://twitter.com/richlitt?ref_src=twsrc%5Egoogle%7Ctwcamp%5Eserp%7Ctwgr%5Eauthor)
Richard Littauer Mastodon (https://mastodon.social/@richlitt) Abby
Cabunoc Mayes Twitter (https://twitter.com/abbycabs?lang=en)
Karthik Ram Website (https://ram.berkeley.edu/) Karthik Ram Twitter
(https://twitter.com/_inundata?lang=en) Karthik Ram GitHub
(https://github.com/karthik) Karthik Ram LinkedIn
(https://www.linkedin.com/in/karthik-ram-93334954) rOpenSci
(https://ropensci.org/) The Journal of Open Source Software
(https://joss.theoj.org/) Arfon Smith-Chatops-Driven Publishing
(https://www.arfon.org/) DJ Patil
(https://en.wikipedia.org/wiki/DJ_Patil) Berkeley Institute for
Data Science (https://bids.berkeley.edu/) URSSI (US Research
Software Sustainability Institute) (https://urssi.us/) Software
carpentry (https://software-carpentry.org/) Report from the URSSI
Winter School pilot
(https://urssi.us/blog/2020/01/29/report-from-the-urssi-winter-school-pilot/)
Kyle E. Niemeyer, Ph.D.
(https://niemeyer-research-group.github.io/) Science-miner
(https://science-miner.com/) GROBID
(https://github.com/kermitt2/grobid) James Howison-Associate
Professor
(https://www.ischool.utexas.edu/people/people-details?PersonID=175)
Issuing a persistent identifier for your repository with
Zenodo-GitHub Docs
(https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content#issuing-a-persistent-identifier-for-your-repository-with-zenodo)
Governance of Open Source Software by Shauna Gordon-McKeon
(https://governingopen.com/) Bertram Ludäscher
(https://scholar.google.com/citations?user=nYx9xasAAAAJ&hl=en)
William Michener
(https://scholar.google.com/citations?user=TJ5xlKsAAAAJ&hl=en)
Patrice Lopez
(https://scholar.google.com/citations?user=xDfUqfcAAAAJ&hl=en)
Credits Produced by Richard Littauer (https://www.burntfen.com/)
Edited by Paul M. Bahr at Peachtree Sound
(https://www.peachtreesound.com/) Show notes by DeAnn Bahr
Peachtree Sound (https://www.peachtreesound.com/) Special Guest:
Karthik Ram.