April 2022 Community Call


New tools lightning talks

The next community call will be on April 14, 2022 at 12ET/11CT/10MT/9PT.

This month’s community call session will feature a series of lightning talks from community members on new technologies. We are planning 5 talks in 50 minutes that will give a quick look at some new RSE related technology that might be of interest to others.

Talk titles and some brief information are given below. To stay on schedule we will limit each talk session to 10 minutes, but will have channels on Slack for any follow up conversation. This call is a bit of an experiment in responding to this issue, so we will see how it goes in practice!

Registration details

Information on how to register for the Zoom meeting will be sent via email and posted in the #general channel on Slack.

Lightning talk titles and presenter information.

Title Abstract Presenter(s)
arXiv.wiki: crowdsourced summaries for papers arXiv has made sharing research papers easy and accessible. But they are often written with expert reviewers in mind, and aren’t always easy for other researchers to digest. The arXiv.wiki lets you read and collect public notes on any arXiv paper — replace “.org” and “.wiki” and you’re there! Kunal Marwaha
Building open science data web application with zero budget During the Open Life Science mentorship program, I collaborated with iNaturalist project organizers to create a web application that allows users to explore iNaturalist data and environmental data (DataExplorers.info). Since my collaborators had zero budget for a web development, I had to deeply rethink the way I build web applications. By blending software ideas from the tech world and the research world, I was able to create an interactive website using Jupyter notebooks and static site generator that runs on CSVs and can be hosted on Github pages for free. Wai-Yin Kwan
Enhancing Python’s ConfigParser Separating the concerns of the configuration of a tool you build versus the tool’s implementation itself is a software engineering best practice. The ConfigParserEnhanced (CPE) package provides extended handling of .ini-style configuration files beyond what ConfigParser provides by adding an active syntax to embed operations with options. Out of the box it allows the user to chain configuration sections together in a directed acyclic graph (DAG). One can subclass CPE to add additional handlers to be used when parsing a configuration file. Jason M. Gates (speaker); William Mclendon
Come for Syntax, Stay for Speed, Understand defects: Defects in Julia Programs Julia has emerged as a popular programming language to develop scientific software, in part due to its flexible syntax akin to scripting languages while retaining the execution speed of a compiled language. Similar to any programming language, Julia programs are susceptible to defects. However, a systematic characterization of defects in Julia programs remains under-explored. A systematic analysis of defects in Julia programs will act as a starting point for researchers and toolsmiths in building developer tools to improve the quality of Julia programs. To this end, we conduct an empirical study with 742 defects that appear in Julia programs by mining 30,494 commits and 3,038 issue reports collected from 112 open-source Julia projects. From our empirical analysis, we identify 9 defect categories and 7 defect symptoms. We observe certain defect categories to be Julia-specific, e.g., type instability and world age defects. Akond Rahman
Storing Time Series Data in Scylla I’ll be discussing time series interval storage in Scylla. Lessons learned over 2 years. @Juan-Carlos Foust

Information about the presenters:

Presenter About
Kunal Marwaha I’m a graduate student in quantum computing at the University of Chicago. I previously worked as a software engineer. I want to build new tools for scientific research.
Wai-Yin Kwan I’m a software developer with an interest in community science.
Jason M. Gates I’m a “DevOps Evangelist”, specializing in CI/CD pipelines and associated infrastructure, helping teams achieve a DevOps paradigm shift in their culture.
Akond Rahman Akond Rahman is an assistant professor in the Department of Computer Science at Tennessee Tech University. His research interests are in software engineering focused on DevOps and Secure Software Development. He is interested in bringing quality assurance and security into the scientific software development process. To learn more about his work visit https://akondrahman.github.io/.
@Juan-Carlos Foust Interested in intersection between software engineering, biotech, and metabolic engineering - https://www.linkedin.com/in/foustjc/