Open Science Newsletter: October 2021

 

The Fall semester is picking up speed and the OSDC program is keeping pace with another round of exciting open science programming, including encore presentations of our popular Reproducible Research MiniSeries! This month, we’re also bringing you the latest in open science news and opportunities. Be sure to check out the long-awaited report from our recent Bioinformatics Hackathon and a special feature from faculty Librarian, Sarah Young!

Please contact us at openscience@andrew.cmu.edu if you have any questions and follow us on social media at #CMUOpenScience.

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Our Reproducible Research MiniSeries is back with Introduction to R!

Fan of The Carpentries? Then we think you’ll love our workshop “Mini-series'' covering the foundational skills and concepts needed to produce reproducible research. OSDC “Minis” are designed to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain. 

On Thursday, October 18th, 1-4 EDT we’re providing an encore presentation of Introduction to R. In this 3-hour virtual workshop, you’ll be introduced to R and the RStudio environment, learn basic R syntax, and move through how to import CSV files, work with data frames, calculate summary statistics, and more. Workshops are taught in a highly-interactive, hands-on format and require no prior programming experience to participate. Register now on LibCal.
 

Recapping and looking ahead at the Collaborative Bioinformatics Hackathons


In January and June 2021, bioinformatics researchers from around the world came together virtually to develop a framework for clinical reporting of RNA-Seq research and multiomics data. CMU Libraries co-hosted the event with Johns Hopkins and Ben Busby of DNAnexus and was on hand to provide support for documenting the project (see https://osf.io/afc7n/ and https://osf.io/hjczs/), organizing resources, and preparing a manuscript.

Many of us think of hackathons as being a competitive exercise with teams vying for a prize, but in these hackathons the participants worked together collaboratively to develop a solution for a clinical problem. Participants came from a variety of backgrounds, including academia, industry, and the clinic, and this wide breadth of expertise allowed the event organizers to create dedicated teams for working on various parts of the framework. Over the course of the four-day events, the teams come together at periodic intervals to collaborate and iteratively develop and improve the framework. Each team had a person assigned to a writer role.  Following the hackathon, the writers collaboratively wrote a preprint manuscript for BioHackrXiv that describes the framework. 

While participants in the hackathon logged in from around the world, Carnegie Mellon University and University of Pittsburgh had great representation at the hackathons. Congratulations to four CMU undergraduates (Shamika Dhuri in Biological Science and Statistics and Data Science, Stephen Price in Computational Biology, and Meghana Tandon in Computational Biology and Computer Science) and a Masters student (Alex Guo in Computational Biology) who are co-authors on the preprint and a poster for the 2021 American Society of Human Genetics meeting that describes the scientific findings of the hackathons.

If these hackathons sound interesting to you, stay tuned for details on our next collaborative hackathon the week of March 9th, 2022! We are hoping for a hybrid event with people participating both in person and virtually.  It is a great opportunity to network, work on solutions to real problems, and contribute to bioinformatics scholarship. You can keep an eye out here for details about this and other hackathons and read more about our collaborative bio hackathons in this blog post from Hannah Gunderman and Ben Busby.
 

CMU Librarian Sarah Young tells us how to move from Open Science to Open Synthesis

In her latest blog post, “From Open Science to Open Synthesis: Removing barriers to knowledge for evidence-based impact,” social science librarian Sarah Young discusses how the open science practices of open data, open access, and open methods allow for research to be more easily discovered and effectively synthesized in ways that support evidence-based policy- and decision-making. Check out the full article here!
 

Fall Workshop Series

 

We have a host of wonderful data and open science-themed virtual workshops lined up for Fall 2021! You can see a complete list of all our workshop offerings for Fall 2021 on the main CMU Libraries website, but we’ve also highlighted some below (each title is a clickable link which will take you to the registration page):
 

Open Science News & Opportunities

Below you’ll find the latest news and opportunities in open science. 

  • The National Academies of Sciences, Engineering, and Medicine’s Roundtable on Aligning Incentives for Open Science will host a public release of Developing a Toolkit for Fostering Open Science Practices: Proceedings of a Workshop on Thursday, September 30, 2021 from 3:30-4:30 pm EDT. Please register in advance to receive information on how to participate in the event. More information on the event and the background work can be found here.

  • ITHAKA is hosting a “Leveraging Data Communities to Advance Open Science” workshop that pairs scientists in data communities with data management professionals. Follow this link for more information.
 
 

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