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Open Science at CMU Newsletter - May 2021

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May is here and summer is just around the corner! Why not take advantage of the lighter workload to treat yourself to some of those extracurricular goodies you’ve been patiently putting off? The summer is packed with awesome OSDC programming and there’s no better time to dip your toes in the water! If you’re a fan of our Carpentries workshops, you’ll love our new half-day “mini” workshops, designed to provide you with high-quality data science instruction in a no-stress learning environment. Also, there’s still time to register for our Collaborative Bioinformatics Hackathon, hosted by our partners at DNAnexus and Johns Hopkins University. Discover what open science is all about while helping contribute to an important (and super interesting) topic in genomics! Finally, take a minute to meet our new OSDC Project Coordinator, Patrick Campbell, in our latest new member highlight.
 

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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Registration Open for Collaborative Bioinformatics Hackathon!

University Libraries is partnering with DNAnexus and the OpenCravatGroup at Johns Hopkins University to host a virtual hackathon titled "Clinical Reporting of MultiOmics Data!" on June 1-4, 2021. A variety of exciting projects from the list below will be built into a comprehensive reporting system for these types of data, building off of previous work from hackathons at CMU, Baylor College of Medicine, and others run by DNAnexus and NCBI.   


After a brief organizational session, teams will spend four days addressing a challenging set of scientific problems related to a group of genomics datasets. Participants will analyze and combine datasets in order to work on crucial problems and opportunities in clinical bioinformatics. Throughout the four days, participants will come together to discuss progress on each of the topics, bioinformatics best practices, coding styles, etc., and receive support from data librarians and academic liaison librarians from CMU Libraries on data management education and recommended practices for writing manuscripts.  


Interested in genomics data and increasing your computational and collaborative skills? Applications are open! Submit your application by May 11th!

1:1 Customized Support for LabArchives


 

All CMU affiliates have free access to LabArchives, a cloud-based electronic research notebook platform that can be used for collaborative research or teaching in any discipline (not just science and engineering!). This tool has proved really useful during this time of remote work for many in the CMU community. LabArchives is offering consultations with individual researchers, instructors, or lab groups to provide customized support on how to get started with the platform or even to just explore if it is the right platform for them. To set up a consultation, please email Linda Cubias (lcubias@labarchives.com) at LabArchives. You can also find more information about how to use our Professional and Educational licenses here: https://www.library.cmu.edu/labarchives/about.

Next Carpentries Workshop: Introduction to Python, Shell, and Git

Registration for our next Carpentries workshop is open! This is a virtual three half-day workshop (15 hours total) that will be held June 7-9th, 12:00-5:00 PM EDT. Participants will learn how to automate tasks and do plotting with Python. There will also be an introduction to Shell and Git. This hands-on workshop is suitable for researchers with little to no programming experience. This is a great opportunity to get started with coding with a small group of folks in a welcoming environment! 


Register here and reach out to openscience@andrew.cmu.edu if you have any questions.

Learn to Use R in Our New Half-Day Workshops

Fan of The Carpentries? Then we think you’ll love our new workshop “Mini-series'' covering the foundational skills and concepts needed to produce reproducible research. The 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. 
 

In the first installment of the series, 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.

Introducing Patrick Campbell, our new OSDC Project Coordinator

Hi everyone! I am an environmental scientist and recent graduate of CMU’s Public Policy and Management master’s program. While my early career was devoted to addressing water quality issues in my home state of Florida, I later relocated to the Peruvian Amazon, where for three years I managed the Amazon Conservation Association’s volunteer and biological monitoring programs. For the past five years, I have been using open source, peer-to-peer, and other collaborative tools and practices to make science and other forms of civic engagement more open and accessible to the public. As OSDC Project Coordinator, I’ll be assisting the OSDC team in expanding our offerings for foundational data science training and increasing the number of citizen science and other informal science opportunities available to students and other members of the CMU research community. I’m thrilled to be joining the OSDC team in their ongoing efforts to improve research and scholarship through open science practices! Feel free to reach out via my staff profile page with any questions or just to introduce yourself.
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