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Open Science at CMU Newsletter - October 2019

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Registration is still open for the second annual Open Science Symposium on November 7, and we are rolling out our new institutional license for LabArchives, an Electronic Research Notebook, this month. Read more about how to take advantage of our trainings and digital tools below.

Contact us at openscience@andrew.cmu.edu and follow us at #CMUOpenScience.

To subscribe to this newsletter, click here.
 

Check out our speaker lineup for the Open Science Symposium on November 7

The second CMU Open Science Symposium, taking place at the Mellon Library on November 7, 2019, will build awareness and support for open research practices and encourage innovative ideas about data sharing in the life sciences and related disciplines.

The full day program will feature talks from guest speakers including researchers, tool developers, and publishers, panel discussions, an interactive poster and demo session on research using open methods, and a reception.

We have 12 speakers lined up from a variety of disciplines including molecular biology, neuroscience, machine learning, and data science.

Dan Allan
Jupyter and scientific Python ecosystem contributor, Brookhaven National Laboratory

Marcel Bruchez
Professor, Department of Biological Sciences and Chemistry; Director of the Molecular Biosensors and Imaging Center, Carnegie Mellon University

Casey Greene
Associate Professor, Integrative Genomics Lab, Perelman School of Medicine, University of Pennsylvania; Director, Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation

Lisa Federer
Data Science and Open Science Librarian, National Library of Medicine

Alexander Mathis
Co-developer of DeepLabCut, Harvard University

Daniela Saderi
Co-founder and Project Director at PREreview; Former Mozilla Fellow for Science 2018

Lynn Schriml
Associate Professor, Department of Epidemiology and Public Health, University of Maryland, School of Medicine; Institute for Genome Sciences; Senior Editorial Board Member at Scientific Data 

Carly Strasser
Director of Alliances and Data Strategy at the Fred Hutchinson Cancer Research Center, Seattle, WA

Lenny Teytelman
CEO and Co-founder of protocols.io

Timothy Verstynen
Associate Professor, Department of Psychology, Neuroscience Institute; Co-Director of the CMU-Pitt BRIDGE Center, Carnegie Mellon University

Gregory Way
Postdoctoral Associate, Image-Based Profiling and Genomics, The Broad Institute of MIT and Harvard

Keith Webster
Dean of University Libraries, Carnegie Mellon University

Sara Weston
Assistant Professor, Department of Psychology, University of Oregon; Past chair, Society for the Improvement of Psychological Science

You can register for the symposium and view the talk titles and schedule here. Registration closes on November 5th.

If you are a trainee (student or postdoc) and sign-up to present a poster or demo during the reception on using open science methods or tools in your research, we will waive the $20 registration fee. Simply click the Submit a Poster or Demo button on our webpage.

Please contact openscience@andrew.cmu.edu if you have any questions.

We look forward to seeing you there!
 

LabArchives institutional license coming to CMU this month
Researchers and instructors at CMU will soon have free access to LabArchives, an Electronic Research Notebook, with an institutional account provided by CMU Libraries.  The platform can be used to record and manage data within a lab or for teaching purposes in lab classes. 

Our institutional license will be live by the end of the month. Look for an announcement in our next newsletter and from departmental emails.

LabArchives will be at CMU for onsite training on Wednesday, November 6th to help users learn more about the platform and how to get started or optimize their current use of it.

The training sessions for instructors will be held: 
  • 11:00-12:00PM in the Den of Sorrells Library (4th floor of Wean Hall) 
  • 4:30 to 5:30PM in Room 411 of Mellon Institute 
The training sessions for researchers will be held:
  • 12:00-1:00PM in the Den of Sorrells Library (4th floor of Wean Hall) 
  • 3:00-4:00PM in Room 411 of Mellon Institute
protocols.io training visit to CMU
The protocols.io platform is a free and open access repository for recording and sharing detailed up-to-date research methods and protocols. Our institutional license allows CMU users to have unlimited private group protocols and storage.

Lenny Teytelman, co-founder and CEO of protocols.io, will be visiting CMU to provide onsite training on Friday, November 8th. Stop by Mellon Institute 355 between 1-4PM to talk to Lenny about how to get started or optimize your use of the platform.  

Lenny will also be giving a talk, "Sharing more openly and reproducibly does not have to be a burden," at the Open Science Symposium on Thursday, November 7th. 

Go here for more info on how to get started with protocols.io
 
Announcing Data Collaborations Lab drop-in hours

Every First Tuesday @ Sorrells Library Den

University Libraries is piloting Data Collaborations Lab to connect the research community across disciplinary borders, and facilitate collaborations between data producers and data scientists. The goal of this new initiative is to match researchers who need help with their datasets with individuals who have data science and computer science skills to work together. Information professionals from the University Libraries will provide support on research data management and project documentation.  

You are invited to join our next Drop-in Hours:  

Time: Tuesday, November 5th, 12:00 - 2:00 pm
Location: Sorrells Library Den, Sorrells Library, 4th Floor Wean Hall 

If you are interested in getting help with your data, building consulting experience, finding potential collaborators, or to learn more about this program, stop by the drop-in hours, have some light food, and chat with others who share the same interest! 

To register as a consultant: 
https://forms.gle/pzS2gDx5P2aTTLtF8 

To register for assistance with your data: 
https://forms.gle/27onEzdXxPwd5F6HA 
 
Upcoming workshops on Open Science and Research Data Management
CMU Libraries is offering the following workshops on Open Science and Research Data Management in October and November:

Publishing Your Research Openly at CMU / Thursday, October 24, 10:00 am
Hannah Gunderman & David Scherer

How can one make their research more open? What are the benefits of making your research data and other scholarly outputs publicly available? How can I comply with my funders open access mandates? This workshop will introduce how to prepare and disseminate research data and other scholarly outputs openly through CMU-provided resources. This will help you to more broadly disseminate  your work and will make it easy for others to find and reuse your data and other outputs.

Register here.

Reproducible Data Visualization in Jupyter Notebooks / Monday November 18, 1:00 p.m.
Ana Van Gulick & Huajin Wang

Hands-on workshop to learn the principles of computational reproducibilty, keeping documention of data analysis projects in Jupyter Notebooks, and using matplotlib to plot scientific figures reproducibly.

Register here.

Cleaning Messy Data with Open Refine / Thursday November 21, 10:00 am. 
Sarah Young

Tired of spending hours and hours cleaning messy data in Excel spreadsheets? Come learn OpenRefine, an easy-to-use, open source tool for data cleaning.

OpenRefine (formerly Google Refine) helps you prepare your data for analysis. Quickly and easily transform data, split and merge columns, remove whitespace, and perform many more common data cleaning tasks. With OpenRefine, you can also easily create JSON scripts for repeating series of tasks across multiple datasets.

No previous experience is required. This will be a hands-on workshop--please bring a laptop.

Register here.

You can register for workshops and see the full list of workshop offerings from University Libraries at library.cmu.edu/workshops.
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