Open Science Newsletter: February 2023

Welcome to a new year and semester full of possibilities! Did you know this is the year of Open Science? Yup, that’s right, the White House of Science and Technology Policy (OSTP) has coined 2023 the Year of Open Science and will take actions spanning the year to advance open science (read more below!). When classes get you down, do you know what you gotta do? No, it’s not “just keep swimming” (though Dory would appreciate that)...you got to seek guidance! The Libraries are here to help, we have a plethora of awesome workshops this semester ranging from cleaning data with OpenRefine, introduction to Python, using Jupyter Notebooks, introduction to social network analysis in R, Project Management, and Pre-Registration in Open Science Framework (OSF), to Licensing and Copyright in Open Education, and more! Also, you can’t forget about Love Data Week! Attention Faculty Researchers! Our Open Science team is recruiting participants for focus group interviews to find out how you are conducting research! Please consider participating, the information learned will contribute to improving services offered, and if this doesn’t already sound wonderful, then you will indirectly benefit from learning more about your research practices!

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Please contact us at openscience@andrew.cmu.edu
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Open Science

On January 11, 2023, the White House of Science and Technology Policy announced 2023 as the Year of Open Science. You have probably heard the term Open Science a dozen times, if not at least once in the last couple of months. You may have even heard Open Science referred to as Open Research or Open Scholarship, but these names all refer to the same concept, openness.

On top of this exciting news, the Office has made an official definition of open science, “The principle and practice of making research products and processes available to all, while respecting diverse cultures, maintaining security and privacy, and fostering collaborations, reproducibility, and equity.

So, why is this a big deal? Well…because research practices are shifting toward a more open structure, and this shift is only gaining momentum. Since and over the course of the pandemic, we have read and, for many, experienced this change of open science practices through mandates, memos, and policies from the government and funders. The challenge for researchers becomes figuring out how to integrate these practices into their research workflow to comply with these requirements, but before becoming overwhelmed, I’ve got good news! Several researchers already incorporate these practices in their research, it’s a matter of identifying them, and asking if there is a way to improve them to better meet funding policies.

Additionally, many researchers believe that to do Open Science means integrating every aspect of the practices, which can create overwhelming amounts of stress. However, the strategy is to rewire how you think about applying open science practices in your research. For example, the National Academies of Science, Engineering, and Medicine (NASEM) identified six core values of science: Objectivity, Honesty, Openness, Accountability, Fairness, and Scholarship. If researchers consider one, two, or even three of these values that are meaningful to them, then this could help identify which Open Science practices fall within those values. Also, it could be beneficial to consider a degree of implementation approach to the practice(s) of choice, which might help alleviate this all-in-or-nothing idea.

The whole concept of Open Science is an approach or set of practices to guide researchers to increase the transparency and accessibility of their research for the greater scientific and community good. There are many common misconceptions of Open Science, as I pointed out with the all-in mindset, but the Libraries, and our Open Science team, are here to help bring clarity to any misconceptions and provide you with the resources you need to be successful as you travel down the Open Science path.

Open Access Publishing Support

The Libraries continue to expand Open Access publishing options for the CMU community. We currently provide Open Access publishing agreements with the following publishers, allowing authors to publish Open Access without a fee:

American Chemical Society (ACS)
Association for Computing Machinery (ACM)
Cambridge University Press (CUP)
Cold Spring Harbor Press
Elsevier
Institute of Physics (IOP)
Public Library of Science (PLoS)
Springer
Wiley

In addition, CMU-affiliated scholars receive a 10% discount when publishing their work in MDPI journals. As part of our dedication to promoting open access in scholarly communication, CMU Libraries is currently negotiating with other organizations to allow CMU scholars to publish in more open access journals. Information on our new partnerships will be released as our contracts are finalized.

The Libraries also maintains an Article Processing Charge (APC) fund to support our CMU authors who wish to publish open access outside of our publisher agreements. Learn more about eligibility and submitting a request on the Article Processing Charges page.

Open Research Focus Group Recruitment

Invitation to participate in the Open Research Focus Group Interviews

Dear Colleagues,

The University Libraries is organizing a focus group to learn more about the research practices at CMU. Our goal is to increase our understanding of how researchers in our community are conducting, discovering, reusing, sharing, and publishing research, as well as hear researchers' perspectives and experiences on these topics.

The focus group interview is very informal and takes around 60 minutes, which includes time for introductions, breaks, and questions.

Your participation is valuable to our understanding of how research is conducted and will ultimately help shape future services and products the University Libraries offer to better support our community.

If you are willing to participate in our focus group, please fill out our three-question participation form. Please reach out to Lencia Beltran, lbeltran@andrew.cmu.edu, CMU Libraries Open Science Project Coordinator, with any questions.

Open Science and Data Collaborations Team
Chasz Griego, Emma Slayton, Emily Bongiovanni, Sarah Young, Melanie Gainey, Katie Behrman, Lencia Beltran

Upcoming Spring Workshops

Project Management and Pre-Registration with OSF

Open Science Framework (OSF) is a research reproducibility and project management platform that is free, open source, and designed to support research across the research lifecycle. OSF allows you to organize all of your research documentation, such as datasets, code, analysis, background literature, and more, into a single space shared by your collaborators. OSF also supports the pre-registration of research protocols and preprint publication.

Instructors: Sarah Young, Principal Librarian; Katie Behrman, Institutional Repository Manager; Melanie Gainey, Open Science Director/Librarian; Lencia Beltran, Open Science Program Coordinator
Date: Monday, February 13, 2023
Time: 12:00 - 1:30 PM EST
Location: Virtual (only)

Cleaning Messy Data with OpenRefine

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.

Instructor: Sarah Young, Principal Librarian
Date: Wednesday, February 15, 2023
Time: 3:00pm - 4:30pm EST
Location: Sorrells Library Den, Wean Hall (in-person only)

Introduction to R Part 1: Getting started with R and RStudio

This 2-part introductory workshop aims to teach basic concepts, skills, and tools for working with data in R so that you can get more done in less time, and apply concepts of reproducibility to your research. This is an introduction to R designed for participants with no programming experience. Part 1 of the workshop covers basic information about R syntax and the RStudio interface, including installing packages and working with vectors. Part 2 will cover importing CSV files, working with dataframes, how to deal with factors, how to add/remove rows and columns using the popular dplyr package, and how to calculate summary statistics from a data frame.

Instructor: Sarah Young, Principal Librarian
Date: Thursday, February 16, 2023
Time: 10:00am - 11:30am EST
Location: Sorrells Library Den, Wean Hall (in-person only)

Introduction to R Part 2: Working with data in R

Instructor: Sarah Young, Principal Librarian
Date: Thursday, February 23, 2023
Time: 10:00am - 11:30am EST
Location: Sorrells Library Den, Wean Hall (in-person only)

Licensing and Copyright in Open Education

Open Educational Resources (OER) are freely available and openly licensed educational materials. OER lower the costs of higher education by replacing commercial educational resources. As openly licensed materials, OER allows instructors to remix and tailor the materials to meet their specific course needs. This Zoom session will explore OER, introduce the basics of copyright and how it applies to OER, and introduce Creative Commons licensing.

Instructor: Emily Bongiovanni, Librarian
Date: Tuesday, February 28, 2023
Time: 10:00am - 11:00am EST
Location: Virtual (only)

Advanced Research Note-Taking with Obsidian

This workshop will introduce Obsidian, a markdown-based note-taking app that helps you organize your personal knowledge base. We will demonstrate how to create and edit markdown files to easily format your notes, then dive in to several of the functions and plug-ins in Obsidian that makes it easier for you to organize, link, and search your recorded thoughts. Finally, we will demonstrate how you can link Obsidian to Zotero to help you connect research notes to items in your bibliography.

Instructor: Chasz Griego, Open Science Postdoctoral
Date: Wednesday, March 8, 2023
Time:10:00am - 12:00pm EST
Location: Sorrells Library Den, Wean Hall (in-person only)

Introduction to Command Line Interface (CLI)

This is a hands-on introduction to using the command line interface. This workshop is designed for those who are beginning their exploration into command-line programming and anyone seeking to refresh their skills. A command line interface (CLI) is a quick and efficient way to perform computing tasks. A few of the topics that will be introduced include navigating the directory structure, commonly used commands, working with files and directories, and more.

Instructor: Lencia Beltran, Open Science Program Coordinator
Date: Tuesday, March 14, 2023
Time:10:00am - 12:00pm EST
Location: Virtual (only)

Open Educational Resources - Platforms and Resources for Developing and Sharing

Instructors: Emily Bongiovanni, Librarian
Date: Tuesday, March 14, 2023
Time: 10:00am - 11:00am EST
Location: Virtual (only)

Tips for Completing and Submitting your Dissertation or Thesis at CMU

In this workshop you will learn about the process for the electronic submission of your dissertation or thesis document into Carnegie Mellon's institutional repository, KiltHub, and the thesis and dissertation database, ProQuest. We will also cover intellectual property considerations like embargos, licensing, and how to manage published materials that are part of the thesis.

Instructors: Jessica Benner, Librarian; Katie Behrman Institutional Repository Manager
Date: Tuesday, March 14, 2023
Time: 11:00am - 12:00pm EST
Location: Virtual (only)

Introduction to Social Network Analysis in R

The data we use in our research is often relational in nature, from legislative bill co-sponsorship to the grooming behaviors in animals; unfortunately, though, we tend to boil these relations down and use them merely as covariates in our research. However, preserving the inherent relational aspect and modeling it as a whole can often lead to novel understandings; for instance, who would have thought that in comparing behavioral networks across species, Senate bill co-sponsorship networks would most resemble the networks of social licking among cows!

In this workshop, we hope to expand your methodological toolkit by providing an overview of the nuts and bolts of social network analysis through the following topics: importing and cleaning data, exploratory analyses, basic statistical tests, an overview of various advanced statistical procedures, and visualizing your results.

Instructors: Scott Renshaw, Postdoctoral Research Associate, Center for Informed Democracy & Social-Cybersecurity (IDeaS)
Date: Wednesday, March 15, 2023
Time: 1:00pm - 3:00pm EST
Location: Sorrells Library Den, Wean Hall (in-person only)

Introduction to Python for Data Science Part 2: Making the Most with Jupyter Lab and Notebooks

This workshop is designed to be an introduction to Jupyter Lab and Notebooks. Some of the topics that will be covered include: how to access these platforms, an overview of platform features like hotkeys and magic commands, the basics of using markdown, publishing notebooks on the web, and how to use and display interactive figures. This is the second part of a workshop series titled “Introduction to Python for Data Science.” Attending the first part is not a requirement, but highly encouraged if you are new to the Python programming language.

Date: POSTPONED!
Time: STAY TUNED!

Introduction to Python for Data Science Part 3: Plotting and Analyzing Tabular Datasets

In the final part of the 3-part workshop series, "Introduction to Python for Data Science," we demonstrate advanced Python programming techniques using the Pandas library to read tabular datasets, perform statistical analyses, and visualize data. The content covered in this workshop will be a continuation of the content covered in part 1, "Introduction to Basic Programming with Data". We highly encourage attending the first part of the series before this workshop, especially to learners that are new to the Python programming language.

Date: POSTPONED!
Time: STAY TUNED!

Finding Data

Have you ever started a project and thought, "wait, where do I find this data" or "where do I even begin searching"? You are not alone! This happens to be quite common. Thanks to the web, several resources are at your fingertips, some open and others not so much. Below are a few good places to start your search for a dataset that fits your needs.

Inter-University Consortium for Political and Social Research (ICPSR)
ICPSR is a vast archive of social and political science data that is made available through the University of Michigan. ICPSR and OPEN ICPSR provides access to an extensive collection of downloadable data. You will need to login and create an account to download data.

Data.gov
Home of the U.S. Government's open data, providing access to over 85,000 datasets. Major topic areas include Agriculture, Consumer, Education, Energy, Finance, Geospatial, Global Development, Health, Jobs & Skills, Public Safety, Science & Research, Weather and more. Some resources allow for online analysis and visualization.

NASA Open Data Portal
NASA’s clearinghouse for open data. Please note, the majority of dataset pages on data.nasa.gov only hold metadata for each dataset and it's common for the actual data to be held on other NASA archive sites. Data.nasa.gov will have the metadata and links to the data as it exists in those many other locations. The type of datasets available come from the Atmospherical Science Data Center, National Snow and Ice Data Center, Land Processes Distributed Data Center, and others (find out more by looking at their visualization of datasets).

LabArchives and Love Data Week!

For Love Data Week, LabArchives is holding sessions that dive into topics like Best Practices and Tips for Establishing Notebooks Structure, Creating Templates to Standardize the Collection and Management of Data, and more.

If you are unfamiliar with how LabArchives works but have been interested in learning more about it for a while, then why put it off any longer?? Attend one of the sessions!

Let us help! You can reach out to Melanie Gainey, mgainey@andrew.cmu.edu, or Lencia Beltran, lbeltran@andrew.cmu.edu or visit the University Libraries, LabArchives page. We are your trusty contacts on the Carnegie Mellon campus for LabArchives-related questions or help!

In Other News

NIH Data Management & Sharing Policy
The Working Group on NIH DMSP Guidance has published a new resource called the Extended Reference Guide. This guide is created for use in conjunction with the previously released DMSP Checklist for Researchers. This guide provides additional context for the requirements in the checklist.

Disclaimer:
The working group is a community-based collaboration of librarians and other stakeholders and has no affiliation with the NIH. The creation of the reference guide is intended for educational purposes only and does not act as a substitute for official guidance from the NIH.

Love Data Week: Virtual CURATE(D) Training Opportunity
The Data Curation Network (DCN) is celebrating Love Data Week with an interactive webinar on curating research data using their CURATE(D) workflow on February 16, from 1-4 pm EST. Register here.

More...

by Lencia Beltran, Open Science Program Coordinator

Feature image by Scott Graham on Unsplash