Digital Scholarship

Knowledge@UChicago featured research: Code for a simple model of evolution of melt pond coverage on Arctic sea ice

July’s featured research in Knowledge@UChicago, the University of Chicago’s open access digital repository, is code by graduate student Predrag Popović and associate professor Dorian Abbot of the Department of Geological Sciences. The code, made available in 2017, supports their model for understanding the evolution of melt pond, or “pools of melted snow and ice,” coverage on Arctic sea ice. Popović and Abbot report on this model in their 2017 article in the open access journal The Cryosphere and point readers to their code in Knowledge@UChicago.

 

Image of Arctic Ocean taken during Office of Naval Research-sponsored study of the changing sea ice, ocean and atmosphere. (US Navy, Image by John F. Williams)

Journal publishers are increasingly requiring or recommending the open availability of research files associated with an accepted publication. For example, Copernicus Publications, the publisher of The Cryosphere, states that the “the output of research is not only journal articles but also data sets, model code, samples, etc. Only the entire network of interconnected information can guarantee integrity, transparency, reuse, and reproducibility of scientific findings.” As a condition of publishing in The Cryosphere, researchers like Popović and Abbot are “are required to provide a statement on how their underlying research data can be accessed” and are encouraged to make these research materials available in an open access repository. 

Knowledge@UChicago is a service that can help researchers meet requirements or expectations from journals like The Cryosphere, Nature Research, Science, and a growing number of others. Researchers can currently deposit small datasets in Knowledge@UChicago and permanent identifiers (DOIs) will be assigned to these deposits, assisting with discoverability and citation. Later this year, new features, including integration with GitHub, will be rolled out. We encourage our research community to make use of this service and to contact knowledge@lib.uchicago.edu for assistance.


This year, we’re highlighting examples of research shared in Knowledge@UChicago, the University’s open access digital repository. By spotlighting items, we hope to illustrate the variety of research that you can find and that UChicago researchers can make available in the repository. University researchers are invited to log in to Knowledge@UChicago and share articles, book chapters, conference materials, datasets, and other scholarly work.  See more digital scholarship news from the Library, including previous featured research on our news site.  

Knowledge@UChicago featured research: Game Mechanics, Experience Design, and Affective Play

June’s featured research in Knowledge@UChicago, the University of Chicago’s open access digital repository, is Patrick Jagoda and Peter McDonald’s book chapter “Game Mechanics, Experience Design, and Affective Play” (2018). Jagoda is an Associate Professor in the Department of English and Department of Cinema and Media Studies at the University of Chicago. Peter McDonald is an assistant professor at DePaul University and earned his PhD from the University of Chicago.

Graphic by Maico Amorim, accessed from Wikimedia Commons

Jagoda and McDonald’s chapter “explores games as a major object of study in both media theory and practice.” The authors consider approaches for game analysis that have characterized the study of games since the early 2000s and probe the concept of “experience design” that “foregrounds the ways players can affect and be affected by a game: experientially, kinesthetically, and ideologically” (p. 174).

The chapter appears in The Routledge Companion to Media Studies and Digital Humanities, a collection of 53 chapters exploring the “intersections of media studies, digital humanities, and cultural criticism through praxis.” The book is available for purchase, but a number of authors, like Jagoda and McDonald, have made their contributions to the volume available for universal access through open access repositories.

We invite University of Chicago researchers to share open access versions of their scholarship in Knowledge@UChicago. Publisher agreements often allow for versions of a published work to be available in an institutional repository, and it is possible to negotiate these rights before signing the agreement. Contact the Library at knowledge@lib.uchicago.edu to discuss your rights as an author and to review your publisher agreement if you are uncertain whether you have permission to submit your work in Knowledge@UChicago.


This year, we’re highlighting examples of research shared in Knowledge@UChicago, the University’s open access digital repository. By spotlighting items, we hope to illustrate the variety of research that you can find and that UChicago researchers can make available in the repository. University researchers are invited to log in to Knowledge@UChicago and share articles, book chapters, conference materials, datasets, and other scholarly work.  See more digital scholarship news from the Library, including previous featured research on our news site.  

Knowledge@UChicago featured work: Migration Stories: A Community Anthology, 2017

April’s featured submission is Migration Stories: A Community Anthology, a collection of stories, essays, poetry, and visual works by individuals at and around the University of Chicago. Edited by Creative Writing Program faculty Rachel Cohen and Rachel DeWoskin, the anthology was produced as a part of the Migration Stories Project, an effort born in 2016 to provide a space to share and experience stories of migration and movement.

Cover of Migration Stories

Cover image by Alejandro Monroy, AM ’17

In the anthology, readers encounter contributions by University of Chicago faculty, undergraduate and graduate students, alumni, high school students in the community, and others. Cohen and DeWoskin write, “From the outset, we wanted the project to focus not on a group of people who are called ‘immigrants,’ but on migration, that human activity, motion, across water, land and air, that is natural to us and that comes to every life in different forms. The stories themselves are a part of these movements; they themselves move from one place to another, one person’s memory to another’s” (p. 9-11). Knowledge@UChicago is pleased to preserve and provide access to this important collection.

We invite University of Chicago faculty and students to share research and writing about our community in Knowledge@UChicago and to use the repository as a place to document and preserve project outputs for the long-term. Contact knowledge@lib.uchicago.edu with any questions!


Each month, we’re highlighting an example of research shared in Knowledge@UChicago, the University’s open access digital repository. By spotlighting an item shared each month, we hope to illustrate the variety of research that you can find and that UChicago researchers can make available in the repository. University researchers are invited to log in to Knowledge@UChicago and share articles, book chapters, conference materials, datasets, and other scholarly work.  See more digital scholarship news from the Library, including previous featured research on our news site.     

Knowledge@UChicago featured research: The Secret Faces of Inscrutable Poets in Nelson Algren’s Chicago

February’s featured research is a master’s thesis completed as part of the University of Chicago’s Master of Arts Program in the Humanities (MAPH).  Graduating students and alumni interested in raising the visibility of and increasing access to their PhD dissertation, master’s thesis, or BA/BS thesis are invited to share their work in Knowledge@UChicago.

Knowledge@UChicago has served as the open access home for University of Chicago PhD dissertations since 2015 and visitors to the repository will find more than 700 open access dissertations by University of Chicago researchers available. While University of Chicago PhD dissertations are also available in the subscription-based ProQuest Dissertations and Theses database, University of Chicago theses can be more difficult to find and, thereby, to use and reference in other research projects.

We’ve been glad to see recent examples of University of Chicago researchers sharing their master’s theses in Knowledge@UChicago. This month, Jeffrey McMahon, a University of Chicago alumnus, lecturer, and MAPH writing advisor shared the thesis he completed in 2002. In “The Secret Faces of Inscrutable Poets in Nelson Algren’s Chicago: City on the Make,” McMahon examines the “symbolic and structural elements” of Algren’s essay and demonstrates the influence that other literary works, particularly Carl Sandburg’s “Chicago,” had on Algren’s text. You can download and read McMahon’s thesis by visiting Knowledge@UChicago.

Figure 5. The Cardiac System: References to the city's heart in "Chicago: City on the Make"

Figure by Jeffrey McMahon, “The Secret Faces of Inscrutable Poets in Nelson Algren’s Chicago: City on the Make,” 2002.

If you are a University of Chicago graduate or current student interested in making your master’s thesis available to the world, visit our site to find more information about Knowledge@UChicago or contact Library staff at knowledge@lib.uchicago.edu. We look forward to reading your work!


Each month, we’re highlighting an example of research shared in Knowledge@UChicago, the University’s open access digital repository. By spotlighting an item shared each month, we hope to illustrate the variety of research that you can find and that UChicago researchers can make available in the repository. University researchers are invited to log in to Knowledge@UChicago and share articles, book chapters, conference materials, datasets, and other scholarly work.  See more digital scholarship news from the Library, including previous featured research on our news site.     

Knowledge@UChicago featured research: The Changing Landscape of Arts Participation

Beginning this month, we’re highlighting an example of a deposit to Knowledge@UChicago, the University’s open access digital repository. By spotlighting an item each month, we hope to illustrate the variety of research that you can find and that faculty and other UChicago researchers can make available in the repository. University researchers are invited to log in to Knowledge@UChicago and share articles, book chapters, conference materials, datasets, and other scholarly work.

January’s featured deposit is a 2014 report entitled “The Changing Landscape of Arts Participation: A Synthesis of Literature and Expert Interviews.” This report is the product of NORC and the former Cultural Policy Center in the Harris School. The report, prepared by Jennifer Novak-Leonard, Patience E. Baach, Alexandria Schultz, Betty Farrell, Will Anderson, & Nick Rabkin, is “oriented to understanding the ‘cultural frames’ of various socio-demographic communities [in California] and to unpacking the many dimensions—meanings, settings, and social context” of participation in the arts. It was submitted to the National Endowment for the Arts, with support from The James Irvine Foundation.

In 2016, the Cultural Policy Center merged with Place Lab. The Library is pleased to have examples of the rich research produced by the Center available in the repository. Access more research created by this Center by visiting Knowledge@UChicago.

We welcome active and past centers to use Knowledge@UChicago for preserving and providing access to their research. Contact knowledge@lib.uchicago.edu for information about Knowledge@UChicago and to request the creation of a repository collection for your center.

Register today for the Library’s Winter Quarter workshops

The University of Chicago Library is offering a variety of workshops and programs during Winter Quarter highlighting tools, resources, and services available to you to support your work. Learn about academic publishing, GIS, data resources, citation management, copyright and more. Space is limited, so register for sessions today!

Center for Digital Scholarship Programs

Open Access, Self-Archiving, and Knowledge@UChicago
January 16, 10:00 – 11:00 a.m. TechBar, Regenstein Library 160 Register
Join the Library for a discussion on the principles of open access, the individual and societal benefits of open research, and authors’ rights and self-archiving. We will consider strategies for expanding access to our scholarship and spend hands-on time with Knowledge@UChicago, the University’s open access digital repository for scholarly work. Bring a laptop to get started sharing and preserving your research!

Creating Digital Collections with Omeka
January 22, 10:00 – 11:00 a.m. TechBar, Regenstein Library 160 Register
This workshop will introduce participants to Omeka.net, a web-based tool that can be used to organize, describe, tell stories with, and share digital collections. Through hands-on exercises, we will navigate and explore the capabilities of Omeka.net. We encourage you to bring your own digital materials to play with during the session and to learn how you might curate them with Omeka!

Librarian Elisabeth Long (left) discusses a data management plan with Professor Stefano Allesina. (Photo by Joel Wintermantle)

Data Management 101
January 23, 11:00 a.m. – Noon, Regenstein Library 523 Register
Data management plans are researchers’ written strategies outlining how they will collect and take care of their data during the life of a project and what approaches they will take for sharing and preserving their data at the end of a project. This session will introduce the basic components of a data management plan, funder requirements related to data management planning, and DMPTool, a free online tool that guides researchers through the creation of a plan.

Working with Spatial Data
January 23, 2:00 – 4:00 p.m. Map Collection, Regenstein Library 370 Register
Come learn the core concepts of working with spatial data, including: spatial thinking for research, Geographic Information Systems (GIS), spatial data formats, finding spatial data, tools & software, spatial analysis & geoprocessing, Spatial Data Management, and geospatial resources.

Version Control with GIT
January 30, 10:00 – 11:30 a.m. Regenstein Library 523 Register
This class teaches about what Git is and how to use it, including an overview of GitHub and GitLab. What are the advantages of using it, and drawbacks to other ways of collaborative development? Laptops recommended for hands-on exercises.

Navigating ARCGIS Online
January 31, 2:00 – 4:00 p.m. Map Collection, Regenstein Library 370 Register
Need to make a web map? Find some spatial data? Come learn how to use ArcGIS Online in this hand-on workshop. No experience is needed – we’ll start with logging in and finish by creating you’re first web map. Please bring a laptop to participate in the workshop.

Introduction to ICPSR
February 6, 10:00 – 11:00 a.m. Regenstein Library 523 Register
This workshop will teach you how to get started with ICPSR (the Inter-University Consortium for Political and Social Research). ICPSR is one of the largest social sciences data archives in the world. During the session, participants will learn how to create an account, browse and search for data, and download datasets. The session will also cover best practices for finding and evaluating datasets. Please bring a laptop to the session; one can be borrowed at the TechBar.

Navigating Social Explorer
February 6, 1:00 – 3:00 p.m. Map Collection, Regenstein Library 370 Register
Social Explorer is a platform for creating interactive maps that explore data from the U.S. Census and the American Community Survey. This session will introduce U.S. demographic data, producing interactive web maps, and how to download data for further analysis. Please bring a laptop to participate in the workshop.

Using the UChicago Map Collection
February 12, 2:00 – 4:00 p.m. Map Collection, Regenstein Library 370 Register
The University of Chicago Library is home to one of the largest map collections in North America, with over 475,000 sheets, in addition to aerial photos, atlases, and reference materials. This session will introduce you to the Map Collection, review how to find and access the maps, and highlight collections of particular interest to researchers.

Introduction to Copyright, Fair Use, and Permissions
February 28, 3:00 – 4:00 p.m.  TechBar, Regenstein Library 160 Register
In academia, we frequently encounter copyright issues in research and teaching and this session will equip participants with tools and a foundation for navigating them. In this session, we will explore the length of copyright terms, probe fair use through case studies, and identify when and how to approach securing permissions for reuse of a copyrighted work. Led by Dan Meyer, Director of the Special Collections Research Center and Nora Mattern, Scholarly Communications Librarian.

Scholarly Communication Drop-In Hours
Mondays, 2:00 – 5:00 p.m. TechBar, Regenstein Library 160
Faculty, students, and staff are invited to drop by the Tech Bar collaborative space to consult with issues related to copyright, data management, and open access. Come talk tools and practices to work through questions like: Do I need to get permission to use this photo in my publication? How can I make sense of (and find) my data in years to come? How can I increase the visibility and impact of my work?

EndNote and Zotero Training  

Introduction to EndNote: Document Organizer and Bibliography Builder
January 16, 4:00 – 5:00 p.m. Crerar Library, Computer Classroom Register
EndNote is a research management tool used to keep track of citations, PDFs and other documents, and create formatted bibliographies as you write your paper. In this workshop, learn how to use the desktop version of EndNote. Topics covered include: creating and managing citation libraries, importing citations from online databases and other sources, importing and managing PDFs and creating bibliographies.

Librarian Rebecca Starkey with 3 students working on laptops.

Rebecca Starkey, Librarian for College Instruction and Outreach (standing), works with students to enhance their research skills. (Photo by Jason Smith)

Introduction to Zotero
January 18, 3:00 – 4:00 p.m. Register
January 28, Noon – 1:00 p.m. Register
January 31, Noon – 1:00 p.m Register
February 8, Noon – 1:00 p.m. Register
February 20, 3:00 – 4:00 p.m. Register
March 26, 1:00 – 2:00 p.m. Register
TechBar, Regenstein Library 160
Learn how to use Zotero, a free citation manager that allows you to save and organize citation information while searching and browsing the Web. With a single click, Zotero saves citations and enables you to create bibliographies in popular citation styles (MLA, Chicago and APA).

Dissertation Support

Dissertation Draft Review Information for Students
January 15, 3:00 – 4:00 p.m. TechBar, Regenstein Library 160 Register
Are you a Ph.D. student planning to submit your dissertation soon? Do you want to know if you are on the right track with formatting your dissertation? Dissertation Office staff offer an optional draft review service during the first few weeks of each quarter. Come to this information session to learn more about draft reviews and the basic requirements for formatting your dissertation. Bring your questions and bring your laptop.

Dissertation Procedures for Students
January 22, 4:00 – 5:00 p.m. Register
January 23, Noon – 1:00 p.m. Register
TechBar, Regenstein Library 160
Are you a Ph.D. student planning to graduate in Winter 2019? Come to this information session about the procedures for submitting your dissertation using a web-based interface, the ETD Administrator. We will review formatting requirements and discuss open access for dissertations via the institutional repository, Knowledge@UChicago.

Love Data Week (February 11-15)

GIS and Maps Librarian and students with map of Chicago on monitor

GIS and Maps Librarian Cecilia Smith (center) discusses mapping tools and resources with (from left) students Paul Gilbert, II, College ’20, and Emil Sohlberg, College ’20. (Photo by Joel Wintermantle)

Introduction to Census Data
February 11, 11:00 a.m. – Noon. Regenstein Library 523 Register
The Census Bureau collects and disseminates demographic and socioeconomic data for the United States. Join us to learn about core data surveys, hear about upcoming changes that will be introduced in the 2020 Census, and find how to locate and download census data using ICPSR and Social Explorer.

Citizen Science Snack Break
February 12, 2:00 – 4:00 p.m.  TechBar, Regenstein Library 160
Citizen science is a movement that encourages the general public to participate in data collection for scientific research. Join us for a fun citizen science activity and a snack. No registration required.

Data Privacy Tips and Tricks
February 13, 11:00 a.m. – Noon. Regenstein Library 523 Register
Data breaches and online tracking scandals are now common occurrences. Are you interested in protecting your personal data but don’t know where to start? Join us for an overview of easy-to-use tools that can help safeguard your privacy.

A Date with Data
February 13, 1:00 – 3:00 p.m. Regenstein Library 122
Do you love data? Join us for cake, button making, demonstrations of open data resources and projects, and a chance to learn about data services offered at the University of Chicago Library. Enter the Census Data Knowledge Challenge for a chance to win a gift card! No registration required.

Open Geospatial Data
February 14, 1:00 – 3:00 p.m. Crerar Library, Computer Classroom
Explore open data sources for your mapping, visualization, and research projects in this session. We’ll review free data sources ranging from the local to the global. We will also cover available resources for supporting your geospatial projects. No registration required.

New developments for Knowledge@UChicago, the University’s institutional repository

The University of Chicago Library is enhancing Knowledge@UChicagothe University’s institutional repository for faculty and student research, in order to better meet growing needs and interests around data sharing and preservation, open access, and reproducible research results. In mid-December, visitors to Knowledge@UChicago will encounter a new, user-friendly interface for sharing and accessing research. Improved capabilities for data and software preservation will follow over the winter quarter.

Launched in 2016, Knowledge@UChicago is an open access repository for sharing and preserving scholarly work created by faculty, students, and staff. It currently serves as a home for UChicago faculty and students’ digital research publications such as articles, book chapters, conference materials, and a small number of datasets, and for dissertations and theses by students who choose to make them open to the public. UChicago faculty and students in divisions and departments that range from the Physical Sciences Division to the School of Social Service Administration to the Humanities Division have already contributed publications and datasets to Knowledge@UChicago.

With the support of capital funding, the Library is migrating the repository to the TIND digital platform. TIND is based on the open source software Invenio, originally developed at CERN, the European Organization for Nuclear Research, to manage its own digital outputs.

This new system will offer more features for handling research data in addition to traditional research publications, and will provide greater flexibility for future customization and integration with researchers’ workflows. The first phase of the project will migrate existing content to the new system by the end of December 2018. The second phase, beginning in January, will add new features that better support research data and software preservation, including richer metadata for data deposits and integration with GitHub.

This move will improve the infrastructure available to our University community to make their data available for reuse, new discoveries, and replication. It will also support researchers as they meet requirements for data sharing from funders and publishers, The new developments to the institutional repository are accompanied by additional library data services, including assistance with data acquisition and transformation, data analysis, and data management. We encourage UChicago faculty, students, and staff to contact the Library at knowledge@lib.uchicago.edu to discuss your data management and sharing requirements and to begin depositing scholarly works. Librarians are available for consultations and instructional sessions on the repository for departments and groups on campus.

Knowledge@UChicago is managed and supported by the Library, in collaboration with IT Services at the University of Chicago.

Expanding services for faculty in a changing environment

Brenda L. Johnson

Brenda L. Johnson, Library Director and University Librarian (Photo by John Zich)

Today’s scholarly environment presents an increasing array of challenges and opportunities for faculty and graduate students. New funding agency requirements call on researchers to present advance plans for openly sharing and preserving their data.  Researchers are seeking ways to obtain data in new formats, to visualize information in new ways, and to rescue and share data for new purposes.  Across disciplines, researchers are constantly challenged to find and adopt new tools and techniques. The Library is meeting this challenge by launching new initiatives, developing cutting-edge skills among our librarians, and bringing on new staff members who can assist researchers in this changing scholarly environment.

Stacie Williams

Stacie Williams, Center for Digital Scholarship Director

The Library’s new Center for Digital Scholarship (CDS) will be an umbrella for many of these services, facilitating the analysis of complex data, the visualization of theoretical relationships, the preservation of core research, and the sharing of research results. Stacie Williams, who joined the Library in August as the inaugural CDS Director, brings experience working with researchers in her previous position managing the Freedman Center for Digital Scholarship at Case Western Reserve University. Williams is working with subject librarians and faculty to identify priorities for establishing new spaces, technical infrastructure, and services that meet research and teaching needs.  Following are some of the key areas in which initiatives are already underway.

Data preservation and sharing

Nora Mattern

Nora Mattern, Scholarly Communications Librarian

The Library is expanding Knowledge@UChicago, the University’s digital institutional research repository, to better support the needs of data preservation. Led by new Scholarly Communications Librarian Nora Mattern, the Library is migrating Knowledge@UChicago to a new platform that was initially developed at CERN to support high energy physics. The new Knowledge@UChicago will launch in January and will provide funder-compliant solutions for researchers to share and preserve their code, data, and research results.  Mattern also provides consultations on good data management practices, writing data management plans, and copyright.

The Library is also partnering with the Energy Policy Institute at Chicago (EPIC) to host a Council on Library and Information Resources Postdoctoral Fellow in Energy Economics Data Curation, Ana Trisovic. Trisovic is focusing on the particular challenges EPIC faculty face in collecting and preserving energy data, which is often available only from private industry or difficult-to-use government websites. She will be building a clearinghouse for EPIC’s data to facilitate discovery and reuse, as well as developing solutions for preserving and sharing the code that researchers use to analyze their data. Trisovic will use the skills she gained earning a PhD in Computer Science and her experience developing similar preservation solutions at CERN, applying them to the field of energy economics.

Data acquisition and use

Kristin Martin

Kristin Martin, Director of Technical Services

The challenge of acquiring data for research is shared by many disciplines. For example, the Library subscribes to thousands of electronic books and journals, but researchers interested in data mining these texts cannot easily do so using the vendor’s PDFs, which are intended for individual reading. Kristin Martin, the Library’s Director of Technical Services, excels at working with publishers to provide alternative access that is optimized for data mining.  The Library’s subject specialists can work with faculty across the disciplines and with Martin to seek such alternative access.

Elizabeth Foster

Elizabeth Foster, Social Sciences Data Librarian

Elizabeth Foster, the Library’s new Social Sciences Data Librarian, can take this one step further, not only helping researchers find and acquire relevant data, but also helping them transform that data, for example, by formatting it to match the requirements of a particular tool.  Foster will offer workshops and will be developing data analysis consultation services, with a focus on using R and Stata.

Geospatial analysis

Cecilia Smith

Cecilia Smith, GIS and Maps Librarian

Faculty in many disciplines are exploring the ways spatial and temporal analysis and visualization can be used to gain new insights into their data. Cecilia Smith, the Library’s new GIS and Maps Librarian, can consult on the use of GIS information and geospatial tools to analyze and visualize trends in data from mapping the shifts in the border of the Roman Empire over time, to plotting the incidence of traffic accidents in relation to red light cameras, to mapping the impact of environmental factors on health outcomes, and more.  Read “Opening a GIS Hub at Crerar Library” for more information.

At-risk data and data rescue

Sarah G. Wenzel

Sarah G. Wenzel, Bibliographer for the Literatures of Europe and the Americas

Researchers interested in documenting historical trends are often stymied when early data are in analog formats not conducive to data analysis.  Heritage data–such as weather data and astronomical observations–are often the only evidence remaining of ephemeral or disappearing phenomena.  The Library is currently partnering with the Humanities Division to ensure that the UChicago Digital Media Archive’s linguistic and ethnomusicology recordings made by former faculty are converted from fragile magnetic tape to a digital form that can be used by researchers today. We are also working with the Ivy Plus Libraries on a web archiving project. Sarah G. Wenzel, Bibliographer for the Literatures of Europe and the Americas, co-developed a proposal with a colleague at Columbia University to create a digital archive of comics and artists’ websites.  Currently, more than 150 websites are being actively archived by this project and can be found at archive-it.org/collections/10181.

The expert and talented staff members of the Library are committed to expanding services that meet faculty needs in this changing environment. We look forward to working with you and encourage you to visit our Center for Digital Scholarship web page and to contact your subject specialist, Stacie Williams, or Elisabeth Long, Associate University Librarian for Information Technology and Digital Scholarship, to discuss your research needs.

Scientific reproducibility, data management, and inspiration

“Science moves forward by corroboration–when researchers verify others’ results,” the journal Nature states in its July special edition on Challenges in Irreproducible Research.  “There is a growing alarm about results that cannot be reproduced. . . . Journals, scientists, institutions and funders all have a part in tackling reproducibility.”

Stefano Allesina discusses a data management plan with Elisabeth Long, who points sto the plan on screen.

Librarian Elisabeth Long (left) discusses a data management plan with Professor Stefano Allesina. (Photo by Joel Wintermantle)

Science faculty across the disciplines are increasingly taking up the challenge to publish their research in ways that are more easily reproduced, and librarians are collaborating with these researchers to ensure that rigorously collected data, metadata, and algorithms are preserved and made accessible to the research community.

“Many of these efforts revolve around teaching, planning, and practicing excellent data management throughout the research life cycle, from grant writing to publication,” said Elisabeth Long, Associate University Librarian for Information Technology and Digital Scholarship.  “The University of Chicago Library is offering a growing set of data management research and teaching services that help UChicago scientists win grants and produce and publish reproducible results that will shape the future of their fields.”

Teaching good data management from the beginning

The UChicago Biological Sciences Division recently played a leading part in improving graduate education in its discipline by developing a National Science Foundation-funded course called Responsible, Rigorous, and Reproducible Conduct of Research: R3CR.  All UChicago first-year BSD graduate students are required to take the course, learning how to use current methods in computational biology in an ethical and reproducible way.  Elisabeth Long has partnered with the course’s creators, Professors Victoria Prince, Stefano Allesina, and Stephanie Palmer, to provide a class session that introduces students to the principles of data management in the lab setting.

“Biology produces a lot of data, and we have seen the kind of mistakes that people can make that are terrifying,” Professor Allesina said. “Elisabeth talked a lot about how you make sure that you’re keeping your data safe throughout your thesis research: how you should name your files, where you should save your files, how you make sure they are saved for posterity, and where there are institutional repositories or online repositories where you can publish your data.”

The Library is partnering with researchers across campus to develop practices and tools that can facilitate the kind of recordkeeping and data curation that is currently demanded of scientists.  Librarians are offering workshops and training sessions that prepare University of Chicago students to graduate with exceptional data management and preservation skills.

Electronic lab notebooks and data management plans

This Autumn Quarter, the Library’s new Center for Digital Scholarship begins offering drop-in consultation hours and customized one-on-one sessions to work with faculty on their data management plans, choosing between the University’s Knowledge@UChicago research repository and disciplinary archives for preserving and sharing research outputs.

The Center will also offer advice on selecting and using research management tools such as electronic lab notebooks and the Open Science Framework.  Research management tools provide platforms where faculty can centralize all their research activities, enabling easy file management, version control, protocol sharing, analysis activities, email, and other interactions between members of a lab. “One challenge confronting researchers is choosing from among the many existing systems,” Long said. “The Center for Digital Scholarship’s consultation services can pair librarians with individual faculty members, or bring sessions to your labs to explore the best solution for your particular research scenario.”

When the data don’t stand alone

Complex research workflows that present particular challenges for reproducibility often occur in fields where data are processed multiple times before final analysis. “In such cases, preserving the data alone is insufficient to support reproducibility,” Long explained. “The computational code for processing the data must also be preserved along with its relation to the data at various stages of processing.”

Marco Govoni, a researcher at the Institute of Molecular Engineering and Argonne National Laboratory, has been developing a tool for mapping and documenting these relationships.  Qresp: Curation and Exploration of Reproducible Scientific Papers (at qresp.org) guides the researchers through the process of documenting the relationship between the datasets, scripts, tools, and notebooks that were used in the creation of a scientific paper. Librarians are working with Govoni to explore ways in which the Library could support his work and potentially integrate it with the Library’s new institutional repository platform.

Data and inspiration

In consulting with librarians, faculty sometimes discover unexpected sources of data, inspiring new research projects.  When Long was talking to the R3CR class about data management and how they will submit their dissertations to ProQuest, a national dissertation repository, Professor Allesina began to consider the value its metadata could provide for the study of careers in science.  “There’s a lot of interest in trying to see if we can improve the situation in the sciences by increasing representations, for example, of women or minorities,” Allesina explained, “but one thing that we lack is some sort of longitudinal analysis, because once PhD students are out the door, it’s very difficult to find them again.”

Librarian Nora Mattern, Professor Stefano Allesina, and a sketch of a computational pipeline. (Photo by Joel Wintermantle)

At Allesina’s request, Long put him in touch with the Library’s Director of Technical Services, Kristin Martin, who worked with ProQuest to obtain the name, institution, and year of graduation for dissertation authors from the U.S. and Canada from 1993 to 2015.  He is now planning to combine that metadata with publication data from Scopus to track the length and locations of scientists’ careers in academia.

Such a study raises specific reproducibility challenges.  In working on a grant proposal to the National Science Foundation to support this research, Allesina turned to Nora Mattern, Scholarly Communications Librarian, and Debra Werner, Director of Library Research in Medical Education, for advice on how to integrate proprietary data owned by ProQuest and Scopus into the data management plan.  “How much can you share with other scientists?” Allesina asked.  “Can you share some summary statistics of the data?  Can you share de-identified data? If you imagine that someone wants to repeat my analysis of PhD students, will they have sufficient data?” Mattern and Werner helped him to structure the data management plan and to consider the legal implications.

When Allesina came to the United States from Italy, he was surprised at the role he found librarians taking in the digital age.  “Here librarians are thinking forward,” he said.  “Nowadays we have this mass of information. How do we navigate that? How do we organize it? How do we make it searchable? I am always amazed that people can be so helpful. I was dreaming of this data about PhDs, and I talked to Elisabeth, and she said ‘let me look into that.’ After a few weeks, I got gigabytes of data.”

His advice to colleagues: “Run it by a librarian before giving up.”

To consult with a librarian on data management and scientific reproducibility, talk to your Library subject specialist or email data-help@lib.uchicago.edu.

 

New Library Guide: Data Sources for Empirical Legal Research

Do you have a research hypothesis or question you’d like to test, but aren’t sure about which data to use or even where to begin looking? Thinking about including some empirical analysis in your substantial paper requirement or journal comment, but don’t know where to find the right dataset? Mastering linear regressions or the Monte Carlo method and need more sample data to crunch?

Consult the D’Angelo Law Library’s “Empirical Legal Research: Data Sources & Repositories” guide to help discover the right data for your next empirical project. This periodically-updated research guide compiles and describes a vast array of data sources (available through Library databases or on the open web) on a wide variety of legal and law-related topics, including U.S. and global economics, law enforcement and criminal justice, litigation, intellectual property, civil and criminal case filings/dispositions, bankruptcy, finance, securities filings and enforcement, and U.S. government agency data.

Check back soon for D’Angelo Law Library’s upcoming research guides, “Empirical Legal Research: Tools and Methodologies” and “Empirical Legal Research: Getting Started.