Research

Posts about citation management, library guides, discovery tools such as the Catalog, betas, summer tips for B.A. writers, online portals, tools.

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.  

College Research Week May 13-17

Student browsing the bookstacks.

Develop important research skills by attending College Research Week programs.

2019 College Research Week will take place from May 13-17 in Regenstein Library. College Research Week is a celebration of undergraduate research and creative inquiry at UChicago. This week-long event will include sessions on research skills, resources, and fellowships; undergraduate researcher and graduate student panels; an Undergraduate Research Poster Showcase, and much more!

College Research Week is brought to you by the College Center for Research & Fellowships and The University of Chicago Library. For more information, visit the College Research Week website.

College Research Week Schedule

Monday, May 13: Research Skills and Resources

Session Schedule:

Location: Regenstein, Room 122

10:00-11:30am: Introduction to Research Proposal Design, led by Sandra Zupan, Assistant Director of Fellowships and Research, CCRF
The goal of this session it to build your academic skills in research design, which can help you engage in undergraduate research. First, you will learn about the process of narrowing your interest to a research topic, followed by developing a research question and a literature review. Second, you will learn about the practicalities of data collection and analysis, ethical research practice and presenting the findings of the research.

11:30am-12:30pm: Undergraduate Research Funding, led by Tracy Nyerges, Assistant Director of Research, CCRF
This session will help you navigate the various undergraduate research funding sources available to College students across the disciplines. Whether you are new to research or an advanced undergraduate researcher, we will discuss research grant programs and options to fund academic year and summer research experiences for students in all majors. This session will also offer guidance and resources to assist you in planning for and preparing applications for undergraduate research grants and funding.

Location: Regenstein TechBar Studio Classroom, Room 160

1:00-2:00pm: Sharing and Archiving your Research with Knowledge@UChicago, led by Nora Mattern, Scholarly Communications Librarian, Library
Join the Library for a discussion on the principles of open access, how you can make your research poster or paper available to others, and why you may want to do so. Knowledge@UChicago is a digital repository where University of Chicago faculty and students can share and archive their scholarly work. Bring a laptop or tablet (or borrow one from the TechBar) and spend hands-on time with Knowledge@UChicago.

2:30-3:30pm: Managing Your Data and Files, led by Elizabeth Foster, Social Sciences Data Librarian, Library
Whether your data are digital photos of archival records or spreadsheets, this session will provide you with practical tips for naming, organizing, documenting, storing and preserving your data. Making a plan for managing your data and digital files can save you time and potential headaches in the long-run. In this workshop, we’ll begin creating data management plans for a current project and talk through challenges and lessons you’ve learned about effective strategies for managing your digital files. This session is given Elizabeth Foster, Social Sciences Data Librarian.

4:00-5:00pm: Getting a Head-Start on Your BA, led by Rebecca Starkey, Librarian for College Instruction and Outreach, Library
Are you apprehensive about writing a BA or honors thesis? Don’t worry, there are many resources to support you! Librarian Rebecca Starkey will help you get a head start on your thesis by offering strategies to ease your research and writing. Learn about specialized research tools for your major, methods for locating primary sources at the University and beyond, GIS and data support services, and how to reach the Library experts who can guide you. After the workshop, you’ll be able to take the first steps towards starting this important research project.

Tuesday, May 14: Research Fellowships and Undergraduate Research Scholars

Session Schedule:

Location: Regenstein, Room A-11

10:00-11:00am: International Research through Fulbright, led by Nicholas Morris, Associate Director of Fellowships, CCRF
The Fulbright US Student Program is an opportunity to conduct research, study, or teach English for a year internationally after graduation. Thisinformation session will investigate how you can launch your research interests through a funded, post-graduate grant. In this session, we will review the broad purpose and specific components of the Fulbright Grant, including essays, affiliations, and recommendations. We will identify essential components of previously successful grants and help you envision ways to start approaching the essays.

11:30am-12:30pm: National Science Foundation (NSF) Graduate Research Fellowships, led by Nichole Fazio, Director, CCRF
The National Science Foundation Graduate Research Fellowship (NSF GRFP) program is one of the most robust and well-recognized national fellowships in support of graduate education (STEM and selective Social Science disciplines). This session will introduce students to the basics of the NSF GRFP, with a focus on the application process and what makes for an especially strong application. Students of any class-standing are invited to attend. We strongly encourage 3rd- and 4th-year students intending to submit applications this coming October to attend. 

Undergraduate Researcher Panels:

2:00-3:00pm: Arts & Humanities College Students
Join for this interative panel featuring UChicago undergraduate researchers and creative sholars in the Arts and Humanities. The participating College students will field your questions, talk about their paths and how undergraduate research and creative scholarship has impacted them. This session will be informative to current and future undergraduate researchers and scholars in a variety of Arts and Humanities majors.

3:00-4:00pm: Social Sciences College Students
Join for this interative panel featuring UChicago undergraduate researchers and creative sholars in the Social Sciences. The participating College students will field your questions, talk about their paths and how undergraduate research and creative scholarship has impacted them. This session will be informative to current and future undergraduate researchers and scholars in a variety of Social Sciences majors.

4:00-5:00pm: STEM College Students
Join for this interative panel featuring UChicago undergraduate researchers and creative sholars in STEM. The participating College students will field your questions, talk about their paths and how undergraduate research and creative scholarship has impacted them. This session will be informative to current and future undergraduate researchers and scholars in a variety of STEM majors.

Wednesday, May 15: Research and Your Future

Session Schedule:

Location: Regenstein A-11

11:30am-1:00pm: Graduate Student Panel and Networking Lunch
Join for this interative panel featuring the five current UChicago graduate students listed below from various fields. These graduate students will field your questions, talk about their paths to graduate school and how undergraduate research impacted their journeys. You will also be able to chat with these graduate students further after the panel during lunch. Lunch will be provided so please RSVP for this session

3:30-4:30pm: Navigating the SBS IRB Process, led by Cheri Pettey, Director, Social and Behavioral Sciences IRB
This session will explore the history of the applicable regulations, explain how to determine whether a project constitutes human subjects research requiring review, define the basic review process/requirements, and provide some helpful tips for navigating the process. There will be time for questions and students who have gone through the process are welcome to share their experiences and suggestions.

Thursday, May 16: Research Mentoring and Toolbox Building

Session Schedule:

Location: Regenstein TechBar Studio Classroom, Room 160

10:00-11:00am: Creating a Digital Portfolio to Share and Present your Research and Creative Scholarship, led by Stacie Williams, Director, Center for Digital Scholarship, Library
Digital portfolios or a personal website can help you to showcase your research, communicate your interests, and develop a professional network. In this session, we’ll explore what makes for an effective digital portfolio and consider decisions when crafting an online identity. This discussion will be followed by a tutorial on using WordPress to create a digital site.

Location: Regenstein A-11

11:30-1:00pm: Research Mentor/Student Pairs and Networking Lunch [lunch provided]
Join us for a lunch-time conversation with student and research mentors across the disciplines to learn more about their work. Students will discuss how they connected with their mentors’ project and together they will talk about the process of undertaking their research together. You will also have the opportunity to hear from faculty and scholars across the university community who pursued unconventional career pathways as a result of their research efforts. 

1:30-3:00pm: Research Proposal Writing, led by Sandra Zupan, Assistant Director of Fellowships and Research, CCRF
The goal of this session is to help you produce a persuasive research proposal, which can be used for successful UChicago and external grants, national fellowships and graduate school applications. First, you will learn about the structure and characteristics of persuasive proposals, as well as common areas of weaknesses in research proposals. Second, you will learn how to develop paragraphs, organize text and write in a clear, detailed, precise manner.

3:30-4:30pm: GRD101: Preparing for the Graduate School Application Process, led by Nichole Fazio, DPhil, Director, CCRF: This information session is designed for current undergraduates considering graduate school as a part of an academic and professional trajectory.  Whether you are certain that you will pursue graduate education or are just beginning to consider the possibility, this session will introduce you to a) the general process of investigating options, b) the application timeline, c) common application components, and d) attempt to demystify the application and admission process. This is a general session and open to all disciplines and years.  Note: this will not cover pre-professional application processes specifically (eg medical or law school), although some of the application components like personal statements, letters of recommendation and CVs will be discussed as universal components to all application processes. 

Friday, May 17: Undergraduate Research Support & Showcase and Reception

Session Schedule:

Location: Regenstein TechBar Studio, Room 160

10:00-11:30am: Zotero Drop-In Support
Drop by the TechBar for one-on-one training and support for Zotero, a free citation manager that allows you to organize, annotate, and cite your sources automatically in standard styles (MLA, Chicago, APA, etc.).

Location: Regenstein 122

Research Poster Showcase and Reception

2:00-2:30pm: Opening Remarks
Professor Peggy Mason, Department of Neurobiology
2:30-3:30pm: Poster Showcase
3:30-4:30pm: Reception 

 

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.     

New center fuses media arts, data, and design

A rendering of people workign together in the MADD Center

A rendering of the Media Arts, Data and Design Center, a new collaborative space in the John Crerar Library at the University of Chicago. (Illustration courtesy of Payette Architects )

Partnership across UChicago explores intersection of technology, creativity, and research

The boundaries between art, design, science, and technology are disappearing in a digital world. Today, artists use algorithms, scientists rely on visualization and designers are often focused on helping people navigate new technologies.

At the University of Chicago, the disciplines come together at the Media Arts, Data, and Design (MADD) Center, creating a new collaborative space for experimentation, discovery and impact. The MADD Center will support work by faculty, other academic appointees, students, staff, and community partners through cutting-edge technologies. The 20,000-square-foot center in the John Crerar Library opens February 25.

“Design, as a field, now encompasses the sum of human interactions with the devices, environments, and communities that shape daily life,” said David J. Levin, Senior Advisor to the Provost for Arts. “The MADD Center gives the University of Chicago a space to address these radical changes, assess their wide-ranging consequences, and comprehend the ways that perception, sensation, and experience are being transformed.”

At the MADD Center, there are opportunities to create, study, and learn about critical technologies driving both culture and science, including video games, virtual and augmented reality, data visualization, and digital fabrication. The MADD Center brings together the College, Division of Humanities, Division of Physical Sciences, UChicago Arts and the UChicago Library.

The MADD Center will host five resource labs:

  • An expanded Computer Science Instructional Labs, providing hardware and software for training and education;
  • The Hack Arts Lab, an open-access digital fabrication, prototyping, and visualization facility;
  • The new Weston Game Lab, offering expanded resources for the study, play, and development of analog, electronic, virtual and online games;
  • The Research Computing Center Visualization Lab in the Crerar Library’s Kathleen A. Zar Room, providing new data visualization technology; and,
  • The UChicago Library’s new GIS Hub, enabling geospatial research and learning activities by providing access to geographical information systems software and hardware and an expert GIS and maps librarian who offers consultations and training.

At the MADD Center, classroom and studio spaces support the teaching of Media Arts and Design and Media Aesthetics in the College, electronic music in partnership with CHIME Studios in the Department of Music, and virtual reality and other media courses as part of the new Media Arts and Design minor in Cinema and Media Studies.  In addition, the MADD Center will provide new opportunities for further collaboration with the Logan Center for the Arts, the Polsky Center for Entrepreneurship and Innovation, and many others.

“I am excited about the new opportunities students and faculty in the College and the Humanities will have to work with colleagues in computer science and other areas as we continue to develop new courses in Media Arts and Design and support the many interests of our students and faculty in this area,” said Christopher Wild, Deputy Dean of the College and Humanities Division.

Collaboration Across Creative Forms

The open floorplan and close proximity of MADD Center labs is designed to create opportunities for crossovers and collaboration. Students designing a new board game can create prototypes on the 3D printers at the Hack Arts Lab, while researchers working with the GIS Hub might reveal new insights by visualizing their data on Research Computing Center resources. The MADD Center is located near the new Department of Computer Science offices and laboratories, a science librarians’ research and teaching suite, and the Library’s collections and study spaces at a renovated Crerar Library, creating new, interdisciplinary opportunities across divisions.

“As our world becomes increasingly digital, designers and artists need to become more engaged with technology and technologists need to become more fluent with design, media and the arts,” said Michael J. Franklin, Liew Family Chair of Computer Science. “By co-locating a critical mass of tech-savvy students and faculty with diverse skills and interests across these varied domains, we will facilitate robust dialogue and collaboration as our disciplines continue to co-evolve.”

People working in the Weston Game Lab

The Weston Game Lab will provide a vibrant new space at UChicago for the research and design of games. (Illustration courtesy of Payette Architects)

Gaming, UChicago-Style

The MADD Center is envisioned as a place for a group of students dissecting the structure of a classic Nintendo game, or sketching out the visual design for a new card game that teaches high school students about teen pregnancy. A cornerstone of the new center, the Weston Game Lab will provide a vibrant new space at UChicago for the research and design of the world’s fastest growing cultural and aesthetic form: games.

The Weston Game Lab is supported by a gift from Dr. Shellwyn Weston and Bradford Weston, JD’77. Within the Lab, students, faculty, and staff will collaborate on the research and development of games that produce social impact or experiment with form. Participants will also be able to research the history of games from technical and theoretical perspectives with the Library’s collection of video games and the Logan Center’s collection of consoles, attend workshops that afford new development skills, and organize collaborative groups for game-based experiments.

“Video games in recent years have become an immensely popular medium and multi-billion dollar industry,” said Patrick Jagoda, Associate Professor of English and Cinema & Media Studies and director of the Weston Game Lab. “For cultural, psychological, and sociopolitical reasons, we need rigorous academic study, across both humanistic and social scientific disciplines. I’m interested in growing a culture of thoughtful, ethical, and experimental game design for ends other than entertainment that includes interdisciplinary teams of faculty, staff, and students. I think the University of Chicago can really shine in this space.”

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.

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.

Riccardo Levi-Setti, physicist and paleontologist

Levi Setti

Levi-Setti with some of his trilobites: https://bit.ly/2DRi4sK

Riccardo Levi-Setti, emeritus professor, died earlier this month.  He began his career as a physicist but also went on to research and publish in paleontology.  Born into a Jewish family in Italy, he survived the Holocaust in hiding.  He earned a PhD in physics in 1947 and started his career at the University of Chicago in 1956 as a researcher in particle physics.  He later developed an interest in the extinct sea creatures trilobites and published multiple books on the subject.

 

 

 

 

His books in physics include:

Elementary Particles, Chicago: University of Chicago Press [1965]. Crerar: QC721.L561

Strongly Interacting Particles, Chicago: University of Chicago Press [1973].  Mansueto: QC793.3.H5L6

 

Some of his books in paleontology:

Trilobites: a Photographic Atlas, Chicago: University of Chicago Press [1975]. Crerar: QE821.L65

Trilobites, Chicago: University of Chicago Press c1993.  Crerar: QE821.L460 1993.

More of his books in the Library: https://catalog.lib.uchicago.edu/vufind/Search/Results?type=AuthorBrowse&lookfor=%22Levi-Setti,%20Riccardo%22

His papers are also held in the Library’s Archival Collections: http://pi.lib.uchicago.edu/1001/cat/bib/8448151

University of Chicago News obituary

Setti-Levi in the university’s Cyclotron pit. https://bit.ly/2SbRjlV

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.