FSCI Course Abstracts
FSCI Course list with links to individual abstracts posted here.
AM1 – Inside Scholarly Communication Today
Instructors:
- Cameron Neylon, PhD, Professor of Research Communications, Centre for Culture and Technology, Curtin University
- Nicky Agate, PhD, Assistant Director, Scholarly Communication and Digital Projects, Columbia University Libraries
Course Chair: Cameron Neylon
Course Syllabus
Description: This course will provide an overview of the Scholarly Communications landscape of today, how we got here, and what we can tell about the current state of the field and how it is changing. The course will provide participants with a broad background on key topics along with knowledge of additional information sources to investigate issues further.
The course will provide a history of scholarly publishing and discussion of the information landscape, data availability, the economics of publishing, and issues surrounding peer review. We will offer a broad overview of major trends into the future, but the focus is primarily on how things are.
There will be four half-day sessions offering a mix of lecture and practical work, particularly information gathering and analysis. The emphasis will be on providing frameworks within which information can be gathered and understood rather than on “fact teaching.”
Proposed Level: Beginner
Intended Audience: The course is aimed at people wanting an overview of the Scholarly Communications landscape and how it has evolved as a starting point for further exploration. This includes those interested in careers in Scholarly Communications in libraries, publishing or other areas; final-year undergraduates and early PhD students in general; research leaders who need an overview of our existing system; and researchers looking to expand their view from their existing disciplinary experience.
Requirements: There are no specific requirements. Readings will be given and some work will be done in documents during the course, so laptops or other devices will be useful but not essential.
AM2 – Author Carpentry: Writing a Research Compendium and the Future of Scientific Reporting
Instructors:
- Thomas Morrell, Research Data Specialist, Caltech Library
- Donna Wrublewski, PhD, Chemistry and Biology Librarian, Caltech Library
Course Chair: Thomas Morrell
Course Syllabus (will be posted June)
Description: Almost two decades ago, computational biologists Robert Gentleman and Duncan Temple Lang proposed a new paradigm for research communication – the research compendium combining text, data, and the code used for analysis (https://biostats.bepress.com/bioconductor/paper3/; https://github.com/ropensci/rrrpkg). They envisioned that a digital compendium of scientific outputs, packaged for inspection, reuse, and publication, could replace the static paper (whether analog or PDF) as a more meaningful and useful research report.
In this workshop, we will explore the paradigm of the reproducible research compendium in three ways:
- by reading and discussing work of Gentleman and Temple Lang;
- by hearing from modern-day followers of the compenium movement (the rOpenSci community, among others);
- by creating a sample mini-compendium in the R environment and publishing it to the web.
R Markdown is an open, powerful, and easy-to-use authoring syntax for combining text, code, figures, and other document features needed for publication, presentations, and websites. Researchers across the disciplines are shifting to this approach, allowing them to “author once” and output to many, and also to create fully open and reproducible reports for human and machine reading and reuse. Participants will gain proficiency authoring a mini-compendium in R Markdown using packages created or adopted by the rOpenSci community, as well as “container technology” such as Docker and Binder.
Combining presenter demonstrations, hands-on sessions, and expert guest lectures, the interactive sessions will take authors step-by-step through a workflow using readily available applications and proven recipes.
Proposed Level: Intermediate
Intended Audience: Participants should be proficient in Windows, Mac, or Linux OS. They should also be able to locate and install pre-compiled open-source software; have experience authoring and publishing research communication; be familiar with the command line; and be fearless about learning enough about the R software environment to follow step-by-step instructions.
Requirements: Students will be required to bring a laptop with R and R Studio installed, along with some R packages. Detailed installation instructions will be provided.
AM3 – Research Reproducibility in Theory and Practice
Instructors:
- Anita Bandrowski, PhD , SciCrunch and University of California, San Diego
- Daniel S. Katz, PhD, Assistant Director for Scientific Software and Applications, National Center for Supercomputing Applications and Research; and Research Associate Professor in Information Sciences, Computer Science, and Electrical and Computer Engineering, University of Illinois Urbana-Champaign
Course Chair: Anita Bandrowski
Description: This course will focus on issues of reproducibility in research from a broad perspective. It will include an introduction to the differing types of reproducibility and a discussion of new grant review guidelines and the philosophy that underpins them.
The course will look at reproducibility in several contexts, including collecting and communication in experimental research, providing a robust record of computational research, and the limitations and debates around these approaches. We will introduce several tools and approaches to support reproducible research practice, including the RRID portal, Zenodo, Jupyter Notebooks, and best practice in research and data management, communication, and open sharing.
There will be four half-day sessions offering a mix of lecture and practical work, particularly information gathering and analysis. The emphasis will be on providing frameworks within which information can be gathered and understood rather than on “fact teaching.”
Proposed Level: Beginner
Intended Audience: The target audience is researchers seeking a deeper understanding of reproducibility in a variety of contexts, as well as those with a need to support researchers – for example, staff from research offices, libraries, service providers, or publishers. Participants should be seeking an introduction to working toward reproducibility in practice and to the tools that can support them in doing this.
Requirements: Participants should have basic computer skills and a laptop.
AM4 – Working with Scholarly Literature in R: Pulling, Wrangling, Cleaning, and Analyzing Structured Bibliographic Metadata
Course Chair / Instructor: Clarke Iakovakis, Scholarly Services Librarian, Oklahoma State University
Description: Developers have created a number of packages for accessing the scholarly literature in R over the last several years, among them rcrossref, rorcid, and roadoi. These packages make use of the APIs in their systems to allow users to execute specific queries and pull the structured data into R, where it can be reshaped, merged with other data, and analyzed.
This session will assume no experience with R, and so will begin with a general introduction to R and the R Studio environment, based partly on my “Introduction to R for Libraries” ALCTS webinar series: http://www.ala.org/alcts/confevents/upcoming/webinar/IntrotoR. This introduction will include reading data into R, installing packages, some functions for cleaning and restructuring data, and basics of visualizing data. Participants will be provided prewritten R scripts as well as explanatory handouts for each section of the course. This not only will help them ease into using R, but will serve as a resource in the future.
As participants become more comfortable using R, we will introduce some of the packages that allow us to access the scholarly literature. rcrossref interfaces with the CrossRef API, allowing users to pull article metadata based on DOIs, keywords, funders, authors, and more. This can be immensely powerful for collecting citation data, conducting literature reviews, creating bibliographies, and more. rorcid interfaces with the ORCID API, allowing users to pull publication data based on a specific ORCID iD, or to input names and other identifying information to find a specific individual’s identifier. Finally, roadoi interfaces with Unpaywall, allowing users to input a set of DOIs and return publication information along with potential locations of open access versions. As we work through the packages, participants will continue to learn R functions for working with data, including dplyr, purrr, and tidyr.
By the conclusion of the session, participants will be able to work with and analyze data in R, and will be familiar with the major functions in each of the listed packages. On a deeper level, they will have more powerful tools for gathering subsets of the scholarly literature in clean and structured formats based on specific parameters.
Proposed Level: All levels
Intended Audience: While some experience working in R will be helpful, this session will assume no knowledge of R. Preparatory work is not required, but it may be useful for participants to download R and R Studio, install the swirl package (https://swirlstats.com/students.html), and run through those exercises in order to get a baseline level of preparedness.
Requirements: Students will be required to bring a laptop with R and R Studio installed, and a few packages installed as well. I will provide detailed installation instructions.
AM5 – FAIR Data in the Scholarly Communications Life Cycle
Course Chair / Instructor: Natasha Simons, Associate Director, Skilled Workforce, Australian Research Data Commons
Description: This course will focus on FAIR research data management and stewardship practices. It will provide an understanding of FAIR (Findable, Accessible, Interoperable, and Reusable) data and how it fits into scholarly communication workflows. Through hands-on exercises, group discussions and presentations, participants will learn about the FAIR Data Principles and how they can be applied in practice.
Good data stewardship is the cornerstone of knowledge, discovery, and innovation in research. The FAIR Data Principles address data creators, stewards, software engineers, publishers, and others to promote maximum use of research data. In research libraries, the principles can be used as a framework for fostering and extending research data services.
This course will begin with an overview of the FAIR Data Principles and the drivers behind their development by a broad community of international stakeholders. Over four half-day sessions, we will explore a range of topics related to putting FAIR data into practice, including how and where data can be described, stored, and made discoverable (e.g., data repositories, metadata); methods for identifying and citing data; interoperability of (meta)data; best-practice examples; and tips for enabling data reuse (e.g., data licensing). Along the way, we will get hands-on with data and tools. There will be opportunities for participants to learn from each other and to develop skills in data management and expertise in making data FAIR.
By the end of the course, participants will be able to:
- Articulate drivers, barriers, and challenges for enabling FAIR data.
- Understand how FAIR data fits into the scholarly communications life cycle.
- Refer to hands-on experience with techniques and tools for making data FAIR.
- Identify best-practice examples of FAIR data.
Proposed Level: Beginner to intermediate
Intended Audience: The course is aimed at individuals working with or expecting to work with data as researchers, publishers, librarians, or in research support, especially those seeking to develop their skills in managing FAIR data in practice and to understand the tools that can support them in doing this.
Requirements: There are no special requirements for the course.
AM6 – When Global is Local: Open Scholarly Communication in the Global South
Instructors:
- Gimena del Rio Riande, PhD, Researcher, Instituto de Investigaciones Bibliográficas y Crítica Textual (IIBICRIT), National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina
- Idowu Adegbilero-Iwari, Library Coordinator, Elizade University, Ilara-Mokin, Nigeria
- Samir Hachani, Lecturer, Algiers University, Algeria
- Daniel O'Donnell, PhD, Professor of English, University of Lethbridge, Canada
Course Chair: Gimena del Rio Riande
Description:
This course will examine the practices and experiences of open scholarly production and knowledge exchange in the Global South, focusing especially on open initiatives in Latin America and Africa.
Free and immediate Open Access is now established in Latin America and the Caribbean as the most prevalent communication model in the academic community, as a method for (trying) to give visibility and value to scientific production at a regional and global level. Also, in Africa, scholarly communication in the Open Access era is facing challenges in relation to its place in the global scholarly communication environment. However, these regions still deal with difficulties that need to be tackled in order to consolidate Open Access and make it fully interoperable with global models.
The course will review these challenges and will highlight initiatives and explore options to advance Open Access in these Global South countries. We will look at national laws on Open Access and specific cases that illustrate its progress and the obstacles it has faced. The course will also present a practical approach to deal with the “different open accesses in the world.” We will examine the impediments Open Access faces in these countries using key statistics such as internet penetration rate, progress on the internet, bandwidth, and presence on Open Access sites (ROAR, DOAR, DOAJ, etc.).
Finally, the course will put Open Access to publications and to research data in the context of the larger Open Science movement. The emphasis will be on the local contexts and relevancies of participation and impact, including those related to publication; technology; access and reuse; dissemination and outreach; funding; credit and attribution; and evaluation.
The course will support a critical examination of the epistemological, geopolitical, spatial, technological, and economic status of the Global South, as well as strategies for positively transforming and opening Scholarly Communications on a global scale in ways that eliminate systematic and biased understandings of participation and success.
There will be four half-day sessions offering a mix of lecture and practical work, particularly information gathering and analysis. The emphasis will be on providing frameworks within which information can be gathered and understood rather than on “fact teaching.” We will encourage participants to engage reflectively with the material, bringing their own experiences to bear.
Proposed Level: Beginner
Intended Audience: Information professionals, researchers, students, and anybody interested in innovation in scientific information from all disciplines are invited to participate in this workshop. The course may also be of interest to those who want to build an understanding of Scholarly Communications in the Global South to meaningfully address (and cease contributing to) inequities, and to allow successful collaborations.
Requirements: No previous knowledge or experience in the topic is needed. Preparatory work won't be required, but we will offer suggested material for participants to read and watch before the course. Students don't need any special equipment, just laptops, and access to the internet.
AM7 – How To Introduce and Implement Policy in Your Institution and Still Have Friends Afterwards
Course Chairs / Instructors:
- Sarah Shreeves, Vice Dean, University of Arizona Libraries
- Danny Kingsley, PhD, Scholarly Communication Consultant, Brisbane, Australia
Description: We face multiple challenges as we develop and implement institution-wide policies to help support an open and information-rich future within our universities. Our ability to work across multiple complex units within the university, to align our priorities and interests, and to understand how decisions are made within our institutions is critical to the success and sustainability of policies and the infrastructure needed to support them.
This course offers an opportunity to engage deeply in how policies and supporting implementing structures are developed, agreed upon, and sustained. Participants will share practice and experiences to broaden the discussion and help find commonalities. Throughout the course, we will be using a range of teaching and workshop tools that in themselves can be repurposed by participants for sessions they might wish to run subsequent to the course.
Proposed Level: All levels
Intended Audience: There are no prerequisites for this course. We believe the course will be useful for a range of roles and participants – anyone who wants to reflect on and improve how policy is set and implemented at the organizational level.
Requirements: We will ask that participants do some pre-work identifying their own institutional structures and workings.
AM8 – Help! How Do I Build Community and Bring About Culture Change for Open Science in My Organization?
Instructors:
- Lou Woodley, Director, CSCCE (Center for Scientific Collaboration and Community Engagement), American Association for the Advancement of Science
- Bruce Caron, PhD, Research Director, New Media Research Institute, Santa Barbara
Course Chair: Lou Woodley
Description: We frequently hear about the need for culture change to make science more accessible, reproducible, and collaborative. These moves toward open science may occur at a grassroots or local level, within the institutions where we work, and more globally across the academy. Wherever it occurs, at the heart of culture change is the adoption of new behaviors that become increasingly supported and reinforced by the group or community. So culture and community are tightly linked.
In this course, we’ll explore what it takes to be a culture change agent, drawing on thinking about culture, community, and systems thinking. If you’ve ever been frustrated by attempts to co-create with others, been puzzled about why new ideas aren’t implemented more rapidly, or struggled to gain stakeholder buy-in, this course is for you!
Via discussions, sharing of models, and practical activities, participants will gain an increased awareness of the culture(s) at play in their own professional lives as well as methods to experiment with and implement new ways of working together more collaboratively.
Topics covered will include:
- How do I recognize culture in my own professional context(s)?
- How do I set up a project for successful community participation from the outset?
- How do I (with others) intentionally change institutional cultural practices to foster open science?
- What role can I play in brokering trust, building engagement, and reviewing success of a community-based project?
- How do I identify the factors that may be blocking a group project – and understand why?
Proposed Level: All levels
Intended Audience: The course is aimed at anyone interested in promoting open science.
Requirements: Participants are expected to have read Module 1 of the Open Science MOOC: https://opensciencemooc.eu.
AM9 – Scholarly Reputation Management in a World of New and Evolving Media
Instructors:
- Christine George, Faculty & Scholarly Services Librarian, Dr. Lillian & Dr. Rebecca Chutick Law Library, Benjamin N. Cardozo School of Law
- Bruce Herbert, PhD, Director, Office of Scholarly Communication, University Libraries, Texas A&M University
- David Hubbard, Associate Professor, University Libraries, Texas A&M University
Course Chairs: Christine George, Bruce Herbert
Description: Academic organizations have embraced scholarly metrics and research analysis as a part of accountability initiatives. This has led to the use of a limited set of metrics that often favors specific disciplines and types of academic work. How can faculty, centers, departments, and colleges construct rich narratives of the impact of their work? And how can those who are at a disadvantage with traditional metrics develop narratives that highlight the rich diversity of their work?
The answer may lie in drawing on altmetrics – alternative methods for calculating scholarly impact. However, altmetrics are only a part of the answer. Faculty engaging in scholarly publishing need an online presence through both scholarly profiles and social media. With the rapid dissemination of information, it’s important not just to make scholarly work available via open access, but to have the authors drawing people to their scholarship. An online presence brings a new set of challenges. Scholarly profiles must be created or claimed and maintained. Training academics to optimize their work via social media can have any number of hurdles such as grasping platform logistics, adapting thoughts to character limits, and managing flame wars or trolling. There are different levels of engagement, and there is no set way for an academic to be on social media.
This course is aimed at those engaging in scholarly publishing and the librarians, scholarly communication officers, and others who offer support within their institutions.
Proposed Level: Beginner to intermediate
Intended Audience: A basic understanding of Twitter and Instagram is helpful. The course is geared mostly toward faculty, researchers, librarians, and other information professionals engaging in scholarly communication.
Requirements: Participants in this workshop will need a laptop that is Wi-Fi enabled. FSCI strongly recommends setting up Eduroam (https://www.eduroam.org/) at your home institution, as it is the most secure and reliable available wireless network though there is an open freely available wireless network on the main campus (UCLA_WEB). Install VOSviewer (http://www.vosviewer.com/), a freely available software tool, on your laptop. There is a web version of VOSviewer that might suffice if installation is not possible. Any data or access to other resources will be provided.
PM – A1 (Repeats Session B) – The Scientific Paper of the Future
Instructors:
- Deborah Khider, PhD, Data Scientist, Information Sciences Institute, University of Southern California
- Daniel Garijo, PhD, Computer Scientist, Information Sciences Institute, USC
- Yolanda Gil, PhD, Research Professor of Computer Science and Spatial Sciences, USC Viterbi School of Engineering
Course Chair: Deborah Khider
Description: This course covers best practices in reproducible research, open science, and digital scholarship that help researchers increase citations for their papers; get credit for all their research products; augment their vitae with data and software that they have written; write compelling data management plans for funding proposals; comply with new funder and journal requirements; and practice open and reproducible science.
We will begin with a motivation for authors through an overview of why scientists, publishers, funders, and the public care about science practices. Next, we will describe how to make research data accessible through publication in a public repository, including metadata and a license for reuse, and how to make data citable using a unique and persistent identifier. We will then show how to make software accessible by making it available in a public repository with a license and a unique and citable persistent identifier.
We will also cover how to document in a software registry key information that helps others reuse research software. We will then discuss how to document provenance and methods by explicitly describing related computations and outcomes in a workflow sketch, a formal workflow, or a provenance record, possibly with a persistent identifier. Finally, we will provide a summary checklist for authors and show how they can manage their scholarly identity, reputation, and impact throughout their careers.
Proposed Level: All levels
Intended Audience: The course will be of interest to graduate students, research scholars, principal investigators, lab and institute directors, and librarians.
Requirements: Participants will need a laptop.
PM – A2 (Repeats Session B) – Evaluation of Scholarly Works: Current Practices and Consequences of Plan S
Instructors:
- Tom Olyhoek, PhD, Editor-in-Chief, Directory of Open Access Journals
- Ivonne Lujano, DOAJ Ambassador for Latin America
Course Chair: Tom Olyhoek
Description: Reliable information about the quality of scholarly communication channels, journals, and platforms is vital to scholars, librarians, funders, and many other parties. Different indexing services use different sets of criteria to assess the quality of journals and platforms. In this course, participants will learn the difference between criteria used in Scopus (Elsevier), Web of Science (Clarivate), and the Directory of Open Access Journals (IS4OA, Infrastructure Services for Open Access).
We will discuss the advantages and disadvantages of ranking, impact factors, and other more recent tools.
Peer review is often cited as the main quality instrument for the evaluation of scholarly output. In this course, we will discuss the performance of conventional methods of peer review and new developments in this area.
Another important topic we will discuss is the relative importance of questionable publishers. We will show that questionable publishing is a) not a big problem and b) not a problem linked to open access journals. A more realistic picture of the problem will be given using the examples of recent articles in the popular press.
Specific time will also be reserved to discuss evaluation of the quality of journals publishing social sciences and humanities content.
The second day of this course will be dedicated to talking about new criteria for evaluating the quality of journals, notably the consequences of Plan S, an initiative for open access publishing launched in September 2018, and to discussing the virtues of new forms of publishing, like preprints and library publishing.
Proposed Level: Intermediate
Intended Audience: The course is intended for all scholars, librarians, funders, and other parties with interest in open access.
Requirements: There are no special requirements for this course.
PM – A3 – Losing Our Scholarly Record and What To Do About It
Course Chair / Instructor: Martin Klein, PhD, Research Library, Los Alamos National Laboratory
Description: Most aspects of scholarly communication happen on the web. The dissemination speed of scholarly knowledge has dramatically increased because of the publishing and accessing of information on the web. However, this environment also poses challenges, as, increasingly, authors reference “web at large” resources such as project web sites, scholarly wikis, ontologies, online debates, presentations, blogs, and videos in their scholarly articles.
While these resources are referenced to provide essential context for the research, they are, just like any other web resource, subject to the dynamic nature of the web and hence likely to disappear or significantly change over time. For scholarly journal articles, we enjoy the benefits of archival systems such as LOCKSS and Portico, but we have no orchestrated preservation infrastructure for “web at large” resources. These observations raise significant concerns regarding the long-term integrity of the web-based scholarly record.
This course aims at outlining the extent of this reference rot problem and how it impacts our ability to revisit web content cited in scholarly articles some time after their publication. The course will also provide participants with an overview of and hands-on experience with approaches and tools available to authors, archivists, librarians, publishers, and others to address this problem.
Proposed Level: All levels
Intended Audience: This course is targeted at scholars, librarians, archivists, and publishers at all levels.
Requirements: The course does not require any special technical equipment or software. However, participants will benefit from having internet-connected laptops or desktop computers available.
PM – A4 – Rethinking Research Evaluation, or How To Start a Campus Conversation About Measuring What You Value Rather Than Valuing What You Can Measure
Course Chair / Instructor: Nicky Agate, PhD, Assistant Director, Scholarly Communication and Digital Projects, Columbia University Libraries
Description: Why do some research outputs “count” and others don’t? Why are single-authored articles in closed-access publications and citations in scholarly literature rewarded above collaborative, innovative projects: open-access writings, projects that bring traditionally underrepresented voices to the table, publicly engaged scholarship, and inclusion in syllabi?
Research assessment so often becomes a numbers game that provides perverse incentives to academics to treat graduate students horribly, steal each other’s ideas, denigrate competitors’ research in peer review – or openly ridicule earnest peer review of hoax papers. The system allows academics to cite only their friends, insist an entire cohort of PhD students cite them in every work, make undergraduates buy their $250 book, or change their research to suit the metrics. But if researchers are evaluated on the end products of their research alone, then how they achieve those products doesn’t matter – the end justifies the means.
Most metrics currently in use are all about the end product rather than the process of research. They represent a numbers game that has everything to do with quantity and little to do with quality. Striving to win at that game often causes scholars to ignore the kinds of collaborative, interdisciplinary, mentoring, or public projects that enrich the academic community as a whole.
On the first day of this course, we will begin by discussing how a change in incentives is necessary to bring about a change in behavior, highlighting several recent initiatives that seek to redress the inequities of article-slanted impact factors and citation scores in favor of more transparent, diverse, and ethical indicators of research assessment (DORA, EvalHum, HumetricsHSS). Participants will be asked to put their cynicism aside and to consider the academy as a locus of shared, if debatable, values. What would a more diverse, more open, more equitable research landscape look like?
On Day 2, using the HuMetricsHSS framework as a guide, participants will work alongside others to argue for, negotiate, and perhaps reformulate their own values to emerge in a space of productive compromise that could form the basis of a new kind of research evaluation. They will then work in small groups to interrogate how that negotiated set of values might be enacted in the processes and production of research writ large – and how such a performance of those values might be assessed. The goal is to model an approach to beginning a conversation about shared values, and values-based evaluation, that could be replicated in a participant’s own department or institution.
Proposed Level: All levels
Intended Audience: The course is intended for librarians, researchers, faculty members, chairs, and deans. It will be of particular interest to those involved with research evaluation, reforming tenure and promotion, recognition of digital and nontraditional forms of scholarly communication, and transforming the culture of higher education.
Requirements: Some advance reading will be required.
PM – A5 – Understanding Copyright: Vital Skills for Navigating Scholarly Communications
Instructors:
- Heather Briston, Head of Curators and Collections and University Archivist, University of California Los Angeles
- Martin Brennan, Scholarly Communication Education Librarian, University of California Los Angeles
Course Chair: Heather Briston
Description: In order to navigate the issues of scholarly communications, every participant in this environment needs to understand the issues in both copyright and privacy/confidentiality, and how they affect scholarship. This course is designed first to provide a basic understanding of the mechanics of copyright law, with a focus on U.S. copyright law but with some exploration of differing application internationally. We will detail the “bundle of rights” inherent in copyright law, as well as review the pertinent exceptions within the law that allow reuse without permission, with a particular emphasis on Fair Use. We will also explore how distinct legal issues of privacy and confidentiality can further complicate the situation, with tips on addressing these issues.
Then we will interactively explore how copyright concerns come into play in the production and dissemination of scholarly work, with a special focus on the move toward openness. Working with their peers, participants will explore scenarios that address common instances of copying, adaptation, publishing, and dissemination within the realm of scholarly communication.
After participating in this session, participants will be able to identify and understand copyright and intellectual property issues as they arise, and will be empowered by a set of tools and resources to address those issues directly when possible. Participants also will be better prepared to articulate their concerns when working with collaborators or legal counsel or within their organizations.
Proposed Level: All levels
Intended Audience: No formal training in copyright is required, but participants will be given training materials to review prior to the course to allow for greater depth in class.
Requirements: Participants should bring their own laptop.
PM – A6 – Managing, Exploring, and Sharing Data with Dataverse
Instructors:
- Gustavo Durand, Technical Lead and Architect, Dataverse, Institute for Quantitative Social Science, Harvard University
- Julian Gautier, Product Research Specialist, Institute for Quantitative Social Science, Harvard University
Course Chair: Gustavo Durand
Description: As data becomes more critical in today’s research, institutions need to provide services for management, exploration, and sharing of data. Data sharing, as the Research Data Alliance defines it, is “the release of research data, associated metadata, accompanying documentation, and software code for re-use and analysis in such a manner that they can be discovered on the web and referred to in a unique and persistent way.”
Dataverse is an open source web application platform to share, preserve, cite, explore, and analyze research data. It facilitates making data available to others and allows a researcher to replicate others’ work more easily. Researchers, journals, data authors, publishers, data distributors, and affiliated institutions all receive academic credit and web visibility.
This course will introduce the Dataverse Project, discussing the project to date and highlighting several recent and upcoming features: the ability to capture provenance metadata, uploading of code from a Github repository, support for working with big data, the modular tool framework for exploring data with external tools, and sensitive data support with Data Tags.
The instructors will also discuss the Dataverse Community as a whole and how anyone can contribute to the project, from documentation to bug fixes to new functionality. Lastly, the class will discuss what data repositories of the future, and Dataverse specifically, should look like.
The course will combine lectures and hands-on work to walk participants through the process of managing, exploring, and sharing datasets with this framework. At the end of this course, each participant will have a clear understanding of the benefits of using a data sharing platform and direct user experience with Dataverse’s approach to addressing these needs.
Proposed Level: All levels
Intended Audience: This course is for researchers, publishers, and repository managers. It does not require any specialized knowledge.
Requirements: Students should bring their own laptops; no special software is needed besides a browser.
PM – A7 – Educating the Next Generation of Open Scholars: Approaches, Tools, and Tactics
Course Chair / Instructor: Robyn Hall, Scholarly Communications Librarian, MacEwan University, Edmonton, Canada
Description: Those who teach and work with students at the undergraduate and graduate level can play an important role in shaping the future of scholarly communications. Drawing students’ attention to the myriad of ways that research and scholarship can be shared openly online can provide valuable opportunities for students to disseminate their own work, engage with the work of others, and develop copyright literacy and improved academic writing and communication skills. Additionally, exposing students to the socioeconomic processes that shape access to knowledge can influence how these budding academics approach scholarly activity and where they choose to publish in their future careers.
On the first day of this course, participants will be asked to reflect upon their own early experiences with scholarly communications and how these have shaped their professional values and practices concerning both teaching and research. As a group, we will then explore and discuss a variety of assignment designs and initiatives from across disciplines that have engaged students with areas of scholarly communications, open pedagogy, and open science, and review some easy-to-use, free software tools and platforms that can facilitate these activities.
On Day 2, participants will have the opportunity to begin building their own assignment, initiative, workshop, or lesson plan that aims to give students experience with open practices and educate them on scholarly communications topics and issues. By the end of this course, participants will have constructed a comprehensive and actionable plan to involve students with open research practices that will both benefit student learning presently, and contribute positively to the future of academic publishing and research dissemination.
Proposed Level: All levels
Intended Audience: This course is for anyone with an interest in educating and engaging students at both the undergraduate and graduate level with the scholarly communications landscape. This includes faculty instructors, graduate students, and academic librarians. Course participants should have a basic understanding of academic publishing and open access.
Requirements: While there are some recommended readings for this course, no preparatory work is required. Participants will need to bring a web-enabled device, preferably a laptop or a tablet.
PM – A8 – Introduction to Open-Knowledge Research
Instructors:
- Ricardo Hartley, PhD, Researcher and Teacher, Universidad Central de Chile
- Martin Perez Comisso, PhD student in Human and Social Dimensions of Science and Technology, Arizona State University
Course Chair: Ricardo Hartley
Description: This course will provide an overview of open-knowledge research, tackling the research design process and considering the epistemological boundaries and evaluation of the process.
The course will provide participants with a broad background on key topics along with knowledge of additional information sources to investigate issues further, considering their historical context, policies, and strategies. The course will also include an open discussion of relevant papers as integrative work.
There will be two sessions offering a mix of lecture and practical work, particularly on information gathering and analysis. After completing the course, participants will be able to:
- Summarize the stages of the research design process.
- Assess tools and strategies to implement research in the open-knowledge field, including policy analysis, content evaluation, scientometry, and data visualization.
- Articulate research questions and strategies to propose a research project in the field of open knowledge.
- Evaluate global contemporary journals, conferences, and research outputs available in the field.
Proposed Level: All levels
Intended Audience: The course is intended for graduate students and faculty researchers wishing to extend their research on topics related to open knowledge.
Requirements: Participants will need a laptop or tablet for web browsing.
PM – A9 – Laboratory Forensics: An Assessment Approach to Data Management in Research Labs
Course Chair / Instructor: Armel Lefebvre, PhD candidate in Research Data Management, Utrecht University, Netherlands
Description: Many research data management initiatives from funders, publishers, and universities focus on the open dissemination of research data to advance reproducibility and reusability of scientific results. At the same time, researchers find data dissemination unrewarding, time-consuming, and unnecessary if it is not mandatory to get articles published. What makes the dissemination of research data a challenge for researchers may also, partially, be explained by the basic storage technology frequently used in research laboratories: hierarchical file systems with digital files and folders.
This course will explore how locally preserved experimental evidence can be reconstructed from the corresponding publication(s). We will also explore how incomplete or fuzzy evidence left by experimentation processes in laboratories can potentially be corrected by engaging with researchers about the issues identified during the investigation of their storage systems. Therefore, research data management and data availability can benefit from “laboratory forensics” to improve critical aspects of preserved experimental evidence.
At the end of the course, participants will have basic knowledge of how to use forensic techniques to explore digital file systems.
Proposed Level: All levels
Intended Audience: This course is suitable for beginners, and everyone is welcome. For the first part, participants will receive material such as lists of file paths and Python scripts (in Jupyter Notebooks). The course requires virtually no knowledge of Python, although students with advanced Python skills will have the opportunity to explore extra material and assignments to keep them interested and busy. The second part focuses more on organizational issues of research data management, which everyone can discuss based on their own experience in data management, stewardship, curation, and publication.
Requirements: A preselected set of publications will be used, so no preparatory work is required. However, participants who have access to real data from their research groups will be invited to use that data during the course if possible. Students need to bring a laptop with Python installed. WinPython (for windows users) and Anaconda both have a Jupyter Notebook server installed.
PM – A10 – Digital Authoring in Scalar
Course Chair / Instructor: Curtis Fletcher, PhD, Associate Director of the Ahmanson Lab, Sidney Harman Academy for Polymathic Study, University of Southern California Libraries
Description: This two-day workshop is designed for scholars, students, and others who wish to compose a project or publication in Scalar and seek training in the platform. The workshop will include basic, intermediate, and advanced training sessions in Scalar. The workshop will also help participants to think through the conceptual, structural, and technical aspects of building digital projects and to situate their own project within the emergent field of digital media and scholarship.
Scalar is a free, open source authoring and publishing platform designed for scholars writing media-rich, born-digital scholarship. Developed by The Alliance for Networking Visual Culture, Scalar allows scholars to assemble media from multiple sources and juxtapose that media with their own writing in a variety of ways. Scalar makes it possible to structure essay- and book-length works in ways that take advantage of the unique capabilities of digital writing, including nested, recursive, and non-linear formats.
Proposed Level: All levels
Intended Audience: This two-day workshop is designed for scholars, students, and others seeking training in Scalar.
Requirements: No prior experience or preparatory work is required.
PM – B1 (Repeats Session A) – The Scientific Paper of the Future
Instructors:
- Deborah Khider, PhD, Data Scientist, Information Sciences Institute, University of Southern California
- Daniel Garijo, PhD, Computer Scientist, Information Sciences Institute, USC
- Yolanda Gil, PhD, Research Professor of Computer Science and Spatial Sciences, USC Viterbi School of Engineering
Course Chair: Deborah Khider
Description: This course covers best practices in reproducible research, open science, and digital scholarship that help researchers increase citations for their papers; get credit for all their research products; augment their vitae with data and software that they have written; write compelling data management plans for funding proposals; comply with new funder and journal requirements; and practice open and reproducible science.
We will begin with a motivation for authors through an overview of why scientists, publishers, funders, and the public care about science practices. Next, we will describe how to make research data accessible through publication in a public repository, including metadata and a license for reuse, and how to make data citable using a unique and persistent identifier. We will then show how to make software accessible by making it available in a public repository with a license and a unique and citable persistent identifier.
We will also cover how to document in a software registry key information that helps others reuse research software. We will then discuss how to document provenance and methods by explicitly describing related computations and outcomes in a workflow sketch, a formal workflow, or a provenance record, possibly with a persistent identifier. Finally, we will provide a summary checklist for authors and show how they can manage their scholarly identity, reputation, and impact throughout their careers.
Proposed Level: All levels
Intended Audience: The course will be of interest to graduate students, research scholars, principal investigators, lab and institute directors, and librarians.
Requirements: Participants will need a laptop.
PM – B2 (Repeats Session A) – Evaluation of Scholarly Works: Current Practices and Consequences of Plan S
Instructors:
- Tom Olyhoek, PhD, Editor-in-Chief, Directory of Open Access Journals
- Ivonne Lujano, DOAJ Ambassador for Latin America
Course Chair: Tom Olyhoek
Description: Reliable information about the quality of scholarly communication channels, journals, and platforms is vital to scholars, librarians, funders, and many other parties. Different indexing services use different sets of criteria to assess the quality of journals and platforms. In this course, participants will learn the difference between criteria used in Scopus (Elsevier), Web of Science (Clarivate), and the Directory of Open Access Journals (IS4OA, Infrastructure Services for Open Access).
We will discuss the advantages and disadvantages of ranking, impact factors, and other more recent tools.
Peer review is often cited as the main quality instrument for the evaluation of scholarly output. In this course, we will discuss the performance of conventional methods of peer review and new developments in this area.
Another important topic we will discuss is the relative importance of questionable publishers. We will show that questionable publishing is a) not a big problem and b) not a problem linked to open access journals. A more realistic picture of the problem will be given using the examples of recent articles in the popular press.
Specific time will also be reserved to discuss evaluation of the quality of journals publishing social sciences and humanities content.
The second day of this course will be dedicated to talking about new criteria for evaluating the quality of journals, notably the consequences of Plan S, an initiative for open access publishing launched in September 2018, and to discussing the virtues of new forms of publishing, like preprints and library publishing.
Proposed Level: Intermediate
Intended Audience: The course is intended for all scholars, librarians, funders, and other parties with interest in open access.
Requirements: There are no special requirements for this course.
PM – B3 – Open Tools for Publishing Education: A Workshop on Pedagogy and Practice
Course Chair / Instructor: John Edward Martin, PhD, Scholarly Communication Librarian, University of North Texas
Description: While a number of publishing tools and platforms have become available for libraries and other organizations that wish to pursue open publishing initiatives, we rarely think about the pedagogical uses of these tools in the classroom or as part of skills-based outreach and educational programming. Yet these systems, many of them open source and community-developed, offer the opportunity to teach a critical approach to scholarly publishing, empowering students to question the biased or capital-motivated systems it can perpetuate.
This course will demonstrate a few of the tools available for open scholarly publishing – Open Journal Systems (OJS), Pressbooks, WordPress, Hypothes.is – and how they might be used for various instructional purposes, whether for a course specifically devoted to scholarly publishing or units/workshops on discrete topics such as peer review, editing, editorial workflows, open licensing, accessibility, metadata, or adapting open resources and developing skills that would allow for an intervention in current systems.
Participants will be encouraged to try out the platforms and start developing a course, unit, or workshop on a topic of particular interest to them that might utilize these or similar tools available at their own institutions. Prior experience with these platforms is helpful but not required.
We will take a look at several examples of pedagogical uses of these tools, and discuss some of the opportunities, challenges, and drawbacks of this kind of skills-based pedagogy for teaching scholarly communication literacy and publishing skills.
Proposed Level: All levels
Intended Audience: This course is aimed at anyone doing instruction in scholarly communications or publishing, including faculty, librarians, or staff members at academic libraries or other organizations that host publishing programs. Prior experience with the platforms or tools under discussion or with scholarly publishing workflows is helpful but not required. Participants will be given access to some of the tools ahead of time, and will have two or three case studies to read in advance.
Requirements: Participants should bring laptops, if possible, in order to access the online platforms under discussion. Information on setting up accounts on these platforms will be sent out ahead of time. Participants may also bring any materials they would like to use in designing a course, workshop, or unit that they would like to develop.
PM – B4 – A Decolonized Approach to Scholarly Communication: Foundations, Challenges, and Perspectives in Practice and Research
Course Chair / Instructor: Thomas Hervé Mboa Nkoudou, PhD student in Public Communication, Université Laval, Canada, and President, Association for the Promotion of Open Science in Haiti and Africa (APSOHA)
Description: Openness and the fast growth of information technology have contributed to reducing many injustices in knowledge diffusion. However, due to the immaterial nature of information, benign threats are still present in practices, research, infrastructure, and policies in academia. That means, once you are dealing with scholarly communication, whether you are a librarian, a researcher, a funder, a policymaker, or a software designer, what you are doing has impact everywhere across the world. But if you are not aware of soft domination, exclusion, and inequities led by knowledge, this impact can be negative. That is why it is so important to learn how to identify and avoid such bad effects. Postcolonial theory seems to offer a good framework to tackle these threats and educate people involved in scholarly communication. That is the raison d’être of this course: to teach how to identify and avoid colonial practices in scholarly communication.
The first day of the course is more theoretical and aims to provide participants with basics on postcolonial theory. We will present and discuss some texts previously shared with participants.
The second day is based on practical activities to scan the landscape of scholarly communication under the lens of postcolonial theory. Then we will focus on best practices we need to adopt to avoid an unconscious colonial impact in scholarly communication.
Proposed Level: All levels
Intended Audience: This course is suitable for all involved in scholarly communication, including researchers, librarians, publishers, policymakers, infrastructure designers, and funders.
Requirements: No technical skills or prerequisites are needed other than familiarity with activities related to scholarly communication. The course will require a laptop and an internet connection.
PM – B5 – Getting Buy-In: How to Plan and Master Open Access Advocacy Sessions
Instructors:
- Amanda Page, Open Publishing and Copyright Librarian, Syracuse University
- Anneliese Taylor, Head of Scholarly Communication, University of California San Francisco
Course Chair: Amanda Page
Description: Advocacy is a core element of scholarly communication (SC) work, particularly when it comes to promoting open scholarship and new communication resources and initiatives. SC officers must know their audience and strike the right balance between educating their community on these resources and advocating for transformations that the community may not be ready to embrace.
This course will present strategies for developing effective SC-related communications ranging from brief “elevator” conversations, to hour-long presentations, to full-length workshops. The course will have two parts and will utilize a variety of pedagogical methods, including lecture, active participation through in-class discussion and live polls, and group and individual exercises. Students will be invited to bring with them examples of real-life scenarios in order to apply the communication strategies covered in class.
Part 1: Advocacy-based Meetings and Conversations, and Project Work
We will begin with an introduction to strategic thinking in communication, which will be the foundation for all forms of SC outreach. Then we will cover the different types of crucial outreach activities and how to apply strategic thinking to these modalities, with an emphasis on one-on-one conversations/consultations and small-group meetings. Examples of project management models and tools will be presented for crafting project proposals and for scoping project work related to SC.
Part 2: Advocacy-based Classes, Workshops, and Events
This part of the course will build upon Part 1 by introducing students to more in-depth techniques to strategically customize communications and advocacy-driven messages, and to include crucial, deliberate methods in presentations and public communications. Additional considerations for facilitating events with larger audiences will be covered, including components of these different types of events, tips for building and tracking campus champions and partners, preparing questions for Q&As, and promoting sessions.
By the end of the class, students will have learned strategies for communicating in a variety of scholarly communication advocacy and outreach scenarios.
Proposed Level: Beginner to intermediate
Intended Audience: The course is intended for those who are new to working in scholarly communications and open access or who are already engaged in this work and are looking to increase their skills in advocacy, education, and stakeholder outreach. Librarians, early-career researchers, administrators, publishers, and graduate students are encouraged to register.
Requirements: Participants should have a basic, conceptual understanding of open access and scholarly communications. Participants will be asked to bring examples of their institutional policies and/or value statements related to scholarly communications, organizational charts, and governance structures. A minimal amount of required reading will be assigned before the class. Shared discussion and activities will occur, respecting confidentiality and consent.
PM – B6 – Citation Context Analysis: Findings and Lessons for Scholarly Communication Development
Instructors:
- Sergey Parinov, PhD, Chief Researcher, Central Economics and Mathematics Institute, Russian Academy of Sciences
- Victoria Antonova, PhD, Professor of Sociology, National Research University Higher School of Economics, Moscow
Course Chair: Sergey Parinov
Description: This course has two parts. The first part examines the current state of the art in citation context analysis: the main methods and achieved results. The second part is a set of interactive sessions discussing the main findings and lessons resulting from citation context analysis for individual researchers, for librarians, and for the research community at large with a focus on scholarly communication.
Part 1 is organized as a set of topics where each topic presents a method of analysis, its current implementations, and available results:
- Counting in-text citations vs. traditional citation index
- Analysis of in-text citation co-occurrence, which demonstrates how references are mentioned together in the same citation context
- Analysis of spatial distribution of in-text citations within papers’ full text
- Finding of common phrases within a corpus of citation contexts, e.g. by the N-gram method (https://en.wikipedia.org/wiki/N-gram)
- Building “topic models” (significant words or abstract topics) over citation contexts based on the Topic Model approach (https://en.wikipedia.org/wiki/Topic_model) and using the LDA method (https://en.wikipedia.org/wiki/Latent_Dirichlet_allocation)
- Recognition of polarity and functions of in-text citations
- Analysis of lexical difference and similarity between citation contexts based on the word-embedding approach (https://en.wikipedia.org/wiki/Word_embedding) and measured by the Word2Vec method (https://en.wikipedia.org/wiki/Word2vec)
- Comparative analysis of citation context analysis results obtained by different methods
Part 2 will be a series of moderated discussions about what important findings and lessons related to scholarly communication we got from Part 1. Suggested topics for discussion:
- Basic function of citations related to scholarly communication and cooperation. Modern diversity of motivations for researchers to make citations. Proper and dangerous motivations.
- Lessons for individual researchers, which could help them improve their skills in making citations in their publications.
- Lessons for librarians. What is the best citation practice to advocate and disseminate?
Lessons for the research community at large, which are important for scholarly communication development, including improvements of traditional publication and citation practice. For example:
o How citation practice should be changed to support better scholarly cooperation and what institutions should be created for this
o Citations as interactive elements and direct scholarly communication between citing and cited authors
o Competition among similar research outputs to be cited
o Scholarly signaling system based on citation data
o Ideal scholarly citation mechanism and proper citation practice
Proposed Level: Beginner to intermediate
Intended Audience: This course is suitable for all involved in preparing and assessing scholarly publications, including researchers, librarians, and others.
Requirements: There are no particular requirements for this course.
PM – B7 – Collecting, Curating, and Publishing Accessible Mobile and Sensor-generated Research Data
Instructors:
- Rosemary Rocchio, Director, Mobile and Web Strategy, Education & Research, Office of Information Technology (OIT), University of California Los Angeles
- Davida Johnson, Managing Director, Community Partnerships, OIT, UCLA
- Travis Lee, Disabilities and Computing Coordinator, OIT, UCLA
Presenters:
- Kent Wada, Chief Privacy Officer, UCLA
- Professor Sandrah Proctor Eckel, PhD, USC
- Professor Jose-Luis Ambite, ISI, USC
- Professor Alex Bui, MII, UCLA
- Nate Jacobs, PhD, recently of UCLA
Course Chair: Rosemary Rocchio
Description: This course will cover three important topics on communicating mobile and sensor research data, from data collection, to accessibility, to publishing mHealth data.
- Collecting New Data in the World of Mobile Devices and Sensors: The genre of data collected with mobile devices and sensors presents an interesting set of challenges with regard to managing, curating, and publishing research data. Many of these research projects include collecting data from physical wearable sensors such as smart watches, air monitors, or on-phone sensors (accelerometer, GPS, etc). Further complicating this effort is the collecting of metadata about the status of each of the devices, such as battery, calibration, configuration, and interdevice communications. Further data about the context of the sensors and phone include the availability of wifi, delivery status of notifications, telemetry, user experiences, and self-report surveys from participants themselves. Additional challenges occur when integrating with commercial sensors and private-sector commercial cloud platforms. The capstone area of data in this realm of research projects includes participatory user survey responses, sometimes motivated by gamified compliance constructs. Attempting to utilize this type of data to measure user engagement encouraged by these techniques is a new area of exploration.
- Making Research Data Accessible: Learn about the challenges facing researchers with disabilities and how you can empower this population through accessible design. People who are blind or low-vision or who have dyslexia rely on assistive technologies and screen reading software to “read text out loud” to them. However, many documents and data sets created are completely inaccessible or just frustrating for screenreader users. Learn accessible design and content management tools to make it easier for people with disabilities to engage with your research content, data, and documents. During this two-hour active-learning session, you will learn the impact of accessible documents and data sets, as well as simple methods for building accessibility into current content. In addition, you will have an opportunity to gain hands-on experience building accessible documents and curating data.
- Publishing Mobile Data and Metadata: Mobile devices and mHealth experiments allow for collection of more granular and personalized research data “in the field” during people’s daily routines. This creates challenges for how to formalize and share this large volume of data and metadata and how to interpret these new types of data. This section will discuss how mobile data, particularly in mHealth projects, can be captured and formalized appropriately for later publication in data repositories or supplemental materials. The value of research data from mobile devices is still emerging; however, it is expected to become highly valuable in aggregate.
Proposed Level: Beginner
Intended Audience: This course is for anyone who is interested in collecting "new data" using mobile devices, wearables, and sensors. This could include professors and researchers in data science or statistics; and those in psychology, sociology, political science, anthropology, or any field that includes the study of people. Work in all of these fields can be improved by enhanced data collection using EMA (Ecological Momentary Assessment) techniques.
Requirements: Participants should download the ohmageX app from either the iOS Store or the Android Store for use during this course.
PM – B8 – Data Citation for Scientific Publishing
Course Chair / Instructor: Gianmaria Silvello, PhD, Assistant Professor of Information Engineering, University of Padua, Italy
Description: Citations are the cornerstone of knowledge propagation and the primary means to assess the quality of research as well as to direct investments in science. Science is increasingly becoming “data-intensive,” where large volumes of data are collected and analyzed to discover complex patterns through simulations and experiments. Hence, most scientific reference works have been replaced by online curated datasets. Yet, for a given dataset, there exists no quantitative, consistent, and established way of knowing how it has been used over time, who contributed to its curation, what results have been yielded, and what its value is.
In this course, we will describe the main challenges we face to effectively cite data. We will analyze the requirements defined by FORCE11 and the Research Data Alliance (RDA) Working Group on data citation, and we will discuss the current solutions. In particular, we will analyze the existing solutions to address:
- identification of and access to the cited data;
- the persistence of data identifiers as well as related metadata (i.e., the problem of fixity);
- the completeness of the reference, meaning that a data citation should contain all the necessary information to interpret and understand the data, even beyond the lifespan of the data they describe; and,
- the interoperability of citations, meaning that they must be interpretable by both humans and machines.
We will present techniques for data citation relying on persistent identifiers such as Digital Object Identifiers (DOI) and Persistent Uniform Resource Locator (PURL) to address the identification problem. We will analyze the RDA proposed solution, which employs a dedicated system to persistently store user queries where these queries are treated as proxies for identifying the cited data. We will also dig into the existing techniques to tackle the completeness problem based on the most diffused data models adopted for managing and accessing scientific data: relational, XML, and RDF databases.
Proposed Level: Intermediate
Intended Audience: The course requires some basic knowledge of computer science. In particular, participants should know the relational model and the XML and RDF frameworks at least at an introductory level. Basic knowledge of the internet and web architecture would be a plus.
Requirements: There are no particular requirements for this course.
PM – B9 – Reveal, Don’t Conceal: How to Avoid Common Data-Visualization Errors and Create More Informative Figures
Course Chair / Instructor: Tracey Weissgerber, PhD, Mayo Clinic and QUEST (Quality, Ethics, Open Science, Translation), Charité Universitätsmedizin Berlin, Germany
Description: This short course will focus on creating informative visualizations for scientific publications. Participants will learn to identify common problems with visualizations in small sample size studies in the basic biomedical, translational, and biological sciences. For example, we’ll discuss the problems with using bar graphs to show continuous data and learn what types of graphs to use instead and how to determine which option is best for your dataset. We’ll talk about strategies for making informative and transparent alternatives to bar graphs, and experiment with free tools for creating better graphs. We will also discuss best practices for other types of graphs, including line graphs and scatterplots.
We’ll learn why it’s important to use study design diagrams and flow charts and how to design these types of figures. We’ll also experiment with free online tools that allow users with no programming expertise to create interactive visualizations. These figures allow readers to gain additional insight by exploring a dataset. We’ll learn strategies for creating informative figures based on images, including photographs, microscopy or electron microscopy images, or images obtained using clinical techniques such as ultrasound or MRI. We’ll test free tools that you can use to determine whether images or figures are color-blind safe. Finally, we’ll discuss how to use figures and infographics to emphasize the message of your paper and simplify the writing process.
Proposed Level: All levels
Intended Audience: All levels are welcome, including students and junior and senior faculty. The course is particularly aimed at those with experience in conducting research and reading literature in small sample size studies, such as basic biomedical science or preclinical studies.
Requirements: Participants will need a laptop with internet connection.
PM – B10 – Publishing Reproducible Experimentation Pipelines: A Hands-on Course
Course Chairs / Instructors:
- Ivo Jimenez, PhD candidate in Computer Science, University of California Santa Cruz
- April Clyburne-Sherin, Director of Scientific Outreach, Code Ocean
Description: Computational analyses are playing an increasingly central role in research. Journals, funders, and researchers are calling for published research to include associated data and code. However, many involved in research have not received training in best practices and tools for sharing code and data. This course aims to address this gap in training while also providing those who support researchers with curated best practices guidance and tools.
This course is unique compared to other reproducibility courses due to its practical, step-by-step design. It is comprised of hands-on exercises to prepare research code and data for computationally reproducible publication. Although the course starts with some brief introductory information about computational reproducibility, the bulk of the course is guided work with data and code. Participants move through preparing research for reuse, organization, documentation, automation, and submitting their code and data to share. Two tools that support reproducibility will be introduced (Code Ocean and Popper), but all lessons will be platform agnostic.
This course is divided into four parts. In the first part, we will briefly introduce DevOps, give an overview of best practices, and show examples that illustrate how these practices can be repurposed for carrying out scientific explorations. The second part will be devoted to hands-on experiences with the goal of walking the audience through the usage of the Popper CLI tool. Participants will create an experimentation pipeline using Git, Bash, Python, Github, Docker, and TravisCI. This pipeline will showcase the concepts and practical aspects of reproducible research. The third part will be devoted to working on the code that attendees bring, with the goal of “popperizing” it. The final part of the course will focus on best practices for sharing data and code in a computationally reproducible publication.
Proposed Level: Intermediate
Intended Audience: The course is targeted at researchers and research support staff who are involved in the preparation and publication of research materials. Anyone with an interest in reproducible publication is welcome. The course is especially useful for those looking to learn practical steps for improving the computational reproducibility of their own research.
Requirements: Participants will need a laptop with internet access. Participants are welcome to bring their own code and data for the exercises and also should go over these setup instructions prior to the course: https://popperized.github.io/swc-lesson/setup.html
