The FSCI 2021 Course List
Click on the linked titles below for abstracts and more details on each course.
Course Abstracts
T10 – Collaborating for open research in your campus' research enterprise and faculty grantsmanship support
Nina Exner, Erin Carrillo, Stephen Bollinger
Abstract: Do you want to see better partnerships between the Office of (Sponsored) Research, the library, research cores, academic departments, and faculty development?
This course is for those who support campus researchers – such as librarians, research development professionals, research administrators, and research managers to discuss support for faculty grant success. We will work on partnerships to support open and public access, and FAIR data services specific to federally funded research. This is the perfect place for librarians to expand from single services like DMP support to wider grant support offerings. It will also be a good class for administrators wanting to build more support partnerships for their new faculty.
Federal funding agencies in the U.S. and many other regions expect faculty to move toward FAIR data and open scholarly communication. But faculty principal investigators (PIs) are not always able to incorporate FAIR and open scholarly communication practices into their workflows. PIs need to be connected to professionals who can support use of modern and emerging scholarly communication approaches in their grant-writing and grant compliance.
Each campus has many units willing to help faculty members. Librarians, mentors, research administrators, and others offer support for PI transitions to better scholarly communication practices. But these support offerings are not always aligned together. Join us for a place to discuss how your campus can grow scholarly communication support in the university “research enterprise.”
In this session, we will share different views of the funded research workcycle. As a group, we will discuss how support offerings align with research administrator and funder priorities. We will then work on plans for outreach to other campus units to partner on FAIR and open practices in faculty grant proposals.
Audience: Librarians, Administrators, Technical Support, Research managers
T11 – FAIR for Data and Texts Not in the Open: Overcoming Legal, Technological, and Economic Barriers
Ye Li, Laura Hanscom, Katie Zimmerman
Abstract: The rise of applied data science, digital humanities, machine learning, and artificial intelligence has resulted in an increased need for computational access and reuse of research data and publications. Researchers have begun to build FAIR (findable, accessible, interoperable, and reusable) and open data practices for data they are generating; however, much computational research requires access to existing structured and well-curated texts and data from proprietary sources that don’t currently meet the FAIR standard. To accomplish this, many researchers are partnering with libraries, which frequently have long-term subscription access to such resources, to gain computational access and rights to reuse for text and data mining (TDM) and machine learning purposes.
Negotiating for such access and rights poses technical, economic, and legal challenges. In some cases, researchers have to negotiate access and reuse at the individual research group or project level. In this course, we will interactively explore these issues through case studies from real-life examples and share resources and tips that will help researchers, librarians, and vendors to “move the needle” toward FAIR data. The joint effort of researchers, librarians, and vendors will be required to sustainably ensure that resources move towards FAIR standards, and that researchers can share their own research output FAIRly.
Class activities include:
- Small-group critique of license terms for computational access and reuse of publications and databases.
- Mock negotiation between researchers/librarians and vendors.
- Hands-on practice accessing a database through publicly available API services (e.g., Crossref, PubChem) and comparison with other computational access models.
- Group discussion of cutting-edge questions on computational access and reuse.
Audience: Researchers, Librarians, Faculty/Scholars, Publishers, Administrators, Technical Support
T12 – Reproducibility for everyone: a train-the-trainer course for teaching reproducibility tools and methods
April Clyburne-Sherin, Ruchika Bajaj, Jeremiah Pietersen, Robyn Price, Vicky Rampin, Hao Ye
Abstract: An ecosystem of tools and methods for improving the rigor and reproducibility of research is thriving. Information professionals at research institutions must stay informed about what tools are available and how they compare. Ideally, they can also onboard researchers to kickstart their adoption. However, developing quality curriculum to train researchers on new tools requires expertise in the tool itself, which leaves many researchers without training on tools that may benefit their research.
This course will train participants to run hands-on, quality modules designed to onboard researchers to four free, open source tools. Participants will experience the module, practice the exercises, and explore the training material needed to run the module themselves. An instructor guide that includes the module outline, objectives, description, frequently-asked-questions, pre- and post- participant surveys, target audience, and instructions for running a successful module is included for each tool taught.
This course will train participants to run modules on unique aspects of reproducibility for researchers:
- Data management
- Electronic lab notebooks
- Organizing and sharing protocols
- Reagent sharing
- Bioinformatics tools
- Data and code sharing
- Data visualization and analysis
- Designing figures with images
Many FSCI participants already run short-duration training events at their institution. This course is ideal for those FSCI participants who wish to improve the quality and variety of the training they already offer to researchers. Participants who do not currently run short-duration training events at their institutions would benefit from the course by learning an accessible and efficient way of getting started with these modules.
For participants of last year’s version of this course, “Open source tools for everyone: a train-the-trainer course for teaching 4 open research tools”, these modules are new but designed to be interoperable with the modules taught at FSCI 2020.
Audience: Researchers, Librarians, Faculty/Scholars
T13 – Fostering Open Scholarship across the Curriculum
Jonathan Grunert
Abstract: Open Scholarship expands the limitations suggested by the term "Open Science." Though many practitioners of Open Scholarship know that values of Open Scholarship are applicable across disciplinary boundaries, it can be difficult to bring them into humanities and social science classrooms, given the historic terminology "Open Science." Principles of Open Scholarship (as holdovers from Open Science) are valuable across disciplines; that is, they are useful in the sciences, social sciences, humanities, and interdisciplinary fields. Acknowledging and teaching them in classrooms across a variety of disciplines and a range of advancement within a discipline can benefit students, their instructors, and academia at large, as they encourage wider promotion of Open principles.
The first part of the course focuses on rationale for teaching Open Scholarship across disciplines, and discussions of who benefits from it. Participants in this course will have opportunities to examine their institutional cultures of Open Science and Open Scholarship, and how instruction can expand the reach of Open Scholarship within their own discipline as well as to other disciplines.
The second part of the course focuses on implementing Open Scholarship within a curriculum. Participants in this course will work to identify specific partners within their institutions and strategize how to leverage those partnerships to endorse the project, and they will map Open Scholarship into a specific curriculum. By the end of the course, participants should have a workable plan to include Open Scholarship principles in existing instruction, and to promote teaching Open Scholarship across a wide range of disciplines.
Audience: Librarians, Faculty/Scholars, Administrators
T15 – How to introduce and implement policy in your institution and still have friends afterwards
Danny Kingsley & Sarah Shreeves
Abstract: As momentum increases toward an open future, questions arise around the implications for research institutions. There are multiple challenges around policy, advocacy, and technology surrounding open research practice. Much of the work in the scholarly communication space involves advocacy – working with many levels of the institutional hierarchy. This course discusses the practical aspects of developing policy and navigating it through an institution – a lengthy and complex process. Participants will consider who the stakeholders are within their institution and collectively will look at the perspectives they might bring to the discussion. There will be some practical work on addressing various objections to provide advocacy and negotiation skills.
The course will be a mixture of synchronous and asynchronous learning. In total the course will take five hours for each of the two weeks of FSCI (10 hours in total). This will include an expected contribution to an introductory process prior to the starting date. You will also need to prepare for scheduled group work by watching a pre-recorded short lecture. Sessions will happen twice a day to allow for different time zones, and group work will occur with people in a time zone close to you. The final day in week two will be a meeting of the whole group – we will work together to decide the best (or least worst!) time zone for everyone.
Collaborators and guest lecturers: TBD
Audience: Researchers, Librarians, Faculty/Scholars, Administrators
T16 – Data Utopia: Building a FAIRer Future in Research Data Management
Emma Anne Harris, Katarzyna Biernacka
Abstract: Are you providing a research data management (RDM) service or services? Do you think RDM would benefit from more Open and FAIR Data? But do you feel like you are constantly reacting to the needs of researchers, the growing variety of software and tools, and the shifting policy landscape, but you are never able to stop and think about strategy? Well, this is the workshop for you!
These hands-on virtual sessions will allow those who are RDM service providers – librarians, IT managers, data protection officers, project officers and managers, trainers, research administrators – to have a rare opportunity to really look at the big picture of RDM strategy and progress. The immense added benefit is that they can do so alongside other RDM service providers, thus revealing common challenges, recurring themes, shared goals, and cross-cutting solutions which all can take away and implement.
In this session we will use an adapted version of the Future Search workshop concept to explore three key areas: challenges, future vision, and implementing solutions. In the first session we will identify challenges in RDM service provision and then look together at the common themes that emerge. In the second session we will be really creative and imagine a utopian future where RDM in universities and research institutes is perfect and FAIR! In the third session we will look at how we can move towards that perfect world today, how we can overcome the challenges, and what practical ideas have worked so far.
Taken together these three sessions will allow a space for RDM service providers to really reflect on the current issues they collectively face, and how the principles of Open Research and the guidelines of FAIR data can be included in strategy management going forward.
Audience: Librarians, Faculty/Scholars, Administrators, Technical Support, IT/Computer Service Managers, Trainers
T17 – Losing Our Scholarly Record and What We Can Do About It
Martin Klein
Abstract: Most aspects of scholarly communication happen on the web. The dissemination speed of scholarly knowledge has dramatically increased because we are able to publish and access information on the web. While this environment comes with lots of new opportunities, it also poses challenges, specifically to the longevity of the scholarly web-based record. Increasingly, as authors of scientific articles we reference resources on the web such as project websites, scholarly wikis, ontologies, datasets, source code, presentations, blogs, and videos.
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 in place for what we call “web at large” resources. These observations raise significant concerns regarding the and long-term availability and access of web-based scholarly artifacts.
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.
Intended Audience: This course is targeted at scholars, librarians, archivists, and publishers at all levels.
Audience: Researchers, Librarians, Faculty/Scholars, Publishers, Administrators
T18 – Unpacking the Role of Preprints in Scholarly Inclusion
Ibraheem Ali
Abstract: Researchers are becoming increasingly aware of preprints: complete and public drafts of unreviewed scientific documents. Preprint publishing and data archiving in repositories has dramatically increased in recent years due to changing researcher priorities and requirements set by funders and publishers. This has created a variety of challenges and opportunities as it relates to scholarly inclusion and academic rigor. In this workshop we will cover an overview of preprint-publishing and research-archiving platforms and the various ways researchers can engage with preprints in their field. We will discuss the challenges that come with the rise in preprint publishing and highlight the importance of creating a culture that fosters open scholarly dialogue to make research more transparent, accessible, and inclusive.
Collaborators and guest lecturers: Raquel Aragón, UCLA; Dr. Shawntel Okonkwo, PhD, ZS Associates, Inc.; Dr. Joe Udeochu, PhD, Regeneron.
Audience: Researchers, Librarians, Faculty/Scholars
T19 – Four recommendations for open source software (4OSS lesson)
Leyla Jael Garcia Castro, Allegra Via, Fotis Psomopoulos, Eva Martin del Pico, Jose Mª Fernández, Dimitrios Bampalikis
Abstract: Scientific data-driven research relies on software to create, process and analyze data, yet software is not always developed following practices that ensure its quality, sustainability and FAIRness. Rather than proposing new software development best practices, this course aims to provide researchers using some code in their projects with four simple recommendations encouraging the adoption of existing best practices. Software development best practices promote better quality software, and better quality software improves the reproducibility and reusability of research. These four recommendations are designed around Open Source values, and provide practical suggestions that contribute to making research software and its source code more discoverable, reusable and transparent. This course is aimed at researchers working with software (or willing to do so) as part of their regular activities.
Collaborators and guest lecturers:
Leyla Jael Garcia Castro. ZB MED Information Centre for Life Sciences. ljgarcia@zbmed.de. Dr. Garcia Castro is a Computer Scientist interested in semantic web, linked data, data science, open science and education. I am currently involved in community projects aiming to make FAIR a reality not only for data but also for software and training materials. I have worked on software development and semantics data integration, project coordination, scientific events organization and chairing, and community-based projects (e.g. Bioschemas and BioJS). I have also worked as a university lecturer on software development and information systems.
Allegra Via, IBPM-CNR, allegra.via@cnr.it. Dr. Via is a physicist and scientific researcher at the IBPM-CNR. In 2009 she moved to the Sapienza University as researcher, and, since January 2014, she is the ELIXIR Italy Training Coordinator. She is involved in the design, organization and delivery of bioinformatics training courses, in Train the Trainer activities, and collaborates with other ELIXIR’s nodes on many training-related initiatives. She has a long track record of academic teaching (Macromolecular Structures, Python programming, Bioinformatics, Biochemistry, Protein interactions). Her main research interests include protein structural bioinformatics, protein structure and function prediction and analysis, and protein interactions. She is also strongly interested in what researchers have discovered about how people learn and how best to teach them, and how research findings in the science of learning (educational psychology) can be translated into common teaching practice. She’s a member of the Global Organisation of Bioinformatics Learning, Education and Training (GOBLET) and a Software/Data Carpentry Instructor and Instructor trainer. Finally, she is the co-lead of the ELIXIR Software Best Practices task together with Fotis Psomopoulos and Eva Martin del Pico.
Fotis Psomopoulos, Institute of Applied Biosciences, Centre for Research and Technology Hellas, fpsom@certh.gr. Dr. Fotis Psomopoulos is researcher leading the Bioinformatics Unit at the Institute of Applied Biosciences, at the Center for Research and Technology Hellas, in Thessaloniki in Greece. His research interests are mainly focused on Bioinformatics and Machine Learning, focusing on the design of new algorithms and pipelines. In addition to his research activities, he is extensively involved in training delivery, also as part of his role as the Training Coordinator of ELIXIR-GR. Finally, he is the co-lead of the ELIXIR Software Best Practices task.
Eva Martin del Pico, BSC / ELIXIR-ES, eva.martin@bsc.es. M.Sc. Martin del Pico is currently a PhD student at the Barcelona Supercomputing Center. Her research interests include FAIR for research software, FAIRness metrics and software best practices. She is co-lead of the ELIXIR Software Best Practices task.
Jose Mª Fernández, BSC / ELIXIR-ES, jose.m.fernandez@bsc.es. Eng. Fernández is a research senior engineer at the Barcelona Supercomputing Center with a background in Bioinformatics. He is an active member of the ELIXIR Software Best Practices task.
Dimitrios Bampalikis, NBIS, dimitrios.bampalikis@nbis.se. M.Sc. Bampalikis is a system developer at NBIS with years of experience in software engineering and development. He did his thesis, related to scRNAseq (single-cell RNA sequencing) with the Bioinformatics Long-term Support (WABI) team at NBIS. He is an active member of the ELIXIR Software Best Practices task."
Audience: Researchers
T20 – Case studies in the Earth Sciences: Current approaches to publishing, data and computation
Sam Teplitzky, Anusuriya Devaraju, Chris Erdmann, Siddeswara Guru, Ivan Hannigan, Dasapta Irawan, Fernando Perez, Olivier Pourret, Natasha Simons, Alison Specht, Shelley Stall, Wynn Tranfield
Abstract: Expectations of collaboration and contribution in the Earth, Space, and Environmental Sciences (ESES) are not always transparent. Increasingly scientists must navigate modern workflows that require an understanding of and attention to changing standards for publications and their associated research products. This course will take emerging and established researchers in Earth Science domains through current approaches to discipline-specific research workflows, including reproducibility, publishing, preserving and sharing data, and setting up computational and software environments at scale.
Attendees will leave with ideas and methods for constructing their own research workflows that incorporate ESES tools and perspectives.
Seven sessions will be offered within the following three themes: Publishing, Data and Computation.
Session 1: Introduction to Open and Reproducible Practices in Earth Sciences
Instructors: Sam Teplitzky, Wynn Tranfield
Description: Serving as an introduction to Case studies in the Earth Sciences course, this session will also introduce participants to the range of topics considered at the outset of an Earth Sciences research project, such as reproducibility, preregistration, and authorship.
Session 2: Your paper is published, it’s not the end of the journey
Instructors: Dasapta Irawan, Olivier Pourret
Description: Publishing a paper is one big effort, but creating engagement and tracking the impact of it is another huge effort that most researchers take for granted. While increasing citations is one goal that people frequently mention when they are promoting their paper, creating engagement has more benefits than just adding some new citations to your portfolio. Olivier and Dasapta will share their experience engaging and collaborating via social media, blogpost, and drawing after a paper is published.
Session 3: Open Discussion Session/Informal Networking
Session 4: FAIR Data & Software Citation
Instructors: Chris Erdmann, Natasha Simons
Description: Citing data and software you created for your research may seem odd and a little bit like self-citation. But Alas! This is exactly what is needed to get credit for the data and software you created for your research. Giving credit to not only your research outputs but also others’ software and data that you used in your research are important. These research outputs are valuable contributions to science and increase the possibility of higher numbers of citations for your published papers. In this session we will provide a checklist of what to cite in your paper as well as data and software management tools and practices that make sharing your data and software at the time of publication easier.
Session 5: Data Management Plans that ensure FAIR principles
Instructors: Anusuriya Devaraju, Alison Specht, Shelley Stall
Description: In the first part of this component of the course, we shall introduce the participants to a Data and Digital Objects Management Plan through a checklist of steps and actions. For each step we shall show how FAIR principle can be incorporated into their work, and how they can assess the adequacy of their efforts. In the second component of the course, we shall invite the participants to bring an example of their own data, and help them to incorporate DMP and FAIR best practice into their own research data management. By this means we shall demonstrate that despite the wide variation in approaches in different discipline fields, there is a similarity of data management practice across all. The participants will take away active tools for their future work.
Session 6: Collaborative, open geoscience in the cloud with Jupyter and Pangeo
Instructors: Fernando Perez
Description: In this session, we will demonstrate how tools in the Jupyter and Pangeo projects can be used to support open, collaborative practices in geoscience in the cloud. Modern cloud infrastructure offers a variety of computational infrastructure that can be deployed elastically, and the availability of geophysical data in the cloud is increasing at a rapid pace. Open source tools and communities like Pangeo and Project Jupyter can unlock this potential with modular components that scientists can use for a variety of scenarios ranging from individual exploration to large-scale, reproducible team science. We will describe some key components of these tools and illustrate how they can be put to use in concrete research scenarios.
Session 7: Introduction to virtual work platforms (using CoESRA)
Instructors: Siddeswara Guru, Ivan Hannigan
Description: In the Earth and Environmental sciences international collaboration is expected. Covid-19 restrictions to travel have only exacerbated an existing challenge: how to work together in a productive manner. The virtual laboratory has gained traction in education, allowing students to collaborate and learn using cloud-based tools from their own desktop. In this component of the course we shall give an introduction to the virtual workspace, using a freeware example, CoESRA. We shall demonstrate how to source and save data, manipulate the data and run analyses, save the results, and ready them for publication, all with multiple colleagues participating. We shall run through the acquisition of a data set that is available on-line, to its analysis and the recording of the steps along the way, and then provide the opportunity for participants to source their own data and, with guidance, learn how to use the tools available, how to add more, and how to export the results.
Audience: Researchers in the Earth Sciences
W21 – FAIR Data in the Scholarly Communications Lifecycle
Natasha Simons, Chris Erdmann, Daniel Bangert, Fiona Murphy
Abstract: 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. 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 provide an overview of the FAIR Data Principles and the drivers behind their development by a broad community of international stakeholders. 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 through self-paced exercises. There will be opportunities for participants to learn from each other and to develop skills in data management and expertise in making data FAIR.
Audience: Researchers, Librarians, Faculty/Scholars, Publishers, Administrators, Technical Support, Research infrastructure project teams
W22 – Research Reproducibility in Theory and Practice (biomedical focus)
Anita Bandrowski, Tracey Weissgerber, Daniel S. Katz
Abstract: This will be a carpentry-like course, instructors will pull together the materials about rigor and reproducibility, important for the scientists. The goal is come out of this with a set of materials.
The 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 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.
Audience: Researchers, Librarians, Faculty/Scholars
W23 – Stakeholder perspectives on negotiating transformative and open access publishing agreements
Colleen Campbell, Curtis Brundy, Mathew Willmott
Abstract: Libraries and national consortia globally are increasingly adopting publisher open access negotiations as a key component in their broader open access strategies. The ESAC Transformative Agreement Registry lists more than 200 agreements currently in place between 45 publishers, large and small, and libraries and national-level library consortia in 30 countries. While the ESAC Market Watch highlights the impact these agreements are having in enabling authors to retain copyright and publish their new research articles immediately open access, the agreements have ramifications that touch all stakeholders in scholarly communication: researchers, publishers, librarians, higher education and research administration, research funders and more.
Featuring the insights of a range of stakeholders, this course will give participants the opportunity to explore the impacts of transformative open access agreements from a variety of different perspectives.
- What are the principles and strategic considerations that motivate stakeholders to engage in this pathway?
- What are the practical and operational implications for each of the stakeholders and how are they addressed?
- As stakeholders inch forward on the path of transformative open access agreements, what new challenges do they see on the horizon and how do they propose to address them?
Through live and recorded presentations, facilitated small-group discussions and other activities, participants will gain a better understanding of the open access scholarly publishing landscape and will come away with their own actionable roadmap for publisher negotiations aimed at driving an open, diverse and equitable scholarly communication system.
Audience: Librarians
W24 – Getting attention and bringing others on board: Applying basics in marketing and communications to advance open research
Jennifer Gibson
Abstract: Getting the attention of faculty, students, decision-makers, and others and convincing them to break out of long-established habits to try something new is a defining aspect of work in scholarly communications. The future of open research is dependent on our ability to change behaviours.
Putting compelling messages in front of the right audiences is a practiced art and science in marketing and communications. The world’s biggest brands are masters at convincing us our shampoo is bad for our hair and to buy more sugary soda – or that specialised indoor bicycle, though we just got rid of the last one.
Social Marketing, which long precedes social media, is the application of commercial marketing principles and practices to effect social and behavioural change. The same systems for understanding an individual’s needs and pains, for communicating to them in their world, on their terms, and convincing them to attempt a change in behaviour can be used to promote adoption of open research practices as well as bacon double cheeseburgers.
This course will explore the basics of marketing strategy and their application in the research environment – advancing open research or any other type of behaviour change.
Audience: Researchers, Librarians, Faculty/Scholars, Publishers, Administrators, Technical Support, Anyone involved in outreach to others with respect to open research practices.
W25 – Working with Scholarly Literature in R: Pulling, Wrangling, Cleaning, and Analyzing Structured Bibliographic Metadata
Clarke Iakovakis, Kay Bjornen, Megan Macken
Abstract: "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 be based on the workshop I provided at last year's FSCI. The course will assume no experience with R; however, a thorough explanation of the R programming language will not be provided.
The course will a mixture of pre-recorded videos and synchronous meeting for discussion and Q&A sessions.
Students will access IPNYB (Jupyter Notebooks) files containing the scripts for the workshop, created with Binder (https://mybinder.org/). The files will include executable code alongside descriptions of what the code is doing. Students can therefore run code that has already been written, but will also write and execute their own R scripts within the Jupyter Notebooks environment. Students will access these notebooks while watching the videos explaining the code.
We will begin with a general orientation of the Jupyter Notebooks environment. We will then discuss R and provide a basic overview of how it works. This introduction will include reading data into R, installing packages, and some functions for cleaning and restructuring data. We will then discuss Crossref, ORCID, and Unpaywall, and the packages developed by the rOpenSci (https://ropensci.org/) organization to access the API services of these organizations, and walk through rcrossref, roadoi, and rorcid.
rcrossref interfaces with the CrossRef API, allowing users to pull article metadata based on ISSN, filter queries by publication date and license information, running queries by title and author, getting funder data, getting citation counts, and exporting to BibTeX, RIS, and CSV. This can be immensely powerful for collecting citation data, conducting literature reviews, creating bibliographies, and more.
roadoi interfaces with Unpaywall, allowing users to input a set of DOIs and return publication information along with potential locations of open access versions.
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.
As we work through the tutorials, students will continue to learn R functions for working with data, including dplyr, purrr, and tidyr.
By the conclusion of the session, students will be able to work with and analyze data in R. 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. Because they will be walking away with executable scripts, they will be able to modify those and collect data based on parameters they are interested in."
Collaborators and guest lecturers: TBD
Audience: Researchers, Librarians, Faculty/Scholars, Publishers, Administrators, Technical Support
W26 – Open science, culture change, and your workplace
Bruce Caron
Abstract:
"The opposite of open isn’t closed. The opposite of open is broken." – John Wilbanks, 2010
We can work together to unbreak science.
This class will open up generous conversations about a wider range of open science topics than is usual for a discussion of “open access.” We will pull key concepts from The Open Scientist Handbook: to discover the wheres and the hows that led science down the wrong pathway, and the hidden “why” of science that is buried under a current, ongoing avalanche of external conflicts of interest.
The opening gambit to open science culture change in your organization is to celebrate the anti-rivalrous logic of science itself. This logic supports what John Wilbanks (paraphrase) also noted is the “unreasonable effectiveness of open [science].” Together we will explore the internal goods of science to anchor open science within an economy and a culture that rejects external incentives in favor of science’s built-in motivations. Science—open and free in its internal cultural logic—promises to deliver new knowledges, and new ways of knowing substantially beyond its current bounded capacity.
Day One:
Before we can point science culture toward an anti-rivalrous, zero-incentive future, we need to learn about science as an infinite game. We will explore some of the toxic practices that currently infest the academy. We will end with a bit of fun, acknowledging that the best science conversations include laughter.
ACTIVITY: We will record personal stories of finite games that dominate activities in the organizations in our careers: libraries, universities, interactions with funders, learned societies, publishers…
Day Two:
Two core logics help illuminate the field of open science practices: Fierce Equality and Demand Sharing. Fierce Equality anchors open science cultural practices at all levels: interpersonal to trans-organizational. This logic counters hierarchies, exclusivity, cumulative advantages, and bullshit excellence. Demand Sharing articulates the primary logic of the science gift economy. This real sharing economy (not science as Uber) powers local scholarly commons, open repositories, and open access to academy goods. We will end with a discussion of how science supports and requires that scientists develop practical wisdom.
ACTIVITY: we will list examples of colleagues, teachers, and others who have shown their practical wisdom in the workplace.
Day Three
Today, the academy needs open scientists as culture change agents. Managing organizational culture is always a local project, but it can benefit from shared resources. Change begins with stating principles that power discussions about new practices that re-place current ones. These new practices celebrate shared values, and valorize normative activities that reward shared virtues instead of toxic, ego-boosting behaviors.
To foster follow-on activities, class members will be invited to join the Open Scientist community on PubPub, and the Open Scientist social community on Hylo.
ACTIVITY: The class will break into small groups and begin to fill in PlayBooks (in Hylo) for their own open science culture change efforts.
Audience: Researchers, Librarians, Faculty/Scholars, Publishers, Administrators, Technical Support
W27 – Why Standards and Best Practices Make Scholarly Communications Better and How You Can Help, Whether You’re a Novice or Seasoned Professional
Nettie Lagace, Todd Carpenter, Alice Meadows
Abstract: Scholarly communication, as a community encompassing many stakeholder groups, relies heavily on the "communication" aspect, as we work together to develop the processes, tools, and policies needed to improve throughput and effectiveness. Development and application of standards and best practices are a huge part of ensuring that scholarly communication supporters aren't "reinventing the wheel" — that we are finding sustainable, interoperable, consensus-developed solutions wherever possible.
But how are information standards and best practices developed? How can scholarly communications professionals identify what standards are needed, contribute to their development, foster their adoption, and assure their maintenance? This training session will examine — through presentations, group discussions, and exercises — the ingredients that make industry standards as effective and useful as possible. Students will leave feeling confident that they have the understanding and knowledge they need to contribute to improving best practices for both their own organization and the wider information community.
Topics to be covered include:
- An introduction to information standards, standards development organizations (SDOs), and the role that consensus plays – why, what, how?
- Building consensus in information standards development — with guest lecturers representing the three main NISO stakeholder groups – librarians, publishers, and the vendors who serve them. Additional discussions will take into account stakeholders in other industry SDOs.
- Information standards in the community – who’s using what and why, exemplars from an array of SDOs and different stakeholder groups
- How to be an “information standardista” – what are the right standards for you and your organization to adopt, what do you need to implement them, where can you find more information, what else do you need? How do you know when it’s necessary, or better, to propose a new standard?
Audience: Researchers, Librarians, Faculty/Scholars, Publishers, Administrators, Technical Support
W28 – Global Overview of the Scholarly Publishing Landscape: Differences Between the North and the South and Possible Consequences of Plan S
Tom Olyhoek, Miho Funamori, Iryna Kuchma, Kathleen Shearer
Abstract: This course will focus on the publisher-dominated scholarly publishing system in the North – subscription and open access, maintained by publisher-controlled metrics and ranking – versus the community-governed open access publishing system in Latin America, national publicly funded infrastructures in African and European countries and the society-based subscription system and governmental infrastructures in Japan and other Asian countries.. We will talk about 3 examples : AJOL, ScienceAfrique and African Continental platform The various indexing services that provide lists of quality journals will be compared and discussed.
To take the discussion of scholarly publishing systems to the next level, we will build on the “Fostering Bibliodiversity in Scholarly Communications: A Call for Action,” which calls on the community to make concerted efforts to develop strong, community-governed infrastructures that support diversity in scholarly communications (referred to as bibliodiversity). We will examine whether the Call for Action can stop the dominance of a handful of Northern publishers.
In the part of the course on Plan S, we will examine the role that Read and Publish agreements between publishers and governments or institutes play in the transformation to a 100 percent open access publishing system. (Examples Germany, Netherlands, UCLA) We will highlight the growing importance of the Rights to Retention Strategy which offers a way to publish in subscription journals and still comply with Plan S. Finally the way the Plan S journal checker tool (JCT) functions will be discussed (it is in place since late 2020)
We will finish by emphasizing the inherent dangers of Plan S-linked transformative agreements and transformative journals , l and present reasons why we think that adoption of this narrow approach in the North and other areas of the world, notably Latin America and Japan, may lead to a global publishing market again dominated by a handful of Northern publishers who will continue to make very high profits.
Audience: Researchers, Librarians, Faculty/Scholars, Publishers, Administrators
W29- When Global is Local: Decolonized Approaches to Scholarly Communication
Thomas Hervé Mboa Nkoudou, Gimena del Rio Riande, Daniel O'Donnell
Abstract: This course will focus on the practices and experiences of open scholarly production and knowledge exchange, focusing on the possible exclusions and inequities that are always part of global debates. Openness and fast growth of information technology have contributed to reducing many injustices in knowledge dissemination. However, strategies are still needed for positively transforming and opening scholarly communication on a global scale in ways that eliminate systematically biased understandings of participation and scholarly success.
To address this need, postcolonial theories seem to offer a good framework to tackle these threats and educate people involved in scholarly communication on identifying and avoiding colonial practices in scholarly communication. Also, theories related to Global South studies have helped in reflecting on alternative ways of examining local and global questions about scholarly communication.
The course will analyze challenges, highlight initiatives, and explore options to contextualize the open movement from a decolonized, open, and Southern perspective. The emphasis will be on the local contexts and relevancies of participation and impact, including debates related to language(s), publication, technologies, access and reuse, dissemination and outreach, and funding.
The class will offer a mix of lecture and practical work, particularly information gathering and analysis. The emphasis will be on providing frameworks for critical episteme and reflection 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.
W30- Data Curation and Code Review in Service of Scientific Reproducibility
Limor Peer, Thu-Mai Christian, Florio Arguillas
Abstract: In 2019, the National Academies published a consensus study report, Reproducibility and Replicability in Science (https://www.nap.edu/catalog/25303/reproducibility-and-replicability-in-science), that addressed issues of reproducibility and replicability that impact the public trust in science. Defining reproducibility as “obtaining consistent results using the same input data, computational steps, methods, and code, and conditions of analysis,” the report noted the lack of consistency in the quality of research artifacts stored in data repositories—resulting in failed attempts to reproduce analytical findings in published reports.
This course introduces the data curation for reproducibility model of curation in which the object of curation goes beyond the dataset to consider the compendium of research artifacts that includes the dataset, documentation, analysis scripts, and all other materials necessary for full understanding and verification of the research processes that yielded the outputs recorded in the scientific record. This model involves quality review of each of the component parts of the research compendium, including code review, to ensure that materials meet the highest quality standards that support reproducibility.
This course will provide participants foundational knowledge for understanding and engaging in discourses around scientific reproducibility while gaining the practical skills needed to effectively curate research data artifacts that serve as the evidence base for reported scientific findings. This includes the application of rigorous data quality review processes as well as inspection and execution of code. The purpose of the course is to enable information professionals to execute data curation for reproducibility workflows that include code review to ensure the reproducibility of published research.
W31 – Advancing the open science agenda: an introduction to responsible resarch intelligence reporting
Armel Lefebvre, Tung Tung Chan, Antonio Schettino
Abstract: In this course, participants will learn about recent developments in the world of research performance evaluation. Together with the instructors, attendees will also practice how to bridge the principles of open science with research intelligence methods and tools to provide actionable knowledge about open science performance in research institutions. This course will provide the means to let participants explore research intelligence, a growing field of interest for professionals in scholarly communication. By learning and using open science evaluation practices, participants will be able to show research intelligence outcomes to policy makers to foster change in their institution. This course is specifically designed for data stewards, librarians, and policy makers who want to discover new approaches to advance the open science agenda in a data-driven way.
In three sessions, the course will cover the landscape of open science evaluation, show how we can gather research information, apply open science evaluation techniques on analyse data related to research institutions, and discuss the outcomes of such analyzes.
In the first module, Antonio will guide the audience through a general overview of open science with a focus on institutional and funding policies on recognition and rewards and societal impact (particularly in Europe and the Netherlands). He will then review and critically examine some of the evaluation criteria typically used to rank institutions as well as individual researchers and their publications, highlighting the inability of such metrics to reflect the amount of transparency, accountability, and reusability of the scholarly output. Afterwards, he will introduce alternative evaluation frameworks that allow a more comprehensive analysis of the content of research rather than quantitative (publication) metrics. The audience will have the opportunity to engage in live discussions and reflect on how research is evaluated in their own institutions. At the end of this session, participants will have contextualized old and new evaluation criteria and be able to choose appropriate metrics that better map onto desirable principles of transparency, accountability, and reusability of intellectual products.
In the second module, Tung Tung will provide an introduction to research intelligence applications and its recent developments in the evaluation of scholarly outputs. The goal here is to introduce participants to a variety of data sources, present a set of standard and alternative metrics through use cases, and define strategic questions that guide research intelligence efforts. During live sessions, the course participants are expected to work on strategic questions that are relevant to their context, and operationalize performance evaluation using both standard and alternative metrics, open science metrics, as well as reflect on the comparison between outcomes from standard approaches and alternative performance assessments.
The course ends with a guided assignment specifically aimed at retrieving and presenting research intelligence outcomes, and therefore contributing to the implementation of responsible research evaluation for advancing open science. The guided assignment will consist of a recorded step by step example as well as two live sessions led by Armel for discussions and presentations with the course participants. Here, participants will introduce an open science analysis on their own organization, using the techniques and tools presented by Tung Tung in the second part of the course.
At the end of this course, participants will feel at ease with the major developments in research intelligence reporting for open science by learning about the concepts of open science, apply (novel) evaluation techniques and practice with open access research information sources.
Audience: Librarians, Administrators, Data stewards
