Open@VT

As part of Open Access Week, the University Libraries and the Graduate School offered a travel scholarship to OpenCon 2017, a conference for early career researchers on open access, open data, and open educational resources. From a pool of many strong essay applications, we chose Alexis Villacis, a Ph.D. student in Agricultural and Applied Economics. Alexis attended the conference in Berlin, Germany on November 11-13, and sent the report below. Be sure to check out the OpenCon 2017 highlights.

Alexis Villacis writes:

The progress of science and access to education varies widely geographically, and sometimes are very limited due to economic, cultural and social circumstances. Open Access, Open Education, and Open Data are key to support those who are left behind and bring empowerment to the next generation. OpenCon brings together the worldwide champions who are working towards the advancement of the Open Movement. Students, early career academic professionals, and senior researchers all come together under one roof to share their initiatives. Participants hear their inspiring stories, from Canada to Nepal, of sparking change during a three-day conference; a conference I am grateful to have had the opportunity to be part of, as a representative of Virginia Tech.

Over these three days, participants showcased how Open is being advanced around the world. The discussion centered on how often higher education models (knowledge access, research questions, and research funding, among many others) marginalize underrepresented scholars and students. It was thought-provoking and sometimes shocking to hear how our western ways of knowing have colonized access to information and how this has impacted the progress of R&D in other parts of the world.

Sharing with participants from other countries and hearing the challenges they face every day made me contrast our everyday realities and the privilege we have at VT. A privilege we take for granted in our everyday lives, where access to all types of tools, research, and content is one click away through our computers. We, as an institution of higher education, promote and share access to knowledge and new technologies throughout Virginia and beyond. The impact of these transfers is what keeps our society thriving every day, but where would we be if this access were restricted to us? Perhaps, VT as a Land Grant Institution would not exist at all, the state of Virginia would not be what it is today and neither many other parts of the US.

As I walked through the halls of the Max Planck Society, where the conference was held, I kept wondering: is this not what we are doing today? What changes are we withholding from the rest of the world by limiting access to data, knowledge, and education? The essence of this and the significance of Open Access clearly goes beyond journals and data, and it is also about social justice, equity, and the democratization of knowledge. We Hokies can make a difference in Open Access. More importantly, we are the key players called to work towards its advancement.

As research becomes increasingly digital, it’s becoming more important to ensure a findable and unchanging scholarly record.  Researchers are probably familiar with the digital object identifier (DOI), which in URL form provides a persistent link to articles (and more), and libraries and publishers provide redundant archiving to ensure  scholarship is preserved for the long term.

However, it’s also important to make sure links (other than DOIs) in articles work, and to make sure web pages represent what the author saw when she cited them.  Some journals are aware of these issues, and I’ve noticed a few authors who employ URLs from the Internet Archive’s Wayback Machine in their manuscripts.  Thinking back to my last article, there are probably some links that won’t work five (or twenty) years from now, or links resolving to web pages that won’t accurately represent what I was referring to at the time.

These problems are usually referred to as link rot and reference rot.  Link rot means a URL can no longer be found (your browser returns a 404 error); reference rot means the information cited at a URL has either disappeared or changed.  Research has shown 50% of the links in Supreme Court decisions from 1996-2010 had reference rot, one in five articles suffers from reference rot, and three out of four URI references lead to changed content.  In the last article, the authors say these problems raise “significant concerns regarding the long term integrity of the web-based scholarly record.”  In this era of fact-checking and “fake news,”  it’s more important than ever to stabilize the evidence base built in peer-reviewed articles.

To help address this problem, Virginia Tech’s University Libraries is pleased to announce that we are now a registrar for Perma.cc, a service to provide archiving of web pages for research purposes.  Researchers at Virginia Tech will be able to archive, manage, and annotate an unlimited number of web pages with persistent shortlinks for citing, and will also receive local support.

Including a Perma.cc link in a citation or footnote may depend on the citation style you are using, but a general recommendation is to include the original URL, followed by “archived at” and the Perma.cc shortlink, for example:

36. Scott Althaus & Kalev Leetaru, Airbrushing History, American Style, Cline Center for Democracy (Nov. 25, 2008), http://www.clinecenter.illinois.edu/airbrushing_history, archived at http://perma.cc/G8PW-798L.

If you click on the Perma.cc link above, you can see how the web page looks in archived form.  In addition, the time of capture is recorded, there’s a link to the live page, and you can download the archive file (under “show record details”).  Perma.cc is intended for non-commercial scholarly and research purposes that do not infringe or violate anyone’s copyright or other rights.   Web pages to be archived should be freely available without payment or registration.  Additionally, some web pages employ a “noarchive” restriction, which Perma.cc archives but makes private.  In other words, the shortlink can be shared, but is available only to the researcher and upon request.

There are some advantages to using Perma.cc over the Wayback Machine (and the Internet Archive is a supporting partner of Perma.cc). Perma.cc provides a more thorough, accurate capture in two forms, a web archive file (WARC), and a screenshot (PNG).  Perma.cc also provides persistent shortlinks that are more convenient for citing, and enables researcher management of the links (with folders, annotation, and public/private control).

Other features of the Perma.cc system include:

• Researchers will be added as organizations, and can add other users within that organization, such as lab members or collaborators
• A bookmarklet and extension are available for easy use in a browser (users must be logged in)
• Links can be deleted within 24 hours

See more information about creating Perma.cc records and links, and check out the FAQ.  Perma.cc is built by Harvard’s Library Innovation Lab, and in alignment with its focus on preservation, the service has a contingency plan and is also open source.

To get started, send an email to permacc@vt.edu and request an account (or to be added as an unlimited user if you’ve already signed up).  You can also send questions and problems to this address, or you can use the Perma.cc contact form.

As part of Open Access Week, the University Libraries and the Graduate School offered two travel scholarships to OpenCon 2016, a conference for early career researchers on open access, open data, and open educational resources. This is the third year we have jointly supported graduate student travel to the conference. From a pool of many strong essay applications, we chose Mayra Artiles, a Ph.D. candidate in Engineering Education, and Daniel Chen, a Ph.D. candidate in Genetics, Bioinformatics, and Computational Biology. In addition, Mohammed Seyam, a Ph.D. candidate in Computer Science, attended. All were in Washington, D.C. for the conference November 12-14, and sent the reports below. Be sure to check out the OpenCon 2016 highlights.

Mayra Artiles writes:

Being as open as possible – OpenCon 2016

This year I had the opportunity to attend OpenCon 2016 in Washington, DC. When I initially applied for the scholarship, I had a vague idea of how the Open agenda tied into my research and why was it important to me. However, I was not prepared for what the conference would spark. While in the US Open is mainly focused on open access to journals, the global idea of open is as diverse as are our problems. Interacting with people from different parts of the globe, who were amazingly passionate about Open in general, I learned that open access to journal articles is relatively a first world problem. While some countries fight for journal access, many more fight for textbooks and others fight for reliable internet. The more people I met, the more I learned how all of these unique issues are all nested under the large umbrella of making knowledge accessible on a global scale. One of the things that came out of these conversations was my involvement in a collaboration to create OpenCon Latin America – a conference similar to the one we had all just attended but held entirely in Spanish, empowering people and spreading the Open ideal in a language spoken mainly by over 425 million people.

This made me think about the following question: How can we, as Hokies, be as open as possible with our research? While fighting the academic tenure process and breaking the paradigms of open access journals is an endeavor of huge proportions, we can take small steps on being more open every day. We need to be as open as possible and as closed as necessary. It is for this reason I have made a list of steps on how we can be open today. The best part is that all these resources are open:

1. Take stock of all your publications and make a list of the journals you’ve published or plan to publish in.
2. Visit Sherpa Romeo and look up these journals. This page will provide information on which parts of your work are shareable and whether or not there is an embargo on your work. If you’re lucky, you can share a copy of your pre-print.
3. Share as much as possible on repositories such as VTechWorks and other sites such as ResearchGate.
4. Create your impact story at ImpactStory – all you need is an ORCID profile. Our work should mean more than amount of times we get cited. This website shows just that: it will give you a score for how ‘open’ is your work, show how many people saved, shared, tweeted, and cited your work and across how many channels, among other great things. As researchers, we are more than our H-index.
5. Have a conversation with your research peers and advisors on the value of open research. While we can’t convince everybody to suddenly publish in open access, we can begin the conversation and break the paradigms. A great resource to learn more about the value of open research is Why Open Research?

Daniel Chen writes:

What is “open”? Merriam-Webster tells us that it is “having no enclosing or confining barrier: accessible on all or nearly all sides”. For OpenCon, access (to academic publications), education, and data lay at the center of its mission.

The conference brings together a select group of like-minded individuals who are all passionate towards openness. Since the conference was single-tracked, it allowed everyone to focus on the various projects, hurdles, and conversations people have about Open around the world. We had plenty of time and space to roam around American University to continue conversations. I was lucky and privileged enough to be one of the select attendees and represent Virginia Tech.

My road to Open revolves mainly though open education and open data. I teach for Software Carpentry and Data Carpentry and support NumFOCUS. It is logical then, that my definition of Open mainly focuses around open source scientific computing. It’s a very specific subset of Open, and OpenCon helped me remember what role I play in the the larger Open movement.

For me Open Education is teaching the Creative Commons-licensed Software Carpentry material the past 3 years. Over the years, my idea of open education revolved around higher education: textbooks for university students, scientific computing materials for graduate students, resources for open source. I was reminded that open education was not just for the graduate students trying to improve the quality of their research, textbooks and educational materials were not just for university students. Open education is used to teach students from all ages, lesson materials and books for elementary school, textbooks for middle school, high school, and university. It allows students and educators to invest resources in other ways to help foster better learning. Here at Virginia Tech, you may notice OpenStax books in the library, but the Rebus Community is another resource and place to get involved with open education materials.

As a data scientist, I am constantly combining disparate datasets from a myriad of sources to answer a research question. I rely heavily on open data sets. Many cities in the United States now have open data portals (e.g., NYC Open Data), and government agencies, such as the Department of Commerce house a plethora of open datasets. These datasets are great for an analyst such as myself, but open data sources such as OpenStreetMap and ClinicalTrials.gov help with urban planning in cities and provide drug trial data and results to people all over the world.

One of my favorite parts of the conference happened on the second day when we shifted from a single-track conference to an un-conference style meeting. Attendees from the conference pitched various discussion topics, and the attendees of the conference dispersed across the American University Law School. I attended a discussion about openness in academia where we talked how we incorporate it in our academic lives. For some of us (including myself), we are lucky that our advisors understand openness. Most, if not all, of my research code has a MIT Open Source License. Others found the challenge of pushing and fighting for ‘openness’ a way of disrupting the traditional ivory tower philosophy. One attendee was an undergraduate freshman who was trying to understand what openness was and how he can incorporate it as he begins his academic career. This was a great metaphor for what OpenCon stands for, empowering and pushing openness to the next generation.

I also attended the breakout discussion about global health, where we talked about how openness plays a role in improving global health. I met many people who work in the health space, and use open data and open access sources to improve health. For example, Daniel Mietchen from the NIH is part of a global infectious disease response team to build the tools and protocols necessary to respond to the next epidemic. The 2014 Ebola and 2015 Zika outbreaks are recent reminders of how much we can improve our global response to infectious disease outbreaks. In this unconference, we also talked about drug results reporting in at ClinicalTrials.gov. The problem is that even though clinical trials are listed there, not all of the results from the trials are reported after the initial trial listing. This takes away the ability for people looking to educate themselves about various treatment options for a disease, and more pressure is needed to make sure this information is adequately distributed in a timely manner.

Our final day at the conference had everyone in the conference work in groups to talk to various funding agencies and senators about openness. Essentially, we became lobbyists for Open. I was lucky enough to be in two groups. My first group talked with Rachael Florence, PhD, the Program Director of the Research Infrastructure program at the Patient-Centered Outcomes Research Institute (PCORI). We talked about how PCORI’s goal is to make study results and data more widely available, brought up the concerns about disseminating clinical trials results, and generally discussed faster reporting, lowering publication bias, reproducible research, and data sharing. We also talked about what OpenCon was, and intrigued Dr. Florence to attend next year.

My next stop was the office of Virginia Senator Mark Warner. We did not get to talk to him directly, but instead talked to his senior Policy Advisor, Kenneth Johnson, Jr. It was during this discussion that I wished we had more training on being an effective lobbyist. We only make 2 passes around the circle during our meeting. The first was introducing ourselves, and the second was how Open played a role in our lives. There was a small conversation about open data, open access, and open education for the state of Virginia, but I wished we were able to have a longer conversation. Senator Warner is already familiar with many aspects of Open, so not too much convincing was needed, but I worried about how other groups fared.

In the end, I felt OpenCon was a great experience. I made new connections with other people from all over the world, and gained new experiences on how to talk about Open. It has also given me some ideas for a side project about using ClinicalTrials.gov data to reporting rates for various clinical trials. I hope I am lucky enough next year to attend as well, and urge everyone at Virginia Tech to learn about Open, and get involved!

Virginia Tech’s fifth observance of Open Access Week took place October 24-28 with seven events, featuring a panel discussion and talks from two visiting speakers.

The first event of the week featured Brian Hole, who is CEO of Ubiquity Press. An archaeologist by training, he had experienced lack of journal access in places like India. Ubiquity Press was begun to provide a good quality, low cost open publishing platform that would be inclusive of the developing world. While the platform does operate using the sometimes controversial APC model, the costs are low ($400 standard, but can be lower depending on services provided) and are often covered by libraries so there is no cost to author or reader. Ubiquity is also involved in publishing books as well as journals for open research software, several for open data, citizen science, and an upcoming open hardware journal. The platform offers an open peer review option, which four journals have implemented. Currently publishing 42 journals, its platform will be open source, and is itself a fork of the Open Journal Systems open source code. It’s an impressive platform and openness is at its core.

On Monday evening, the forum “For the Public Good: Research Impact and the Promise of Open Access” was held, hosted by Peter Potter (Director of Publishing Strategy, University Libraries) and featuring panelists from a variety of perspectives: graduate students Siddhartha Roy (Civil and Environmental Engineering) and Mohammed Seyam (Computer Science) as well as Montasir Abbas (faculty, Civil and Environmental Engineering), Karen DePauw (Dean of the Graduate School), and Brian Hole (Ubiquity Press). The conversation was wide-ranging, covering pre-prints, publishing costs, metrics, and peer review. Other topics included the importance of open licensing for reuse of scholarly material and the role of openness for a public land-grant university. Faculty open access mandates were briefly addressed, with comments focusing on saving faculty time and showing benefits. Transparency of data and code were a theme, as well as the possibility of researching completely in the open. See the video below for the full forum (and here are Peter’s introductory slides).

Thanks to the University Libraries’ Event Capture Service for the video below.

In the session “Where Can I Post My Publications?” Ginny Pannabecker and I covered the landscape for article archiving, including research networking sites, researcher profiles, disciplinary and institutional repositories, and personal and departmental websites. It’s important to know about journal permissions, which sites can host research as opposed to linking to it, and about limits to sharing and preservation on proprietary platforms. We got great feedback on this session, and one faculty member signed up for an ORCID identifier and used the new EFARS system to deposit scholarship to the VTechWorks faculty collection.

“Publishing Services at Virginia Tech,” hosted by Gail McMillan and Peter Potter covered the journal and conference hosting services provided by the Libraries. Attendees showed particular interest in the student journals hosted, such as Philologia and the Virginia Tech Undergraduate Historical Review (and more are on the way).

We were very pleased that our librarian exchange with the Cape Peninsula University of Technology in Cape Town, South Africa coincided with Open Access Week, since Veliswa Tshetsha focuses on scholarly communication there. Her presentation Access to Research in South Africa gave an overview of open access initiatives in that country as well as on the continent. Recently CPUT signed the Berlin Declaration on Open Access, joining 45 other African universities. The main funding body, the National Research Foundation, like funding bodies in the U.S., is requiring article archiving, supporting article processing charges, and developing a policy on data archiving. Paywalls are only one of the problems contributing to what she referred to as an African “access drought.” Others include telecommunications access, high APC charges in some open access journals, embargoes, and researchers submitting to open access journals with little or no peer review.

The week ended with two sessions regularly offered by the Libraries. In “Scholarly Publishing Trends” I covered a lot of ground, from open science to peer review to ORCID, and Gail McMillan introduced attendees to our Open Access Subvention Fund and its guidelines.

Beyond our own events, there were other developments of note:

• There is a survey for Virginia Tech faculty on open access practices and attitudes that is now available. Help a graduate student on this thesis research!
• A great new tool for finding open research was unveiled, oadoi.org. Enter a DOI and be redirected to an open version- give it a try!
• The federal government’s Office of Science and Technology Policy (OSTP) announced new public access policies for three agencies, and a new working group on open science.

Thanks to all who attended an Open Access Week event, and thanks for reading!

Few areas in scholarly publishing are undergoing the kind of examination and change that peer review is currently undergoing. Healthy debates continue on different models of peer review, incentivizing peer reviewers, and various shades of open peer review, among many other issues. Recently, the second annual Peer Review Week was held, with several webinars available to view.

Since peer review is currently such a dynamic topic, the University Libraries and the Department of Communication are especially pleased to host a talk about peer review in science by Dr. Malte Elson of Ruhr University Bochum. Dr. Elson is a behavioral psychologist with a strong interest in meta-science issues. Dr. Elson has created some innovative outreach projects related to open science, including FlexibleMeasures.com, a site that aggregates flexible and unstandardized uses of outcome measures in research, and JournalReviewer.org (in collaboration with Dr. James Ivory in Virginia Tech’s Department of Communication), a site that aggregates information about journal peer review processes. He is also a co-founder of the Society for Improvement of Psychological Science, which held its first annual conference in Charlottesville in June. Details and a description of his talk, which is open to the public, are below. Please join us! (For faculty desiring NLI credit, please register.)

Wednesday, October 12, 2016, 4:00 pm
Newman Library 207A

Is Peer Review a Good Quality Management System for Science?

Through peer review, the gold standard of quality assessment in scientific publishing, peers have reciprocal influence on academic career trajectories, and on the production and dissemination of knowledge. Considering its importance, it can be quite sobering to assess how little is known about peer review’s effectiveness. Other than being a widely used cachet of credibility, there appears to be a lack of precision in the description of its aims and purpose, and how they can be best achieved.

Conversely, what we do know about peer review suggests that it does not work well: Across disciplines, there is little agreement between reviewers on the quality of submissions. Theoretical fallacies and grievous methodological issues in submissions are frequently not identified. Further, there are characteristics other than scientific merit that can increase the chance of a recommendation to publish, e.g. conformity of results to popular paradigms, or statistical significance.

This talk proposes an empirical approach to peer review, aimed at making evaluation procedures in scientific publishing evidence-based. It will outline ideas for a programmatic study of all parties (authors, reviewers, editors) and materials (manuscripts, evaluations, review systems) involved to ensure that peer review becomes a fair process, rooted in science, to assess and improve research quality.