Open@VT

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.

Virginia Tech Libraries and the Pamplin College of Business are pleased to announce publication of Fundamentals of Business, a full color, 440+ page free online textbook for Virginia Tech’s Foundations of Business course. This Virginia Tech course averages 14 sections with over 700 students in Fall semesters. The textbook is an open educational resource, and may be customized and redistributed non-commercially with attribution.

The book is the work of Prof. Stephen Skripak and his team of faculty colleagues from the Pamplin College of Business, Anastasia Cortes and Richard Parsons, open education librarian Anita Walz, graphic designers Brian Craig and Trevor Finney, and student peer reviewers Jonathan De Pena, Nina Lindsay, and Sachi Soni. Assistive Technologies consulted on the accessibility of the textbook.

The first openly licensed book of its kind created at Virginia Tech, the book is in direct response to two problems faced by Pamplin’s team of professors: a used edition of the previous textbook was priced as high as $215, and students were not engaged by the previous text.

Skripak and his colleagues started with an openly licensed textbook created in 2011 (licensed with a Creative Commons Attribution-NonCommercial-ShareAlike license) which legally allows modification and non-commercial redistribution with attribution. The team significantly updated, redesigned, and contributed new content to create a learning resource that fits course learning objectives and reduces student textbook costs for this course to zero. Through a grant from the University Libraries, three students were hired to peer review drafts of the text. The team worked together through details of updating data, designing new figures, and ensuring web and print-on-demand ready layout. The resulting work, Fundamentals of Business, is licensed with a
Creative Commons Attribution-NonCommercial-ShareAlike license.

In addition to faculty members’ ability to customize content and resolution of student affordability issues, the availability of an openly licensed text in common, editable file format bodes well for faculty at other institutions seeking to leverage academic freedom in support of student learning and affordability. The book is representative of a larger movement to empower faculty to freely adopt, adapt, and author a myriad of course types. We hope that many other institutions will take advantage of the opportunity to adopt, adapt or remix the book to fit their needs.

Fundamentals of Business is available in VTechWorks, Virginia Tech’s institutional repository, in PDF and editable Microsoft Word formats. Print-on-demand copies are available at the cost of manufacturing and shipping in color and black & white from Lulu Press. The book is also featured in the Open Textbook Library, OER Commons, and MERLOT II.

Credits for cover images:
“Hong Kong Skyscrapers” by Estial, cropped and modified by Trevor Finney CC BY-SA 4.0; “Paris vue d’ensemble tour Eiffel” by Taxiarchos228, cropped and modified by Poke2001 and Trevor Finney CC BY 3.0; “London Bridge” by Skitterphoto, cropped and modified by Trevor Finney, Public Domain; “New York” by Mscamilaalmeida, cropped and modified by Trevor Finney, Public Domain.

Last week Virginia Tech’s University Libraries hosted its inaugural Open Data Week with six programs on a variety of open data topics. The new format builds on last year’s Open Data Day, which incorporated a hackathon and roundtable discussions. However, the weekend scheduling and a conflict with spring break this year spurred us to create a new event friendlier to academic schedules, with programs throughout the week. Though we hadn’t heard of anyone having an Open Data Week before, we know that Virginia Tech is supposed to “Invent The Future,” so we did. Here’s a summary of the week’s programs.

In our first program of the week, Data Anonymization: Lessons from an Millennium Challenge Corporation Impact Evaluation, Ralph P. Hall (Urban Affairs and Planning) and Eric Vance (Director, LISA- Laboratory for Interdisciplinary Statistical Analysis) described their evaluation of a rural water supply project in Mozambique, which involved household surveys (slides, MCC documentation).

The first lesson learned from their evaluation was that everything is linked to the informed consent. The primary takeaway here is the importance of distinguishing between anonymity and confidentiality (see slide 18), the latter of which provides researchers much more flexibility. In addition, there were difficulties with the translation of informed consent into Portuguese and local languages. Other lessons include not underestimating the time required to anonymize data, and designing surveying instruments to minimize anonymization challenges. Unfortunately, the anonymization challenges resulted in an analysis that is not reproducible and data that cannot be shared with a follow-up evaluation team. Data anonymization is a persistent and complex issue that needs to be discussed more frequently, and will certainly be on the agenda of future Open Data Weeks.

Our session on The Freedom of Information Act (FOIA) featured three speakers: Wat Hopkins (Dept. of Communication), Steve Capaldo (University Legal Counsel), and Siddhartha Roy (Flint Water Study team).

Wat Hopkins focused on FOIA in Virginia. FOIA first emerged at the federal level from a 1964 Supreme Court case, and subsequently Virginia was among the first to implement FOIA at the state level in the late 1960s. FOIA laws vary greatly from state to state. In Virginia, FOIA applies to records and meetings. Record requests must receive a response within 5 days and do not need to be in writing (though federal FOIA does require it), and there are around 130 exemptions. Requests must come from a Virginia citizen, or a news organization with circulation or broadcast in some part of the state. For more information, see Virginia’s Freedom of Information Advisory Council, and the Virginia Coalition for Open Government’s FOI Citizens Guide. Ultimately, we can’t be responsible citizens without access to government information.

Steve Capaldo said that since Virginia Tech is a state agency, it is governed by Virginia FOIA. However, the university responds to requests from everyone, not just residents or the media, and will do so within 5 days. There are many exemptions, including some involving research (proprietary or classified research, and grant proposals), personnel records, and records involving security, such as building plans. He emphasized the importance of making requests as specific as possible in order to reduce the time and effort required to respond. And although it’s not required, Capaldo suggested that it can be helpful when requestors explain the context of their request, because sometimes information needs can be met in alternative ways.

Sid Roy, a member of the Flint Water Study team and a graduate student in Civil and Environmental Engineering, described the Flint water crisis which has spanned 18 months and affected 100,000 people. In the process, an EPA employee was silenced and the fallout has included several resignations. The crisis response involved FOIA requests to the city of Flint, the Michigan Department of Environmental Quality, and the EPA. Interestingly, federal FOIA requires an acknowledgement of the request within 2 weeks, but there is no time limit for responding with the requested information. Roy relayed the FOIA advice of the project’s leader, Dr. Marc Edwards: first, be as specific as possible in your request, and second, make requests to a related agency that is not the primary target. For example, the team made FOIA requests to Flint in order to obtain communications and data from EPA. Although we ran out of time to discuss FOIA costs, according to the Flint Water Study GoFundMe page, their FOIA expenses came to $3,180 (while you are on that page, consider a donation!). In short, Roy recommended that FOIA should be in every scientist’s toolbox.

In Library Data Services: Supporting Data-Enabled Teaching and Research @ VT , Andi Ogier gave an overview of the three services offered: education (data management and fluency), curation (capturing context and ensuring reuse), and consulting (embedding informatics methods into research, and teaching about proprietary formats and the need for using open standards). Data Services strives to help researchers have their data achieve impact on the scholarly record, remain useful over time and across disciplines, and have it openly shared for the benefit of humanity. The library helps with data management plans required by funders, and can assign DOIs to datasets. The presentation coincided with the beta release of VTechData, a data repository to help Virginia Tech researchers provide access to and preserve their data.

Show Me the (Open) Data! with librarians Ginny Pannabecker and Andi Ogier was a conversational, exploratory session devoted to identifying open data sets. At the session, they introduced a new guide to finding data, which in addition to listing data sources also includes definitions and information on citing data.

Scraping Websites: How to Automate the Collection of Data from the Web was led by Ben Schoenfeld of Code for New River Valley, a Code for America brigade that meets biweekly to work on civic projects. As the slides explain, some programming skills are needed to effectively obtain and clean up data from websites lacking an API, and the basic steps are outlined. The live demonstration, using local restaurant health inspection data, did a good job of showing what is possible. One of our developers in the library, Keith Gilbertson, wrote a blog post about the session and how he applied the skills he learned to a database of state salaries.

Intro to APIs: What’s an API and How Can I Use One? was led by Neal Feierabend, also of Code for NRV (slides follow the scraping slides with slide 17). After an explanation of what APIs (application programming interfaces) are and what types are available, the live demo explored a few APIs, beginning with the Google Maps API. Use of this API is free up to a certain number of page loads, and usage beyond that requires a fee– a model used by many popular APIs. This is one reason Craigslist switched from Google Maps to OpenStreetMap, which as an open mapping tool enables download of the data. Generally, good APIs are those that are well documented. Both Neal and Ben attested to the value of using Stack Overflow and searching the web when encountering coding problems. After the session I found out there are also web services for data extraction like import.io.

Thanks to all of our presenters and attendees, and please let us know if you have suggestions for Open Data Week programs. We hope to do it again next year!