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The LIINES Commitment to Open-Information

Good science is reproducible.   This means that it must be publicly available, its contributions transparently communicated, and its data accessible.  These are principles that drive the everyday work of every individual’s research at the LIINES.  We now wish to go further and make a commitment to Open-Information.
Beginning today, the LIINES will seek to leverage its website to make all of its research 100% reproducible by the public at large.   This includes:
  • Sharing all input datasets used to conduct the research for which no prior proprietary or security commitments have been made.
  • Producing scientific publications in such a way that scientific peers can accurately verify & validate the work.
  • Making the content of all conference, journal and book-chapter publications freely available in author preprint form.  (Note: Most publishers allow self-archiving and open-distribution of author preprints).
We believe that the LIINES’ research has broad applicability to academia, industry, government and the public at large.   However, traditional publication venues are often only subscribed by academic universities and a handful of well-funded industrial companies.   All-too-often the people that can benefit from this work, never get a chance to see it.   This slows down the work’s potential impact and is counter to the LIINES mission.   It is for these reasons, that the LIINES makes its Open-Information commitment.
While it is natural that making all of this information available will take some time, we will be sure to keep blogging to keep you up to date of new additions to the LIINES website.  For now, feel free to visit the LIINES Datasets Repository which includes both data from our publications as well as a collation of several relevant and openly available datasets.

Mendeley @ the LIINES

Reference management is a key competence in any research group or laboratory.   Think of a research workflow.

  1. Get papers
  2. Get paper reference information
  3. Read them from anywhere in the world.  Take notes.
  4. Share them with colleagues
  5. Do the research – referring to papers as required.
  6. Cite the papers easily in any document preparation system.
  7. Build the reference list easily and accurately.
  8. Be ready to change the reference list in subsequent revisions.
Reference management supports all steps of the research flow and can save dozens of hours for any given paper.  This compounds with the numbers of papers that are produced every year and the number of researchers and collaborators with whom you work.  Despite the associated controversies  journal editors and academic departments will continue to increasingly use bibliometric analysis in key decisions.  Therefore, systematic approaches to reference management is even more necessary.
At the LIINES, we use Mendeley in 2011 after a migration from EndNote.  While EndNote had been the default reference management software for many years, it did have several key disadvantages which others have also noted.
  1. Cost:  Endnote required a license for every LIINES researcher at a relatively hefty price tag.  Sharing with collaborators was an every harder proposition.  Furthermore, yearly upgrade licenses was an even tougher pill to swallow.
  2. PDF Organization:  Managing the filesystem associated with PDF files of all the references is a big challenge.  EndNote did not provide a headache-free solution to this.  Even worse, an EndNote database could lose links to PDF files making it quite difficult to find again.
  3. Collaboration & Sharing:  The above challenges were compounded when it came to share Endnote Libraries across the LIINES.  Endnote sharing through Dropbox across multiple operating systems can get quite hairy!
  4. Proprietary Platform & Database:  When reference databases get large, one increasingly becomes interested in automating tasks for its management.   While EndNote does provide plenty of built in automated functionality, the power user ultimately does need to manage records automatically.
Of course, when migrating from one reference management system to another, it is important to make an educated well-researched decision.  The folks at PhdOnTrack.net have provided an excellent introduction.  The University of Rhode Island library has made a comparison of leading options, while Wikipedia provide a comprehensive comparison
Ultimately, Mendeley did come out on top @ the LIINES for a number of reasons.
  1. Cost:  The Mendeley desktop application is free!  This meant that every LIINES researcher could work individually without paying a penny.  That said, the associated cost was in the cloud-based monthly data storage plan.   While this was a recurring cost, Mendeley’s “Solar System”, “Milky Way”, and “Big Bang” subscription plans were very much priced reasonably.   Since Elsevier’s purchase of Mendeley, the cost of new plans has risen; perhaps out of reach for many.  Fortunately, with a little computer savvy one could also use other cloud-based storage services like Dropbox or Google Drive to easily store and share reference libraries.  Alternatively, many institutions including MIT have recognized the need to provide a uniform platform for their researchers and so have purchased Mendeley Institutional Edition.
  2. PDF Organization:  Probably one of Mendeley’s strongest features is its ability to automatically name and organize PDF files based upon key reference information such as Author Name, Year, and Title.  This became a headache free solution.
  3. Collaboration & Sharing:  Another real strength of Mendeley’s is its recognition of Web 2.0 and social media.   Mendeley databases are easily shared and synchronized between multiple computers, operating systems, tablets, smart phones, and users in a seamless way.   For the LIINES, this meant native support for Windows, Mac OS X, Linux, iOS, and Android for dozens of researchers across the world.
  4. Standard Database:  Finally, Mendeley’s database is written in SQL.  This meant that for the advanced database programmer, Mendeley offers the potential to develop automated scripts to manage reference data.  This particular strength overcomes some of the feature limitations within the Mendeley desktop application itself.
And yet, the migration to Mendeley was not without its disadvantages.
  1. Integration with LatTeX/BibTex:  Mendeley is able to create and maintain an automatically synced BibTeX database file.  However, it provides no user control to the highly important Citation Key!  In the course of regular use, Mendeley can change these citation keys which will then cause LaTeX citation links to break in your document.  Make sure to keep backups of your BibTeX database unless you want to redo all the links!
  2. PDF File Import:  The jury is still out on this one. Mendeley can directly import PDF files.  It will scan the PDF for reference information and insert it into the database.  For many files of standard format (e.g. IEEE, Elsevier journals), it does this accurately.  However, for many others, it creates lots of errors; forcing the researcher to manually correct the information.  At the LIINES, we recommend going to established online reference databases (IEEE XploreScienceDirectCompendex & Google Scholar  to download the associated .ris or .bib files instead.
  3. Batched PDF Import:  Many researchers new to reference management have troves of organized pdf files.  Others are migrating to Mendeley.  Beware that a batch PDF import can create lots of duplicates in the Mendeley database!
  4. Duplicates Management:  Mendeley desktop does provide a “Check for Duplicates” feature but in then requires manual deletion of these duplicates.  For large databases, this can be very time consuming.
  5. Association with Elsevier:  Finally, some academics have chosen to boycott Elsevier’s service on ethical grounds.  Others distinguish Mendeley from its parent company, and then there is official Mendeley perspective from William Gunn   While the LIINES does not participate in this boycott, we recognize its existence out of academic respect and encourage awareness amongst our readership.  Ultimately, one must recognize that Mendeley is now a fully commercial product and service.  For those that maintain reservations, many highly functional, free and open-source reference management solutions continue to exist.
We hope to return to some of these weakness in coming blog posts.

IEEE Statement on Appropriate use of Bibliometric Indicators

The use of bibliometric analysis has become an increasing part of scientific publishing today.   While bibliometric analysis has brought about a degree of quantified objectivity, many have raised concerns about the potential pitfalls of their usage.   We refer our LIINES readership to the recent IEEE Statement on the Appropriate use of Bibliometric Indicators.   The associated video can be found below.



LIINES Website: http://amfarid.scripts.mit.edu