Reviews, organization, rewrites

Today’s a mixed bag of activities. Finished a journal review, comments confidential, recorded in my reviewed papers archive.  I then organized documents library (more below) and then back to paper revisions.

The reference manager software Mendeley recently upgraded the way it handles groups and sharing, and I’ve been waiting to revise how it impacts my workflow around articles.  Articles can be organized into folders (collections) or kept unsorted within the library,  and can be part of as multiple collections.  Completely independent of this organization, articles can also be added to groups.  Articles added only to a group are still considered unsorted in terms of collections.  Groups can be public or private.  Public groups can have members and followers, and can be moderated or open.   I sort papers by the broad topics I am interested in. The challenge here is to find topics narrow enough to be useful but broad enough that articles can be easily classified, neither falling between the gaps or  falling into too many categories.  In this way, my organizational scheme reflects the use of categories in my lab notebook.  Unfortunately, while I have the option of tags, I do not have the option of sub-categories.  Further, it is harder to browse one’s list of tags in Mendeley than here in Wordpress.  Also, the categories I read extend somewhat beyond the categories I normally work in.  How many categories are useful?

Here’s how I’ve chosen to break it down so far:

  • Phylogenetic Methods – anything I’m reading pertaining to phylogenetic methods development and application.  This focuses primarily on comparative methods, primarily in continuous traits.  But this also includes comparative methods in discrete traits, rates of diversification (branching), inferring phylogenies from DNA data, and inferring divergence times from phylogenies.    I’ve pulled some highlights from this focus into a separate group (below).  A separate but related alternative might be an adaptive radiations list, which would stretch beyond phylogenetic literature as well.

  • A special focus subset of my phylogenetics collection focuses on those examples that show evolutionary regime shifts – again, primarily in continuous traits (methods like Brownie or OUCH), but also in diversification/branching.  Represents most of my personal focus out of the broader above category.

  • Theoretical Ecology.  Articles on theoretical ecology and modeling. The public list is a kind of best-of subset drawn from all of the theoretical ecology literature in my collection. Dominant themes include persistence and coexistence results, stochasticity, and population-level dynamics. The list is significantly biased to my own focus and interest rather than a more broad view.

  • Early Warning Signs is another collection and public group.  Properly a subset of theoretical ecology, just as regime shifts are a subset of Phylogenetics.

  • Math Methods and Model Inference is a collection of papers on some of the methods central to my research.  Currently the collection has two major themes – stochastic processes theory and approximations following Thomas Kurtz, van Kampen and others, and likelihood and Bayesian inference of models.

  • Education Research papers on effective teaching methods, with focus on science education and active learning.

  • Future of Science Articles on the process of science, with emphasis on Open Science, Open Access, Open Source, Science2.0, collaborative research, large databases, reproducible results, and high-performance computing.

Before the update, I simply curated my collection and it generated a feed.  Some of the articles fell outside the original definitions I’d set for the collections, phylogenetic comparative methods becoming all phylogenetic methods, and stochastic population dynamics becoming pretty much anything in theoretical ecology, though both reflecting primarily their original titles.  Now I find myself curating both the public groups and the list.  In some ways this is good, since I can have a lower threshold to add something to my own list then to a public collection.

There are some challenges to keeping both lists updated.  When I select an article, I can immediately see which collections it’s in due to the highlighting of the labels, but not which groups it has been included in.  It seems a group is an independent copy of the article with its own timestamp, etc, and edits to the metadata of one do not impact the other.  In some ways this is good – allows private copy and a public copy of notes on the article.  But in tracking it is annoying that the objects are not the same and I cannot easily check if an article in a collection is in a group or vice versa.  Another challenge is that duplicates aren’t removed automatically, either in groups or collections.