Last week I wrote about software.lagotto.io, an instance of the lagotto open source software collecting metrics for the about 1,400 software repositories included in Sciencetoolbox. In this post I want to report the first results analyzing the data. If you want to follow along, please go to https://github.com/mfenner/software-analysis, this repository holds all the data, as well as the R code used for analysis.

The iTunes Store was opened by Apple in 2003 to sell digital music and other digital assets. Since 2009 music purchased in the iTunes store is free of Digital Rights Management (DRM). Apple became the largest music vendor worldwide in 2010, and by 2013 had sold 25 billion songs. Scholarly articles are distributed almost exclusively in digital form.

One of the challenges of collecting metrics for scholarly outputs is persistent identifiers. For journal articles the Digital Object Identifier (DOI) has become the de-facto standard, other popular identifiers are the pmid from PubMed, the identifiers used by Scopus and Web of Science, and the arxiv ID for ArXiV preprints. For other research outputs the picture is less clear.

Last month at the Force15 conference in Oxford Ian Mulvany and I ran a workshop on data citation support in reference managers. The report of that workshop isn’t done yet, but I can say that it was a success - we now have a pretty good idea what the problems are and what needs to be done to fix them. The short summary of the workshop is in this slide deck of the presentation that summarized the workshop for the other Force15 attendees.

This is the title of an upcoming workshop next Sunday organized by Ian Mulvany and myself. The workshop is a pre-conference event of the Force15 conference in Oxford. This blog post summarizes some of the issues and work that needs to be done.

In a blog post two weeks ago I argued for the need for reference managers to properly support data citation, if we want data citation to become a standard activity. I am happy to announce two events working towards that goal.

This year’s SpotOn London conference takes place November 14-15 and the registration has opened this Monday. I am helping organize this conference since 2009, and I again look forward to the sessions, and - more importantly - the discussions with people in and between sessions this year.

In my last post I wrote about the importance of keeping things simple in scholarly publishing, today I want to go into more detail with one example: citations in scholarly documents. Citations are an essential part of scholarly documents, and they are summarized in the references section at the end of the article or book chapter. The problem is that not everything that is cited in a scholarly document ends up in the references list.

Doing scientific research is becoming increasingly complex, both in terms of the tools and technologies used, and in the collaboration across disciplines and locations that is increasingly commonplace. While the way we write up and publish research is of course also very different from 25 years ago, I would argue that our tools and services haven’t quite evolved at the same pace.

One of the important outcomes of the Markdown for Science workshop that took place in June 2013 was a decision on a name - Scholarly Markdown - and a brief definition: 1. Markdown that supports the requirements of scientific texts 2. Markdown as format that glues open scientific text resources together 3. A reference implementation with documentation and tests 4. A community In my eyes this is still a great definition.

One of the major challenges of writing a journal article is to keep track of versions - both the different versions you create as the document progresses, and to merge in the changes made by your collaborators. For most academics Microsoft Word is the default writing tool, and it is both very good and very bad in this.