Why should we work where we live? 28 Jun 2015

At the SciFoo Camp this weekend Erin McKiernan and I moderated an unconference session on the topic Why should we work where we live? This was a spontaneous idea after we had talked about this topic on Friday (Erin lives in Mexico with a job in Canada, I live in Germany and work for an organization in San Francisco).

Persistent Identifiers and URLs 03 Jun 2015

Just like the rest of the internet, much of our scholarly infrastructure is built around the Hypertext Transfer Protocol (HTTP), increasingly HTTPS for security, and soon HTTP/2 for better performance. In this infrastructure Universal Resource Locators (URLs) are essential to locate resources (sic) such as scholarly articles, datasets, researchers, organizations, or grants. Read this recent Thomson Reuters report for a good recent perspective on this topic. While this works for the most part, there are some issues with URLs - not specific to scholarly content, but particularly import here:

Human-readable and machine-readable Persistent Identifiers 27 May 2015

Yesterday Julie McMurry and co-authors published a preprint 10 Simple rules for design, provision, and reuse of persistent identifiers for life science data (McMurry et al., 2015). This is an important paper trying to address a fundamental problem: how can we make persistent identifiers both human-readable and machine-readable? McMurry, J., Blomberg, N., Burdett, T., Conte, N., Dumontier, M., Fellows, D. K., … Parkinson, H. (2015). 10 Simple rules for design, provision, and reuse of persistent identifiers for life science data. doi:10.5281/zenodo.18003

Introducing the Scholarly Markdown Bundle 23 Apr 2015

Using Markdown to author scholarly documents is an attractive alternative to the standard authoring tools Microsoft Word and LaTeX. The feeling shared by many is that Scholarly Markdown is 80% there, and that more effort is needed for the remaining 20% - moving markdown from a niche into the mainstream. What is mainly needed is building tools that connect the existing tools and ideas, resulting in one or more services attractive to a critical number of users. But maybe we also need to rethink the essential parts of Scholarly Markdown. In this post I propose that we expand the concept and define the Scholarly Markdown Bundle.

Blogging Beyond Jekyll 23 Mar 2015

This blog has been on four different platforms since starting in 2007: a custom blogging engine and then Movable Type on Nature Network 2007-2010, Wordpress on the PLOS Blogs Network 2010-2013, and the static blogging engine Jekyll hosted on Github Pages since 2013. It might be time for yet another blogging platform change.

Metadata in Microsoft Word documents 20 Mar 2015

Metadata such as author, title, journal or persistent identifier are essential for scholarly documents, and some of us are spending a significant part of our time adding or fixing metadata. Unfortunately we sometimes don’t pay enough attention to the flow of metadata, i.e. we ignore already existing metadata, or reinvent the wheel in how we describe or store them.

First analysis of software metrics 28 Feb 2015

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.

Why there is no iTunes for science papers 23 Feb 2015

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.

Metrics for scientific software 19 Feb 2015

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.

Manifests and Reference Lists 05 Feb 2015

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 slidedeck of the presentation that summarized the workshop for the other Force15 attendees.

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