Sunday: Mendeley, Workflow Classification

I’ve decided that the act of writing these things at the end of the day is actually a bit of a put-off, for me. It seems like an extra task, on top of what I am doing, just remembering what I am doing. So, hopefully, from now on I will try to keep these open in another window, publish them as I go and not on a day-to-day basis, and just use them like I would otherwise use an EtherPad. I’ve added the Open Science Notebooks icon to the sidebar. For a better description of what I plan to do, see who I plan to copy – in particular, Carl Boettiger’s page on why and how he uses an open notebook. I’ll be doing the same thing. Apart from this, I also use a Mendeley group – look there for updates as to what I am reading.

I’ve now sent out emails to Kepler-users, Taverna-users, Ecoinformatics, LTER, and Ecolog asking for feedback and help, either with recommendations of articles, or with actual workflows. I’ve gotten a few results, but by far the most results have come from direct email – and from direct twitter messages. I set up a Mendeley open group for Scientific Workflows and Workflow Systems, and already have seven followers, a few more personal connections, and at least one additional article I wouldn’t have otherwise gotten, from Jonathan Eisen (UC Davis). Eisen is (from what I’ve gathered, anyway) pretty big in the field of microbiology, so it is fairly interesting to me that he’s only published one article using a workflow out of 209 articles. This isn’t a very good sign for their use! Particular as the article in question, “Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences,” seems to be about a workflow itself, and not about it’s use. It may be that he’s been using them all along, and this is just the one time that he published specifically on them.