researchr on Linux (Addemdum to Computer-aided Scientific Workflow)


In my last blog entry, I presented the extemporary, yet neat solution for an academic workflow, which was unfortunately limited to Mac. Though I own a MacBook myself, I am also very passionate about Linux and like to find solutions that are plattform-independent.

I already suspected, that given setup should be easily portable to Linux, only the Open Source tools Skim and BibDesk would take some deeper programming, as they depend on the Cocoa Library. But one could find alternatives:

So the presented workflow should be more or less reproducible on a Linux system. Get a feel for why this workflow is – in my opinion – ingenious, and then try porting it to Linux. The community of scientists using Linux will most definitely appreciate it.

One way to replace Skim and BibDesk would be to turn to an integrated solution, such as the Cross-Platform solution Mendeley, which uses the Qt framework and is therefor available for Linux, Mac and Windows. It is similar to Papers, but in my opinion, Mendeley seems to be much leaner. It also offers some social-network features, that other reference management systems lack.

The Ph.D. student Bodong Chen (who incidentally also studies at the University of Toronto) tried it, and seems to have succeeded. On his researchr-Wiki he gives some pointers on how it’s done (and it seems, like he also tried to do so on Windows, but as I suspected, there seems to be no success).

So, to all you Linux-Heads out there, here’s a solution for you, too. Try it out, make it better, document it, and give me a link, if you do 😉

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Computer-aided Scientific Workflow


In Hamburg (at least ten years ago) when you went to Gymnasium, at some point you would learn about something called methodological competences, a “learn to learn” course showing you how to conduct research for the topic of interest, how to then efficiently read through texts, take notes, organize these notes and finally – as a preparation for the finals – how to learn and present these things.

It was this course, that at our school was thought in a two weeks seminar on Sylt, that got me interested in this topic. Of course, in 1999, when we had that course, it was still all about the analogue world – literature was obtained at the library (we even learned how books are sorted in the Staatsbibliothek), texts were photocopied, we were told to use highlighters, write flashcards, etc. Still every now and then when my interest on this topic awoke again, I started reading about new ideas on how to efficiently and effectively process knowledge that you obtain while reading and how to preserve this knowledge in a way that makes it usable even in ten years time. Now the most famous person managing this would be Niclas Luhman who was meticulously writing down every thought on every book he ever read onto little papers, numbering and tagging them, keeping handwritten indices in lookup-table. In many interviews he explained how he worked, stating, that he wouldn’t even need to write a book anymore – with this system, called Zettelkasten he’d look up important words, and the story would tell itself. He even spoke of it as a person with whom he was leading a discussion – his alter ego (see this German article on Sciencegarden as well as the following interview).

After his dead in 1998 the Bielefeld University bought the Zettelkasten from the heir: 20 000 sheets, in 80 boxes, everything Luhman was thinking in his lifetime – and as he was well recognized for his works, this was treated as the holy grail of wisdom on sociological systems theory, and as far as I know it’s even analyzed today.

But what to do, when you don’t have that much time? When you simply cannot afford to spend your every days evenings creating, tagging, indexing and sorting new sheets of papers into a giganteous pile, that most people would rather consider to be the symptoms of a hoarding personality disorder?

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