chem-bla-ics: April 2016

Sci-Hub succeeds where publishers fail (open and closed)

Knowledge dissemination is a thing. It's not easy. In fact, it's a major challenge. Traditional routes are not efficient anymore, where they were 200 years ago. The world has moved on; the publishing industry has not. I have written plenty in this blog about how the publishers could catch up, and while this is happening, progress is (too) slow.

The changes are not only technical, but also social. Several publishers still believe we live in a industrial area, where the world has moved on into a knowledge era. More people are mining and servicing data than there are making physical things (think about that!). Access to knowledge matters, and dealing with data and knowledge stopped being something specific for academic and other research institutes many, many years ago.

Apr

Programming in the Life Sciences #22: jsFiddle

My son pointed me to jsFiddle which allows you to edit JavaScript snippets and run them. I have heard of them before, but never really got time for it. But I'm genuinely impressed with the stuff he is doing, and finally wanted to try sharing JavaScript snippets online, particularly, because I had to update the course description of Programming in the Life Sciences. In this course the students work with JavaScript and there are a number of example, but that has a lot of HTML boiler plate code.

Apr

Splitting up Bioclipse Groovy scripts

... without writing additional script managers (see doi:10.1186/1471-2105-10-397). That was what I was after. I found that by using evaluate() you could load additional code. Only requirements, you wrap stuff in a class, and the filename need to match the class name. So, you put stuff in a class SomeName and safe that in a Bioclipse project (e.g. SomeProject/) with the name SomeName.groovy.

Apr

Still a draft: The Amsterdam Call for Action on Open Science

It was on the agenda: "Presenting the Amsterdam Call for Action". However, a day of hard work by some 300 participants of the Dutch Presidency's meeting on Open Science did not allow for the draft to be finalized today. Instead, the editors will work the next 24h (a bit less by now) on a new draft that will be send around to the participants which will then have about a week to send in further comments.

Apr

The Amsterdam Call for Action on Open Science #2: 10% Open Science

Some of the discussions here are about data sensitivity, privacy, etc. Excellent points! One confusion that should be put aside is that you cannot be an open scientist if you do not release everything. That is nonsense, FUD perhaps.

The The Amsterdam Call for Action on Open Science may very well set some goals; I do not think it currently does. It may set a goal of 10% by the end of this year (already made, probably), 20% at the end of 2018, and 30% at the end of H2020.

Apr

The Amsterdam Call for Action on Open Science

First, it is very regrettable the participants of #EU2016NL #openaccess did not get access to The Amsterdam Call for Action on Open Science document (read it in this Trello) until minutes before the break out sessions. So, I am still reading it (it's 21 pages), while in the Innovation session, which will only discuss actions #8 and #9.

Here's the first page:

All participants split up in various break out sessions, and I ended up in the Innovation session.