chem-bla-ics: January 2011

GitHub Tip: download commits as patches

Some time ago, the brilliant GitHub people gave me the following tip. Rajarshi is lazy, and might find it interesting. By appending .patch to the commit URL, a commit can easily be downloaded as patch. That way, developers can easily download it with wget or curl and apply it locally with git am, without having the fetch the full repository.

For example, Dmitry made this commit in his branch, having the URL https://github.com/dmak/cdk/commit/9b0478d50c7b5ca10f77fb01d89329db5fe80625. The patch for this commit can then be downloaded at this URL https://github.com/dmak/cdk/commit/9b0478d50c7b5ca10f77fb01d89329db5fe80625.patch.

Willighagen, E. (2011, January 30). GitHub Tip: download commits as patches. Chem-bla-ics.

Jan

My professional network (according to LinkedIn)

LinkedIn has a nice new visualization app, InMaps. I quite like LinkedIn, though not all aspects, but most anyway. I particularly like it focuses on work-relationships. This new app visualizes my professional network, and colors it by network organization:

This one is just a static image, but as creator, you get a zoomable and interactive version. In the image I have labeled the various colored groups that were mined in my network. It is nice to see my positions to show up.

Jan

"Atomic weights are not constant" !!!

In case you missed it, "standard atomic weights are not constants of nature" (doi:10.1351/PAC-REP-10-09-14)! Wow, chemistry upside down. This is bigger than the new arsenic life they found!

Calm down, calm down. Nothing to see here, move on.

It was actually news a some weeks back, but a tweet by @MatToddChem and a question by Antony on the Blue Obelisk eXchange, made me write up this post.

Facts: 1. atomic weights have never been constant; 2. isotopic weight are constants of nature.

Jan

GitToDo Install Guide #1: the command line utilities

Some years ago I was in need of a todo list tool. Of course, the requirements were simple: distributed, version controlled, command line support (I must be able to access it with minimal requirements). I also hooked it up with the Freemind mindmapping tool. I am in the process of installing it on my new laptop, so thought a walk-through might be useful.

Jan

Is Nature really clueless about Blogs, Twitter, etc? WTF ?!

My apologies for this rant in the early morning, but WTF?? (what the fuzz??) I just got pointed to this Peer review: Trial by Twitter (doi:10.1038/469286a) by Mandavilli. Cool title, but before I even finished seventeen words of the intro... WTF?? Here it is:

Blogs and tweets are ripping papers apart within days of publication, leaving researchers unsure how to react.

Jan

Re: How can cancer research be open-sourced?

Mark asked on Quora on how can cancer research be open-sourced. So, far I found Quora to be rather noisy, even after signing up only to science related groups, themes, whatever it is called. However, every now and then there is an interesting question like this one.

The question resonated with discussions I had earlier this week. During Peter's Symposium the discussion was restarted on why publishing data in databases is currently not rewarded.

Jan

The 9th International Conference on Chemical Structures (ICCS)

Later this year the ninth International Conference on Chemical Structures (ICSS) conference will be held in the Netherlands. I had the pleasure of joining this meeting, I think, eight years ago, when I was doing my PhD in Nijmegen.

Jan

#pmrhack and #pmrsymp (or: what to do the next days?)

The next few days there will be a disturbance of the force: #pmrhack and #pmrsymp. Because I have an important meeting early next week in my new position, I am unable to attend these events.

Jan

Karolinska Institutet

Hi all, and a happy 2011! After a turbulent December (finishing up in the Oscar project), holidays, etc, I am starting to get some sense of organization in my new position at the Institutet för miljömedicin at the Karolinska Institutet in Stockholm. I will be using cheminformatics and chemometrics methods in toxicology studies, and work in the groups of Prof. Roland Grafström and Prof. Bengt Fadeel.

The actual work will crystallize in the next weeks, but here are two pointers.