chem-bla-ics: September 2014

Slides at the Open PHACTS community workshop (June 26)

It seems had not posted my slides yet of the presentation at the 6th Open PHACTS community workshop. At this meeting I gave an overview of the Programming in the Life Sciences course we give to 2nd and 3rd year students of the Maastricht Science Programme (MSP; some participants graduated this summer, see the photo on the right side).

This course will again be given this year, starting in about a month from now, and I am looking forward to all the cool apps the students come up with! Given that the Open PHACTS API has been extended with pathways and disease information, they will likely be even cooler than last year.

Sep

OpenTox Europe 2014 presentation: "Open PHACTS: solutions and the foundation"

Where the OpenTox Europe 2013 presentation focused on the technical layers of Open PHACTS, this presentation addressed a key knowledge management solution to scientific questions and the Open PHACTS Foundation. I stress here too, as in the slides, that the presentation is on behalf of the full consortium!

For the knowledge management, I think Open PHACTS did really interested work in the field of "identity" and am happy to have been involved in this [Brenninkmeijer2012].

Sep

Do a postdoc with eNanoMapper

Details will still have to follow as they are being worked out, but with Cristian Munteanu having accepted an associate professorship, I need a new postdoc to fill his place, and I am reopening the position I had almost a year ago.

Sep

CDK: Element and Isotope information

When reading files the format in one way or another has implicit information you may need for some algorithms. Element and isotope information is a key example. Typically, the element symbol is provided in the file, but not the mass number or isotope implied. You would need to read the format specification what properties are implicitly meant. The idea here is that information about elements and isotopes is pretty standardized by other organizations such as the IUPAC.

Sep

CDK 1.5.8, Zenodo, GitHub, and DOIs

John released CDK 1.5.8, which has a few nice goodies, like a new renderer. The full changelog is available. Interesting aspect of this release is, that it uses one ZENODO to make the release citable with a DOI. And that is relevant because it simplifies (making it a lot cheaper!) to track the impact of it, e.g. with #altmetrics. And that matters too, because no one really has a clue on how to decide which scientist is better than another, and which scientist should and should not get funding.

Sep

Open knowledge dissemination (with @IFTTT)

An important part of science is communication. That is why we publish. New insights are useless if they sit on some desk. Instead, reuse counts. This communication is not just about the facts, but also a means to establish research networks. Efficient research requires this: you cannot be an expert in everything or at least not be experienced with everything. That is, for most things you do, there is another researcher that can do it faster.

Sep

First steps in Open Notebook Science

I blogged a few weeks back I blogged about my first Open Notebook Science entry. The post suggest I will look at a few ONS service providers, but, honestly, Open Notebook Science Network serves my needs well.

What I have in mind, and will soon advocate, is that the total synthesis approach from organic chemistry fits chem- and bioinformatics research. It may not be perfect, and perhaps somewhat artificial (no pun intended), but I like the idea.