science

Our team is working with a number of task forces in bioinformatics. Each of those task forces was started to collaborate on the development of a platform for their sub-field: a set of software tools that work together to solve the problems that everyone in the field needs to solve. Developing the platform does not require any newbioinformatics developments: the purpose is to put existing tools together.

The advantage of having these platforms available is obvious:

• to a biologist the advantage consist of having all the de facto standard tools available under the press of a button.
• to a specialist bioinformatics researcher working on a new tool the advantage is that he does not have to deal with the intricacies of all the other tools, and is able to plug his new tool into the platform using well described protocols.

To get to the development of such a platform there is a bootstrapping problem. The situation is like a table with biologists sitting on one side, bioinformaticians at the other side. Above the table, a thick (volcanic?) fog. The layout of the platform is drawn in diagrams on the table: all the tools making up the common work flow, with all their relations. On the side of the bioinformaticians, the diagram shows the concrete tools. Through the fog, they can vaguely see the workflow on the other side of the table. For the biologists, the situation looks completely different: they have a clear view on the concrete workflow they need, but the tools are vague entities that are only visible through the thick fog.

Without good support from a project leader that can listen to people on both sides of the table, the bioinformaticians will try to solve the very concrete problems they encounter on their very concrete individual tools. A little optimization here, a better data storage facility there. None of this is visible for the biologists.

This is why we put project leaders from our engineering team into each of the task forces. They will direct the focus of the bioinformaticians towards more visible changes. Work on common data formats. Work on (common) user interfaces.

Getting things to work together will bootstrap the true collaborative advantages. It will blow away the fog. Suddenly the biologists will be able to see what is going on. They will be able to provide directed feedback. And the bioinformaticians will be able to see the workflow even from their side, and build upon it.

Image credit: Three views of three tables, by EJP Photo on Flickr.

The BiGGrid user event is organized in the Beurs van Berlage in Amsterdam. If you break through the modern glass ceiling, you end up in the old monumental building. #conference

I've never seen as many post-its as on the brainstorm day for Open PHACTS in Manchester. #work #openphacts #conference #postit

Coffee to start the NBIC communication day. #work

Computer infrastructure used in universities is not part of a market, let alone of a "transparent market" in which everyone has a clear view on what alternatives exist and what their relative merits and costs are.

Nobody in a university research group finds it strange to pay for pens and paper.

Nobody in a research group finds it strange to pay for state-of-the art lab equipment.

But very often computer services have been offered for free. Like water, and electricity, they have been discounted into general costs of running the university.

This situation is unsustainable in a world in which life-science research becomes driven by big data. And it also becomes unsustainable in a world where large storage and computer infrastructure suitable for routine jobs can be rented commercially.

The sustainable way to the future is to properly budget for data handling and storage. Budgeting for computing needs means people are required to balance cost and value, like with every other aspect of a research project.

Photo: CC-BY-SA-NC on Flickr by John Flinchbaugh

Some of the computing services at universities become paid services. And the primary reaction in the science groups often is a fight because the realistic costs of operating the existing infrastructure are high. And if the fight does not work, there is a flight towards running decentralized infrastructure. This can look cheaper but maintenance and incident control are rarely accounted for.

We will need good documentation to convince people of the true costs of the alternatives. It is such a waste if the rare time of good bioinformatics experts is spent on inefficient server management.

Photo: CC-BY-SA, Hollingsworth on flickr.com

The #conference hall for the Galaxy community Conference in Lunteren is #packed! #usegalaxy

Two planets and a very thin slice of moon in the early evening.

#astronomy

NBIC hackathon just started. What can we interconnect? #nbic #hackathon #work

Via twitter, I saw a very cynical remark about asking questions after a scientific lecture with a flow diagram discouraging most people to ask anything at all. This does not at all correspond to my experience organizing symposia and conferences. Most of the time, questions are very welcome, and people are way too shy to share their visions. I therefore made a rebuttal in the form of the following flow diagram which I think is a better representation of the line of thought to follow.

Many people went outside for lunch at the #nbic #conference…. But it is still quiet. Have they disappeared in the woods? #summer

Quality of software workshop at the fifth NBIC conference. The topic is introduced by Machiel Jansen from SARA. #nbic5

A partial solar eclipse at the opposite side of our street. #home #eclipse

I have been grabbed (a bit late) by the December 2003 Puzzling Adventures by Dennis E. Shasha in Scientific American: the surprising strings.

#momentum #ngi #conference

Chemistry as a noun has two completely distinct meanings in every day life:

• A good social relationship: 

 "It was visible that there was chemistry between those two people"

• Something related to a compound that is supposedly bad for people or the environment. "Chemical" is often used as synomymous with poisonous:  

"A chemical leaked from the container into the sea, endangering the fish"

How come these two meanings of the same word have such extremely different connotations? After all, the scientific word chemistry represents any kind of reaction between two compounds and does not have any positive nor negative meaning in itself. Water is a chemical. Life is chemistry.

As a chemist, I wish I could change the negative connotation of molecular chemistry in the news. But if I really do not succeed, maybe I can influence the social meaning of chemistry to make things consistent:

"There was chemistry between those two! When they first met, she tried to poison him. As soon as he recovered he exploded in anger."

 Somehow I feel this would not be as satisfying.

[image credit: Nic McPhee on flickr]