Sunday, July 7, 2013

An Hourglass representing Research and Technology

The programming we choose to do in our team is like the neck in the hourglass representing life science research and technology:
  • There are many grains of sand above us. Those represent all the software tools developed in life science research.
  • There is a large void below us. This represents the need for widely applicable tools in the life sciences.
  • At the bottom there are also grains of sand. They are well settled. These represent the current technology: commercially available tools and well-serviced open source packages.
How does the sand get from the top to the bottom? Via the neck of development. It is narrow; only few academic tools make it to the bottom. The flow through the neck is powered by:
  • push: a few academic groups that have the capability and capacity to make their tools available
  • pull: a few companies that look far ahead and are able to see and use the potential of an academic tool
In our hourglass of life science tools, new sand is being added at the top all the time. And most of it overflows the beaker after a while. Some tools never deliver what the author thought they would do. Some are made to solve a single problem and rightfully abandoned when that is done. But many tools are published and left as orphans. Only a selection of tools that promise to be useful for a larger audience ever make it to the neck.

In practice, the neck is too narrow. There are many more valuable tools than are taken up. A team like ours can help to make the neck larger by making existing research tools applicable for wider use as a service to life scientists with a clear need (we call it professionalization). But it is sometimes hard to convince funding parties to pay for this. It is also hard to convince researchers to work on making their software better: professionalization does not generate new high-impact papers. We work on convincing the funding parties that it is better to professionalize existing successes than to reinvent them using research money. And we work on convincing the scientists that professionalization of their output will lead to higher citation scores on their existing publications.

Science wants novelty. And the current Dutch finance climate is directed towards applied science, towards innovation in society. Look at the picture, and you can see that these are hard to combine. Innovation starts where novelty ends. The only way to make the combination is to include development.

Photo by graymalkn on flickr

Saturday, March 30, 2013

Fight or flight reactions to the cost of computing

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

Sunday, February 24, 2013

Commodies are not free

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