Academic software

A lot of very good software in academia is developed by PhD students or post-docs. Both groups have temporary contracts, and very often the software dies at the end of the contract.

One can compare academic software with a Formula 1 race car: it is very fast, beautiful, technologically advanced. But it is very difficult to drive and needs frequent service. The only way of keeping it on the road is to have the driver and the designer working closely together.

To make it possible to use the technology that is developed for the Formula 1 race car in practice, the car must be redesigned:

  1. It must be possible for anyone with a normal drivers license to drive it.
  2. It has to be possible to drive on different types of road, not only a polished race track.
  3. It must be possible for a regular trained service engineer to service it.
  4. The service interval must be raised from 200 km to 25000 km.

It is obvious that in car design, these changes are not the responsibility of the designers in the Formula 1 team. There are other designers that are specialized in normal cars.

The equivalent concepts in software design are:

  1. The program must be made user-friendly. It must be usable by casual users that are not also computer hackers.
  2. It must be robust enough to work on real data as encountered by real users.
  3. Running and installation must be well documented.
  4. It must be able to run unsupervised for many data sets and not break down after limited time e.g. through a seemingly unrelated upgrade to the operating system or a minor change to an underlying web service.

Funny enough, in many larger projects it is expected that the designers of the Formula 1 software will also do this redesign. This is a strong contrast with car design! In NBIC-II we will not make this mistake. Taking software the extra step will be one of the important tasks of our Central Engineering Team. And this team will contain specialists in industrial strength software engineering.

We will turn the Ferraris into Volkswagens. And we will be proud of them!

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We have a business plan!

This week, the Management Team of NBIC has agreed to a new operation plan for the BioAssist unit. This now puts the BioAssist Engineering Team on firm ground. We will have three important tasks:

  • Guarantee interoperability of biological data
  • Be consultant and project leader for the academic task forces within BioAssist
  • Accept academic software and make it usable by others

I am excited to get going.

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New job; the purpose of this blog

Last Tuesday, September 1st 2009, I started a new job as CTO of NBIC. NBIC is a Dutch not-for-profit organization (foundation) that has as prime target to bring BioInformatics in the Netherlands to a higher standard.

Until now, NBIC has been run as a small administrative office in Nijmegen, coordinating research ("BioRange" program), education ("BioWise" program) and support ("BioAssist" program) at several different academic locations in the Netherlands.

We are now setting up a virtual workshop as part of the NBIC office, operating as part of the BioAssist program. This office will be working on data and on software development. We will start where the research groups end. We will take what is produced, and continue development by applying industrial design standards to it. Above the virtual door to our virtual office there is a virtual sign:


No thinking beyond this point.


Sometimes, however, in the office, we can not help having our own thoughts. I will use this blog to write about the way we run our office together, including obstacles. And occasionally, I may add a little thought I have had.

[Note: The postings of the blog have been merged in 2019 into the rest of my own web site instead of being hosted separately on "blogger". You can find back most of the specific postings under the tag BioAssist]

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Venus passing the sun

The morning of June 8, 2004 the planet Venus moved in front of the sun. Since it was beautiful weather, I mounted my telescope on top of our office building in Delft and projected the image of the sun on a white sheet of paper. During the six hours of the event, we regularly paid a visit with different colleagues to take a live look.

Read more: Venus passing the sun

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