Wednesday, November 20, 2013

Bioinformaticians look at bioinformatics

Bioinformatics as a term dates back to the 1970s, usually credited to Paulien Hogeweg, of the Bioinformatics group at Utrecht University, in The Netherlands, although it apparently did not make it into print until 1988 (Paulien Hogeweg. 1988. MIRROR beyond MIRROR, puddles of Life. In: Artificial Life, C. Langton, ed. Addison Wesley, pp. 297-315.).

In the 1990s the field expanded rapidly and became recognized as a discipline of its own, as a subset of computational science. However, Christos A. Ouzounis (2012. Rise and demise of bioinformatics? Promise and progress. PLoS Computational Biology 8: e1002487) has noted a distinct decrease in the use of the term itself, as shown by this graph.

Ouzounis recognizes three (admittedly artificial) periods in the history: Infancy (1996-2001), Adolescence (2002-2006) and Adulthood (2007-2011). Along the way, the practice of bioinformatics has received a lot of criticism. I have noted some of this before, in previous blog posts:
Poor bioinformatics?
Archiving of bioinformatics software

What is perhaps most important is that much of this criticism comes from bioinformaticians themselves, rather than from biologists. Moreover, this criticism does not seem to have had much effect on how bioinformatics is practiced, given the length of time over which it has been made.

For example, Carole Goble (2007. The seven deadly sins of bioinformatics. Keynote talk at the Bioinformatics Open Source Conference Special Interest Group at the 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2007) in Vienna, July 2007) produced this list of what she called "intractable problems in bioinformatics":
1. Parochialism and insularity.
2. Exceptionalism.
3. Autonomy or death!
4. Vanity: pride and narcissism.
5. Monolith megalomania.
6. Scientific method sloth.
7. Instant gratification.
More recently, Manuel Corpas, Segun Fatumo & Reinhard Schneider (2012. How not to be a bioinformatician. Source Code for Biology and Medicine 7: 3) pointed out what they call "a series of disastrous practices in the bioinformatics field", which look very similar:
1. Stay low level at every level.
2. Be open source without being open.
3. Make tools that make no sense to biologists.
4. Do not provide a graphical user interface: command line is always more effective.
5. Make sure the output of your application is unreadable, unparseable and does not comply to any known standards.
6. Be unreachable and isolated.
7. Never maintain your databases, web services or any information that you may provide at any time.
8. Blindly believe in the predictions given, P-values or statistics.
9. Do not ever share your results and do not reuse.
10. Make your algorithm or analysis method irreproducible.
You can peruse the originals to check out the details of these problems, and whether they sound uncomfortably familiar.

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