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Missing topics and incentives to fulfill them for an online bioinformatics curriculum

Posted by RNajmanovich on 15 Oct 2012 at 17:40 GMT

As the author clearly states, any online curricula depends on the shifting availability of courses. Anyone who masters all the material present in the described curses would be more than qualified to become a bioinformatician. Yet, such person wouldn't be one at all. There are a multitude of topics that are specific for bioinformatics that are not addressed by these courses. To name one, the whole theory behind sequence alignments isn't part of any course (unless I missed it). There are plenty of other examples where it can be argued that bioinformatics is not just the sum of biology, maths and informatics. So my opinion is that we are not quite there yet. There are serious gaps for any bioinformatics online curriculum that cannot yet be fulfilled with what is currently available.

This brings me to the second point. How can we create the courses to fill the gaps?

It takes:
1. one or more professors/lecuturers/intructors to do it.
2. the technological infrastructure to create it.
3. production support to make it usable/nice/etc.

While items 1 and 2 are generally there, the last item is not generally present in universities. This is not present probably because of a vicious circle of lack of interest. Professors don't demand this, universities don't see the demand for it. At the core of this vicious circle is the lack of incentives (in terms of counting the time towards professors' teaching requirements and its contribution to their career advancement).

Ultimately the exposure given by such courses would be enough to make it advantageous for the institution to create the mechanisms and incentives so that such courses can be created - but for the most part, it is not the case at the moment.

Rafael Najmanovich (http://bcb.med.usherbrook... :: @RNajmanovich)

No competing interests declared.

RE: Missing topics and incentives to fulfill them for an online bioinformatics curriculum

dbsearls replied to RNajmanovich on 21 Oct 2012 at 17:33 GMT

To your two points:

I believe the curriculum does indeed cover many topics "specific to bioinformatics" though of course whether there are enough is a matter of opinion. However, regarding your specific example of sequence alignment, I would refer you to (1) Prof. Brutlag's course "Computational Molecular Biology" in the virtual Biology Department, which covers sequence alignment in lecture 6, sequence similarity search in lecture 7, and multiple alignment in lecture 8; and (2) Prof. Skiena's course "Computational Biology" in the Computer Science Department, which covers algorithmic details of string matching, dynamic programming (including space-efficient versions) and Smith-Waterman local alignment in lectures 8-12.

Your second point is that what is lacking in order to fill the gap is "production support to make it usable/nice/etc." I would urge you to examine the efforts ongoing in Coursera and edX, which offer enough such support to motivate the participation of a large number of eminent university faculty. Things are happing fast on this front.

Competing interests declared: I am the author of the original article.