Similarly, bioinformatics research splits into the same two categories: 1) there is bioinformatics as methods development (what I call “theoretical bioinformatics”), and 2) there is what is called “applied bioinformatics”, where existing methods are applied to extract knowledge from available data. However, in bioinformatics, unlike in other life sciences, the split in commercialization between the two categories is different: generally, if you are a bioinformatics Principal Investigator (PI), you are expected to work primarily on methods development, while applying these methods to biological problems merely as a proof-of-concept. Theoretical bioinformatics, while more likely to be funded as independent research, does not benefit from the same commercialization as other areas of biological research – most commonly utilized tools continue to be maintained by academic labs and individual researchers and distributed under use-at-your-own-risk licenses.
The case for privatization and commercialization in bioinformatics is strong and supported by several necessary features that software has to adhere to:
These important features are really hard to achieve in the academic settings, for many reasons, but I will name two that I find most influential:
As a result, the plethora of good bioinformatics software becomes unmaintained and loses its relevance.
A bioinformatics core facility is a department that provides sequencing services on a commercial basis or part of academic collaborations. The emergence of such facility generally comes from a research group in the academic institution who purchases a sequencer, and since the capacity of a sequencer is usually higher than a need of a single group, it is filled up by collaborative projects.
Core facilities have been some of the most aggressive opposers of commercial bioinformatics, which is understandable, if we consider that bioinformatics analyses is one of the key services they provide. They are also key skeptics of commercialization of bioinformatics, because (and I quote) “Why would someone use a commercial service if we can do it for free?”
Core facilities indeed have an economic advantage – they are generally cheaper than the services of commercial partners. The main reason for this is that their services often come with “bioinformatics analyses included for free”. Another advantage comes from the licensing by academics under “free-for-academics-but-not-commercial-use” licenses.
However, as it often is, lower price-tag comes at a price (pun-intended). The hiring strategies of universities would not allow to build a team of senior researchers to support necessary bioinformatics workload, and the work is often done by students with limited ability for follow-ups or customized analysis. And we see a result of this in the growing number of bioinformatics service companies founded by PhD students, who saw the increasing demand from within by working for those facilities (Ecseq, Lifebit, Omiqa and many others).
In my vision, such shielding of core facilities from commercial partners is unnecessary – they play an important role in scientific research, but it is important to understand the appropriate use-cases for potential clients – when to use it and when to turn to commercial partners instead. But that’s a topic for a different post.