Covering the bioinformatics niche and much more

SciView: Scientific Interviews, Part 2

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After the first interview with Joe Felsenstein, I am continuing with this small project, SciView, with an interview with Brian Golding, from the McMaster University in Hamilton, Canada. For those who don’t know, Brian is the person behind EvolDir, where many researchers find new jobs, solve problems and check for next meeting. I would like to thank him for taking the time to answer my (sometimes) dull questions.

_In your opinion is there any difference about the Bioinformatics research done in Canada and in the US? The number of companies, universities and institutes in Canada is evidently smaller than in the US, would that be an obstacle for the development of Canadian Bioinformatics? _

BG: Canada has often had a “branch-plant” economy for many companies. So little primary research is done for the major pharmaceutical companies here. Because genomics and pharmaceutical research is expensive, the research here is probably less per capita and of a different nature (for example more testing). I don’t think that this is an obstacle, it simply means that the research for bioinformatics is mainly centered in universities and mainly in a few concentrated areas.

I asked this question to Joe Felsenstein: How do you see the “publish or perish” in science, with the increasing number of retracted papers, fake results, rushed publications and sometimes publication of extremely similar results in different papers and journals? What are your views?

BG:Yes, the paradigm to publish is getting worse than when I was younger. Indeed, I would not have had enough papers to get a job. It has also lead to many more authors per paper than in the remote past when I was younger. The increased pressure has an obvious consequence that you note above. However, this is not limited to research. The need for “accountability” is a buzz word in politics today and any government venture has to be “made accountable” (since for some reason it is perceived not to have been in the past). Research with government dollars is painted with the same brush. Unfortunately, for much of science, increased accountability in an already very open system, simply leads to more paperwork and less productivity (less accountability).

You have been an advocate of free/open source software. In your opinion what is the importance of this type of software for the Bioinformatics research? Do you agree of academic researcher to pursue copyright/patents of applications that are developed using public money?

BG: I do not agree with this though I find my opinion to be in the minority. I have always found open source software to be excellent work (people base their reputations rather than their cash on the software). You do require some willingness to accept strange bugs but people that pay for software seem to be willing to accept these same bugs that they are intolerant of in open source. I think that many are living by the adage that “you get what you pay for”. I think that there are many exceptions to this and a community based software project is one of these exceptions.

Another question that will become a favourite of this interview series is about computer graphic interfaces. There are many scientific software that does not have interfaces. Based on that, do you think that the lack of GUI would be an obstacle for the adoption of a program in research?

BG: Having a command line option for a program is a requirement for me. I find the command line to be the natural place to “get things done” in LINUX. It provides a way to use the power of the shell, the operating system and other programs to easily interface with whatever other program I may be running. Without it, you are limited to the interface that was created by the programmers.

How do you see that some bioinformatics companies create proprietary packages that are mere wrappers of open source academic software? Geneious, CLC Workbench, etc are excellent GUIs but the main engine is/was developed using academic research.

BG: This is common practice. They are selling value added software. So are the LINUX distribution packagers. They sell LINUX and a package of software that goes with it, each itself usually free but checked to make sure they all play nice together. The community is one where they usually also make available a lesser package that contians the essentials for free. If it is important to people to have a package that they need not worry about piecing together then they can pay for it. I am however, surprised to find any people that have paid big bucks for packages that I piece together for free often with a more powerful interface. Difference is, I am willing to spend some time to try to learn.

EvolDir is a great service for the scientific community (I found my first post-doc through it). I know that it is run using your own software, based on scripts and homebrew code. Why did you decide to rely on your own scripts instead of using Mailman or Majordomo? How EvolDir was started?

BG: Mailman and Majordomo did not exist when I started the EvolDir. The EvolDir was started simply as a file that contained a list of emails that I knew (this was before the days of web browsers or even gopher browsers and the only way to get an email was to ask someone for it (by voice only). A friend saw it and asked if he could get a copy. The list changed shortly after so I thought that I should send him another, updated copy. Another person asked and so on; strictly via word-of-mouth (literally in those days). This is why it is called a Dir (directory; a list of names and emails). Notices of general interest to people came later.

What would be your advice for someone that starting in the field? You came from the wetlab and probably have used punch cards in the early days of informatics. Is the life of the young bioinformatician easier than in the old days?

BG: A bioinformatician today can do things that I could not imagine when I started as an undergraduate. This morning I BLAST’ed over 5000 proteins against more than 500 complete genomes (in about 20 minutes). When one thinks of all that this entails it is staggering. The computers are so fast today that the trick to getting things done is no longer how quickly you can contrive to get back into the queue for those few precious cpu seconds. Now most people, except for some specific programs or gaming, cannot keep a computer busy … hence the creation of the grid to give this idleness to others that can. The world is a much different place, biology is much different and what it even more exciting, I would surely anticipate (given the advances that one sees today) that in another ten/fifteen years, the world and biology will be different anew.