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What is bioinformatics anyway?
June 24th, 2008 under Bioinformatics, Devel, rengolin. [ Comments: 4 ]

After almost three years in the field I’m pretty sure I have no idea. A few months ago I though I knew and wrote an essay about software quality on bioinformatics but I now figured out that, even though those things might make sense to the rest of us, for bioinformatics it doesn’t.

Wikipedia (which have a much higher quality than many papers I’ve read) defines software as: “a general term used to describe a collection of computer programs, procedures and documentation that perform some tasks on a computer system”. It also defines programming as: “the process of writing, testing, debugging/troubleshooting, and maintaining the source code of computer programs”.

So, every one that writes programs (let’s forget about documentation, tests, maintenance etc for now) is a programmer. But a computer programmer IS NOT a software engineer. Programmers can write as much code as they want but without formal definitions, metrics, good design decisions and practices, tests, documentation and so on, they are useless as ants without pheromone.

Quick tip: Whenever you see a job for a software engineer in a bioinformatics institute, beware: It generally means a developer to maintain random code and make random changes in random environments.

So what?

I might not have a clue about what bioinformatics is, but now I’m pretty sure what it ISN’T: Software Engineering. You will find a huge amount of code, scripts, programs, databases but rarely find a fair piece of software. Therefore, my previous ideas could be valid for software quality, but not at all to bioinformatics.

Don’t get me wrong, I know some bioinformaticians (and programmers around) that understand the basic ideas about software and quality and why we should have them, but the whole structure, the scientific community, the people that give them money, have no idea whatsoever of what software really is or where it fits in the loop.

Still, bioinformaticians are getting half-programming and half-biology degrees, on two fields that each has more to know than the whole humanity can hold on their brains added up. How is it possible (and fair) to put those poor guys to work on such sub-human conditions, without any guidance or quality control, without any clue, in fact, to what they really should be doing in the first place.

Some of them come out pretty well, so well that they abandon the field and go work on better companies, with much better software strategies, proper engineering, scientific development in the right place (sandboxes) and production code done by real engineers with solid experience in mission-critical environments.

In the end, it leaves bioinformatics (to be fair, the informatics part only) in the hands of inexperienced people in all sorts of fields and levels, students writing production software, people that never saw a mission-critical environment coordinating databases, filesystems and development, with one bad decision after the other.

Is it just a rant, then?

No, not really. It’s a liberation. For a while I struggled to understand the motives behind those weird decisions. I knew that, in every industry, you have a whole set of values and people can, sometimes take completely awkward decisions, which turns out to be the right one. I’ve seen it happening when moving between jobs, especially when I worked at Yahoo! (big company, big culture). But with time, the awkward decisions still sounded awkward, even after considering all the new information I had.

Other people got fed up with all this and left, one after the other. I talked to them, and the answer was always the same: random (generally bad) decisions, ego in astronomic proportions and zero technical knowledge from all parts. Now I’m leaving for good and you won’t need to ask me why, will you?

I generally need a very good reason to leave a work place. I was feeling out-placed but couldn’t leave without a very good reason, but now I got a good bunch of them…

A liberation indeed!

Is there a way out?

Seriously, no. In 10 years definitely no. In 15 quite likely no. In 20, maybe… but things must start changing now!

Being optimistic, assuming they stop running like headless chickens, they would still need a strong guidance, which is virtually impossible to happen because of the strong ego of scientists in general. Bioinformatics exists for decades already, who is the software engineer that will tell them they’re doing all wrong?

Besides, the people that grant them money (governments) have no clue about software engineering (nor they should) and they will keep sending money every year, as long as, in the reports, they pretend to be doing great things. In fact, most could’ve been done in a few weeks with two or three people prepared to compromise.

Who doesn’t want a job where they can do almost nothing at all, get paid every month without even the remote fear of loosing their jobs and still pretend they’re doing great things? Who say no to this and start working for real gets a really bad reputation… While this win-win situation keeps going, there is little or zero chance of doing real stuff in the field and bioinformatics is doomed to constant failure and ineffectiveness.

At last, it’s not a specific problem, where you can just change a couple of people and everything will be all right, as many believe. This is nobody’s fault, it’s just the way the two fields: biology and informatics, joined together some decades ago and was never straightened. If there is a way out, I’d be very glad to see and will congratulate those who managed to do it, but this is much more politics than software development and I am, very luckily, just a programmer…


Bioinformatics and its problems
February 21st, 2008 under Bioinformatics, Biology, Computers, Devel, rengolin. [ Comments: none ]

For the last two months I’ve been writing a text about software quality in bioinformatics and the first part is done: I finally finished the basic concepts and tasks on why and how to perform software quality assurance in bioinformatics.

The big reasons why I focused in bioinformatics are:

  1. I’m working in a bioinformatics institute
  2. Bioinformatics has LOTS of problems

If you liked the first part (link just above) or would like to know more about my solutions and ideas keep reading. Use the root link as your entry point and go reading by chapter.

I couldn’t do the next/previous links as the wiki software doesn’t have this automatically and I didn’t want to hard-code it in the text (it’s a software quality text, isn’t it?).

Disclaimer:

  • The text was written very fast, you’ll probably find lots of incoherent phrases and grammar errors, ignore them for now as I’m re-reading and re-writing everything.
  • I’ve put more than I think I should and am now filtering what’s worth staying. I might also add a few more new things.
  • Most code samples won’t work, they’re a simplified language for clarification only.

Do let me know if you think you could add something I forgot or disagree on any concept, the text is in a very immature state yet.


 


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