Bioinformaticians in the service of bench biologists

Stumbled out of bed to the feed reader and came close to spraying cereal over the screen when I read this exchange on a Nature Network blog:

Original post:

Like them or loathe them, it’s not really possible to analyze a genome-wide screen without a large number of [Excel spreadsheets]

Comment #1 from our Pierre:

Oh please, please, please, no, don’t that with excel, please

He’s quite right, of course. Unfortunately, the ensuing debate is heading down a familiar track: “that’s all very well for you hardcore computer types, but we’re just simple bench biologists”.

Well look – a lot of us “computer types” were, or are, bench biologists too. We weren’t born with magical computer skills, nor did we learn them overnight. We know what we know and recommend it to others not out of geekiness or snobbery, but because we believe that if there’s a better way to perform a task, we owe it to ourselves to learn it. If others can’t make that commitment, we’re more than happy to help out and share what we’ve learned.

Just be prepared to meet us half-way, OK?

8 thoughts on “Bioinformaticians in the service of bench biologists

  1. Pierre

    and as I wrote in another comment, Nature Network would be the place where she might find someone to help her and start a real scientific collaboration.

  2. Cameron Neylon

    I think Richard’s point is fair though. Happy to meet /you/ half way (where is that anyway, about Abu Dhabi?) but it can be hard to get your local computer guru to be interested in your specific problem. This is why we need open shared data and social networking tools to get the right people in touch with each other!

  3. Deepak

    *rolls eyes* … sad part is this battle is so old and one would think that things would have changed by now. And its not just an issue in academia. You get clinical submissions in excel and people think they can do the same with large genomic studies.

  4. nsaunders Post author

    Just to note briefly that the comment thread at the original NN blog post is the most enjoyable and productive one that I’ve ever seen there. May it continue!

  5. chall

    ahh… but it is sooo hard to talk to geeky computer bioinformatic people ;) (seeing I am half one I am making a joke.) I remember my prof’s comment when I did my PhD project and compared similarities between proteins we believed being in the same [functional] family “I didn’t get the same e-value as you. What do you mean with matrices? Is is based on math? Can you change the parameters…”

    and it wasn’t because he didn’t know math, he just didn’t think of databases as ‘possible to program how you want to search them”.

    Then again, I still think it is hard to be excellent in both bioinformatics and programming AND the wet biology stuff…

    like the blog btw!

  6. kevinl

    LOLZ.. large numbers of excel spreadsheets?
    ROFL.. I had a colleague who sent me a bunch of sequences to be analysed but he didn’t expect that there’s a char limit in each excel cell.

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