A bioinformatician’s peeves (some of them)

As resident bioinformatician in many places over the years, I got many of requests to help. Anything from a short blast run to a full-fledged collaboration. I love that. I always like learning about new problems, and those requests may blossom into full research collaborations. So yes, drop me an email or step into my office any old time. But here are some sure-fire ways to tick me off:

  • Send me sequence data in a MS-Word,  PDF or pretty much anything else that is not a text file. No, PowerPoint is not an acceptable file format either.
  • Send me sequence data not in FASTA format. Unless there is a compelling reason, FASTA only please.
  • Please compress big files before you email me. Or let me know in advance that they are big, we’ll get them across by FTP or somesuch.
  • Send me image files of protein structure prediction from some online server with the tag “what do you think”? How should I know what to think?About what?  Nice colors man, try using green for your beta strands the next time, brings out your eyes. Also, if you want to perform structure prediction, approach it just like any other experiment. Take time to think what you are doing. Or come to me if you are not sure before you do a 3 day run.
  • Say “78% homology”.. OK, but I wrote about that before. More than once.
  • “Can you please BLAST this sequence for me and tell me what you think”? Huh? What is this? Why this particular sequence? How did you come by it? Why do you want to BLAST it? What is your scientific question?
  • Actually, the above is probably the most common problem. No question on hand.  Usually, when I manage to pry the question out of you, we find out that BLAST against the nr database with default values might not be exactly what the doctor ordered. (At least not Dr. Friedberg).
  • “I really need to get some nice blast/tree/multiple sequence alignments for this grant application I am writing”. Always happy to help, but not 48hrs before the submission deadline. I have my own research and a life too, such as it is.
  • No follow-up: OK, my lab did some work for you, anything between a couple of days and a couple of  months.  Now what? Can you give a sign of life letting me know if anything came out of it? Most hypotheses go down the drain, sure. Or sometimes funding runs out, things get prioritized differently, a postdoc leaves… but let me know! I worked quite a bit on this problem, I think that I deserve to know what happened with my work.  Have some common courtesy.


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4 Responses to “A bioinformatician’s peeves (some of them)”

  1. Chris Miller says:

    See also the Saunders Principle: “The first step in any collaboration is to reformat the data sent by your collaborators.”

  2. My favorite is a variation on the “No question on hand” theme. Somebody comes to me with data from an already performed and poorly designed high-throughput experiment, which they have failed to find anything in themselves. They then expect me to drop everything, work on their data, and somehow magically make a scientific discovery. And if I manage that feat, I will get an insignificant position on the author list of their paper. Let me think about that … how about “No!”?

  3. Max says:

    Other ones:
    – “This is highly significant” meaning that whoever said it thinks it is significant but actually has no clue what a statistical test or a p-value is.
    – “I know you can do this in 10 minutes”, meaning that it will basically take around week to program and whoever said it won’t care about the results anyways
    – “Well, first please plot the data and than we’ll look at it”, which is a variation of the “no question at hand problem”
    – “I have to see the data before we can continue with this” which often means that the collaborator has no idea who one could visualize the data in a format he could display in Excel

  4. @tomtubbs says:

    Put another way:
    Sequence in FASTA format only.
    Zip files, or send via DropBox/FTP
    Here’s a link to a post on homology. Before you start using percentages – here (link)
    Maybe have a You have to answer all these questions before getting through?

    What is your scientific question?
    What is it you want to do?
    Why the particular data you want to use/create?
    What’s the background?
    How did you/are you going to get the data

    Rough Turn around times for requests…

    No follow-up – Easier to set up a date for gettting an update whilst doing the work for someone?
    Both parties could help. Just having an autoremind with standard coookie cutter email with fields filled in would work for this. Saves you time, they get reminder to get back to you.

    Sounds like some prep bioinformaticians end would help reduce these problems? What’s the current solution for these issues people use?