Galaxy, and writing code

I don’t write code.  There.  I said it.  Yes, I have been a bioinformatics professional for over a decade and I don’t write code. galaxy_logo

I’ve taken the classes and I own the books.  I’m down with the philosophy.  I get the need. But writing code makes me cranky and miserable.  Chasing a stray comma or semi-colon for 45 minutes makes we want to pull my hair out.  I have the ultimate respect for the people who have the patience for this.  But I’m not one of them.

Personally, I’m interested in finding the leads, and answering the biological questions.  That’s what drives me.  I’m essentially a super-end-user.  And that’s what I really like.

Recently we did a training on Galaxy and we were working with some grad students/post-docs who shared my phenotype.  They had been trying really hard to write some scripts to accomplish what they needed to do.  They also reported that comma-crazies affected them too.   After we showed them Galaxy, they were ready to put down those scripting books.  In fact, one of the comments to us was {paraphrased}, “We’ve been trying to teach ourselves programming.  I think that’s over.”  They said it would be more worth it to them to spent time learning Galaxy than learning programming.

That’s what I think, too.  Learning to use Galaxy is worth your time.

Now, I’m glad I know something about programming.  Probably the best back-end thing I ever learned was writing SQL statements. (Thanks, Rick :) At the Jackson Lab I shared an office with a very patient programmer who helped me with that.) Both of these have helped me to converse with professional programmers.  I know what to ask for in development projects better.  And I know enough that when handed some code I can sometimes get it to do what I need (or, ah, find someone who can help me locally….).

Galaxy is developing a user community that is doing that now–bridging the people with the questions and the people who like to build the bridges.  Across the mailing list the other day came word from Ido Tamir about a very helpful series of blog posts he’s going to do that offers help with Galaxy tasks.  The first one is importing data into Galaxy.  (There are some built-in import strategies already, Ido just created one that offers a bit more customization for additional features.)

Visit Ido’s Adventures in the galaxy Pt.1 to learn more–and see the code.  But spend some time learning Galaxy.  Our free tutorial (sponsored by the Galaxy team) will get you started.  We provide an overview of what Galaxy is, and the fundamentals of the interface and how and why to use it.   The great screencasts the team does that address specific tasks will really get you further.

And if you are like me, you can skip the scripting and go right to answering the biological questions. If you are developer helping people like me in your local group–get them using Galaxy and you can build stuff that they can use, and stop bugging you.

Use Galaxy.  It’s worth your time.

4 thoughts on “Galaxy, and writing code

  1. Mark Fortner

    Hi Mary,
    I read your posting and found your comments about programming to be quite familiar. In fact, wanting an answer to a biological question without having to write code was the primary reason that Taverna (the open source workflow engine) was written. With Taverna you simply drag and drop the operations you want into place, and then run the workflow. You can reuse services and workflows written by other scientists around the world. A related site ( provides a catalog of workflows that one can learn from, or incorporate into new workflows. Taverna is open source, works on all platforms, and written by scientists for scientists. Give it a go, and let me know what you think.

  2. Mary

    Hi Mark–

    Yeah, I knew there would be people that understood! (And a bunch of people afraid to admit that they don’t like to write code ;) )

    I’ve been also watching the Taverna project, and I agree–that’s exactly what non-programmers need.

    We’ve been using Galaxy workflows and sharing those and I think the utility of that is just tremendous. Very much like sharing reagents at the bench.

    I think what we are seeing is what many of us were yearning for as this field developed–lowering the barriers so the field specialists can use the tools without having to learn computer science. We’re really getting there now.

  3. Mark Fortner

    Hi Mary,
    One of the things that I find appealing about Taverna is that it has the notion of “provenance” built into it. So you never have to wonder “how did they come to THAT conclusion”. You can see their data, run their workflow, and know exactly how they arrived at their conclusion.

  4. Trey

    I can’t argue to the merits of Taverna vs. Galaxy vs other workflow tools,

    but Galaxy has “provenance” also with histories and workflows that can be created and shared.

    It’s one of those things that has been sorely missing, and I’m glad to see available.

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