>grad school – phase II?

>I’m trying to keep up with my one-posting per-day plan, but I considered abandoning it today. It’s just hard to keep focussed long enough to write a post when you’ve been coughing all day. Fortunately, the coughing let up, the fever went away, and – even if my brain isn’t back to normal – I’m feeling much better this afternoon than I was this morning.

Anyhow, spending the day on the day on the couch gave me lots of time for reflection, even if my brain was at 1/4 capacity. I’ve been able to follow several email threads, and contribute to a couple along the way. And, of course, all this sitting around and watching email go by made me re-evaluate my attitude to grad school. Of course, this posting could just be because I’m sick and grumpy. Still, there’s a nugget of truth in here somewhere…

Until today, I’ve been trying to write good quality code that can be used in our production pipelines – which some of it has. FindPeaks has been a great success in that respect. [EDITED]

However, several other pieces of my work were slated to be put into production for several months, until a few days ago. Now, they’ve all been discarded by the GSC in favour of other people’s work. Of course, I can’t complain about that – they’re free to use whatever they want, and – despite doing my research at the GSC – I have to remind myself that I’m not a GSC employee, and they have no obligation to use my code.

To be fair, the production requirements for one element of the software changed this morning, and my code that was ready to be put in production a year ago is no longer cutting edge.

However, in hindsight, I guess I have to ask some questions: why have I been writing good code, when I could have been writing code that does only what I want, and doesn’t handle the 100’s of other cases that I don’t come across in my research? What advantages were there for me to do a good job?

  • If I want to sell my code, it belongs to UBC. Clearly this is a non-starter.
  • If I want the GSC to use my code, I won’t get any recognition for it. (That’s the problem with writing a tool: Many people will get the results, but no one will ever know that it was my code in use, and unlike lab work, pipeline software doesn’t seem to get included on publications.)
  • If I’m doing it just for myself, then there’s the satisfaction of a job well done, but it distracts me from other projects I could be working on.
  • If I want to publish using my code, it doesn’t have to be production ready – it only has to do the job I want it to, so there’s clearly no advantage here.

Which leaves me with only one decent answer:

  • develop all my code freely on the web, and let other people participate. The more production-ready it is, the more people will use it. The more people who use it, the more my efforts are recognized – which in a way, is what grad school is all about:
Publications and recognition.

I seem to have more or less already adopted that model [EDITED]

Some time last year, I came to the recognition that I should stop helping people who just take advantage of my willingness to work, but I think this is a new, more jaded version of it.

Viva la grad school.

[EDITED] I guess now I understand why people leave Academia.

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