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Re:What's the point of writing good scientific software? by JohnBooty on Friday February 08, 2013 @01:23PM (#5189293)
"I have previously believed that converting any code you've created into a open-source library benefits the community and prevents reinvention of the wheel [...]

I have however started to realise that perhaps something I thought would be very useful may be of little interest to anyone else. Furthermore the effort I have put into testing and documentation may not have been the best use of my time if no one but I will use it. As my time as a post doc is limited, the extra time effort spent on improving these tools could have instead have been spent elsewhere."

From a purely selfish perspective, I've found that documenting and cleaning up my own code benefits me in the future. Even if it's a one-off, single-purpose utility that I'll never use again in the future, I often find myself needing to borrow bits of code from my old projects. ("Oh, I solved this problem before. How did I do it? Let's dig up that old, old project...") At which point, present-day me benefits if my past self bothered to actually document things and make sure they're reasonably robust.

There are countless other reasons (moral and pragmatic) to document, test, and open-source one's code, of course! Many of them more important than the ability to crib one's old code, I'd argue.

But the author seems to have considered (and discarded) them...

Re:What's the point of writing good scientific software? by michaelbarton on Friday February 08, 2013 @03:28PM (#5189924)
I am the author of this post. I don't disagree with anything you wrote. Several posts on my blog say exactly this. The software I wrote however is open source on github [1], has it's own website [2], has man pages for each command [3], example projects [4] and three screencasts guiding how to install and use it [5].

I did this because I wished that all bioinformatics software had this attention to usability and documentation. However now I wonder what was the point of all of this if no one ever ends up using it? I could have done the minimum for publication then spent this time working on finishing other manuscripts I have waiting.

As I wrote though, I agree with what you wrote in your comment. I just don't think there is any incentive for post-docs in academia to prioritise writing good software over pushing out additional papers.

[1]: https://github.com/michaelbarton/genomer

[2]: http://next.gs

[3]: https://github.com/michaelbarton/genomer-plugin-view/tree/ma...

[4]: https://github.com/michaelbarton/chromosome-pfluorescens-r12...

[5]: http://www.youtube.com/user/BioinformaticsZen

Re:What's the point of writing good scientific software? by JohnBooty on Wednesday February 13, 2013 @10:19AM (#5213440)
Instead of, "But the author seems to have considered (and discarded) them"

I ought to have written, "But the author has considered them and concluded that their benefits don't outweigh their costs in his case."

I totally support what you're saying! IMHO it's definitely not worth it to document/open-source/etc code at the cost of one's career or happiness, especially when the code is of questionable utility to others.