What do people hope to gain from microarray experiments in 2008? What relevance does transcriptional profiling on a genome/transcriptome wide scale have when thousands of these experiments have already been done and made publicly available through GEO and MGED? And what about the more recent realizations that short, non-coding RNAs (that were thrown away during sample preparation) are orchestrating another level of regulation - you can’t go back to the original samples to measure the microRNAs? What techniques could make microarray data more usable and meaningful? The GEO interface is god-awful for the occasional user, but look at what Atul Butte can do with these data. Is there still a meaningful discovery aspect of transcriptional profiling studies? How many of the people doing microarrays have the infrastructure to do the kind of followup studies that really demonstrate relevance of their discoveries? I’d wager not many.

Now, a few thoughts on collaboration:

Collaboration is certainly the key to moving knowledge forward in an increasingly interdisciplinary world, but the paradigm we have been brought up in (at least on the science side) is that to be successful academically you have to the one with the idea, the persistence and the ability to tell a story. It doesn’t help to be the third guy from the left when you’re getting credit. Unless everyone feels that their interests are protected, no one (except the young and foolish) will move forward with a collaboration.

So is there a unique role for a small company in this process? I think there are several. But that’s a topic for a future post.

Funny you should ask. I’m almost finished porting the chained examples stuff to a more recent RSpec version, because we were sick of being stuck at 1.0.8 or whatever it was at work. I should have something released in the next couple weeks, and I will be releasing it to spec/ui (which is part of rspecext). specselenium will probably be deprecated (although we’ll see how it all goes in the next couple weeks).

Cheers for the update! I only see it now though: I did not check you blog

http://rubyforge.org/projects/spec-selenium/ is great! I am going to use it. I also use selenium-grid.

Any chance you update the chained example for RSpec >= 1.1.3 ?

it looks like it can work using before :all, I am a bit confused at this stage. What’s up the spec/ui project?

The use_chained_examples option is something we implemented locally at CDD, and is only available through the spec-selenium plugin right now (available via svn on rubyforge: http://rubyforge.org/projects/spec-selenium/).

Recently I was added as a committer on RSpec to roll some of our work into spec:ui. I will keep you posted.

Interesting ideas in your blog post, I would like to see something similar, too. It’s an especially interesting idea for clinical informatics, particularly in the case of validated systems, when you need to document everything your software does. This is traditionally done in Word, leading to unacceptable bureaucratic overhead.

Sorry it took a while to approve your comment, I was on vacation last week.

I did not know about the “use_chained_examples” option and I am going to give a try right now. Thank you for blogging about it. I have had been thinking to create a specific matcher to generate a description from all selenium actions but it would not have been very readable …

Yes, if you could share your work through a plugin, it would be great! Jean-Michel