[BioRuby] BioRuby Digest, Vol 77, Issue 20

[Yannick Wurm]

On 24 Feb 2012, at 07:59, Raoul Bonnal wrote:
> ++1
> 
> On 23/02/12 19.37, "Yannick Wurm" <yannick.wurm at unil.ch> wrote:
>> * making it idiot-proof
> This is a key point, user experience is everything.



Thanks Raoul. 
Yes, I think there is still a lot of potential for idiot-proofing (or should one say biologist-proofing??) at all levels between biological stuff and machines (most interfaces of PCR machines, robots, online bio* forms suck *really* *bad*!). Getting ruby/apple/google minimalist philosophies into things can only make the world a better place :)  
Thats the kind of idea driving our approach with our blast server/wrapper http://www.sequenceserver.com  (still a work in progress - e.g. hoping to elminate the necessity of choosing blast algorithms soon - http://goo.gl/nP8u8 )


Have you watched some noobs code? I was surprised to see that some biopython users new to programming don't actually ever execute whole scripts. Instead, they use the python shell... and copy-paste individual lines or blocks of code from their MS Word document. Similarly to the manner in which most run analyses in R.
Going line by line & seeing where things screw up definitely reduces the initial hurdle. I wish I had known about 'Bioruby in the shell' when I started...


>> * people should be able to test it without having to install
>> anything. (I recently tried running the BioRubyOnRails & failed). 
> *It was developed a long time ago and Ror is great but life time cycle of
> each release is very short.

Sure I understand. Noob's don't. Thus if it doenst work out of the box as advertised one should make it work or get rid of it. Making it work everywhere is likely quite intense. The best compromise might be to remove the biorubyonrails from the documentation in its current form, and instead set up an online server that people can simply use (without local install).

Cheers
yannick

ps: don't forget to show you use ruby in Mike Barton's http://bioinfsurvey.org/


Yannick Wurm
Ants, Genomes & Evolution ⋅ y.wurm at qmul.ac.uk ⋅ skype:yannickwurm ⋅ +44 207 882 3049
5.03A Fogg ⋅ School of Biological & Chemical Sciences ⋅ Queen Mary, University of London ⋅ Mile End Road ⋅ E1 4NX London ⋅ UK