[BioRuby] Bio-projects comparison

Yannick Wurm Yannick.Wurm at unil.ch
Thu Nov 23 09:46:35 UTC 2006

Hi Moses & List,

the comparison at http://sciruby.codeforpeople.com/sr.cgi/BioProjects
is definitely a great initiative. Thanks also to those that replied  
about ruby's alternative XML parser.
Moses commented:
> One thing that bothers me about the open bio software libraries is  
> that they are all or nothing. That is,
> you can download and install all of the pieces of bioperl or bioruby,
> or install none of them.
> it would be much nicer if I could just install the sequence
> manipulation bioruby gem, and then install my restriction site gem of
> choice, or vice v

In my day-to-day work, I do not want to worry about installing  
things. Disk space is insanely cheap, so I don't mind having  
unnecessary extras lying around. What could be interesting is if  
installation of "non-core" libraries happened auto-magically, without  
my having to do anything other than confirm. For example: add the  
"require XXX" line to your code. Run your script --> ruby figures out  
its missing somethings, finds out where to get it, confirms that you  
want to install it, does, and your code runs.



          yannick . wurm @ unil . ch
Ant Genomics, Ecology & Evolution @ Lausanne

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