[BioRuby] Bio-projects comparison

Moses M. Hohman mmhohman at northwestern.edu
Sun Nov 26 23:19:53 UTC 2006

Hi Yannick,

I should clarify my point: My concern is not about disk space, but  
rather that I might want to be able to select separately which  
restriction site library and which sequence manipulation library I  
wanted to use. With any openbio project currently it's all or  
nothing, so as a result people are not encouraged to develop a better  
sequence library, for example (not that I'm complaining specifically  
about the sequence library, I'm just giving an example). That is,  
because the sequence manipulation part of bioruby is "already  
written", no one will write another one. In some ways this is good,  
because people can just use existing software, but in other ways this  
slows down the pace of innovation. I would imagine someone could  
improve on the design of one or two libraries in any of the openbio  
projects, but people generally don't. It'd be nice to have some kind  
of way of doing this in bioruby, IMHO, something like plugins in  
Rails. And, I think this could distinguish bioruby from other openbio  


On Nov 22, 2006, at 11:46 PM, Yannick Wurm wrote:

> 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.
> Cheers,
> yannick
> --------------------------------------------
>           yannick . wurm @ unil . ch
> Ant Genomics, Ecology & Evolution @ Lausanne
>    http://www.unil.ch/dee/page28685_fr.html
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