[BioRuby] Bio-projects comparison

Yannick Wurm Yannick.Wurm at unil.ch
Mon Nov 27 08:31:03 UTC 2006

Hi MOses,

Ok, good point. But how big is the bioruby community anyway? Anybody  
else using Bioruby in Switzerland?



On Nov 27, 2006, at 12:19 AM, Moses M. Hohman wrote:

> 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 projects.
> Moses
> On Nov 22, 2006, at 11:46 PM, Yannick Wurm wrote:
>> 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

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