[BioRuby] Bio-projects comparison

Moses M. Hohman mmhohman at northwestern.edu
Tue Nov 28 00:13:53 UTC 2006

Doesn't seem like it's that big, but perhaps that's because there  
currently isn't really an incentive for most people to switch from  
bioperl. Beyond that, I think it would be useful even for our small  
community. I think it would be cool if bioruby could leverage more of  
what ruby has to offer to build a more compelling platform than  
bioperl, biopython and biojava offer.

Maybe I'm getting ahead of myself, though, and we should just wait on  
this until someone feels energetic and wants to write an alternative  
library for something already in bioruby.


  Nov 27, 2006, at 12:31 AM, Yannick Wurm wrote:

> Hi MOses,
> Ok, good point. But how big is the bioruby community anyway? Anybody
> else using Bioruby in Switzerland?
> Cheers,
> Yannick
> 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
>    http://www.unil.ch/dee/page28685_fr.html
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