[Bioperl-l] Offering to help

Bryan Bishop kanzure at gmail.com
Tue Mar 3 15:05:22 EST 2009


On Tue, Mar 3, 2009 at 12:49 PM, Adam Witney wrote:
> On 3 Mar 2009, at 17:21, Bryan Bishop wrote:
>> On Tue, Mar 3, 2009 at 11:14 AM, Chris Fields wrote:
>>> For a Moose-based bioperl implementation I suggest a separate repo
>>> completely.  We're using svn currently on dev.open-bio.org, though I and
>>> a
>>> few others are also using git.  I'm neutral on the matter but it's
>>> possible
>>> the consensus may be to keep everything in the open-bio svn repo (not
>>> everyone has git or uses it).
>>
>> Yes, I've been figuring that the protocols work should be done in a
>> separate repository for now anyway, I just haven't got around to
>> starting the code, although with XML::Simple it should be easier or
>> quicker to do than I'm making it out to be. Part of the issue is that
>> there needs to be some good thought put into what exactly the schema
>> should be or how exactly to represent the information, which I've
>> always had a little bit of anxiety over. It would be fantastic if I
>> could somehow come up with an easy format and a wizard creation tool
>> front-end for something like protocol-online.org, since all of those
>> protocols truly deserve to be in some sort of microformat, whether
>> CLP-ML or something based off of YAML. Maybe I'll post a thread soon
>> outlining what a discussion would have to go over to make sure there's
>> no shooting of self in the foot, to come up with that relatively
>> mature API or microformat, and see what others on the list have to say
>> about it? My background is more computer science than bioinformatics
>> and biology (even though I've been in biology labs longer (strange)),
>> so it would be great to get some support on that front.
>
> The FuGE folks have modeled Protocols as part of their object model. I
> haven't looked at it recently but it is supposed to be fairly generic for
> any kind of protocol. We have used the MAGE (FuGE's almost predecessor)
> version of Protocol within our database for several years and it covers most
> cases.
>
> The FuGE project pages can be found here:
>
> http://fuge.sourceforge.net/
>
> Maybe that would be a good place to start?

Thanks Adam, I hadn't seen that before. I glanced over their API documentation.

http://fuge.sourceforge.net/dev/V1Final/FuGEv1-refManual.html#Action

So, it looks like they are defining individual steps with an ordinal
number (which is good), also equipment via make and model tags. One of
the ideas that I have been working on is the concept of instructions
being "solved" by equipment: so you can either execute a PCR protocol
by manually dunking test tubes into warm and cold baths, or you can
use a thermocycler or microfluidic chip using some standardized
interface. This is also the same problem that "semantic web" advocates
have to put up with: UDDI, WSDL, B2B, "service discovery", etc.,
without overly restricting the standards to the point that nobody can
do anything new. But anyway, getting off track.

There is a link to "example files"- which is broken-
http://fuge.sourceforge.net/dev/V1Final/Instances/

Although this one does work:
http://fuge.sourceforge.net/presentation/master_example.xml
though it might be too meta for me :-).

Ultimately I'd like to come up with a system that I can dump into EXPO
(like The Robot Scientist) but also into a human readable format
(comparably, instructables?).

http://expo.sf.net/
videos: http://www.aber.ac.uk/compsci/Research/bio/robotsci/video/

- Bryan
http://heybryan.org/
1 512 203 0507



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