[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.


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-

Although this one does work:
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?).

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

- Bryan
1 512 203 0507

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