Wiki forum now active!
Yes, I'm aware of how silly it may seem to have a forum discussing a wiki that came from a forum...but mediawiki's discussion possibilities are downright awful. May I never edit another User:Talk page.
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Originally posted by ECO View PostThanks to an immense amount of work by "dan" for which I am eternally grateful, the wiki is ready for more widespread use.
Currently (without DB access) I can't make a detailed summary of the 'top contributors', but I'll try to set that up ASAP. See here (with the help of "ECO" ;-)
Please do use the feedback page to discuss how the NGS software archive on the wiki can be improved. For example... do we need a dedicated forum for the wiki?
IMPORTANT NOTE: I put some notes about what I have been doing on the wiki here, which includes attribution for the source data.
Please note that the work I have been doing is purely through the 'wiki interface', so any user can login and change / expand what I have been doing.
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Thanks to an immense amount of work by "dan" for which I am eternally grateful, the wiki is ready for more widespread use.
Please browse the software collection, and most importantly enter and update any new software packages with the new handy form: http://seqanswers.com/wiki/SoftwareLast edited by ECO; 09-17-2009, 10:46 PM. Reason: dan put so many features into the wiki i could not possibly capture with my first attempt
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Beta version of the SEQwiki software database up and running...
Check it out...
Dan.
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Good work ECO and dan
I'll chip in somewhat when I get the time... presently I'm furiously analysing some SOLiD reads before a conference abstract submission date rolls around.
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Originally posted by ECO View PostVery cool, and exactly what I had in mind for getting users to help submit the packages to the wiki.
Any chance you could help me set the thing up here? Or do you think this again falls into the category of unnecessary replication?
I am worried about duplication... here is my chain of thoughts: Any successful wiki project depends on a community of users. Users are motivated for many reasons, but one strong motivation is peer 'pressure' (or peer recognition) within a ... community of users! So building up a community is a big part of building up a wiki. So if we create many similar wikis we kind of split the community and furthermore it doesn't feel good (from a user perspective) to not really know where one should edit...
Thinking about it though - This forum is very successful, so I don't see why we shouldn't try to build on that success with a nice well defined and focused wiki project :-)
Originally posted by ECO View Postedit: I found the holy grail....http://www.mediawiki.org/wiki/Extension:Semantic_Forms
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Originally posted by dan View Post
Any chance you could help me set the thing up here? Or do you think this again falls into the category of unnecessary replication?
edit: I found the holy grail....http://www.mediawiki.org/wiki/Extension:Semantic_Forms
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Originally posted by ECO View PostIf anyone has experience with that type of wiki form, please let me know!
:-D
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Originally posted by dan View PostDo you mean, this is the thing that is most difficult to model? Or do you mean this is the thing that is the most difficult to get people to do? Or the most difficult thing for people to decide? Or do you mean this is technically the mostly tricky thing with the wiki? Sorry for being a pain!
Do you know any ontologies related to software? SMW can be set up to work with ontologies, but this is one feature I haven't looked into in detail. i.e. if we could tag software programs with terms from well defined ontologies, that could help a lot with organizing the content of the wiki. Thinking about it, something related to this must be being developed by people interested in 'standard operating procedures' (SOPs) and web service 'resource descriptions', pipeline frameworks, etc. etc. I wonder how technical we can (usefully) get ;-)
This is kind-of what I mean when I say we don't want to duplicate work... I'm sure people at O|B|F / BioCatalogue could provide input, and there is so much on Wikipedia already... This site has a good focus, which is useful for any project, but it would be nice to be able to actually make use of the semantic web features of SMW with the proper use of ontologies (and it should be a big help with the vague idea of software 'tagging' that we have). Basically, the risk is that we go off and do something different, and miss the opportunity to 'plug-in' to wider efforts.
However, the scope of what I'm talking about is probably a full time research project! Whatever we do we should keep it as simple as possible.
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Originally posted by ECO View Postthe main difficulty is the tagging/properties used...
I'm guessing you mean some of the above... it's 'the most difficult to decide', and from there, hardest to implement 'properly'...
Do you know any ontologies related to software? SMW can be set up to work with ontologies, but this is one feature I haven't looked into in detail. i.e. if we could tag software programs with terms from well defined ontologies, that could help a lot with organizing the content of the wiki. Thinking about it, something related to this must be being developed by people interested in 'standard operating procedures' (SOPs) and web service 'resource descriptions', pipeline frameworks, etc. etc. I wonder how technical we can (usefully) get ;-)
This is kind-of what I mean when I say we don't want to duplicate work... I'm sure people at O|B|F / BioCatalogue could provide input, and there is so much on Wikipedia already... This site has a good focus, which is useful for any project, but it would be nice to be able to actually make use of the semantic web features of SMW with the proper use of ontologies (and it should be a big help with the vague idea of software 'tagging' that we have). Basically, the risk is that we go off and do something different, and miss the opportunity to 'plug-in' to wider efforts.
However, the scope of what I'm talking about is probably a full time research project! Whatever we do we should keep it as simple as possible.
Dan.
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Will do this evening Dan! I really like the ngs sandbox you started...the main difficulty is the tagging/properties used...
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Nice work!
Can you please install the 'semantic bundle' extension? There are lots of crucial extensions for working with SMW, such as semantic forms and semantic drilldown.
You can see a subset of the bundle in action here:
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SEQanswers Experimental Wiki!
THREAD UPDATED 9/17/2009!
Based on some recent experience, and some feedback from this thread, I've just installed and configured a MediaWiki instance for the community.
Find the wiki here: http://wiki.seqanswers.com
Forum credentials *should* work on the wiki, so you won't have to re-register. Also, Semantic MediaWiki (SMW) has been installed so the smarter amongst you can help us organize the data.
My first goal at this point is to capture and organize the information in the above thread. It's grown to the point where a single forum thread cannot contain it, and sci_guy and I cannot maintain it alone. Not to mention that we would all benefit from a format that could be used to slice the entries to get what we want efficiently (ie...SMW will allow quick queries to get say all the open source programs that support illumina data and miRNA).
Anyway, stay tuned and please post here if you're a SMW whiz, a MediaWiki whiz, or have suggestions. =]
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