OpenWetWare:Software/Ideas

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'''Please post any ideas you have about OpenWetWare software development here.'''
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Feel free to add further ideas for future implementation or discussion
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== Features and priorities ==
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==Blogs==
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This is the list of prioritized features that came out of the [[OpenWetWare_steering_committee/Software_development_meeting_3-8-06| 3-8-06 meeting]]. They're listed in the order in which George is going to be working on them. Also included are the folks George needs to talk to in order to nail down exactly how the feature is going to work.
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===Plugins===
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* '''Related Articles''' - A wordpress plugin that could display a certain number of articles related to the topic of the post itself. This could be achieved through proper usage of tags in the blogging software and would allow the plugin to search OWW for related articles based on the tags. This plugin could be used internally on OWW blogs but also on any blog, thus providing great outreach if used on a fair number of top blogs.
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=== Priority 1 ===
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* '''Inline Links''' - Similar the previous plugin, it could be of great interest to have certain keywords in a text automagically become links to relevant articles. Such plugins are used for advertisement in blogs where keywords in the blog post become links to sites related to them. This feature would add a wiki-feel to the blog if implemented seamlessly
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* Bulk image upload (Austin)
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* Better support for "scientific" markup ie formulae etc (?)
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* Easier user account creation (Sri, Jason)
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* Ability to make categories invisible (?)
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* "Cite this page" support
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**'''[[User:Austin|Austin]] 14:45, 2 May 2006 (EDT)''': I've installed http://meta.wikimedia.org/wiki/Cite/SpecialCite.php now that we're running MW 1.6. Each page in the toolbox now has a cite this page link (actually only pages in the main namespace).
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* Improvements to current support for turning wiki pages into static pages (Austin)
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=== Priority 2 ===
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* User-defined sidebar
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=== Priority 3 ===
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* More data conversion tools
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* Semantic Mediawiki integration
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* Support for tagging
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==Tags==
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*Using '''"tags"''' (similar to sites such as delicious or flikr) so end-users could help categorize protocols with minimal effort.  This idea was suggested by Ishan.
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===Proposed implementation===
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In thinking about this issue some more, I think Austin might be right.  We may want to initially try to use Categories as '''tags''' and see how that works.  It seems like the easiest thing to do as it requires no new functionality in MediaWiki.  It seems that the easiest way to enforce this is to only have a single layer of categories and no subcategories.  We could also avoid tags like ''E. coli protocol.''  For example, the page [[Electrocompetent cells | Preparing electrocompetent cells]] would get tagged with <font face="courier">Category:Escherichia coli</font> and <font face="courier">Category:Protocol</font> so that it would fall under both categories.  This would enable users to collect together pages in different groupings.  Someone viewing the category <font face="courier">Escherichia coli</font> would see equipment pages, protocol pages, material pages, and information pages.  I think for our purposes, this might be a more useful application of categories. This would also have the advantage that some pages whose categorization is ambiguous could be labelled with multiple tags.  For example, [[Miniprep]] could be tagged with <font face="courier">Category:DNA</font> and <font face="courier">Category:Escherichia coli</font> and <font face="courier">Category:Protocol</font>.
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Some useful categories off the top of my head (please edit)
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#OpenWetWare
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#*for community related pages
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# Protocol
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# Equipment
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# Material
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#In vivo
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#In vitro
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#In silico
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#DNA
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#RNA
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#Protein
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#Escherichia coli
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#*and one for every other species
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#Reference
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#*For information resources like [[Web resources | listings of online tools]] and the [[E. coli genotypes | genotypes]] pages.
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#Mimulus
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#* and one for every research area (like [[Synthetic Biology]])
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#Course
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#*to indicate class-related pages
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#BE.109
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#*to indicate pages related to a certain course
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#*note that BE.109 should not be a subcategory of course because there might be pages that are useful for BE.109 and thus tagged as BE.109 that are not actually true Course pages.
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#Organization
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#*to indicate pages that are maintained by a certain organization
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#ICSB SC
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#*and one for every other organization (like [[BE Board]] and [[Students for Global Sustainability Wiki | SfGS]])
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# MIT
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#*and one for every other institution
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#Wittrup
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#*and one for every other lab
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#Microfluidics
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#Flow cytometry
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#Microscopy
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#Measurement
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#*would something like this be useful for collating measurement methodologies?  I'm not sure
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#Safety
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#Quality/data management categories (to dynamically generate to-do lists)
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#*Needs attention
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#*Needs formatting
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#*Needs content
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#*Needs categorization
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#*Great page
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Later, if this scheme proves useful and maintainable, we could consider trying to customizing the mediawiki software further by renaming '''Categories''' to '''Tags'''.
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Such an approach may also help the generation of tailored [[Special:Recentchanges]] pages.
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--[[User:Rshetty|RS]]
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I really like this idea, though I am concerned about the implementation and usefulness to the user.  Just for clarification I'm going to call what you've descibed above "categories" and make a distinction between that and "tags."  In tagging a user has a set of labels that are specific to them, so they can create a categorization scheme that is most useful to them personally.  For instance, I may want to tag only the e.coli protocols I actualy use as "E.Coli" and then I can click on that tag and bring up my personal list of favorite e.coli protocols.  just to be clear, this is different from categorizing in that I only bring up things I have labeled, not every protocol categorized as "E.Coli".  The reason I like this better is that I think it will be more useful to the user, and as a result, the user will be more inclined to bother categorizing things (in other words, I think it scales better).
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OK, so tags ''may'' be more useful to the user,  but what about generating protocol pages for the larger community to browse through?  Its clear how the categories scheme allows dynamic generation of protocols pages, i.e. if Category = E.Coli and Category = Protocol then include a link in the E.coli protocols page.  Well, tags enable something similar (and perhaps better), they can aggregate all the tags associated with a page and look at the most popular tag and assign the page under that label on the main protocols page.  Or more complicated things like creating heirarchical categories simply by clustering the tags on pages, see [http://www.flickr.com/photos/tags/biology/clusters/  Flikr's biology clusters] as an example.  The big downside to using tags in my opinion is that it will require some serious changes to the software to implement them in a way that is convenient for the user. 
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--[[Jason Kelly|JK]]
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Also, it's worth noting that since each article has its own URL, we could do this in the framework of existing tagging sites such as [http://del.icio.us/ del.icio.us] -- could at least be a way to easily explore if this whole thing is useful anyway.
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There has been a some [http://meta.wikimedia.org/wiki/Del.icio.us-style_Tags_for_MediaWiki discussion] about implementing tags for wikipedia, so maybe we could get some development help?
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:I like the tag idea a lot but until we find a nice way of implementing it within OWW, I think the usefulness of categories merits implementing them.--[[User:Bcanton|BC]] 17:49, 22 February 2006 (EST)
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Semantic MediaWiki extension seems to accomplish a lot of this:
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*[[Wikipedia:Semantic_MediaWiki|Semantic MediaWiki]]
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*[[Wikipedia:Semantic_Wiki|Semantic Wiki]]
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*[http://wiki.ontoworld.org/ Live demo 1] and [http://semanticwiki.jp/jabionpedia live demo 2]
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--[[User:Ilya|Ilya]] 13:31, 26 April 2006 (EDT)
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==Other==
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*'''Discussion boards''' similar to [http://www.fluwikie.com/index.php?n=Forum.Forum these] found on the Fluwiki site.  Actually, there are a number of cool things on the Fluwiki site that might be worth implementing:
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**Better [http://www.fluwikie.com/index.php?n=Main.RSSFeeds RSS feeds]
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**Easily changeable [http://www.fluwikie.com/index.php?n=Site.StyleOptions site viewing options].
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:--[[Jason Kelly|JK]]
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*Multiple image upload (or upload of a directory of images).
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**This would be very desirable.  There are some posts on the mediawiki message boards saying that this is on the list of things to do so maybe this could be done in collaboration with the mediawiki community?
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*Tailored [[Special:Recentchanges]] viewing so that you could look at all the recent changes associated with a particular namespace like [[BE.109]] or [[Synthetic Biology]] or the [[Mimulus Community]].  It helps new users track those changes that they care about more easily.
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**'''[[User:Austin|Austin]] 15:48, 26 April 2006 (EDT)''': [[User:Austin/Extensions/Recentchangesfilter|Done]]
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*'''[[User:Ilya|Ilya]] 01:06, 2 May 2006 (EDT)''': WikiMedia announced [http://meta.wikimedia.org/wiki/Summer_of_Code_2006 software development ideas] for the [http://code.google.com/soc/ Google Summer of Code] 2006.
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*[http://www.biodirectory.com/biowiki/Monobook_bookmarklets Bookmarklets] --[[User:Ilya|Ilya]] 16:00, 5 February 2007 (EST) (via [[User:Johncumbers|John]])
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*Wildcard search --[[User:Ilya|Ilya]] 13:26, 6 February 2007 (EST) (via [[User:Johncumbers|John]])
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Current revision

Feel free to add further ideas for future implementation or discussion

Blogs

Plugins

  • Related Articles - A wordpress plugin that could display a certain number of articles related to the topic of the post itself. This could be achieved through proper usage of tags in the blogging software and would allow the plugin to search OWW for related articles based on the tags. This plugin could be used internally on OWW blogs but also on any blog, thus providing great outreach if used on a fair number of top blogs.
  • Inline Links - Similar the previous plugin, it could be of great interest to have certain keywords in a text automagically become links to relevant articles. Such plugins are used for advertisement in blogs where keywords in the blog post become links to sites related to them. This feature would add a wiki-feel to the blog if implemented seamlessly
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