OpenWetWare:Software/Extensions

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Installed Extensions Go to Special:Version to see the definitive list of installed extensions and their versions. See OpenWetWare:Feature test to check that the extensions are working. If you wish to discuss extensions on openwetware, sign up for the mailing list. The following extensions are installed on OpenWetware: Critical Extensions Critical extensions are either those which if they break would cause many pages to "break" and as such, these extensions should be considered as important to support (for upgrades, etc). Another way to look at this: if we aren't willing to support these, then we shouldn't encourage people to use these. The known dependencies of these are listed to help in smooth upgrades. Biblio: for citing from PubMed. (Requires php w/ builtin curl support) Calendar: extension for fancy calendars Dewikify: for helping with dewikifying (The mediawiki 'extension' itself only provides the wikionly tags. The dewikify script itself relies on the default format of the monobook skin. If that changes, the script is likely to break.) Recent Changes Filter: extension that augments the recent changes list with the ability for complex filtering (depends quite heavily on the internal structure of MediaWiki so extension likely to break on all major version upgrades, although it is also quite easy to update the extension to match the MediaWiki version) Jasonk 22:44, 12 March 2006 (EST): I think this extension may end up being critical in order to manage discussions. It will enable each discussion area to have recent changes listed. It also enables users to better manage recent changes in areas important to them, something which will be increasingly important as the site scales up. This may be possible via the watchlist, which is the only reason I wouldn't designate this immediately as critical, but I certainly wouldn't call it non-critical yet. Austin 13:27, 13 March 2006 (EST): Good point, I actually hadn't thought about using this as an includable page rather than just for each user using it to filter their own recent changes. Bill Flanagan 8:27, 11 August 2007 (EST): I'm going to look into the extension. If we can create a map that exists as a wiki page that controls the behavior of the filtering, we can isolate at least some of the problems associated with upgrading. Content can be managed independent of the structure. Development can be done by more than one person: the technical details of modifying the code can be separated from the way the site is categorized. This may be more of a meta-goal than a specific outcome but I'll look into it and find out. Austin Che 11:13, 11 August 2007 (EDT): I'm not sure what you're suggesting but there's already nothing in the extension that has anything to do with content. Bill Flanagan 12:00, 11 August 2007 (EST): I'll look into the extension to see how it works. ParserFunctions and StringFunctions: useful for simplifying templates greatly. RSS Extensions: Display the contents of RSS feeds from external sources on OpenWetWare.org pages. Google Analytics: Inserts the Google Analytics script for this site into the appropriate wiki pages (not all) Unknown criticality Dynamic Page List: dynamically create lists of pages based on sophisticated selection criteria. PartsRegistry: for connecting with the Registry of Standard Biological Parts. Use the bbpart tag such as <bbpart>B0010</bbpart> to get <bbpart>B0010</bbpart> Jasonk 22:44, 12 March 2006 (EST):Is it hard to just link to registry parts via HTML links? Austin 23:17, 12 March 2006 (EST): not really, but you also get the ease of entering it and auto-updating if the link changes (given the URL, this seems likely). This may also be implementable using the interwiki linking feature in the same way we link doi's so we would be able to do something like [[part:B0010]]. The benefit of using an extension is that allows for future more complicated expansion. For example, we could perhaps insert the part description or a part sequence or whatever else we wanted. RS 17:44, 26 May 2006 (EDT): As an example, we may now want to update this extension to point to the "new" registry. (And by we, I mean Austin :) ). Austin 18:03, 26 May 2006 (EDT): right...ok, done. Bill Flanagan 8:36, 11 August 2007 (EDT): I notice this extension's link has "gone missing". Is there another place we can link to it for information? Thanks! Austin Che 11:13, 11 August 2007 (EDT): Nope...This is one of those extensions that probably is better if it didn't exist, at least in it's current form. Once the registry actually gets an API for getting more information about parts other than just linking to it, then it might actually be more useful. Bill Flanagan 8:36, 11 August 2007 (EDT): OK. Just researching what's here and seeing how it works. I'll track it over time. Cite: 'Cite this page' support LatexDoc: For writing a LaTeX document on the wiki (see example at OpenWetWare:Feature test/LatexDoc). Now supports images and bibtex! WikiTex: Supports embedding LaTeX objects such as chemical structures with XyMTeX. Wibbit: Extension for using Exhibit and also includes a table editor that can be used for non-Exhibits also. PreferencesExtension: This extension hooks into the default Special:Preferences page and allows other extensions to easily add new preferences. UserMerge: Merge all documents owned by a given user into the set of documents owned by another user. After merging documents, the 'merged' username can optionally be deleted. HeaderFooter: Set a header and/or footer for individual namespaces. Non-critical extensions Non-critical extensions are defined as those which don't significantly change pages or remove important functionality. Users may use these as they wish and they should be able to easily adapt if we turn them off suddenly. Renameusers: rename OWW user including moving all user pages to a new username. Multiupload: allow upload of multiple images simultaneously. SyntaxHighlight: syntax highlighting for many languages WikiChat Bill Flanagan 8:36, 11 August 2007 (EDT): This is a fantastic extension. But I've heard that it puts a big load on the server when 20 or more folks are using it. Have there been any measurements done on the load it's responsible for? Since it uses AJAX (i.e., receiving and sending tons of small messages from every client while in use), even a bigger server may not allow it to scale very well. There may be a way to do the same thing with IM clients such as GoogleTalk. The log of the IM sessions could be scrolled onto the chat page interactively while the chat is executed within GoogleTalk. This is a long-term item but I wanted to make a note of it here. Please reply if you have anecdotal evidence of how useful it is and how it could change to work better. Austin Che 11:13, 11 August 2007 (EDT): See this thread. Some seem to be able to get it to scale while others can't. It also links to this WebChat2.0 which looks neat but seems to be less browser compatible (doesn't work on my Opera). But I think the idea of using a web chat program that talks with IRC is great. Bill Flanagan 8:36, 11 August 2007 (EDT): Ilya told me that GoogleTalk is a good candidate rather than IRC. I'll look at the htread you mentioned. I love AJAX. But the performance hit on the server is major. If a single GoogleTalk bot monitoring a chat is updating the server in real time, it still can be a problem if it's going into a Wiki page: every update is a new document. The database gets creamed. But if it's a "special page" being updated, the overhead is a lot less. The bot can then write the entire log from the chat into a "discussion" page as a single write when the chat is over. I have a GoogleTalk bot that I downloaded last week that does some of this. It's another long-term item but one that I think has some possibilities. Editcount: Show edit stats for users. Can be linked as [[Special:Editcount/user]] and included {{Special:Editcount/user}} UserDefaultPage: allow users to change their default page in their preferences UserSidebar: allow users to change their sidebar Deprecated extensions Do not use these extensions. They may be removed at some point in the future. Removed extensions ShowHide extension to dynamically show/hide sections. Use the more powereful toggle functionality. Some pages still use showhide. Change to use toggle as described here. Google MapsGenerate google maps You can use Wibbit to make a google map on the wiki. See OpenWetWare:Map Desirable or pending extensions List extensions you would like to install here and vote or de-vote for ones you'd like. See http://meta.wikimedia.org/wiki/Category:Mediawiki_Extensions for some extensions. I'd really like to see the SlideShare extension, to embed presentations from Slideshare. I suspect a lot of OWW users know of or use this service. *Neil Saunders 18:13, 21 February 2008 (EST): Semantic MediaWiki: add semantic data to pages. This is potentially an extremely important extension. Our current MW requires a one-line patch to Parser.php as noted in the INSTALL file This has been fixed in SVN: http://bugzilla.wikimedia.org/show_bug.cgi?id=8578 Extension adds a couple of tables and namespaces Also semantic forms. Make it much easier to edit pages via forms to fill in templates ArticleComments: allow easy adding of comments to pages ShareThis: add links for many social bookmarking sites to sidebar Dynamic Article List - would allow us to dynamically generate lists of the most popular articles, newest articles etc. Check out the sandbox for a test. (Requires >php5) Forum extension: Demo WikiDrops: Add to the top of pages automatically a 'breadcrumbs' path back to the main page. navimages: for allowing images to link to any URL (was uninstalled as it wasn't working) I'd like to see an extension which treated genbank accession numbers in a way similar to PMIDs. --TK 9 April 2006 Lucks 21:10, 14 April 2006 (EDT): Excellent idea. Perhaps a generalization for any ID numbers in any of the NCBI databases. Or even citing giving a DOI would be great.Toan 12:07, 20 July 2007 (EDT) Genbank ids work via interwiki linking. Give examples for other IDs to be added. WikiDB: create arbitrary databases on the wiki, demo site. Cite extension (different from SpecialCite that is already installed) SubPageList so that pages are automatically linked. This would make Help:Page_naming_conventions#Sets of related pages more useful.*Kathryn Muratore 17:15, 8 June 2011 (EDT): Will not be installed MediaWiki extension for R R is an Open Source 'Matlab-like' software (great for statistics, multivariate analysis and ploting] see demos: HTML ouput, Graphics, Interactions. OWW community could benefit from it when it comes to sharing analytical methods. need to investigate further server-side security issues. Writing new extensions or special pages Tutorial on how to write an extension Tutorial on how to write a new special page Hooks in MediaWiki