User talk:Spencer Bliven

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Moved to User:Spencer Bliven/sandbox

Thanks Spencer!

It's nice to be here!

Do you know of any work to build a better reference system for wikitext? It seems there is now enough critical mass for it to be really worth while developing a better system for managing references in MediaWiki. Cheers, --Dan Bolser 06:41, 22 April 2012 (PDT)

Combining the Cite.php and Pubmed extensions worked pretty well for us, since almost all our references come from pubmed. Wikipedia has the {{cite journal}} family of templates, which let you specify all the parameters individually. But this seems like more work for authors. Wikipedia's {{cite pmid}} and {{cite doi}} seem like good compromizes–a bot automatically populates the reference after a short period of time, allowing it to be easily edited.
What other features would you request for a wiki reference system? EndNote integration probably isn't going to happen. --Spencer Bliven 14:34, 23 April 2012 (PDT)


Fantastic work running this system! I was wondering - is it possible to enable VisualEditor on this wiki? I think the version as of late 2016 is pretty stable and would help authors who are not already markup-familiar to contribute more easily. Ineed, even for thos who are competant at wikimarkup, VisualEditor is often much easier to use.
All the best, T Shafee (talk) 15:25, 12 January 2017 (PST)

Excellent suggestion. It's enabled on almost all wikipedias, so it would make sense for us to support it as well. The VisualEditor extension does require some additional components to be installed on the system. I'd be generally supportive of installing it, but it increases my maintenance burden somewhat. I'll check with the editors, and it will probably take some time to get set up after that. Spencer Bliven 02:06, 13 January 2017 (PST)
I think it would be good to have VisualEditor here as an option, perhaps even the default, particularly along with Citoid. I agree that this increases the maintenance burden, but it really simplifies contributions by people who are not used to wiki formatting. If that burden becomes too high, we always have the backup option of going to the live Wikipedia, e.g. to subpages of WikiProject Computational Biology, but then, we would have the burden to ensure that contributions to the drafts remain both useful and compatible with CC BY. --Daniel Mietchen (talk) 06:35, 16 January 2017 (PST)
Ok, I will add VisualEditor and Citoid to my TODO list. --Spencer Bliven 00:56, 19 January 2017 (PST)
VisualEditor (and the parsoid service) is installed! Citoid is not installed because it has a ton of dependencies: a node.js service, Scribunto, TemplateData, VisualEditor's Citation Tool, and probably some transitive dependencies. Apparently the management isn't bad if deploying using a vagrant VM (might be nice anyway for updates), but I don't have any experience with that. I did switch references to using PubmedParser, which is quite a bit faster than the previous extension. Maybe that's enough for our citation needs? --Spencer Bliven 10:45, 19 January 2017 (PST)
Sounds good so far — thanks! Let's see for a while whether anything unexpected pops up. --Daniel Mietchen (talk) 11:48, 19 January 2017 (PST)
Champion. It seems to be working well for the Transcriptomics manuscript. T Shafee (talk) 14:38, 19 January 2017 (PST)

Citoid Installation Progress

☐ Node.js and citoid service
Is this needed if using wikipedia's endpoint?
☑ Extension:VisualEditor
☑ Extension:Scribunto
☑ Extension:Cite
☑ Extension:TemplateData
☑ Extension:ParserFunctions
☐ Extension:Citoid
Is this needed if using wikipedia's endpoint?
☐ VisualEditor's Citation Tool
Enabled but template copy was incomplete. Perhaps /do
☑ zotero (wikipedia endpoint seems to work)
☐ Parsoid


  • Scribunto may have some issues with the PCRE version php uses. How do we get it to use the current system version short of recompiling php?