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Use of Mediawiki commons on OWW?

Steve Koch 03:16, 16 April 2008 (EDT):Has it been discussed previously the possibility of using images from Mediawiki commons on OWW. The way Wikipedia does it, so that you can use the same [[Image:whatever.png]] and if it doesn’t exist on OWW it will try to grab it from the commons? I would use this in my research pages and my courses. (It would also be convenient if private wikis could use public wiki images (and templates) in a similar manner.) I have no clue how hard this is to implement (I was just reminded of it today due to our discussion about tracking MediaWiki with OWW)…maybe it is easily copied from Wikipedia?


  • Jason R. Kelly 08:44, 8 August 2007 (EDT): Should have a button/page that allows people to easily invite their friends/labmates to join OWW. This is more relevant if we establish lab groups, etc, where we are storing the connections between users. E.g. a person could join and then invite their whole lab, adding all of them to the group 'Endy lab' or whatever all in one shot.
Agree--Dan 14:04, 13 February 2008 (CST)
    • wjf 14:10, 13 February 2008 (CST):I did something like this before. It's pretty simple. Al would be needed would be a form and an emai message. Hmm... let's think about it. I like the idea. You would also get an email message when the user joined.

Search within tags/categories

  • Jason R. Kelly 09:56, 17 July 2007 (EDT): Would be nice to be able to have a 'search protocols' box. If we had tags/categories working well, it seems like this is something that could be implemented fairly easily. If it was well done it would probably remove the need for an auto-generated, well-organized summary page (e.g. Protocols could be replaced by a search box). This will become more important down the line as I suspect the single summary page won't scale.
  • Alethea 09:02, 5 September 2008 (EDT): Is there a tag search capacity somewhere? Am I the only person who still can not conduct a successful search from either the lefthand navigation pane, or from within my lab notebook, and does this have more to do with my navigator or platform than with OWW?

Private/public lab notebooks

  • Jason R. Kelly: A post here mentions an idea we've kicked around before that is similar to the "publish to OWW button" where a page from a private wiki is published automatically to the public OWW. One thought is that we might consider private wikis that are specifically dedicated to be lab notebooks, they would publish to a subpage on the userpage User:Jason Kelly/notebookName, so the collisions problem of the publish to OWW button might not be a problem. Also, we could have tools -- like the calendar, preloaded on the lab notebook wikis. I think a set of powerful lab notebook tools would be powerful for both the private and public wikis. The best way to get content on OWW is if scientists are digitizing right when they are doing the work.
    • Bill Flanagan11:45, 13 August 2007 (EDT): I have part of the "publish to OWW" button close to working. I wrote a class that will take all of the templates, images, file attachments, and the wiki text itself from any wiki page and copy it to a new page in another wiki without loss of any detail or formatting information. This would be a mechanism for the publishing of the page itself. I'm creating a new Publish to OWW Button page to track this feature. I'll put together a demo to let folks see how it works. There are a number of issues that need to be handled in doing this including security, preservation of OWW content (we don't want this walking over similarly named templates or images in OWW, for example), how to select new page names, how to specify multiple pages, etc.
    • Bill Flanagan11:52, 13 August 2007 (EDT): I can create a set of pages that will be pre-populated in a lab notebook. These pages can contain references to specific extensions which also would be included. There would be a canned set of templates, pages, and images that would be used to seed all new lab notebooks as they are created. Over time, the specific contents of these can be customized as different specializations are required for different labs.
    • Bill Flanagan11:56, 13 August 2007 (EDT): Getting content into OWW fast seems and keeping it there is a great challenge. I've spoken to a few folks about what would make the OWW Lab Notebook more useful. As it is, if it takes longer to do it here than in a paper lab notebook, there still is a good reason to use it. Hopefully we can introduce compelling features that will make them a lot more useful.
      • Steven J. Koch 15:26, 13 August 2007 (EDT):One thing I want in my lab is one or a couple "cheap" computers that are pretty much just for entering notes on the wiki. In this case, seemingly trivial barriers to using the wiki can prevent users from entering things in their lab notebook. For example, making sure the computer is always on, unlocked, with browser on OWW page, and keyboard usable with gloves on. Here are some things that come to mind that can help from the OWW side:
        1. Group signons (such as "Koch Lab") for making edits. Users could sign their entries with the group identity (~~~~) followed by their real name (which they can manually type). The reason this may help is because users are reluctant to use other people's signon and as trivial as it sounds, people aren't going to log off and back on to add a simple lab notebook entry. Also, group work is common. As far as I know, this wouldn't require code, just a policy to allow user accounts of the type "Koch Lab."
          • Bill Flanagan 7:36, 16 August 2007 (EDT): Steve, if this is for "write-only" updates, there may be another way to do this. I like your idea of a "group login". Let me understand your requirement a little better. Do you need this for general OWW access, where you would be skipping around between several pages or would most of the updates be to a single page? If the updates for each user were all to go to one page, such as a page in a lab notebook, I can imagine a model where we could continuously append updates for a user to the end of a page or within a specified section within a page. Maybe something like "live journal". You could then go back to clean up the page when you take off the gloves (or not!) and get back to your own PC. All of the captured updates could be tagged with their update time. You could append a line or even an entire page. If you specified a section that didn't exist within the page, it could be appended to the end of it.
            Steven J. Koch 09:15, 16 August 2007 (EDT):I haven't used LiveJournal (yeah I know, behind the times), but here is what I was thinking that wouldn't require code: We have a regular OWW account with name "Koch Lab". We have a cheap computer in the lab that is always logged on to OWW as "Koch Lab." Multiple browser windows or tabs are open to various project lab notebooks. So, two students could be working on project #1 and go to that page and add an entry such as: "~~~~:Me and so and so made this sample and we saw this and that." and the entry would be signed as "koch lab." I don't know if that is the best idea, but that's what I was thinking. It would be easy, but maybe there's a problem I'm not seeing.
          • Jason R. Kelly 20:50, 16 August 2007 (EDT):The reason we currently don't allow group logins is mostly because knowing who makes an edit helps OWW members be more comfortable with allowing others to edit their work. There's more social pressure against inappropriate edits when you are using you own name than if you are shielded by a group account. Also, you can use it as another metric for quality (e.g. "oh, steve's a smart guy, his change to this protocol is probably legit...") I hadn't considered the shared computer issue though, don't know if solving that is worth the trade off of allowing anonymity.
        2. Longer-lived sign-on cookies. For some reason, my public OWW account expires very quickly. Private wiki doesn't seem to ever expire. In terms of conveneneince mentioned in item #1 above, a very long-lived sign on would be good.
          • Austin Che 15:44, 13 August 2007 (EDT): Under your preferences on the public wiki, click 'remember me' (and do this when you log in also). On the private wiki, this option is automatically set for you.
            • Steven J. Koch 16:04, 13 August 2007 (EDT):I did have the "remember me" checked, and have since the beginning (and I just double-checked). I remember some discussion of this from several months ago. Maybe it is some other quirk, such as because I am a member of a private wiki? (I actually have no problem being signed on permanently to the private wiki, even though my public wiki session expires very quickly.)
            • Ricardo Vidal 20:18, 27 August 2007 (EDT): I too have noticed that the cookie expires too quickly. Could it be a browser issue? I don't have access to the private wiki so it's probably not related.

RSS digests

  • So we have the capability to provide RSS feeds of labs or projects (see Endy:Screening plasmid RSS feed.), though it's not especially obvious how to set it up. However with every edit showing up it overwhelms the ol feed reader -- would be nice to provide a daily digest. LifeHacker does this so might be model there on how to implement.

Add a reference

  • Jason R. Kelly 18:25, 10 June 2007 (EDT):A wizard for adding a reference in the biblio format automatically.

Wiki to PDF converter

  • Reshma 15:11, 23 May 2007 (EDT): At a panel discussion on use of wiki's in education at MIT yesterday, there were several comments from educators that while wiki's were great for collaboration, they aren't great for putting together proper reports. For example, they said that if a group of students start writing stuff up on a wiki, eventually they have to move everything to a Microsoft Word document in order to make a report that was submittable for the class assignment. My guess is that part of this sentiment is psychological ... since the wiki feels like a work in progress, users don't feel as much need to clean up errors and spelling mistakes. And part of this sentiment is the practical problem of it being hard to print out a wiki page and make it look "polished". Right now, since we can compose latex docs on the wiki that look "polished", it shouldn't be very difficult to write an extension that goes from wiki markup direct to a latex-generated PDF. It might be useful to be able to generate a "polished" version of a page.
    • Jason R. Kelly 18:05, 24 May 2007 (EDT): This would be especially valuable for the Reviews section. If you wanted to submit a review periodically for peer-review and publication in traditional journals then it would be nice to be able to dump it straight from the wiki.
    • Cameron Neylon 22 July 2007: Agreed. Even just if people want to print something out of have a portable version of it this would be useful.

Gel annotater

  • Jason R. Kelly 16:54, 16 May 2007 (EDT):Basically same technology that you use to tag images in facebook, but used to tag relevant lanes/bands on a gel or other image.
  • Austin Che 20:20, 16 May 2007 (EDT): See also OpenWetWare:Software/Image_Editor
    • Sri Kosuri (talk) 19:09, 17 May 2007 (EDT): Doesn't seem very easy to use. I wonder if we could incorporate something like this into the site.

Tell user about this edit

  • Jasonk 08:46, 23 April 2007 (EDT): One of the more annoying things about the wiki is that when I post a reply to someone on a random talk page I don't know for sure that they will notice it. A lot of time I end up emailing them "I replied to your comment, follow this link", just to be sure. Would be nice to include a feature on the edit page that had a box to type in the username of anyone you wanted to get an email telling them about the edit. (would include a link, etc). People could opt out of receiving the emails in the their preferences, and the email itself could explain how -- so don't think it would bother people too much or anything.

Add protocol to my notebook

Could have a click feature on protocol pages that would automatically put a link to the protocol on a sub-page of the userpage like User:Jasonk/Protocols. This could also automatically add the protocol to the user's watchlist.

Down the road features that I would like

  • From Social Text, I learned of the possibility of emailing to a wiki. The personal wiki they set up for me by default allows me to email to the main page, or to email and automatically create new pages. They also have a "blog"-type page. When you create a blog, it gets it's own email address, and then when you send an email, it gets added to the top of the blog. I think it is set to only accept email from certain addresses. I have no clue how hard it would be to add this to OWW. It would help me in that I often have ideas or notebook entries that would be nice to quickly add without editing wiki text. I know that sounds lazy, but in general, the lower the barriers to editing the more stuff will get in.
    • I wrote the Wikilist extension with the idea of slowly integrating email with the wiki. Every page currently does have an email ID (e.g. Special:Wikilist/OpenWetWare:Ideas). If you go there, you can see the email address of a page (e.g. wikilist+SOMEID). Any emails to that address are sent to all users listed on the page (thus it acts like a mailing list). I've also thought about automatically posting the email to the discussion page of the target page. However, the main issue has been figuring out the right way to deal with authentication. Email is inherently unauthenticated. I guess checking the from address against the entire OWW database and then doing a lookup of the OWW user is possible. --Austin Che 16:41, 23 January 2007 (EST)
    • I hadn't thought about the spam or authentication problem. Your idea sounds good, but I guess it's still easy to fake a "from address" right? Maybe in the near term I should figure out an off-line solution (just send email to myself and then cut and paste when I have time). Thanks for your answers, Austin! And thanks for showing me that email extension, I will keep it in mind--Skoch3 17:01, 23 January 2007 (EST)
    • Yes faking from addresses is trivial. If you are willing to (and your email client is capable of it), it would be possible and easy to implement a way for authentication to be passed in extra email headers. So you would have to add to every email to the wiki something of the form X-OpenWetWare-Password: Secret which would kind of authenticate you. Some mail clients let you do this trivially while I believe it's impossible with others, but I could possibly implement this and see who has use for it. --Austin Che 18:44, 23 January 2007 (EST)
    • I'd say hold off, since it's not clear anyone else needs it, and I am still learning. Thank you for thinking about this --Skoch3 21:37, 23 January 2007 (EST)
  • In the same vein as emailing to the wiki, I have a dream of being able to call and leave messages on the wiki. This is for when I am in my car and remember something. Of course, an actual voice recording would be a lot of data and too annoying to ever manually convert into text. So, one would want the wiki to have voice recognition software to convert the voicemail into a text notebook entry. Yes, I know this is a long way off!
    • This isn't that much harder than the email. The main thing is how are you going to specify a page name on your phone? Also, voice recognition really isn't that great. --Austin Che 16:41, 23 January 2007 (EST)
    • Yeah, I can see that the voice recognition wouldn't work too well. Maybe for this and the email idea above, a better solution is to handle these things "off the wiki" and then manually "dump" information into the right place via normal mechanisms. Actually I guess what I really want is an assistant who I can call. :) --Skoch3 17:01, 23 January 2007 (EST)
  • OK, I know this idea is really tough too, but maybe there's work going on I don't know of. I am a user of evil microsoft products. I actually like Outlook and I suspect that since I will be doing email, I will also use the Outlook Calendar, and task list (to do). Would there be some way of "synching" outlook with a wiki? So that I could use the convenient way on Outlook of adding calendar events and task lists, but have it synched with public wiki pages? Some kind of wiki outlook plug in? OK, I know the market for that would be small. Synching with Outlook would then also make it easier to somehow add stuff to the wiki via a PDA--Skoch3 16:25, 23 January 2007 (EST)
    • Reshma 17:01, 23 January 2007 (EST): It is possible to view Google calendars on a wiki. See Endy:Victor3_plate_reader#Plate_reader_schedule for an example. So if you could get Outlook to sync with a Google calendar, then you could just display the Google calendar on a particular wiki page. That is the most straightforward way to do it right now (or at least the way that requires no new coding/functionality).
    • Very interesting, that looks like it would work for me, so I will look into it. Thank you!--Skoch3 17:04, 23 January 2007 (EST)

OWW journal clubs

  • --Vincent 05:58, 7 December 2006 (EST): Organizing a section of OWW where several journal clubs would be hosted (Computational Biology, Synthetic Biology, Lab Techniques in Microbiology ...) -- Has it been tried before ? Not at the lab level but with article discussions openly discussed by OWW users.

A given OWW journal club would have a focus on a defined area (use of categories), a place where people could suggest articles to be reviewed , and a selected article (voted every 2 weeks for example) being open for discussion through an open forum. It could be concluded by a conference call if people are motivated (more constraining to organize). It would be great to build a rich literature review that OWW could share and point to in the rest of the wiki.

Dear OWWers, I started an online journal club page with a draft here: Journal Club. Have a look and extend at your leisure. So far it's only a static article review. But with the excellent chat feature that was added recently, people could gather on a specific article page and really discuss world-wide. Jasu 09:41, 18 April 2007 (EDT)

OWW Short Course

  • Lon 13:33, 30 November 2006 (CST): Although there are protocol and course pages on OWW, both containing educational information and objectives, it might be good to have some more refined experiments. By this, I mean for newcomers to the biological sciences (new lab members, new labs) or those moving into new areas to have a set of standard experiments they could perform to establish good laboratory techniques and to be able to communicate problems with OWW members and/or their labmates. This could also be an alternative for lab instructors to use. This could be something like an updated and more encompassing Short Course in Microbial Genetics (or any another good lab manual).

Academic Job Openings

  • Jasonk 11:52, 10 November 2006 (EST): Came up at the last SC meeting, could have a place to post open post-doc positions, faculty, etc. Could also have corporate job postings, but that's probably already covered pretty well by type websites.

Calendar with all scientific conferences

  • Jasonk 11:52, 10 November 2006 (EST): Suggested by Tom. This would be a calendar strictly for scientific conferences, since it's often tough to find out about conferences you might be interested in.

OWW Journals

  • Jasonk 01:50, 25 October 2006 (EDT): Based on conversations with Chris Surridge, our 2nd OWW Open Science Seminar series speaker, it looks like starting a journal may get much easier. The general idea is to use PLoS One as a commoditized peer-reviewing service. Articles that get through the PLoS One filter have been verified for publication-quality science, but have not been subjected to any subjective merit criteria (e.g. is this good enough for publication in Nature?) This is where OWW can come in, user groups on OWW could aggregate and "re-publish" open access (OA) content that has made it onto PLoS One (or any other OA journal). Basically, we would serve as an aggegator of articles that conform to some quality standard set by an editorial board from that community. An author published in the OWW Journal of Synthetic Biology could site their PLoS one reference as well as a 're-publication' reference. If the OWW Journal actually gained some clout, an author would probably simply list being published in the aggregator rather than the PLoS One reference, since it would carry more weight (e.g. the paper had to get over the merit quality bar -- "is this good enough for publication in OWW Journal of Synth Bio?"). a very high bar, indeed ;) Additionally, we could provide commentary on the papers that are of interest, "blog-esque" posts from notable community members, etc...
  • open source journal management software


  • Jasonk 09:26, 6 October 2006 (EDT): Along the lines of adopt-a-protocol, it might be great to have adopt a topic area as well. Basically, trying to solve the problem of review articles always being out of date. It seems like the job of writing reviews would be much simpler if it was done on the fly as new papers came out. THat way when a new paper came accross your desk in the area you review you could read it, and then add the relevant details and the reference to the OWW Review page. This is in contrast to coming back to that same paper a year later when you're asked to write a review and having to re-read it, re-analyze it, etc. Seems like a win-win for the both the review-writer (less work) and the readers (who get a more up-to-date source.)


Moved to Talk:Protocols/Template.

Page Authorship

  • Jasonk 22:57, 8 August 2006 (EDT): There might be a benefit to having the option to lock in an "author" at the time of page creation. We could limit this to pages with a namespace in front of them (e.g. 'Endy:foo'), to prevent someone from locking down a 'shared area' page like DNA ligation. Other people could edit the page, but there would be an official author -- that means the author would have the benefit of getting credit for the content of the page (e.g. perhaps when you hit cite this page, only the offical author would come up), but also be saddled with ensuring some level of quality (whatever they were comfortable attaching their name to). This might help enable some downstream OWW applications, like providing real scientific attribution for OWW contributions or for publishing results, etc. I suspect that assigning a page an official authorship would be the exception rather than the rule, but might be a useful option to have -- just something to think about longer term, wanted to write it down.


  • Jasonk 16:38, 27 July 2006 (EDT):The customize sidebar extension is great, but I don't think any new user would notice it. Maybe at the bottom of the side bar we should include a link be default that says update my sidebar and would take the user to a pregenerated sidebar page for them with comments on how to change it. once they figured it out they could remove the link themselves from their sidebar if they don't want it there.


  • --Johncumbers 16:38, 16 July 2006 (EDT): A big problem I've found with OWW, and I'd like to see if anyone else has the same problem. I can't stay logged in, e.g Flickr, Amazon retains who I am, but OWW doesn't. Is this just me? This leads to the seconds part of the problem. When I go to log-in, it always returns me the link to go back to the main page, I then have to use the back button to go back to the page I want to edit. These are not huge problems, but they really confuse new people that I introduce to the site. They find it really frustrating to navigate at the beginning. Anyone else found this when trying to introduce new people to OWW/Mediawiki?
    • Smeister 07:38, 17 July 2006 (EDT) OWW keeps me logged in unless I log in from another computer - in that case I get logged out from the first. Are you maybe sharing your account? I assume you do not have any cookie setting problems since Flickr etc works for you...
    • Jasonk 09:25, 17 July 2006 (EDT): I stay logged in as well normally... However, to avoid getting linked back to the main page, use the link at the top right corner to log in - it will then offer a link back to the page you were coming from, rather than a link to the Main Page (I agree it is annoying when it links to the Main Page).
    • Austin 13:59, 17 July 2006 (EDT): On one computer, I can't stay logged in. On another, I always stay logged in. I've not been able to figure out the cause.
    • Skoch3 16:14, 23 January 2007 (EST): I always seem to have to re-log in. I use one computer, but it's a laptop with a lot of different IP addresses during the day I think. It seems I have to log in to my private wiki more often than the public, but not sure. I have been assuming that it was just some quirk between the private wiki log on and the OWW.

Page watch function

Smeister 08:20, 17 July 2006 (EDT) I love the "watch page" function and would like to organize more activities in the lab, taking advantage of it. However, there is no way of knowing who in the lab is watching a page at any moment. You basically never know if anybody is paying attention at all. Would a query page for this be very hard to incorporate? It sure would enhance overall transparency and I guess it would also be useful for some of these OWW discussion pages...

  • --Johncumbers 13:14, 17 July 2006 (EDT) I agree, I don't use the page watch as much as I'd like. I like you ridea Steven, It would be also nice if it had a little number like 'my watchlist(44)' to let you know what's inside there each day and encourage you to click on it.

Comment button

  • --Johncumbers 13:14, 17 July 2006 (EDT) could the signature button be changed to include the * and ''' that we put in for comments. Another idea would be a protocol notes button that creates a note link for a protocol. Currently if you want to add a note to a protocol, you have to either put it at the bottom, it would be better if it created a link within the page without you having to type it all out. e.g if the protocol is located at Protocols:Drosophila/chip on chip then when I post a note, it automatically creates a link to Protocols:Drosophila/chip on chip/note1 without me having to do it. get the idea?

Active Discussions

Lucks 20:16, 3 April 2006 (EDT):The topic on Flexible Science Databases has been moved to OpenWetWare:Software/Flexible_Science_Databases.


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