OpenWetWare:Ideas: Difference between revisions
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*Distribute information from [[OpenWetWare:Ideas/IdeasArchive]] to respective areas. | *Distribute information from [[OpenWetWare:Ideas/IdeasArchive]] to respective areas. | ||
*Firm up one of these ideas and put it on the official [[OpenWetWare:To do list|to do list]]. | *Firm up one of these ideas and put it on the official [[OpenWetWare:To do list|to do list]]. | ||
==Use of Mediawiki commons on OWW?== | |||
[[User:Steven J. Koch|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 <nowiki>[[Image:whatever.png]]</nowiki> 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? | |||
== | ==Invitations== | ||
*'''[[User:Jason R. Kelly|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--[[User:Dan Bolser|Dan]] 14:04, 13 February 2008 (CST) | |||
**'''[[User:Bill Flanagan|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== | |||
*'''[[User:Jason R. Kelly|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. | |||
*'''[[User:Etchevers|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== | |||
*'''[[User:Jason R. Kelly|Jason R. Kelly]]:''' A [http://chem-bla-ics.blogspot.com/2007/06/nature-should-host-our-electronic-lab.html 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. | |||
**'''[[User:Bill Flanagan|Bill Flanagan]]11:45, 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 [[OpenWetWare:Software/Publish to OWW Button|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. | |||
**'''[[User:Bill Flanagan|Bill Flanagan]]11:52, 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. | |||
**'''[[User:Bill Flanagan|Bill Flanagan]]11:56, 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. | |||
***'''[[User:Steven J. Koch|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: | |||
***# Group signons (such as "Koch Lab") for making edits. Users could sign their entries with the group identity (<nowiki>~~~~</nowiki>) 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." | |||
***#*'''[[User:Bill Flanagan|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. | |||
***#*:'''[[User:Steven J. Koch|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: "<nowiki>~~~~</nowiki>: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. | |||
***#*'''[[User:Jason R. Kelly|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. | |||
***#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. | |||
***#*'''[[User:Austin J. Che|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. | |||
***#**'''[[User:Steven J. Koch|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.) | |||
***#**'''[[User:Ricardo Vidal|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]] [http://openwetware.org/index.php?filter=Endy:Screening_plasmid&feed=rss&title=Special:Recentchanges 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. [http://lifehacker.com LifeHacker] does this so might be model there on how to implement. | |||
==Add a reference== | |||
*'''[[User:Jason R. Kelly|Jason R. Kelly]] 18:25, 10 June 2007 (EDT):'''A wizard for adding a reference in the biblio format automatically. | |||
==Wiki to PDF converter== | |||
*'''[[User:Reshma P. Shetty|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 [[User:Austin J. Che/Extensions/LatexDoc|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. | |||
**'''[[User:Jason R. Kelly|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. | |||
**'''[[User:Cameron Neylon|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== | |||
*'''[[User:Jason R. Kelly|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. | *'''[[User:Jason R. Kelly|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. | ||
*'''[[User:Austin J. Che|Austin Che]] 20:20, 16 May 2007 (EDT)''': See also [[OpenWetWare:Software/Image_Editor]] | |||
**'''[[Sri Kosuri]] ([[User talk:Skosuri|talk]]) 19:09, 17 May 2007 (EDT)''': Doesn't seem very easy to use. I wonder if we could incorporate something like [http://www.frankmanno.com/ideas/css-imagemap/ this] into the site. | |||
==Tell user about this edit== | ==Tell user about this edit== | ||
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Dear OWWers, | 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 | 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. [[User:Jasu|Jasu]] 09:41, 18 April 2007 (EDT) | ||
==OWW Short Course== | ==OWW Short Course== | ||
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==OWW Journals== | ==OWW Journals== | ||
*'''[[User:Jasonk|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... | *'''[[User:Jasonk|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... | ||
*[http://pkp.sfu.ca/?q=ojs open source journal management software] | |||
==[[OpenWetWare:Reviews]]== | ==[[OpenWetWare:Reviews]]== |
Latest revision as of 06:02, 5 September 2008
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Welcome to Ideas discussion area. How you can help
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? Invitations
Search within tags/categories
Private/public lab notebooks
RSS digests
Add a reference
Wiki to PDF converter
Gel annotater
Tell user about this edit
Add protocol to my notebookCould 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
OWW journal clubs
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
Academic Job Openings
Calendar with all scientific conferences
OWW Journals
OpenWetWare:Reviews
Adopt-a-protocolMoved to Talk:Protocols/Template. Page Authorship
Sidebar
Page watch functionSmeister 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...
Comment button
Active DiscussionsLucks 20:16, 3 April 2006 (EDT):The topic on Flexible Science Databases has been moved to OpenWetWare:Software/Flexible_Science_Databases. SubarticlesRecent Changes in IdeasList of abbreviations:
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