Talk:Protocols

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(inserted Sri's graphic)
Current revision (15:17, 6 April 2010) (view source)
(Consensus Protocols)
 
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'''This is a proposed restyling of the protocols page.  I thought I would put it here to see what people thought before making it go live on the real page.  Comments welcome.  I just thought the page could be made more compact and easy to viewFeel free to retweak if you have a better idea.  A similar thing has been suggested for the materials page.  My only concern is whether it makes it more difficult/intimidating for those new to wikis to edit?  Which is definitely not what I want.''' --[[Reshma Shetty | RS]]
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==Goals==
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The protocol page is intended to organize the protocol information contributed by different labs and individualsAs an example of what a community protocol might look like, see [[DNA Ligation]].
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I made a protocols [[Template:Protocols|template]].  It has all the formatting from the layout below.  Power users can edit the template to add new categories, formats etc.  This [[Protocols v2| page]] has the new version of the protocols using that template.  This makes it a tiny bit easier for people to edit the protocols list without dealing with all the formatting.  This is good but it means that users need to go edit the template page if they want to add new categories so there is trade off between making some editing simple and higher level editing more difficult.
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==Active Discussions==
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:It looks like the ease of editing afforded by using the template as described above probably doesn't merit the extra complexity of having templates as well as pages.  It might however be beneficial if the protocols, materials, help pages etc, were all formatted in a common way.  Then you could just change the template and style changes would be applied to all pages.--[[User:Bcanton|BC]] 12:14, 11 January 2006 (EST)
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''add new discussion topics to the top of this list''
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*agreed on both points - template probably not worth it for the page, though eventually moving to a common template would be pretty nice.  Also, this is WAY better, I think we should go live with this ASAP. Though might be nice to have a graphic saying 'protocols' beneath the OWW logo...-- [[Jason Kelly|JK]]
 
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*yeah that was Austin's objection to the page as well.  That it looked TOO similar to the frontpage.  I just didn't know how the openwetware graphic was made and if we could easily make a "Protocols" graphic to go under it and similarly for the Materials page.  As for the templating, I kind of like it.  It does make things easier to look at. --[[Reshma Shetty | RS]]
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===Consensus Protocols===
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*'''[[User:Rene Kessler|Rene Kessler]] 6 April 2010 (EDT)''': All consensus protocols should be organized in a single location.  What other consensus protocols exist besides DNA ligation?
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*I was going to suggest removing the OWW logo altogether. Maybe replacing it with a protocols graphic will work, but most people will have navigated their way here, so they'll know what they're looking at. I think the template may be bit too complicated for now and may inhibit the addition of new protocols to the shared page. I also don't think the categories we have now are anywhere near "all-encompassing" especially given that some real biology labs are joining up now. I do agree that a template to standardizing formatting will be a good thing in the future, though.--[[User:Kathmc|Kathleen]] 15:22, 11 January 2006 (EST)
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===New Category===
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**i don't like the implications of your "real biology labs" comment, kathleen ;) --[[Jason Kelly|JK]]
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*'''[[User:Cameron Neylon|Cameron Neylon]] 07:19, 29 April 2008 (EDT)''': Added new category of chromatography and appropriate category page. Will probably run around a few of the protocols and add the new category as appropriate
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**I was talking about our lab, too. Some of these people work with what most people in the world would consider as critters, not the single-celled guys we play around with, and do things like study behavior. Anyone up for studying the ecology of E. coli? Didn't mean to offend. :)--[[User:Kathmc|Kathleen]]
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*In all my offending, I forgot to mention that I like this organization scheme. It makes it much easier to find stuff. --[[User:Kathmc|Kathleen]]
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:We have two levels of info. on this page - protocol categories and actual protocols. When the real biologists start adding more protocols, it may make sense to put the actual protocols on subpages.  Were we to come up with a more "all-encompassing" set of categories and scrape any extra protocols that are lying around we might not be too far away from needing to do that.  This looks great for now, I agree with replacing OWW with Protocols.--[[User:Bcanton|BC]] 18:31, 11 January 2006 (EST)
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::Sri kindly offered to do a "Protocols" graphic that is similar in flavor to the OWW graphic.  He should be doing it tonight supposedly.  Once that happens, perhaps we can replace the old protocols page since most people chiming in here seem to be in favor of it.  Sri ... want to make a Materials graphic too while you're at it? :) --[[User:Rshetty|RS]] 18:38, 11 January 2006 (EST)
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<div style="padding: 2px">[[Image:Oww-protocols.jpg|753px]]</div>
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===Dynamically generated protocols pages===
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*'''[[User:Bcanton|BC]] 18:49, 11 May 2007 (EDT)''':  I like the idea of dynamically generating the protocols page.  However, there are still some minor drawbacks.  For one, each page is now labeled with its page name rather than a piped version of it.  As a result the list of protocols looks a little uglier than it once did.  Second, instead of there being one link for, say, Colony PCR, there are now multiple links to lab specific colony PCR protocols.  Since the list is alphabetical, the colony PCR protocols aren't in consecutive order making it difficult to browse.  Another point to consider is that if this is the route we want to take, we might need multiple levels of categorization.  For example, currently there is an listing for Colony PCR, Knight:Colony PCR and Endy:Colony PCR.  It seems like they need different categories since they are at different levels in the hierarchy, i.e. general protocol page versus lab specific protocol.  In general though, I'm all in favor of dynamic generation of this page.
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**We could probably filter out all protocols with a ":" in the title thereby omitting all lab specific protocols if we choose.
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***'''[[User:Bcanton|BC]] 10:13, 13 May 2007 (EDT)''':Yeah, that should be easy given that you can filter by namespace with the dpl extension.  If we did that though, we would also get rid of all the protocols for which a lab specific protocol is the only one we have and I think we should try and keep those. We could solve that problem by making a general protocol page for every protocol for which a lab specific protocol exists (i.e. a <nowiki>[[Bar protocol]]</nowiki> for every <nowiki>[[Foo:Bar protocol]]</nowiki>).  For now, <nowiki>[[Bar protocol]]</nowiki> could just be a template of how community protocol pages should look and include a link to <nowiki>[[Foo:Bar protocol]]</nowiki>.  Hopefully, all those general pages would be used in the long run anyway.
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***'''[[User:Torsten Waldminghaus|Torsten Waldminghaus]] 05:04, 28 February 2008 (EST)''': Would it be possible to include the lab specific protocols in the alphabetic list of the others by changing the titel from labX: My protocol to My protocol (labX) or something similar? Is that a technical problem? I would think it's good to have all the protocols including the lab specific ones in one list and I agree that it is confusing to not find the Colony PCR protocols at one spot in the list.
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*'''[[User:Rshetty|Reshma]] 17:22, 2 May 2007 (EDT)''': The [[OpenWetWare:Steering committee|steering committee]] is discussing moving to a dynamically generated protocols page.  See [[Escherichia coli]] for an example.  Thus rather than explicitly adding protocols to this page, people would simply tag their own protocols with the relevant [[Categories|categories]].  Please comment on this proposal here.
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*'''[[User:Austin|Austin Che]] 18:37, 8 May 2007 (EDT)''': For inspiration, see [[Protocols/Dynamic]] (probably requires some more work and formatting), but it won't get any more dynamically generated than something like this.
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{| cellspacing="3"
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==Archived Discussions==
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|- valign="top"
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*[[Protocols/Template]] - a template for posting a protocol on OpenWetWare
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|width=247px class="MainPageBG" style="border: 0px solid #CCCCCC; color: #000; background-color: #CCCCCC"|
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*[[Talk:Protocols/Example protocol|Example protocol]] - what is the best example of a protocol that we can point users to?  What could make it better?
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<div style="padding: .4em .9em .9em">
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*[[Talk:Protocols/Tags|Tags]] - can we effectively use tags to organize protocols?
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*[[Talk:Protocols/Appearance|Appearance]] - suggestions for improvements to the appearance of the page.
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*[[Talk:Protocols/In silico|In Silico]] - should we include in silico protocols?
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==''In vivo''==
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===Content===
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===''Escherichia coli''===
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*'''[[User:Rshetty|RS]] 18:46, 3 May 2006 (EDT)''': I've added additional links under general resources.  However, I am not sure if these resources are generally available or if MIT happens to have an institutional subscription.  Remove links that require subscriptions ... they can be listed under [[Web resources]] or elsewhere.  (Will try and check on this later.).
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*[[beta-Galactosidase Assay (A better Miller)]]
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*[[Bacterial cell culture]]
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*[[Chemically competent cells]]
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*[[Electrocompetent cells]]
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*[[Electroporation]]
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*[[Miniprep]]
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*[[Colony PCR]]
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*[[Pulse-chase protein production]]
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*[[Pour plates|Pour LB plates]]
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*[[S_N Chemostat Protocol]]
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===Yeast===
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*[[High Efficiency Transformation]]
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*[[Yeast Colony PCR]]
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*[[Yeast DNA Prep]]
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*[[Cell Cycle Arrest]]
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*[[Fixing cells]]
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*[[B-galactosidase assay]]
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*[[Silver: Time-Lapse Microscopy|Time-Lapse Microscopy]]
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*[[Silver: Lysate for Western|Simple Yeast Lysate]] (for Western etc.)
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*[[Assaying mating]]
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*[[Pour YPD plates]]
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*[[Dropout plates for yeast]]
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*[[Layered plates]]
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===T7===
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*[[Studier Lysate Prep|Simple lysate protocol from plaque or lysate]]
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*[[Cesium Chloride Purification of T7]]
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===''Mesoplasma florum''===
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*[[Mesoplama florum:Culture media|Culture Media]]
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</div>
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==Active Community Members==
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|width=247px class="MainPageBG" style="border: 0px solid #cc3300; color: #000; background-color: #99CCFF"|
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[[Barry Canton]], [[Jason Kelly]],  '''add yourself here'''
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<div style="clear: right; text-align: left; float: left; padding: .4em .9em .9em">
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==''In vitro''==
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===Nucleic acids===
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*[[Quantification of nucleic acids]]
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*[[Phenol/chloroform extraction]]
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*[[Nucleic acid precipitation]]
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*[[Denaturing acrylamide gel purification of nucleic acids]]
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====DNA====
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*[[Agarose gel electrophoresis]]
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*[[Annealing Primers]]
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*[[Designing primers]]
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*[[DNA Ligation]]
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*[[Library Generation]]
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*[[Miniprep]]
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*[[PCR]]
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*[[Phosphatase treatment of linearized vector]]
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*[[PNK Treatment of DNA Ends]]
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*[[Purification of DNA]]
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*[[Reconstituting primers]]
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*[[Restriction digest]]
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*[['Round-the-horn site-directed mutagenesis]]
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*[[Sequencing DNA]]
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*[[Site-directed mutagenesis]]
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*[[Templiphi]]
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====RNA====
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*[[RNA Extraction]]
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*[[Northern Blot, 32P End-Labeled Probes |Northern Blot, <sup>32</sup>P End-Labeled Probes]]
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*[[Probe Prep, 32P End-Labeled Probes|Probe Prep, <sup>32</sup>P End-Labeled Probes]]
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*[[RNase Protection Assay]]
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*[[In vitro transcription with T7 RNA polymerase]]
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*[[RNA Half-life]]
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===Protein===
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*[[Acrylamide Gels|Acrylamide gels and SDS-PAGE]]
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*[[Silver: Coomassie Stain|Coomassie Stain]]
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*[[Silver: Destain|Coomassie Destain]]
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*[[Sauer:Silver staining|Silver staining]]
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*[[Western Blot]]
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*[[Keating:Experimental Protocols:HPLC|HPLC]]
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</div>
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|width=247px class="MainPageBG" style="border: 0px solid #cc3300; color: #000; background-color: #CCCCCC"|
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<div style="padding: .4em .9em .9em">
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==Other==
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===Microfluidics===
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*[[Design a Microfluidic Chip]]
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*[[Order a Microfluidic Chip from the Foundry]]
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*[[Operate Microfluidic Chemostat]]
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===Microscopy===
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*[[Agarose Pads for Microscopy]]
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*[[Quantitative Microscopy]]
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*[[Silver: Time-Lapse Microscopy|Time-Lapse Microscopy]]
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===Flow Cytometry===
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*[[Flow Calibration]]
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===Plate reader===
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*[[Endy:Victor3 counteracting evaporation in long time courses|Counteracting evaporation from wells in a Victor3 plate reader]]
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</div>
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|}
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__NOTOC__
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Current revision

Contents

Goals

The protocol page is intended to organize the protocol information contributed by different labs and individuals. As an example of what a community protocol might look like, see DNA Ligation.

Active Discussions

add new discussion topics to the top of this list


Consensus Protocols

  • Rene Kessler 6 April 2010 (EDT): All consensus protocols should be organized in a single location. What other consensus protocols exist besides DNA ligation?

New Category

  • Cameron Neylon 07:19, 29 April 2008 (EDT): Added new category of chromatography and appropriate category page. Will probably run around a few of the protocols and add the new category as appropriate

Dynamically generated protocols pages

  • BC 18:49, 11 May 2007 (EDT): I like the idea of dynamically generating the protocols page. However, there are still some minor drawbacks. For one, each page is now labeled with its page name rather than a piped version of it. As a result the list of protocols looks a little uglier than it once did. Second, instead of there being one link for, say, Colony PCR, there are now multiple links to lab specific colony PCR protocols. Since the list is alphabetical, the colony PCR protocols aren't in consecutive order making it difficult to browse. Another point to consider is that if this is the route we want to take, we might need multiple levels of categorization. For example, currently there is an listing for Colony PCR, Knight:Colony PCR and Endy:Colony PCR. It seems like they need different categories since they are at different levels in the hierarchy, i.e. general protocol page versus lab specific protocol. In general though, I'm all in favor of dynamic generation of this page.
    • We could probably filter out all protocols with a ":" in the title thereby omitting all lab specific protocols if we choose.
      • BC 10:13, 13 May 2007 (EDT):Yeah, that should be easy given that you can filter by namespace with the dpl extension. If we did that though, we would also get rid of all the protocols for which a lab specific protocol is the only one we have and I think we should try and keep those. We could solve that problem by making a general protocol page for every protocol for which a lab specific protocol exists (i.e. a [[Bar protocol]] for every [[Foo:Bar protocol]]). For now, [[Bar protocol]] could just be a template of how community protocol pages should look and include a link to [[Foo:Bar protocol]]. Hopefully, all those general pages would be used in the long run anyway.
      • Torsten Waldminghaus 05:04, 28 February 2008 (EST): Would it be possible to include the lab specific protocols in the alphabetic list of the others by changing the titel from labX: My protocol to My protocol (labX) or something similar? Is that a technical problem? I would think it's good to have all the protocols including the lab specific ones in one list and I agree that it is confusing to not find the Colony PCR protocols at one spot in the list.
  • Reshma 17:22, 2 May 2007 (EDT): The steering committee is discussing moving to a dynamically generated protocols page. See Escherichia coli for an example. Thus rather than explicitly adding protocols to this page, people would simply tag their own protocols with the relevant categories. Please comment on this proposal here.
  • Austin Che 18:37, 8 May 2007 (EDT): For inspiration, see Protocols/Dynamic (probably requires some more work and formatting), but it won't get any more dynamically generated than something like this.

Archived Discussions

  • Protocols/Template - a template for posting a protocol on OpenWetWare
  • Example protocol - what is the best example of a protocol that we can point users to? What could make it better?
  • Tags - can we effectively use tags to organize protocols?
  • Appearance - suggestions for improvements to the appearance of the page.
  • In Silico - should we include in silico protocols?

Content

  • RS 18:46, 3 May 2006 (EDT): I've added additional links under general resources. However, I am not sure if these resources are generally available or if MIT happens to have an institutional subscription. Remove links that require subscriptions ... they can be listed under Web resources or elsewhere. (Will try and check on this later.).

Active Community Members

Barry Canton, Jason Kelly, add yourself here

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