Talk:Protocols: Difference between revisions

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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)
::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)


<div style="padding: 2px">[[Image:Oww-protocols.jpg|753px]]</div>


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'''Making this revised version go live. Feel free to revert back or change it as you see fit.''' --[[User:Rshetty|RS]] 20:02, 11 January 2006 (EST)
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<div style="padding: .4em .9em .9em">
 
==''In vivo''==
===''Escherichia coli''===
*[[beta-Galactosidase Assay (A better Miller)]]
*[[Bacterial cell culture]]
*[[Chemically competent cells]]
*[[Electrocompetent cells]]
*[[Electroporation]]
*[[Miniprep]]
*[[Colony PCR]]
*[[Pulse-chase protein production]]
*[[Pour plates|Pour LB plates]]
*[[S_N Chemostat Protocol]]
===Yeast===
*[[High Efficiency Transformation]]
*[[Yeast Colony PCR]]
*[[Yeast DNA Prep]]
*[[Cell Cycle Arrest]]
*[[Fixing cells]]
*[[B-galactosidase assay]]
*[[Silver: Time-Lapse Microscopy|Time-Lapse Microscopy]]
*[[Silver: Lysate for Western|Simple Yeast Lysate]] (for Western etc.)
*[[Assaying mating]]
*[[Pour YPD plates]]
*[[Dropout plates for yeast]]
*[[Layered plates]]
===T7===
*[[Studier Lysate Prep|Simple lysate protocol from plaque or lysate]]
*[[Cesium Chloride Purification of T7]]
===''Mesoplasma florum''===
*[[Mesoplama florum:Culture media|Culture Media]]
 
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==''In vitro''==
===Nucleic acids===
*[[Quantification of nucleic acids]]
*[[Phenol/chloroform extraction]]
*[[Nucleic acid precipitation]]
*[[Denaturing acrylamide gel purification of nucleic acids]]
====DNA====
*[[Agarose gel electrophoresis]]
*[[Annealing Primers]]
*[[Designing primers]]
*[[DNA Ligation]]
*[[Library Generation]]
*[[Miniprep]]
*[[PCR]]
*[[Phosphatase treatment of linearized vector]]
*[[PNK Treatment of DNA Ends]]
*[[Purification of DNA]]
*[[Reconstituting primers]]
*[[Restriction digest]]
*[['Round-the-horn site-directed mutagenesis]]
*[[Sequencing DNA]]
*[[Site-directed mutagenesis]]
*[[Templiphi]]
====RNA====
*[[RNA Extraction]]
*[[Northern Blot, 32P End-Labeled Probes |Northern Blot, <sup>32</sup>P End-Labeled Probes]]
*[[Probe Prep, 32P End-Labeled Probes|Probe Prep, <sup>32</sup>P End-Labeled Probes]]
*[[RNase Protection Assay]]
*[[In vitro transcription with T7 RNA polymerase]]
*[[RNA Half-life]]
===Protein===
*[[Acrylamide Gels|Acrylamide gels and SDS-PAGE]]
*[[Silver: Coomassie Stain|Coomassie Stain]]
*[[Silver: Destain|Coomassie Destain]]
*[[Sauer:Silver staining|Silver staining]]
*[[Western Blot]]
*[[Keating:Experimental Protocols:HPLC|HPLC]]
 
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==Other==
===Microfluidics===
*[[Design a Microfluidic Chip]]
*[[Order a Microfluidic Chip from the Foundry]]
*[[Operate Microfluidic Chemostat]]
===Microscopy===
*[[Agarose Pads for Microscopy]]
*[[Quantitative Microscopy]]
*[[Silver: Time-Lapse Microscopy|Time-Lapse Microscopy]]
===Flow Cytometry===
*[[Flow Calibration]]
===Plate reader===
*[[Endy:Victor3 counteracting evaporation in long time courses|Counteracting evaporation from wells in a Victor3 plate reader]]
 
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Revision as of 18:02, 11 January 2006

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 view. Feel 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. -- RS

I made a protocols template. It has all the formatting from the layout below. Power users can edit the template to add new categories, formats etc. This 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.

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.--BC 12:14, 11 January 2006 (EST)
  • 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...-- JK
  • 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. -- RS
  • 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.--Kathleen 15:22, 11 January 2006 (EST)
    • i don't like the implications of your "real biology labs" comment, kathleen ;) --JK
    • 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. :)--Kathleen
  • In all my offending, I forgot to mention that I like this organization scheme. It makes it much easier to find stuff. --Kathleen
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.--BC 18:31, 11 January 2006 (EST)
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? :) --RS 18:38, 11 January 2006 (EST)


Making this revised version go live. Feel free to revert back or change it as you see fit. --RS 20:02, 11 January 2006 (EST)

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