User talk:Jamesh008

Consensus protocols

Sri Kosuri comments

Hi James,

Welcome to OWW. Hope you are finding the site useful. I thought I would send along a few comments.

1. First, check out this page. It's a custom recent changes that only looks at Recent Changes of pages that begin with CRI Genomics Core.
2. Nice posting of the idea that you had about protocol aggregregation. Actually, we've been thinking of the same solution. Check out the DNA Ligation page. There is an overall page, and then links to individual lab protocols. While this is only one example, we haven't had a lot of bandwidth to do aggregation. We've been thinking of an alternative way to do this too, where all protocols are posted with custom lab names in front of them. Then people use the categorization tools to group their protocols with others. Anyways, so far a work in progress. Thanks for you input, and please give us more as time goes on.

Anyways, that's it for now... let me know if you have questions as well.

--Sri Kosuri (talk) 08:27, 13 October 2006 (EDT)

James Hadfield

Hello Sri,

• I like the recent changes pages and the history options as well. I think both will be very useful for consensus protocols.
• The DNA Ligation is going in the right direction but so far it is not what I would consider a consensus protocol. I would like to see the consensus protocol page actually have a protocol on it; probably biased by the editor (?) but certainly reflecting the general trends in that prtocol i.e. methodology and materials. Links in the protocol could be to reference protocols and another option would be to have a 'contentious issue' link where there are unresolved differnces of opinion for open discussion e.g. xNA precipitation protocols and temperature of precipitation. The consensus protocol page would hopefully become the starting point for anyone not used to doing a particular process.
• The biggest problem I see is who looks after a consensus protocol page?

Protocol editing

What happens if someone makes a mistake when editing a protocol? Is there some way of using the history functions to create a 'stable' version of a protocol?

• First, thanks for all your comments on trying to make the site better. It's great to have a lot of feedback. As to a beginnings to answer your question. For now, on the page, you can link to a stable link (rather than the current page), to have a stable copy of what you entered. In practice though, very few people edit others' protocols. Also, in the future, MediaWiki is working on creating vetted versions that they show, while edits can be made on more dynamic pages, and aren't put into practice until they are vetted by the user. They are doing this b/c of problems on wikipedia, but i'm sure in the future we can incorporate this once the updated software arrives. So something to keep on our minds.

Latex markup

James Hadfield question to Austin Che

Hi Austin, Is there a way to easily intergrate the LatexDoc ability to create a PDF into all protocols? This would make them way easier to print out for the lab!

Austin Che

Can you clarify exactly what you would like to see? Each page can already be printed out so I assume printing out in some "fancy" format? Or are you suggesting a way to collect a group of protocols and somehow print them all out together? I have thought a bit about automatically converting mediawiki syntax into latex syntax but I'm not sure exactly what that would get us. Maybe have templates for converting from web to print versions? If you can figure out how you would do such a thing by hand, I'm sure we can figure out how to get a computer to do it.

James Hadfield

I would like to be able to get a pdf for any prtocol, or any page at all, on OWW. A PDF is easily printable and savable on any PC, the printable page option on OWW is not so nice to look at? The problem I see is that you need to format an OWW page for Latex markup and this is different from Latex markup. Perhaps some converter to automatically swap between the two?

Austin Che

An alternative which may be make 'prettier pages' which would be easier than a general converter is a different stylesheet for printing. This is already within the wiki's capabilities. So if you know anything about CSS and think it would be possible to make the printed output look nice simply by CSS formating, then we can change the CSS on the wiki.