User talk:Jamesh008

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Visit to Boston

Hey James,

That's great that you're visiting Boston on Monday. If you have time, you should definitely stop by to chat. A few (but not all) of the steering committee members reside in the Endy and Knight labs at MIT. You can either just stop by or we can set up a time.

Directions to the Endy lab: Endy:Contact

Building 68, Room 68-558, 564, 570, and 580

617-258-8684 (ask for Jason)

Directions to the Knight lab: Knight:Contact

Stata Center, MIT

32 Vassar Street Room 32-311

Cambridge, MA 02139

617-258-5244 (ask for Reshma or Austin)

Sorry that it took so long to reply to you about this. Your note just fell through the cracks for a bit.


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?

  • Sri Kosuri (talk) 11:35, 18 October 2006 (EDT):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.
  • User:Jamesh008 21:18, 18 October 2006 (GMT):I will add a link to a stable historical version of the protocols I feel it is necessary for. I am satisfied that ther will be virtually nil malicious editing and that mistakes are unlikely but will occur rarely. I also think I am the one most likely to get things wrong as I am doing all the editing!

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.


Hey James,

I just wanted to make a few comments on the possibility of making things restricted to editing. There are a couple of things to note

  1. Almost all protocols with User:protocol or Group:protocol are only edited by those users and groups that posted them. Those few protocols (there are not more than 5 or so) that are edited by people outside the member/group are almost all formatting help.
  2. We have never had a case of vandalism
  3. All histories are tracked. Each user is documented in the system to an actual person with institutional affiliation. It makes little sense to edit someone else's protocol. Not only for public embarresment, culpability, and being kicked off... but are there really scientists that are that malicious (User:Jamesh008 No, probably not).
  4. The only imaginable problem is accident. This has never happened on a protocol page, but once or twice we had a user try to copy code, and accidently changed the code when doing this. This is rare, and usually happens to the OWW template pages. The one good thing is that anyone can revert to any point in the history of a page. Mistakes are very easy to fix. This is so rare though, people rarely look at the history everytime there is a problem. Is it likely that someone would change something so small that the original user wouldn't notice? I guess it's possible. We haven't had a problem so far, so it seems a bit premature to create a whole mechanism by which to restrict edit access to pages. There are also ways to get around such a problem. For example, if you have a set of protocols you use, link to a stable copy (Every page has a permanent link button on the left hand side).

On the other hand though, I do understand the necessesity for private pages, and it is something we are working on. Austin, as you've seen, hopefully might have already solved some of the problem for us (User:Jamesh008 Private wikis look like a solution, they will certainly help to convert some people here!).

Anyways, thanks for all your comments. We really need users to push all of us to make the site better. We would love if you would consider joining the Steering Committee, so that you can take part in votes and other ideas that you may have. And please, keep the comments coming.(User:Jamesh008 Steering committee sounds cool, I would worry about telephone conferencing from the UK!)

--Sri Kosuri (talk) 12:03, 18 October 2006 (EDT)

ps. One of the things we've been dealing with on the steering committee how hard it is to keep track of discussions. We are in the process of starting a discuss mailing list that may make things easier in the future.

where have the cool pictures gone?

Hi James,

Just surfed again to your nice page about RNA Quality Control but many of the sample pictures were gone. Any idea what happened there? Let's find out. I would love to see the page restored to it's full gallery state. Very nice work btw.


Jakob 04:15, 10 July 2009 (EDT)