Paris/DISCUSSION

From 2007.igem.org

Revision as of 06:19, 13 July 2007

Discussion Page

This page is for questions, answers and discussions on the project, a kind of open forum.

Test of DapA deletion transduction, Thursday, July 5

How did you test for the success of this transduction? Simply with a normal culture without supplemented lysine in the medium, and seeing that the bacteria grows neverthless? Or is it that in the original DapA- strain tha DapA gene was replaced by an antibiotic resistance gene, that should then be present in the transfected bacteria?

For the modellers

Have a look at the Cambridge team wiki. They have a detailed page on [http://www.ccbi.cam.ac.uk/iGEM2007/index.php/Software_Modelling_for_Synthetic_Biology modelling and iGEM. ]

For everybody

Have a look at the Edinburgh team wiki. They also present a Cre/Lox box in one of their constructions !

Team Notebook and Protocols

I suggest that the Team Notebook section summarizes the work progress, the meaning of the different steps, and intermediate results. All protocols should be in the protocols section with links.

Question: how to link directly to a subsection of a page in a wiki?

Answer: click here to read July 2nd entry.

Concerning the wiki

The notebook is now accessible via a calendar. I hope that you will prefer the notebook like that. I moved some pages from their places to Paris/, and it is a good idea to take care that every page we create begins by Paris/... Nicolas C.

Samuel B.: The calender is a nice feature, however isn't it possible to have also everything in a single page. It is useful to have an overall view of the notebook. There is a risk with wikis to split informations on too many pages. This is clearly the case by presenting all in a calender...

I discussed with Eimad and David (P) and the idea is to make two notebooks :

• one accessible via the calendar, where we put all that we do during the day (still separated from protocols), for the people in the lab
• another one which will summarize goals and progresses step by step. We will begin this one soon. Nicolas C.
• Ok, but it should be possible to generate from the calender a single page with all the entries. It would be useful in any case to get an overview of the calender... Samuel B.
• Ok, it's done. Nicolas C.
• Finally I removed it because the two ways of watching the notebook are not compatible. I have to find another solution. Nicolas C. 07:38, 11 July 2007 (EDT)
• There is a way to generate pages from other pages. You can write a page that will include dynamically all entries from a given week (see this example Week page) for the applications below. This can be used to:
  • generate week pages, month pages...
  • quote a particular day into a different page...
  • quote a particular section of a day into a different page...
  • include code at the end of each page (links to the main page, the notebook, the forum, etc...), to help us organize our wiki. (as in the kinetic array)

It is based on templates:

• • http://en.wikipedia.org/wiki/Help:TemplateWikipedia:Wikitext_examples#Templates
  • http://en.wikipedia.org/wiki/Help:Template

Pablo

• I tried this transclusion stuff, but the problem is that it's loading dynamically the page only after editing the page : if you modify the page July_2 after having generated the page transclusion_example, the page transclusion_example won't be updated until you edit and save it again. Moreover, if somebody wants to edit directly the page transclusion_example, it will be lost on the next edit/save page. I think it's a bit dangerous. Maybe we can keep in mind this solution but not use it to fill the wiki. Nicolas C.
• May be there is something I am missing to me it does what it should be. Example:
  • I log in the wiki and add "TEST" to the end of July2
  • I open the Week page above
  • I find TEST without problems

May be is a problem of the cache of your browser !? Pablo 02:19, 13 July 2007 (EDT)

Boston team

Have a look at the Boston team wiki main page

I find it very clear. Maybe a good inspiration for a next version of ours... Samuel B.

Concerning kinetic measurements

I made a template in order to present growth experiments clearly when we use the 96 plate array. Click here to see an example. Nicolas C. If you want to use it, just copy and past this example after clicking on the edit link. Then, fill the appropriate cells.

Berkeley UC notebooks

It is very interesting to visit the other teams' wikis... Very inspiring ! Have a loog at the Berkeley UC wiki. They organize their work differently: each member has his own notebook, and they are very detailed (see for instance David Tulga Notebook. Impressive.

Another idea to keep in mind: share spreadsheets on google documents (for instance for oligos).

Otherwise their wiki structure is similar. Not bad! Samuel B.