Paris/DISCUSSION

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< Paris(Difference between revisions)

Latest revision as of 02:32, 27 October 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. ]
Shouldn't we write from the begining a list of parameters (in fact, the things we would like to characterize) together with the variables we discussed, and separate input (probably independent) and output (probably dependent) variables for clarity? Pablo 07:21, 13 July 2007 (EDT)

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.
Ok, I tried. The first time I added something to July_2, I could see it inmediately on the week page. Then I tried again adding something else, but this change is not shown now. Therefore, I agree it is a weak solution, it is updated in an impredictable way (at least it does not appear inmediately) :( Pablo

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.

Templates

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.

Kinetic Array :le titre ici
	1	2	3	4	5	6	7	8	9	10	11	12
A
B
C
D
E
F
G
H

PCR

Each time you make a PCR, try to fill the following form properly and put it in the wiki. To use this template, just copy and paste the example in the edit page here, and replace the cells with your parameters.

PCR : le titre ici

PCR Settings	Buffer (5x)	Expected size
Annealing (°C)	MgCl₂ 10µM	{{{Size}}}
	dNTP 10µM	Success
Time Elongation	Oligo F 10µM	{{{Success}}}
	Oligo R 10µM	Image (click to enlarge)
Number cycles	Water	[[Image:{{{Image}}}\|30px]]
	Polymerase	Band (0=ladder)
	DNA	{{{Band}}}

Try to fill it like the example below.

PCR : DGAT amplification

PCR Settings	Buffer (5x)	5x 10µL		Expected size
Annealing (°C)	MgCl₂ 10µM	10µM 0µL		{{{Size}}}
55°C	dNTP 10µM	10µM 1µL		Success
Time Elongation	Oligo F 10µM	6	10µM 1µL	{{{Success}}}
1m30'	Oligo R 10µM	7	10µM 1µL	Image (click to enlarge)
Number cycles	Water	40µL		[[Image:{{{Image}}}\|30px]]
30	Polymerase	FinnZymes 2µL		Band (0=ladder)
	DNA	lambda plasmid 1µL		{{{Band}}}

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.

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

Otherwise their wiki structure is similar. Samuel B.

What essential gene?

Not to forget to add the details for the choice of FtsZ in the description of the project here Samuel B.

@@ Line 2: / Line 2: @@
 This page is for questions, answers and discussions on the project, a kind of open forum.
 ==Test of DapA deletion transduction, Thursday, July 5==
@@ Line 10: / Line 9: @@
 ==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. ]
+* 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. ]
+* Shouldn't we write from the begining a list of parameters (in fact, the things we would like to characterize) together with the variables we discussed, and separate input (probably independent) and output (probably dependent) variables for clarity? [[User:PTortosa|Pablo]] 07:21, 13 July 2007 (EDT)
 ==For everybody==
@@ Line 35: / Line 35: @@
 * 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...[[User:Bottani| Samuel B.]]
 * Ok, it's done. [[User:Nicolas C.|Nicolas C.]]
+* Finally I removed it because the two ways of watching the notebook are not compatible. I have to find another solution. [[User:Nicolas C.|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 [[Paris/transclusion_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
+[[User:PTortosa|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. [[User:Nicolas C.|Nicolas C.]]
+* Ok, I tried. The first time I added something to July_2, I could see it inmediately on the week page. Then I tried again adding something else, but this change is not shown now. Therefore, I agree it is a weak solution, it is updated in an impredictable way (at least it does not appear inmediately) :( [[User:PTortosa|Pablo]]
 ==Boston team==
@@ Line 42: / Line 54: @@
 I find it very clear. Maybe a good inspiration for a next version of ours... [[User:Bottani| Samuel B.]]
-==Concerning kinetic measurements==
+==Templates==
+=== 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 [[Paris/July_3|example]]. [[User:Nicolas C.|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.
 {{Paris_KineticArray| Title = le titre ici
-|A1=|A2=|A3=|A4=|A5=|A6=|A7=|A8=|A9=|A10=
+|A1=|A2=|A3=|A4=|A5=|A6=|A7=|A8=|A9=|A10=|A11=|A12=
-|B1=|B2=|B3=|B4=|B5=|B6=|B7=|B8=|B9=|B10=
+|B1=|B2=|B3=|B4=|B5=|B6=|B7=|B8=|B9=|B10=|B11=|B12=
-|C1=|C2=|C3=|C4=|C5=|C6=|C7=|C8=|C9=|C10=
+|C1=|C2=|C3=|C4=|C5=|C6=|C7=|C8=|C9=|C10=|C11=|C12=
-|D1=|D2=|D3=|D4=|D5=|D6=|D7=|D8=|D9=|D10=
+|D1=|D2=|D3=|D4=|D5=|D6=|D7=|D8=|D9=|D10=|D11=|D12=
-|E1=|E2=|E3=|E4=|E5=|E6=|E7=|E8=|E9=|E10=
+|E1=|E2=|E3=|E4=|E5=|E6=|E7=|E8=|E9=|E10=|E11=|E12=
-|F1=|F2=|F3=|F4=|F5=|F6=|F7=|F8=|F9=|F10=
+|F1=|F2=|F3=|F4=|F5=|F6=|F7=|F8=|F9=|F10=|F11=|F12=
-|G1=|G2=|G3=|G4=|G5=|G6=|G7=|G8=|G9=|G10=}}
+|G1=|G2=|G3=|G4=|G5=|G6=|G7=|G8=|G9=|G10=|G11=|G12=
+|H1=|H2=|H3=|H4=|H5=|H6=|H7=|H8=|H9=|H10=|H11=|H12=}}
+=== PCR ===
+Each time you make a PCR, try to fill the following form properly and put it in the wiki. To use this template, just copy and paste the example in the edit page here, and replace the cells with your parameters.
+{{Paris_PCR_0| Title = le titre ici
+|Name=
+|Annealing=
+|Elongation=
+|Cycles=
+|Buffer=
+|MgCl2=
+|dNTP=
+|n_oligoF=
+|v_oligoF=
+|n_oligoR=
+|v_oligoR=
+|water=
+|pol=
+|DNA=
+|}}
+Try to fill  it like the example below.
+{{Paris_PCR_0| Title = DGAT amplification
+|Name= DGAT
+|Annealing= 55°C
+|Elongation= 1m30'
+|Cycles= 30
+|Buffer=  5x 10µL
+|MgCl2= 10µM 0µL
+|dNTP= 10µM 1µL
+|n_oligoF= 6
+|v_oligoF= 10µM 1µL
+|n_oligoR= 7
+|v_oligoR= 10µM 1µL
+|water= 40µL
+|pol= FinnZymes 2µL
+|DNA= lambda plasmid 1µL
+|}}
 == 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 [https://2007.igem.org/David_Tulga_Notebook David Tulga Notebook]. Impressive.
+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 [https://2007.igem.org/David_Tulga_Notebook David Tulga Notebook].
 Another idea to keep in mind: share spreadsheets on google documents (for instance for oligos).
-Otherwise their wiki structure is similar. Not bad! [[User:Bottani| Samuel B.]]
+Otherwise their wiki structure is similar. [[User:Bottani| Samuel B.]]
+==What essential gene?==
+Not to forget to add the details for the choice of FtsZ in the description of the project [[Paris/A_synthetic_multicellular_organism#What essential gene ?|here]] [[User:Bottani| Samuel B.]]

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