ETHZ/Internal
From 2007.igem.org
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<center><font size = '+2'><b> .:: ETH Zurich - EducatETH ''E. coli'' ::. </b></font></center><br> | <center><font size = '+2'><b> .:: ETH Zurich - EducatETH ''E. coli'' ::. </b></font></center><br> | ||
- | ====='''.:: Task List ::.''' | + | =='''.:: Task List ::.'''== |
+ | |||
+ | ==='''.:: Project Task List ::.'''=== | ||
The things to do, from the most pressing (timewise), to the least pressing (timewise) is below. Please put your name next to the task that you believe that you can undertake. | The things to do, from the most pressing (timewise), to the least pressing (timewise) is below. Please put your name next to the task that you believe that you can undertake. | ||
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# '''T-Shirts''' <br> ''Sylke'': in print (2007-09-24) | # '''T-Shirts''' <br> ''Sylke'': in print (2007-09-24) | ||
- | + | ==='''.:: Wiki Task List ::.'''=== | |
- | + | '''''Katerina'':Please write here your remarks on the wiki. Thank you.''' | |
+ | |||
+ | =='''.:: In the Lab ::.'''== | ||
+ | |||
+ | ==='''.:: List of system building blocks ::.'''=== | ||
+ | |||
+ | Here is a list of all the registry parts we used as bulding blocks for our system parts. This list has to be updated and extended for the new, concatenated parts that the ETH Zurich has submitted to the registry. | ||
# [http://partsregistry.org/Part:BBa_B0034 B0034] | # [http://partsregistry.org/Part:BBa_B0034 B0034] | ||
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# [http://partsregistry.org/Part:BBa_Q04510 Q4510] | # [http://partsregistry.org/Part:BBa_Q04510 Q4510] | ||
- | ====='''.:: Week 1 ::.''' | + | ==='''.:: Lab book ::.'''=== |
+ | |||
+ | ===='''.:: Week 1 ::.'''==== | ||
{| class="wikitable" border="1" cellspacing="0" cellpadding="2" style="text-align:left; margin: 1em 1em 1em 0; background: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" | {| class="wikitable" border="1" cellspacing="0" cellpadding="2" style="text-align:left; margin: 1em 1em 1em 0; background: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" | ||
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| | | | ||
* Preparing the Solutions | * Preparing the Solutions | ||
- | | Sylke | + | | Sylke<br>Raphael<br>Stefan<br>Markus<br>Martin<br>Christos<br>Joe |
|- | |- | ||
| Tue, 07. Aug. 2007 | | Tue, 07. Aug. 2007 | ||
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* Prepare competent cells for all parts | * Prepare competent cells for all parts | ||
* Transformation of all the parts | * Transformation of all the parts | ||
- | | Sylke | + | | Sylke<br>Raphael<br>Stefan<br>Markus<br>Martin<br>Christos<br>Joe |
|- | |- | ||
| Wed, 08. Aug. 2007 | | Wed, 08. Aug. 2007 | ||
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| | | | ||
* Preparing the grown cultures (12) for the MINIPREP <br> (o/n cultures) | * Preparing the grown cultures (12) for the MINIPREP <br> (o/n cultures) | ||
- | | Raphael | + | | Raphael<br>Stefan |
|- | |- | ||
| Thu, 09. Aug. 2007 | | Thu, 09. Aug. 2007 | ||
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* MINIPREP of the grown (10) o/n cultures | * MINIPREP of the grown (10) o/n cultures | ||
* Gelelectrophoresis of the grown cultures (step: 0.8% Agarose) | * Gelelectrophoresis of the grown cultures (step: 0.8% Agarose) | ||
- | | Raphael | + | | Raphael<br>Stefan<br>Martin<br>Christos<br>Joe |
|- | |- | ||
| Fri, 10. Aug. 2007 | | Fri, 10. Aug. 2007 | ||
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|} | |} | ||
- | + | ===='''.:: Week 2 ::.'''==== | |
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| | | | ||
* Ligation didn't work due to bad quality of enzymes (probably) | * Ligation didn't work due to bad quality of enzymes (probably) | ||
- | | From 12:<br> Martin | + | | From 12:<br> Martin<br>Markus<br><br> |
|- | |- | ||
| Thu, 16. Aug. 2007 | | Thu, 16. Aug. 2007 | ||
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* Transformation of #13 (Q04121) and #14 (C0053) <br> Numbers #13 and #14 are now growing in the 37°C incubator (step 13 in the transformation procedure) | * Transformation of #13 (Q04121) and #14 (C0053) <br> Numbers #13 and #14 are now growing in the 37°C incubator (step 13 in the transformation procedure) | ||
| | | | ||
- | Markus | + | Markus<br>Christos<br>(Martin) |
|- | |- | ||
| Fri, 17. Aug. 2007 | | Fri, 17. Aug. 2007 | ||
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|} | |} | ||
- | + | ===='''.:: Week 3 ::.'''==== | |
Little rearrangements of the parts. Planning of the sequences to order them. | Little rearrangements of the parts. Planning of the sequences to order them. | ||
- | + | ===='''.:: Week 4 ::.'''==== | |
{| class="wikitable" border="1" cellspacing="0" cellpadding="2" style="text-align:left; margin: 1em 1em 1em 0; background: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" | {| class="wikitable" border="1" cellspacing="0" cellpadding="2" style="text-align:left; margin: 1em 1em 1em 0; background: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" | ||
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|} | |} | ||
- | + | ===='''.:: Week 5 ::.'''==== | |
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* 2 boxes of blue pipette tips are in the autoclave | * 2 boxes of blue pipette tips are in the autoclave | ||
* Stefan ran the agarose gel (?) | * Stefan ran the agarose gel (?) | ||
- | | Martin | + | | Martin<br>Stefan |
|- | |- | ||
| Tue, 04. Sept. 2007 | | Tue, 04. Sept. 2007 | ||
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* Miniprep of pcyc177 and pck01 (but not yet tested) | * Miniprep of pcyc177 and pck01 (but not yet tested) | ||
* Prepared 3 o/ns of pbr322 (finally ;-) and each 1 o/n of pcyc177 and pck01, just in case there are problems with the miniprep | * Prepared 3 o/ns of pbr322 (finally ;-) and each 1 o/n of pcyc177 and pck01, just in case there are problems with the miniprep | ||
- | | Martin | + | | Martin<br>Christian |
|- | |- | ||
| Wed, 05. Sept. 2007 | | Wed, 05. Sept. 2007 | ||
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|} | |} | ||
- | + | ===='''.:: Week 6 ::.'''==== | |
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|} | |} | ||
- | + | ===='''.:: Week 7 ::.'''==== | |
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Christian <br> | Christian <br> | ||
- | Martin | + | Martin<br>Raphael |
|- | |- | ||
| Wed, 19. Sept. 2007 | | Wed, 19. Sept. 2007 | ||
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|} | |} | ||
- | + | ===='''.:: Week 8 ::.'''==== | |
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| | | | ||
|} | |} | ||
+ | |||
+ | ==='''.:: Cloning plan::.'''=== | ||
==== '''.::Plasmid 1 ''(pbr322ap)''::.''' ==== | ==== '''.::Plasmid 1 ''(pbr322ap)''::.''' ==== | ||
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# [[ETHZ/pbr322-4| pbr322-4]] | # [[ETHZ/pbr322-4| pbr322-4]] | ||
- | + | Four linkers are tested for pbr322, as two are used for the tetracycline-resistance version of pbr322 and two are used for the ampicillin-resistnace version. |
Revision as of 14:19, 13 October 2007
![Eth zh logo 2.png](/wiki/images/7/7e/Eth_zh_logo_2.png)
Contents |
.:: Task List ::.
.:: Project Task List ::.
The things to do, from the most pressing (timewise), to the least pressing (timewise) is below. Please put your name next to the task that you believe that you can undertake.
- Team descriptions (overdue) and team photograph
Christian: I guess I am the only semiprofessional photographer of the group. I can do some group pictures etc. but for this we need some ideas... - I would like to do something special. I also made the group-pics of the Synth. Biology 3.0 conference. Some references ;-) : [http://www.fotocommunity.de/pc/pc/mypics/461397]
Raphael: What about a short movie of us? - Team rosters due (1.9.)
Martin: Does somebody know, what exactly should be done here?
Nan: A list of team members, including some basic personal info.? (e.g. nationality, background, pet peeves...? )
Katerina: Guys, to make this easier, either write things about you on your personal page on the wiki or link to a page about you. This way it'll be easy to put it all together afterwards. - Labwork (parts have to be at the registry in Boston on 26.10.)
Joe: I can be in the lab at least 2 evenings a week and some times through the weekdays.
Martin: From Monday I can work every day for the whole day. At the moment I only work for several hours...
Rico: I have my exam on Tuesday. Afterwards I can assist.
Christian: I can do the introduction of the polylinker into the vectors beside my normal labwork on the Hoenggerberg. I could also do the whole biobrick assembly if you want this (I will go on holiday from the 5.10-24.10.07)
Raphael: That's the part where I will mainly contribute, from 14.09. on I can work several days/week
Christos: I can assist at the afternoons, if needed.
Katerina: 7.09 - 30.09 generally plenty of time, apart from when I do my semester project presentation, will keep you posted when that is.
Sylke: I'll not be available until 14th of October but from then on I can work several days per week fulltime. - Testing/ Analysis/ Detection (due to 02.11.)
Sylke: Meeting with Alfredo Franco-Obregon (FACS guy from center) on 18.09. concerning devices available for detection of GFP/ derivatives. - Simulation and sensitivity analysis
Martin: From 10. Sept. I've got plenty time to work on it. I think Markus would join here too ;-)
Tim: I can contribute in running stuff and help identify parameters from literature
Rico: I can do simulations, sensitivity analysis.
Nan: I would like to do simulations and sensitivity analysis.
Christos: Yeap, I guess I can be here too. I will check some toolboxes to automate things, this weekend.
Katerina: Want to help (parameter identification, programming, sensitivity analysis). Discuss in upcoming meeting tasks, versioning and ask Christian about parameters. - Presentation
Joe: I'm American... I can sale anything.
Martin: I'm bad in Layout stuff, but maybe I can help as an idea supplier or so.
Rico: I like giving presentations. For preparation we will need a mixture of different background and excellent pictures!!!
Christian: I can provide the molecular biology knowledge and part.
Nan: I can work on the slides.
Christos: I like this part, I guess everyone will contribute anyway...
Katerina: I believe I can be of help in structure, layout and fancy stuff. Could help train a bit the people we decide to do the presentation (question answering, style). I also think that Joe and Christos could be good for doing the presentation (structured, pleasant voices and lively), can discuss this in a meeting.
Sylke: I can help with the bio-part and I'm good at doing graphics and stuff. Can be a help when it needs to look good :-) - Poster
Joe: See 5. above
Rico: I can help.
Christian: I can provide the molecular biology knowledge and part.
Nan: Partly art. I will help.
Christos: You can sell, but can you trick? lol :)
Katerina: Not my strong point, but have an eye for typos, fonts, layout etc, so can help in final checking.
Sylke: See above. Good at layout. - Wiki (Project and part documentation due on 26.10)
Martin: See the points above, from next Monday I will give everything, now I'm doing my best...
Rico: I can help. I guess this will have to contain the materials that we will also use for poster and presenttion anyway.
Nan: Shouldn't it be updated with every going on process?
Christos: I am trying to put stuff in, as it comes along. I will update the bio pages with the presentation material, this weekend (I hope).
Katerina: You guys have done a great job so far, will help with whatever needed. - T-Shirts
Sylke: in print (2007-09-24)
.:: Wiki Task List ::.
Katerina:Please write here your remarks on the wiki. Thank you.
.:: In the Lab ::.
.:: List of system building blocks ::.
Here is a list of all the registry parts we used as bulding blocks for our system parts. This list has to be updated and extended for the new, concatenated parts that the ETH Zurich has submitted to the registry.
- [http://partsregistry.org/Part:BBa_B0034 B0034]
- [http://partsregistry.org/Part:BBa_R0062 R0062]
- [http://partsregistry.org/Part:BBa_R0053 R0053]
- [http://partsregistry.org/Part:BBa_J23100 J23100]
- [http://partsregistry.org/Part:BBa_J37033 J37033]
- [http://partsregistry.org/Part:BBa_E0434 E0434]
- [http://partsregistry.org/Part:BBa_B0015 B0015]
- [http://partsregistry.org/Part:BBa_Q04400 Q04400]
- [http://partsregistry.org/Part:BBa_R0010 R0010]
- [http://partsregistry.org/Part:BBa_E0422 E0422]
- [http://partsregistry.org/Part:BBa_R0040 R0040]
- [http://partsregistry.org/Part:BBa_R0051 R0051]
- [http://partsregistry.org/Part:BBa_Q04121 Q04121]
- [http://partsregistry.org/Part:BBa_C0053 C0053]
- [http://partsregistry.org/Part:BBa_Q04510 Q4510]
.:: Lab book ::.
.:: Week 1 ::.
Date | TODO's | Completed | People |
---|---|---|---|
Mon, 06. Aug. 2007 |
| Sylke Raphael Stefan Markus Martin Christos Joe | |
Tue, 07. Aug. 2007 |
| Sylke Raphael Stefan Markus Martin Christos Joe | |
Wed, 08. Aug. 2007 |
| Raphael Stefan | |
Thu, 09. Aug. 2007 |
| Raphael Stefan Martin Christos Joe | |
Fri, 10. Aug. 2007 |
|
Christos | |
Sat, 11. Aug. 2007 | no labwork | ||
Sun, 12. Aug. 2007 | labwork cancelled |
.:: Week 2 ::.
Date | TODO's | Completed | People |
---|---|---|---|
Mon, 13. Aug. 2007 start at 3 pm |
|
| Martin Markus Christos Tim |
Tue, 14. Aug. 2007 | Morning Shift:
Evening Shift:
| Morning Shift:
Evening Shift:
| Morning Shift (9am-1pm?): Markus, Tim Evening Shift (5pm-...): Martin, Christos |
Wed, 15. Aug. 2007 |
|
| From 12: Martin Markus |
Thu, 16. Aug. 2007 |
|
|
Markus |
Fri, 17. Aug. 2007 |
|
| Martin |
Sat, 18. Aug. 2007 | |||
Sun, 19. Aug. 2007 |
.:: Week 3 ::.
Little rearrangements of the parts. Planning of the sequences to order them.
.:: Week 4 ::.
Date | TODO's | Completed | People |
---|---|---|---|
Mon, 27. Aug. 2007 | |||
Tue, 28. Aug. 2007 | |||
Wed, 29. Aug. 2007 | |||
Thu, 30. Aug. 2007 | |||
Fri, 31. Aug. 2007 | |||
Sat, 01. Sept. 2007 |
|
| Stefan |
Sun, 02. Sept. 2007 |
|
| Stefan |
.:: Week 5 ::.
Date | TODO's | Completed | People |
---|---|---|---|
Mon, 03. Sept. 2007 |
|
| Martin Stefan |
Tue, 04. Sept. 2007 |
|
| Martin Christian |
Wed, 05. Sept. 2007 |
|
| Martin |
Thu, 06. Sept. 2007 |
|
| Christian |
Fri, 07. Sept. 2007 |
|
| Martin |
Sat, 08. Sept. 2007 | |||
Sun, 09. Sept. 2007 |
.:: Week 6 ::.
Date | TODO's | Completed | People | |
---|---|---|---|---|
Mon, 10. Sept. 2007 |
all digests o/n |
Christian | ||
Tue, 11. Sept. 2007 |
|
|
Christian | |
Wed, 12. Sept. 2007 |
|
Christian | ||
Thu, 13. Sept. 2007 |
|
Christian | ||
Fri, 14. Sept. 2007 |
|
*pBR322-MCS (Tet-selection) clone2 positive |
Christian | |
Sat, 15. Sept. 2007 | ||||
Sun, 16. Sept. 2007 |
.:: Week 7 ::.
Date | TODO's | Completed | People |
---|---|---|---|
Mon, 17. Sept. 2007 |
|
|
Christian |
Tue, 18. Sept. 2007 |
|
> no DNA on pACYC177 digest-gel, only degradation smear
|
Christian |
Wed, 19. Sept. 2007 |
| ||
Thu, 20. Sept. 2007 | |||
Fri, 21. Sept. 2007 | |||
Sat, 22. Sept. 2007 | |||
Sun, 23. Sept. 2007 |
.:: Week 8 ::.
Date | TODO's | Completed | People |
---|---|---|---|
Mon, 24. Sept. 2007 | |||
Tue, 25. Sept. 2007 | |||
Wed, 26. Sept. 2007 | |||
Thu, 27. Sept. 2007 | |||
Fri, 28. Sept. 2007 | |||
Sat, 29. Sept. 2007 | |||
Sun, 30. Sept. 2007 |
.:: Cloning plan::.
.::Plasmid 1 (pbr322ap)::.
- Put parts 1,2,3 in pbr322ap plasmids.
- Merge plasmid containing part 2 (donor) with plasmid containing part 3 (acceptor). You should get a plasmid containing a 2.3 composite part.
- Merge plasmid containing part 1 (donor) with plasmid containing composite part 2.3 (acceptor). You should get a plasmid containing a 1.2.3 composite part.
.::Plasmid 2 (pck01cm)::.
- Put parts 4,5,8,9 in pck01cm plasmids.
- Merge plasmid containing part 4 (donor) with plasmid containing part 5 (acceptor). You should get a plasmid containing a 4.5 composite part.
- Merge plasmid containing part 8 (donor) with plasmid containing part 9 (acceptor). You should get a plasmid containing a 8.9 composite part. Note: this step can be done simultaneously with the above.
- Merge plasmid containing composite part 4.5 (donor) with plasmid containing composite part 8.9 (acceptor). You should get a plasmid containing a 4.5.8.9 composite part.
.::Plasmid 3 (pacyc177km)::.
- Put parts 6,7,10,11 in pacyc177km plasmids.
- Merge plasmid containing part 6 (donor) with plasmid containing part 7 (acceptor). You should get a plasmid containing a 6.7 composite part.
- Merge plasmid containing part 10 (donor) with plasmid containing part 11 (acceptor). You should get a plasmid containing a 10.11 composite part. Note: this step can be done simultaneously with the above.
- Merge plasmid containing composite part 6.7 (donor) with plasmid containing composite part 10.11 (acceptor). You should get a plasmid containing a 6.7.10.11 composite part.
.::Linkers::.
Four linkers are tested for pbr322, as two are used for the tetracycline-resistance version of pbr322 and two are used for the ampicillin-resistnace version.