Team:DTU-Denmark/Notebook

From 2013.igem.org

(Difference between revisions)
Line 34: Line 34:
===July===
===July===
-
Week 27  
+
'''Week 27'''
* Hello World project is successful.  From a cytoplasmic extraction, we have observed GFP in the periplasm and RFP in the cytoplasm. See a nice picture [[Team:DTU-Denmark/Notebook/6_July_2013|here.]]
* Hello World project is successful.  From a cytoplasmic extraction, we have observed GFP in the periplasm and RFP in the cytoplasm. See a nice picture [[Team:DTU-Denmark/Notebook/6_July_2013|here.]]
* 2013-07-06 "Hello World" pilot project complete
* 2013-07-06 "Hello World" pilot project complete
* Biolector experiment complete, initial data analysis complete. See some graphs [[Team:DTU-Denmark/ToxicityExperiment|here]]
* Biolector experiment complete, initial data analysis complete. See some graphs [[Team:DTU-Denmark/ToxicityExperiment|here]]
-
Week 28
+
'''Week 28'''
* Made media and began growing ''Nitrosomonas'' culture
* Made media and began growing ''Nitrosomonas'' culture
* Designed, ordered and received primers to extract genes from ''Nitrosomonas'' and ''Pseudomonas''
* Designed, ordered and received primers to extract genes from ''Nitrosomonas'' and ''Pseudomonas''
* Began work on cloning genes out of ''Nitrosomonas europaea'' and ''Pseudomonas aeruginosa''.  All isolations successful except Nir.
* Began work on cloning genes out of ''Nitrosomonas europaea'' and ''Pseudomonas aeruginosa''.  All isolations successful except Nir.
-
Week 29
+
'''Week 29'''
* Performed first nitrate -> nitrite experiment
* Performed first nitrate -> nitrite experiment
-
Week 30
+
'''Week 30'''
* Only have colonies for the cytochromes -- other genes do not give cultures
* Only have colonies for the cytochromes -- other genes do not give cultures
* Will try to extract Nir gene in two pieces
* Will try to extract Nir gene in two pieces
* Began work on arabinose inducible system
* Began work on arabinose inducible system
-
Week 31
+
'''Week 31'''
* Began work on Synthetic Promoter Library
* Began work on Synthetic Promoter Library
* BBQ with KU this Saturday
* BBQ with KU this Saturday
Line 58: Line 58:
===August===
===August===
-
Week 32
+
'''Week 32'''
-
*  
+
* The week no PCR worked -- ran 96 PCRs with varying conditions to debug
 +
* Began work on modelling
 +
* Began work on presentation
-
Week 33
+
'''Week 33'''
 +
* Began daily meetings to coordinate
 +
* Arabinose inducible promoter works as of 2013-08-11
 +
* One Nir fragment has been amplified with USER primers (changed DMSO, Mg, temperature, etc), one to go
 +
* E coli experiment will be run again this week
-
Week 34
+
'''Week 34'''
 +
* Decided on final human practices event
-
Week 35
+
'''Week 35'''
 +
* Attended Scandinavian meetup in Odense hosted by SDU team
 +
* Biobricks in progress
 +
* Biolector for SPL in progress
 +
* sequencing for SPL in progress
 +
* first draft of presentation
 +
* first draft of poster
 +
* measure Nir, AMO, HAO transformants
 +
* modelling of kinetics and design of a reactor: Vanessa
 +
* Title and abstract finished; Title: Requiem for a Stream
 +
* Reviewed presentation with Julie, who gave us very good advice on pitching our project
 +
* measure AMO, HAO transformants complete
===September===
===September===
 +
'''Week 36'''
 +
* Have biobricks for AMO and cytochromes (are going to sequence these), the others are coming.
 +
* Running last biolector experiment today
 +
* sequencing for SPL is in progress
 +
* Kristian is working on a page in the parts registry for the parts registry
 +
* first draft of presentation completed
 +
* first draft of poster complete
 +
* modelling of kinetics and design of a reactor: using Continuous Stirred Tank Reactor
 +
* Began reactor design -- ask Mikael Rordham in 223 for 2 1L chemostats
-
Week 36
+
'''Week 37'''
-
Week 37
+
'''Week 38'''
-
Week 38
+
'''Week 39'''
-
 
+
-
Week 39
+
=== October ===
=== October ===
-
Week 40
+
'''Week 40'''
* Wiki complete!
* Wiki complete!

Revision as of 13:05, 28 September 2013

Notebook

Contents

Timeline

January

  • 2013-01-15 Budget completed
  • 2013-01-29 Human Practices: Workshop for highschool students

February

  • 2013-02-25 Project selected: Conversion of ammonia to nitrous oxide in E. coli

March

  • 2013-03-11 Biobrick workshop hosted for KU and SDU
  • 2013-03-13 Project kickoff meeting

April

  • 2013-04-15 Team contract signed
  • 2013-04-28 Human Practices: Outreach for highschool students

May

  • 2013-05-29 "Hello World" pilot project kicked off

June

  • 2013-06-04 Team competency mapping
  • 2013-06-09 Work on wiki started
  • 2013-06-29 Team BBQ

July

Week 27

  • Hello World project is successful. From a cytoplasmic extraction, we have observed GFP in the periplasm and RFP in the cytoplasm. See a nice picture here.
  • 2013-07-06 "Hello World" pilot project complete
  • Biolector experiment complete, initial data analysis complete. See some graphs here

Week 28

  • Made media and began growing Nitrosomonas culture
  • Designed, ordered and received primers to extract genes from Nitrosomonas and Pseudomonas
  • Began work on cloning genes out of Nitrosomonas europaea and Pseudomonas aeruginosa. All isolations successful except Nir.

Week 29

  • Performed first nitrate -> nitrite experiment

Week 30

  • Only have colonies for the cytochromes -- other genes do not give cultures
  • Will try to extract Nir gene in two pieces
  • Began work on arabinose inducible system

Week 31

  • Began work on Synthetic Promoter Library
  • BBQ with KU this Saturday

August

Week 32

  • The week no PCR worked -- ran 96 PCRs with varying conditions to debug
  • Began work on modelling
  • Began work on presentation

Week 33

  • Began daily meetings to coordinate
  • Arabinose inducible promoter works as of 2013-08-11
  • One Nir fragment has been amplified with USER primers (changed DMSO, Mg, temperature, etc), one to go
  • E coli experiment will be run again this week

Week 34

  • Decided on final human practices event

Week 35

  • Attended Scandinavian meetup in Odense hosted by SDU team
  • Biobricks in progress
  • Biolector for SPL in progress
  • sequencing for SPL in progress
  • first draft of presentation
  • first draft of poster
  • measure Nir, AMO, HAO transformants
  • modelling of kinetics and design of a reactor: Vanessa
  • Title and abstract finished; Title: Requiem for a Stream
  • Reviewed presentation with Julie, who gave us very good advice on pitching our project
  • measure AMO, HAO transformants complete

September

Week 36

  • Have biobricks for AMO and cytochromes (are going to sequence these), the others are coming.
  • Running last biolector experiment today
  • sequencing for SPL is in progress
  • Kristian is working on a page in the parts registry for the parts registry
  • first draft of presentation completed
  • first draft of poster complete
  • modelling of kinetics and design of a reactor: using Continuous Stirred Tank Reactor
  • Began reactor design -- ask Mikael Rordham in 223 for 2 1L chemostats

Week 37

Week 38

Week 39

October

Week 40

  • Wiki complete!

Lab Book Entries

June
MTWTFSS
          [http://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Notebook/1_June_2013&action=edit 1] [http://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Notebook/2_June_2013&action=edit 2]
[http://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Notebook/3_June_2013&action=edit 3] [http://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Notebook/4_June_2013&action=edit 4] [http://2013.igem.org/Team:DTU-Denmark/Notebook/5_June_2013 5] [http://2013.igem.org/Team:DTU-Denmark/Notebook/6_June_2013 6] [http://2013.igem.org/Team:DTU-Denmark/Notebook/7_June_2013 7] [http://2013.igem.org/Team:DTU-Denmark/Notebook/8_June_2013 8] [http://2013.igem.org/Team:DTU-Denmark/Notebook/9_June_2013 9]
[http://2013.igem.org/Team:DTU-Denmark/Notebook/10_June_2013 10] [http://2013.igem.org/Team:DTU-Denmark/Notebook/11_June_2013 11] [http://2013.igem.org/Team:DTU-Denmark/Notebook/12_June_2013 12] [http://2013.igem.org/Team:DTU-Denmark/Notebook/13_June_2013 13] [http://2013.igem.org/Team:DTU-Denmark/Notebook/14_June_2013 14] [http://2013.igem.org/Team:DTU-Denmark/Notebook/15_June_2013 15] [http://2013.igem.org/Team:DTU-Denmark/Notebook/16_June_2013 16]
[http://2013.igem.org/Team:DTU-Denmark/Notebook/17_June_2013 17] [http://2013.igem.org/Team:DTU-Denmark/Notebook/18_June_2013 18] [http://2013.igem.org/Team:DTU-Denmark/Notebook/19_June_2013 19] [http://2013.igem.org/Team:DTU-Denmark/Notebook/20_June_2013 20] [http://2013.igem.org/Team:DTU-Denmark/Notebook/21_June_2013 21] [http://2013.igem.org/Team:DTU-Denmark/Notebook/22_June_2013 22] [http://2013.igem.org/Team:DTU-Denmark/Notebook/23_June_2013 23]
[http://2013.igem.org/Team:DTU-Denmark/Notebook/24_June_2013 24] [http://2013.igem.org/Team:DTU-Denmark/Notebook/25_June_2013 25] [http://2013.igem.org/Team:DTU-Denmark/Notebook/26_June_2013 26] [http://2013.igem.org/Team:DTU-Denmark/Notebook/27_June_2013 27] [http://2013.igem.org/Team:DTU-Denmark/Notebook/28_June_2013 28] [http://2013.igem.org/Team:DTU-Denmark/Notebook/29_June_2013 29] [http://2013.igem.org/Team:DTU-Denmark/Notebook/30_June_2013 30]
July
MTWTFSS
[http://2013.igem.org/Team:DTU-Denmark/Notebook/1_July_2013 1] [http://2013.igem.org/Team:DTU-Denmark/Notebook/2_July_2013 2] [http://2013.igem.org/Team:DTU-Denmark/Notebook/3_July_2013 3] [http://2013.igem.org/Team:DTU-Denmark/Notebook/4_July_2013 4] [http://2013.igem.org/Team:DTU-Denmark/Notebook/5_July_2013 5] [http://2013.igem.org/Team:DTU-Denmark/Notebook/6_July_2013 6] [http://2013.igem.org/Team:DTU-Denmark/Notebook/7_July_2013 7]
[http://2013.igem.org/Team:DTU-Denmark/Notebook/8_July_2013 8] [http://2013.igem.org/Team:DTU-Denmark/Notebook/9_July_2013 9] [http://2013.igem.org/Team:DTU-Denmark/Notebook/10_July_2013 10] [http://2013.igem.org/Team:DTU-Denmark/Notebook/11_July_2013 11] [http://2013.igem.org/Team:DTU-Denmark/Notebook/12_July_2013 12] [http://2013.igem.org/Team:DTU-Denmark/Notebook/13_July_2013 13] [http://2013.igem.org/Team:DTU-Denmark/Notebook/14_July_2013 14]
[http://2013.igem.org/Team:DTU-Denmark/Notebook/15_July_2013 15] [http://2013.igem.org/Team:DTU-Denmark/Notebook/16_July_2013 16] [http://2013.igem.org/Team:DTU-Denmark/Notebook/17_July_2013 17] [http://2013.igem.org/Team:DTU-Denmark/Notebook/18_July_2013 18] [http://2013.igem.org/Team:DTU-Denmark/Notebook/19_July_2013 19] [http://2013.igem.org/Team:DTU-Denmark/Notebook/20_July_2013 20] [http://2013.igem.org/Team:DTU-Denmark/Notebook/21_July_2013 21]
[http://2013.igem.org/Team:DTU-Denmark/Notebook/22_July_2013 22] [http://2013.igem.org/Team:DTU-Denmark/Notebook/23_July_2013 23] [http://2013.igem.org/Team:DTU-Denmark/Notebook/24_July_2013 24] [http://2013.igem.org/Team:DTU-Denmark/Notebook/25_July_2013 25] [http://2013.igem.org/Team:DTU-Denmark/Notebook/26_July_2013 26] [http://2013.igem.org/Team:DTU-Denmark/Notebook/27_July_2013 27] [http://2013.igem.org/Team:DTU-Denmark/Notebook/28_July_2013 28]
[http://2013.igem.org/Team:DTU-Denmark/Notebook/29_July_2013 29] [http://2013.igem.org/Team:DTU-Denmark/Notebook/30_July_2013 30] [http://2013.igem.org/Team:DTU-Denmark/Notebook/31_July_2013 31]
August
MTWTFSS
      [http://2013.igem.org/Team:DTU-Denmark/Notebook/1_August_2013 1] [http://2013.igem.org/Team:DTU-Denmark/Notebook/2_August_2013 2] [http://2013.igem.org/Team:DTU-Denmark/Notebook/3_August_2013 3] [http://2013.igem.org/Team:DTU-Denmark/Notebook/4_August_2013 4]
[http://2013.igem.org/Team:DTU-Denmark/Notebook/5_August_2013 5] [http://2013.igem.org/Team:DTU-Denmark/Notebook/6_August_2013 6] [http://2013.igem.org/Team:DTU-Denmark/Notebook/7_August_2013 7] [http://2013.igem.org/Team:DTU-Denmark/Notebook/8_August_2013 8] [http://2013.igem.org/Team:DTU-Denmark/Notebook/9_August_2013 9] [http://2013.igem.org/Team:DTU-Denmark/Notebook/10_August_2013 10] [http://2013.igem.org/Team:DTU-Denmark/Notebook/11_August_2013 11]
[http://2013.igem.org/Team:DTU-Denmark/Notebook/12_August_2013 12] [http://2013.igem.org/Team:DTU-Denmark/Notebook/13_August_2013 13] [http://2013.igem.org/Team:DTU-Denmark/Notebook/14_August_2013 14] [http://2013.igem.org/Team:DTU-Denmark/Notebook/15_August_2013 15] [http://2013.igem.org/Team:DTU-Denmark/Notebook/16_August_2013 16] [http://2013.igem.org/Team:DTU-Denmark/Notebook/17_August_2013 17] [http://2013.igem.org/Team:DTU-Denmark/Notebook/18_August_2013 18]
[http://2013.igem.org/Team:DTU-Denmark/Notebook/19_August_2013 19] [http://2013.igem.org/Team:DTU-Denmark/Notebook/20_August_2013 20] [http://2013.igem.org/Team:DTU-Denmark/Notebook/21_August_2013 21] [http://2013.igem.org/Team:DTU-Denmark/Notebook/22_August_2013 22] [http://2013.igem.org/Team:DTU-Denmark/Notebook/23_August_2013 23] [http://2013.igem.org/Team:DTU-Denmark/Notebook/24_August_2013 24] [http://2013.igem.org/Team:DTU-Denmark/Notebook/25_August_2013 25]
[http://2013.igem.org/Team:DTU-Denmark/Notebook/26_August_2013 26] [http://2013.igem.org/Team:DTU-Denmark/Notebook/27_August_2013 27] [http://2013.igem.org/Team:DTU-Denmark/Notebook/28_August_2013 28] [http://2013.igem.org/Team:DTU-Denmark/Notebook/29_August_2013 29] [http://2013.igem.org/Team:DTU-Denmark/Notebook/30_August_2013 30] [http://2013.igem.org/Team:DTU-Denmark/Notebook/31_August_2013 31]
September
MTWTFSS
            [http://2013.igem.org/Team:DTU-Denmark/Notebook/1_September_2013 1]
[http://2013.igem.org/Team:DTU-Denmark/Notebook/2_September_2013 2] [http://2013.igem.org/Team:DTU-Denmark/Notebook/3_September_2013 3] [http://2013.igem.org/Team:DTU-Denmark/Notebook/4_September_2013 4] [http://2013.igem.org/Team:DTU-Denmark/Notebook/5_September_2013 5] [http://2013.igem.org/Team:DTU-Denmark/Notebook/6_September_2013 6] [http://2013.igem.org/Team:DTU-Denmark/Notebook/7_September_2013 7] [http://2013.igem.org/Team:DTU-Denmark/Notebook/8_September_2013 8]
[http://2013.igem.org/Team:DTU-Denmark/Notebook/9_September_2013 9] [http://2013.igem.org/Team:DTU-Denmark/Notebook/10_September_2013 10] [http://2013.igem.org/Team:DTU-Denmark/Notebook/11_September_2013 11] [http://2013.igem.org/Team:DTU-Denmark/Notebook/12_September_2013 12] [http://2013.igem.org/Team:DTU-Denmark/Notebook/13_September_2013 13] [http://2013.igem.org/Team:DTU-Denmark/Notebook/14_September_2013 14] [http://2013.igem.org/Team:DTU-Denmark/Notebook/15_September_2013 15]
[http://2013.igem.org/Team:DTU-Denmark/Notebook/16_September_2013 16] [http://2013.igem.org/Team:DTU-Denmark/Notebook/17_September_2013 17] [http://2013.igem.org/Team:DTU-Denmark/Notebook/18_September_2013 18] [http://2013.igem.org/Team:DTU-Denmark/Notebook/19_September_2013 19] [http://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Notebook/20_September_2013&action=edit 20] [http://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Notebook/21_September_2013&action=edit 21] [http://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Notebook/22_September_2013&action=edit 22]
[http://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Notebook/23_September_2013&action=edit 23] [http://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Notebook/24_September_2013&action=edit 24] [http://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Notebook/25_September_2013&action=edit 25] [http://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Notebook/26_September_2013&action=edit 26] [http://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Notebook/27_September_2013&action=edit 27] [http://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Notebook/28_September_2013&action=edit 28] [http://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Notebook/29_September_2013&action=edit 29]
[http://2013.igem.org/wiki/index.php?title=Team:DTU-Denmark/Notebook/30_September_2013&action=edit 30]