Revision as of 13:41, 15 October 2018

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1 Notebook
2 Team page
- 2.1 May 10
- 2.2 Team page
- 2.3 May 10
3 Footer
- 3.1 May 20
- 3.2 Footer
- 3.3 May 20
4 Footer
- 4.1 May 21
- 4.2 Footer
- 4.3 May 21
5 Notebook
- 5.1 May 24
- 5.2 Notebook
- 5.3 May 24
6 Header
- 6.1 May 27
- 6.2 Header
- 6.3 May 27
7 Main template
- 7.1 May 28
- 7.2 Main template
- 7.3 May 28
8 Header
- 8.1 May 28
- 8.2 Header
- 8.3 May 28
9 Team
- 9.1 May 29
- 9.2 Team
- 9.3 May 29
10 Main page
- 10.1 June 7
- 10.2 Main page
- 10.3 June 7
11 Team
- 11.1 June 9
- 11.2 Team
- 11.3 June 9
12 Header
- 12.1 June 9
- 12.2 Header
- 12.3 June 9
13 Header
- 13.1 June 10
- 13.2 Header
- 13.3 June 10
14 Construction pages
- 14.1 June 13
- 14.2 Construction pages
- 14.3 June 13
15 Header
- 15.1 June 14
- 15.2 Header
- 15.3 June 14
16 Main page
- 16.1 June 14
- 16.2 Main page
- 16.3 June 14
17 Architecture design [TC]
- 17.1 June 18
- 17.2 Architecture design [TC]
- 17.3 June 18
18 Human Practices page
- 18.1 June 22
- 18.2 Human Practices page
- 18.3 June 22
19 Main page
- 19.1 June 23
- 19.2 Main page
- 19.3 June 23
20 Architecture design [TC]
- 20.1 June 24
- 20.2 Architecture design [TC]
- 20.3 June 24
21 First prototype [TC]
- 21.1 June 25
- 21.2 First prototype [TC]
- 21.3 June 25
22 Team
- 22.1 June 26
- 22.2 Team
- 22.3 June 26
23 Second prototype [TC]
- 23.1 June 26
- 23.2 Second prototype [TC]
- 23.3 June 26
24 Assessing CooA Production
- 24.1 June 26
- 24.2 Assessing CooA Production
- 24.3 June 26
25 Testrun [TC]
- 25.1 June 27
- 25.2 Testrun [TC]
- 25.3 June 27
26 Assessing CooA Production
- 26.1 June 29
- 26.2 Assessing CooA Production
- 26.3 June 29
27 Draft decision
- 27.1 July 2
- 27.2 Draft decision
- 27.3 July 2
28 Assessing CooA Production
- 28.1 July 2
- 28.2 Assessing CooA Production
- 28.3 July 2
29 Architecture design [TC]
- 29.1 July 5
- 29.2 Architecture design [TC]
- 29.3 July 5
30 Electrical circuit design [TC]
- 30.1 July 8
- 30.2 Electrical circuit design [TC]
- 30.3 July 8
31 Electrical circuit design [TC]
- 31.1 July 9
- 31.2 Electrical circuit design [TC]
- 31.3 July 9
32 Electrical circuit design [TC]
- 32.1 July 11
- 32.2 Electrical circuit design [TC]
- 32.3 July 11
33 Stock up
- 33.1 July 11
- 33.2 Stock up
- 33.3 July 11
34 Basic parts
- 34.1 July 11
- 34.2 Basic parts
- 34.3 July 11
35 Board layout [TC]
- 35.1 July 12
- 35.2 Board layout [TC]
- 35.3 July 12
36 Basic parts
- 36.1 July 12
- 36.2 Basic parts
- 36.3 July 12
37 Board layout [TC]
- 37.1 July 13
- 37.2 Board layout [TC]
- 37.3 July 13
38 Basic parts
- 38.1 July 13
- 38.2 Basic parts
- 38.3 July 13
39 Blue White screening on paper
- 39.1 July 13
- 39.2 Blue White screening on paper
- 39.3 July 13
40 Board layout [TC]
- 40.1 July 15
- 40.2 Board layout [TC]
- 40.3 July 15
41 Basic parts
- 41.1 July 16
- 41.2 Basic parts
- 41.3 July 16
42 Blue White screening on paper
- 42.1 July 16
- 42.2 Blue White screening on paper
- 42.3 July 16
43 Notebook
- 43.1 July 17
- 43.2 Notebook
- 43.3 July 17
44 Basic parts
- 44.1 July 17
- 44.2 Basic parts
- 44.3 July 17
45 Stock up
- 45.1 July 18
- 45.2 Stock up
- 45.3 July 18
46 Notebook
- 46.1 July 19
- 46.2 Notebook
- 46.3 July 19
47 Basic parts
- 47.1 July 19
- 47.2 Basic parts
- 47.3 July 19
48 Notebook
- 48.1 July 21
- 48.2 Notebook
- 48.3 July 21
49 Assessing Gas Production BioBricks in E.Coli
- 49.1 July 23
- 49.2 Assessing Gas Production BioBricks in E.Coli
- 49.3 July 23
50 ATP sensor
- 50.1 July 24
- 50.2 ATP sensor
- 50.3 July 24
51 Gas output
- 51.1 July 24
- 51.2 Gas output
- 51.3 July 24
52 Notebook generator
- 52.1 July 24
- 52.2 Notebook generator
- 52.3 July 24
53 Transformation
- 53.1 July 24
- 53.2 Transformation
- 53.3 July 24
54 Assessing Gas Production BioBricks in E.Coli
- 54.1 July 24
- 54.2 Assessing Gas Production BioBricks in E.Coli
- 54.3 July 24
55 Notebook generator
- 55.1 July 25
- 55.2 Notebook generator
- 55.3 July 25
56 Google Drive API
- 56.1 July 25
- 56.2 Google Drive API
- 56.3 July 25
57 Automatic uploader
- 57.1 July 25
- 57.2 Automatic uploader
- 57.3 July 25
58 Transformation
- 58.1 July 27
- 58.2 Transformation
- 58.3 July 27
59 Assessing Gas Production BioBricks in E.Coli
- 59.1 July 27
- 59.2 Assessing Gas Production BioBricks in E.Coli
- 59.3 July 27
60 Automation program
- 60.1 July 29
- 60.2 Automation program
- 60.3 July 29
61 Automatic uploader
- 61.1 July 29
- 61.2 Automatic uploader
- 61.3 July 29
62 Page generator
- 62.1 July 31
- 62.2 Page generator
- 62.3 July 31
63 Google Drive API
- 63.1 July 31
- 63.2 Google Drive API
- 63.3 July 31
64 Automation program
- 64.1 July 31
- 64.2 Automation program
- 64.3 July 31
65 Automation program
- 65.1 August 1
- 65.2 Automation program
- 65.3 August 1
66 Notebook
- 66.1 August 2
- 66.2 Notebook
- 66.3 August 2
67 Transformation
- 67.1 August 9
- 67.2 Transformation
- 67.3 August 9
68 Assessing Gas Production BioBricks in E.Coli
- 68.1 August 10
- 68.2 Assessing Gas Production BioBricks in E.Coli
- 68.3 August 10
69 Urea and sodium pyruvate test for resistance E.coli
- 69.1 August 10
- 69.2 Urea and sodium pyruvate test for resistance E.coli
- 69.3 August 10
70 Assessing Gas Production BioBricks in E.Coli
- 70.1 August 13
- 70.2 Assessing Gas Production BioBricks in E.Coli
- 70.3 August 13
71 Assessing Gas Production BioBricks in E.Coli
- 71.1 August 13
- 71.2 Assessing Gas Production BioBricks in E.Coli
- 71.3 August 13
72 Assessing Gas Production BioBricks in E.Coli
- 72.1 August 13
- 72.2 Assessing Gas Production BioBricks in E.Coli
- 72.3 August 13
73 Testing gas production
- 73.1 August 16
- 73.2 Testing gas production
- 73.3 August 16
74 Testing gas production
- 74.1 August 23
- 74.2 Testing gas production
- 74.3 August 23
75 Testing gas production
- 75.1 August 23
- 75.2 Testing gas production
- 75.3 August 23
76 Testing gas production
- 76.1 August 23
- 76.2 Testing gas production
- 76.3 August 23
77 Assessing Gas Production BioBricks in E.Coli
- 77.1 August 27
- 77.2 Assessing Gas Production BioBricks in E.Coli
- 77.3 August 27
78 Assessing Gas Production BioBricks in E.Coli
- 78.1 August 27
- 78.2 Assessing Gas Production BioBricks in E.Coli
- 78.3 August 27
79 Urea and sodium pyruvate test for resistance E.coli
- 79.1 August 28
- 79.2 Urea and sodium pyruvate test for resistance E.coli
- 79.3 August 28
80 Assessing Gas Production BioBricks in E.Coli
- 80.1 September 7
- 80.2 Assessing Gas Production BioBricks in E.Coli
- 80.3 September 7
81 Assessing Gas Production BioBricks in E.Coli
- 81.1 September 7
- 81.2 Assessing Gas Production BioBricks in E.Coli
- 81.3 September 7
82 Assessing Gas Production BioBricks in E.Coli
- 82.1 September 11
- 82.2 Assessing Gas Production BioBricks in E.Coli
- 82.3 September 11
83 Assessing Gas Production BioBricks in E.Coli
- 83.1 September 11
- 83.2 Assessing Gas Production BioBricks in E.Coli
- 83.3 September 11
84 Assessing Gas Production BioBricks in E.Coli
- 84.1 September 13
- 84.2 Assessing Gas Production BioBricks in E.Coli
- 84.3 September 13
85 Assessing Gas Production BioBricks in E.Coli
- 85.1 September 14
- 85.2 Assessing Gas Production BioBricks in E.Coli
- 85.3 September 14
86 Assessing Gas Production BioBricks in E.Coli
- 86.1 September 17
- 86.2 Assessing Gas Production BioBricks in E.Coli
- 86.3 September 17
87 Testing gas production
- 87.1 September 17
- 87.2 Testing gas production
- 87.3 September 17
88 Assessing Gas Production BioBricks in E.Coli
- 88.1 September 20
- 88.2 Assessing Gas Production BioBricks in E.Coli
- 88.3 September 20
89 Assessing Gas Production BioBricks in E.Coli
- 89.1 September 26
- 89.2 Assessing Gas Production BioBricks in E.Coli
- 89.3 September 26
90 Assessing Gas Production BioBricks in E.Coli
- 90.1 September 27
- 90.2 Assessing Gas Production BioBricks in E.Coli
- 90.3 September 27
91 Assessing Gas Production BioBricks in E.Coli
- 91.1 September 27
- 91.2 Assessing Gas Production BioBricks in E.Coli
- 91.3 September 27
92 Assessing Gas Production BioBricks in E.Coli
- 92.1 October 8
- 92.2 Assessing Gas Production BioBricks in E.Coli
- 92.3 October 8
93 Testing gas production
- 93.1 October 11
- 93.2 Testing gas production
- 93.3 October 11

Notebook

<input type="checkbox" class="wetlab-filter" checked>show wetlab entries
</input> <input type="checkbox" class="hardware-filter" checked>show hardware entries
</input> <input type="checkbox" class="software-filter">show software entries
</input>

Team page

May 10

Rens Boeser

Created the first prototype for the team page

01

Team page

May 10

<style>

#switch-2:checked ~ #card-2 { width: 100%; height: auto; } #switch-2:checked ~ #card-2 .entryform { display: block; } #switch-2:checked ~ #card-2 .cardform, #switch-2:checked ~ #card-2::before, #switch-2:checked ~ #card-2::after { display: none; } </style>

Footer

May 20

Rens Boeser

Social media created

01

Footer

May 20

<style>

#switch-3:checked ~ #card-3 { width: 100%; height: auto; } #switch-3:checked ~ #card-3 .entryform { display: block; } #switch-3:checked ~ #card-3 .cardform, #switch-3:checked ~ #card-3::before, #switch-3:checked ~ #card-3::after { display: none; } </style>

Footer

May 21

Rens Boeser

Social media buttons same color and fixed iGEM style issues

02

Footer

May 21

<style>

#switch-4:checked ~ #card-4 { width: 100%; height: auto; } #switch-4:checked ~ #card-4 .entryform { display: block; } #switch-4:checked ~ #card-4 .cardform, #switch-4:checked ~ #card-4::before, #switch-4:checked ~ #card-4::after { display: none; } </style>

Notebook

May 24

Rens Boeser

Multiple week summary styles created for the notes

01

Notebook

May 24

<style>

#switch-5:checked ~ #card-5 { width: 100%; height: auto; } #switch-5:checked ~ #card-5 .entryform { display: block; } #switch-5:checked ~ #card-5 .cardform, #switch-5:checked ~ #card-5::before, #switch-5:checked ~ #card-5::after { display: none; } </style>

Header

May 27

Rens Boeser

Added the header with mobile compatibility als resized logos and readded them to the header

01

Header

May 27

<style>

#switch-6:checked ~ #card-6 { width: 100%; height: auto; } #switch-6:checked ~ #card-6 .entryform { display: block; } #switch-6:checked ~ #card-6 .cardform, #switch-6:checked ~ #card-6::before, #switch-6:checked ~ #card-6::after { display: none; } </style>

Main template

May 28

Rens Boeser

Added template header and footer with 'under construction' content

01

Main template

May 28

<style>

#switch-7:checked ~ #card-7 { width: 100%; height: auto; } #switch-7:checked ~ #card-7 .entryform { display: block; } #switch-7:checked ~ #card-7 .cardform, #switch-7:checked ~ #card-7::before, #switch-7:checked ~ #card-7::after { display: none; } </style>

Header

May 28

Rens Boeser

Small fixes and menu adjustments

02

Header

May 28

<style>

#switch-8:checked ~ #card-8 { width: 100%; height: auto; } #switch-8:checked ~ #card-8 .entryform { display: block; } #switch-8:checked ~ #card-8 .cardform, #switch-8:checked ~ #card-8::before, #switch-8:checked ~ #card-8::after { display: none; } </style>

Team

May 29

Rens Boeser

Added a PI list with the secondary PI

02

Team

May 29

<style>

#switch-9:checked ~ #card-9 { width: 100%; height: auto; } #switch-9:checked ~ #card-9 .entryform { display: block; } #switch-9:checked ~ #card-9 .cardform, #switch-9:checked ~ #card-9::before, #switch-9:checked ~ #card-9::after { display: none; } </style>

Main page

June 7

Rens Boeser

Designed and added content holders to the index Page

01

Main page

June 7

<style>

#switch-10:checked ~ #card-10 { width: 100%; height: auto; } #switch-10:checked ~ #card-10 .entryform { display: block; } #switch-10:checked ~ #card-10 .cardform, #switch-10:checked ~ #card-10::before, #switch-10:checked ~ #card-10::after { display: none; } </style>

Team

June 9

Rens Boeser

Added myself to the teammember Page and did some bugfixing

03

Team

June 9

<style>

#switch-11:checked ~ #card-11 { width: 100%; height: auto; } #switch-11:checked ~ #card-11 .entryform { display: block; } #switch-11:checked ~ #card-11 .cardform, #switch-11:checked ~ #card-11::before, #switch-11:checked ~ #card-11::after { display: none; } </style>

Header

June 9

Rens Boeser

Started working on a better looking menubar

03

Header

June 9

<style>

#switch-12:checked ~ #card-12 { width: 100%; height: auto; } #switch-12:checked ~ #card-12 .entryform { display: block; } #switch-12:checked ~ #card-12 .cardform, #switch-12:checked ~ #card-12::before, #switch-12:checked ~ #card-12::after { display: none; } </style>

Header

June 10

Rens Boeser

Added the ability to add sub-menus to items in the menu bar. Integration into the website and added indication for which Page you are on

04

Header

June 10

<style>

#switch-13:checked ~ #card-13 { width: 100%; height: auto; } #switch-13:checked ~ #card-13 .entryform { display: block; } #switch-13:checked ~ #card-13 .cardform, #switch-13:checked ~ #card-13::before, #switch-13:checked ~ #card-13::after { display: none; } </style>

Construction pages

June 13

Rens Boeser

Updated all Pages to the new style with an under construction sign

01

Construction pages

June 13

<style>

#switch-14:checked ~ #card-14 { width: 100%; height: auto; } #switch-14:checked ~ #card-14 .entryform { display: block; } #switch-14:checked ~ #card-14 .cardform, #switch-14:checked ~ #card-14::before, #switch-14:checked ~ #card-14::after { display: none; } </style>

Header

June 14

Rens Boeser

Added a way to recognise Pages under construction using the menubar

05

Header

June 14

<style>

#switch-15:checked ~ #card-15 { width: 100%; height: auto; } #switch-15:checked ~ #card-15 .entryform { display: block; } #switch-15:checked ~ #card-15 .cardform, #switch-15:checked ~ #card-15::before, #switch-15:checked ~ #card-15::after { display: none; } </style>

Main page

June 14

Rens Boeser

Updated the content containers so that they are responsive

02

Main page

June 14

<style>

#switch-16:checked ~ #card-16 { width: 100%; height: auto; } #switch-16:checked ~ #card-16 .entryform { display: block; } #switch-16:checked ~ #card-16 .cardform, #switch-16:checked ~ #card-16::before, #switch-16:checked ~ #card-16::after { display: none; } </style>

Architecture design [TC]

June 18

Tom van Dijk | Mike Vrieswijk

The first draft of the architecture design for the temperature controller was made.

01

Architecture design [TC]

June 18

<style>

#switch-17:checked ~ #card-17 { width: 100%; height: auto; } #switch-17:checked ~ #card-17 .entryform { display: block; } #switch-17:checked ~ #card-17 .cardform, #switch-17:checked ~ #card-17::before, #switch-17:checked ~ #card-17::after { display: none; } </style>

Human Practices page

June 22

Rens Boeser

Content added to the human practices page

01

Human Practices page

June 22

<style>

#switch-18:checked ~ #card-18 { width: 100%; height: auto; } #switch-18:checked ~ #card-18 .entryform { display: block; } #switch-18:checked ~ #card-18 .cardform, #switch-18:checked ~ #card-18::before, #switch-18:checked ~ #card-18::after { display: none; } </style>

Main page

June 23

Rens Boeser

Content created and added to the main page

03

Main page

June 23

<style>

#switch-19:checked ~ #card-19 { width: 100%; height: auto; } #switch-19:checked ~ #card-19 .entryform { display: block; } #switch-19:checked ~ #card-19 .cardform, #switch-19:checked ~ #card-19::before, #switch-19:checked ~ #card-19::after { display: none; } </style>

Architecture design [TC]

June 24

Tom van Dijk | Mike Vrieswijk

Today a few changes have been made to the architecture design of the temperature controller. The choice was made to use a premade power supply as opposed to a self-made one, because this was considering the time left to finish this device the best choice. A few alterations were made to make the architecture design better readable.

02

Architecture design [TC]

June 24

<style>

#switch-20:checked ~ #card-20 { width: 100%; height: auto; } #switch-20:checked ~ #card-20 .entryform { display: block; } #switch-20:checked ~ #card-20 .cardform, #switch-20:checked ~ #card-20::before, #switch-20:checked ~ #card-20::after { display: none; } </style>

First prototype [TC]

June 25

Tom van Dijk | Mike Vrieswijk

A 3d drawing was made for the casing that will hold the temperature controller. The first prototype was printed, but was determent to be inadequate due to the lack of enough space for the cooler block.

01

First prototype [TC]

June 25

<style>

#switch-21:checked ~ #card-21 { width: 100%; height: auto; } #switch-21:checked ~ #card-21 .entryform { display: block; } #switch-21:checked ~ #card-21 .cardform, #switch-21:checked ~ #card-21::before, #switch-21:checked ~ #card-21::after { display: none; } </style>

Team

June 26

Rens Boeser

Added the remaining instructors to the team

04

Team

June 26

<style>

#switch-22:checked ~ #card-22 { width: 100%; height: auto; } #switch-22:checked ~ #card-22 .entryform { display: block; } #switch-22:checked ~ #card-22 .cardform, #switch-22:checked ~ #card-22::before, #switch-22:checked ~ #card-22::after { display: none; } </style>

Second prototype [TC]

June 26

Tom van Dijk | Mike Vrieswijk

In the drawing space was added to fit the cooler block for the temperature controller. Slits were added to the drawing for the nuts to slide into. The altered drawing was printed. The newly printed parts, cooler block, fan and Peltier element were assembled. Everything fit together.

02

Second prototype [TC]

June 26

<style>

#switch-23:checked ~ #card-23 { width: 100%; height: auto; } #switch-23:checked ~ #card-23 .entryform { display: block; } #switch-23:checked ~ #card-23 .cardform, #switch-23:checked ~ #card-23::before, #switch-23:checked ~ #card-23::after { display: none; } </style>

Assessing CooA Production

June 26

Dustin van der Meulen

To start testing the production of CooA, we firstly resuspended and transformed the BioBricks from the kit witch we wanted to use (Table 1). This has been done using the iGEM Kit plate instructions (Protocol 1, step 1 - 3) and the NEB 10 béta transformation protocol adapted New England Biolabs (Protocol 2), using bought cells with a reported transformation efficienty of 1-3 10^9 cfu/μg pUC19. Inucbation was at 37°C.

Table 1 : Resuspended BioBricks from the iGEM 2018 Distribution kit and their uses.

BBa_K592009	Blue Chromoprotein AmilCP
BBa_B0031	Ribosomal binding site (strong), derived from BBa_B0030
BBa_B0032	Ribosomal binding site (medium), derived from BBa_B0030
BBa_B0030	Ribosomal binding site (weak)
BBa_B0015	Double terminator (BBa_B0010 & BBa_B0012)
BBa_J23100	Strong Constitutive Anderson Promotor
BBa_J23105	Medium Constitutive Anderson Promotor
BBa_J23113	Weak Constitutive Anderson Promotor
BBa_J45199	Banana odor enzyme (ATF1) generator
BBa_K1184000	Killer Red
BBa_K352001	CooA
BBa_K352011	CooA responsive system

After checking the plates on the 28th of June, we recieved the following results (Table 2):

Table 2 : Kolonies found after overnight growth.

BBa_K592009	20 colonies
BBa_B0031	4 colonies
BBa_B0032	5 colonies
BBa_B0030	1 colonies
BBa_B0015	6 colonies
BBa_J23100	1 colonies
BBa_J23105	98 colonies
BBa_J23113	19 colonies
BBa_J45199	0 colonies
BBa_K1184000	4 colonies
BBa_K352001	2 colonies
BBa_K352011	4 colonies

01

Assessing CooA Production

June 26

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Testrun [TC]

June 27

Tom van Dijk | Mike Vrieswijk

A short test run was done with the newly assembled cooler. The test concluded that the temperature controller could cool a water droplet to the point of freezing and heat it back up to its boiling point.

03

Testrun [TC]

June 27

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Assessing CooA Production

June 29

Dustin van der Meulen

<p>After making a 20 mL overnight culture of our NEB 10 béta cells containing our BioBricks, we performed a mini prep (Protocol 3). Using our nanodrop spectrophotometer which gave us the following DNA concentrations:

BBa_K592009	72,5 ng/μL
BBa_B0031	118,9 ng/μL
BBa_B0032	52,5 ng/μL
BBa_B0030	488,6 ng/μL
BBa_B0015	53,5 ng/μL
BBa_J23100	148,3 ng/μL
BBa_J23105	96,3 ng/μL
BBa_J23113	151,8 ng/μL
BBa_K118400	140,4 ng/μL
BBa_K352001	77,7 ng/μL
BBa_K352011	76,8 ng/μL

After assessign our results, in the future we will perform the ethanol carry-over steps.

Also from the previously mentioned overnight culture 1 mL has been used to make Glycerol Stock (Protocol 4)</p>

02

Assessing CooA Production

June 29

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Draft decision

July 2

Tom van Dijk | Mike Vrieswijk

The choice to use a computer PSU as a power supply was made. The choice was made on the grounds, that computer PSU have a standard 12, 5 and 3.3V output. This is beneficial because these are the voltages necessary for the selected components.

01

Draft decision

July 2

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Assessing CooA Production

July 2

Dustin van der Meulen

<p>Today we performed a digestion, dephosphorilation and ligation (following protocols 4 and 5) of a few promotor and RBS BioBricks. Because of administrative compliations only the variants with J23113 and a RBS could be made.

</p>

03

Assessing CooA Production

July 2

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Architecture design [TC]

July 5

Tom van Dijk | Mike Vrieswijk

Changes were made to the architecture design of the temperature controller. Different voltage regulators were selected to fit the newly chosen power supply. To better readability of the architecture design a legend was added.

03

Architecture design [TC]

July 5

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Electrical circuit design [TC]

July 8

Tom van Dijk | Mike Vrieswijk

Custom footprints were made for multiple components and added to the parts library in the PCB design software.

01

Electrical circuit design [TC]

July 8

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Electrical circuit design [TC]

July 9

Tom van Dijk | Mike Vrieswijk

The provisional electronic circuit design for the temperature controller was made.

02

Electrical circuit design [TC]

July 9

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Electrical circuit design [TC]

July 11

Tom van Dijk | Mike Vrieswijk

The electronic circuit design for the temperature controller was finished. Measuring point were added to the electronic circuit design.

03

Electrical circuit design [TC]

July 11

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Stock up

July 11

Elise Grootscholten | Loraine Nelson | Paul Reusink

To have some basic biobricks ready, we stocked them by doing a plasmid isolation and freeze the DNA.

01

Stock up

July 11

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Basic parts

July 11

Elise Grootscholten | Loraine Nelson | Paul Reusink

To start on a basic construct we did a digestion and ligation with the parts we isolated earlier. To prevent original constructs we did a defosphorylation after the digestion. We controlled the digestion by doing a gelelktroforeses.

01

Basic parts

July 11

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Board layout [TC]

July 12

Tom van Dijk | Mike Vrieswijk

Started working on the board layout for the PCB of the temperature controller.

01

Board layout [TC]

July 12

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Basic parts

July 12

Tom van Dijk | Randall de Waard

We continued with the ligated DNA by transformating it to Neb10Beta. This was plated onto agarplates and incubated for 1 day.

02

Basic parts

July 12

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Board layout [TC]

July 13

Tom van Dijk | Mike Vrieswijk

Further work was done to the board layout for the temperature controller.

02

Board layout [TC]

July 13

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Basic parts

July 13

Elise Grootscholten | Randall de Waard

The results of 7/12/2018 were collected, in action of this we decided to plate some ligated and transferred DNA from 7/12/2018 again. This we did because there wasn't a clear grow of colonies on the plates.

03

Basic parts

July 13

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Blue White screening on paper

July 13

Elise Grootscholten | Randall de Waard

We tried to let bacteria grow on paper, therefore we used our own buisnesscards. We let the buisnesscards absorb some LB-medium and put them inside petridishes.

01

Blue White screening on paper

July 13

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Board layout [TC]

July 15

Tom van Dijk | Mike Vrieswijk

Work has been done on the board layout for the temperature controller. The board layout is now finished.

03

Board layout [TC]

July 15

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Basic parts

July 16

Mei Ju Goemans | Elise Grootscholten | Dustin van der Meulen | Randall de Waard

To know if the ligation was succesfull we will controll the DNA, therefor we ented the bacteria's with DNA in LB-medium to grow overnight. We also plated the used bacteria's onto new plates to use for further experiments.

04

Basic parts

July 16

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Blue White screening on paper

July 16

Mei Ju Goemans | Elise Grootscholten | Dustin van der Meulen | Randall de Waard

We did a blue white screening on our buisnesscards to see if bacteria had grew on them. We transferred the buisnesscards to new petrydishes and added ITPG and X-gal to the petrydishes.

02

Blue White screening on paper

July 16

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Notebook

July 17

Rens Boeser

Frontend design for the notebook

02

Notebook

July 17

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Basic parts

July 17

Rens Boeser | Dustin van der Meulen | Loraine Nelson | Suzanne Romeijn | Randall de Waard

The resulst of 7/16/2018 showed that the DNA didnt ligate as planned. To be able to digest enough DNA we did a plasmid isolation again. We digested this DNA and froze it for further use.

05

Basic parts

July 17

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Stock up

July 18

Dustin van der Meulen | Loraine Nelson | Suzanne Romeijn | Mike Vrieswijk | Randall de Waard

We did another round of plasmid isolation for stocking.

02

Stock up

July 18

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Notebook

July 19

Rens Boeser

Designed a way to follow experiments that take up multiple days and eventually designed a notebook entry page and made it a responsive page

03

Notebook

July 19

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Basic parts

July 19

Dustin van der Meulen | Mei Ju Goemans| Randall de Waard

We digested all DNA we have in stock to test for our basic construct. We tested the DNA by doing a gelelktroforeses.

06

Basic parts

July 19

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Notebook

July 21

Rens Boeser

Created a one page notebook. Made the notebook entry page more suited for the entry length

04

Notebook

July 21

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Assessing Gas Production BioBricks in E.Coli

July 23

Elise Grootscholten | Randall de Waard

<p>Transformations of the biobricks K133071, K173003 and I13453 are performed. K133071 will produce CO2 if there's pyruvate present and K173003 will produce CO2 if urea is present. I13453 is a promotor which will work if there's arabinose present.
The biobricks were transformed first into electrocometent cells and later into chemical competent cells from the strain NEb10Beta. After transformations the culture was plated on agar plates with antibiotics. The first transformations didn't work out, but the second did, because then the right competent cells were used.

</p>

01

Assessing Gas Production BioBricks in E.Coli

July 23

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ATP sensor

July 24

New biobricks, used to make an ATP sensor, were transformed into NEB10Beta. The culture was than plated onto agar and incubated for 1 day.

01

ATP sensor

July 24

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Gas output

July 24

New biobricks, which produces gasses, were transformed into NEB10Beta. The culture was than plated onto agar and incubated for 1 day.

01

Gas output

July 24

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Notebook generator

July 24

Rens Boeser

Started working on an automatic notebook creator

01

Notebook generator

July 24

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Transformation

July 24

Loraine Nelson | Elise Grootscholten | Paul Reusink

<p>Today we did a transformation with new biobricks. The biobricks were built into chemically competent cells from the strain NEb10Beta. After transformation the culture was plated on agar plates with antibiotics. The results were checked the next day.

</p>

01

Transformation

July 24

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Assessing Gas Production BioBricks in E.Coli

July 24

Elise Grootscholten | Randall de Waard

<p>To be able to always get the necessary biobricks, there have been made glycerolstocks of the transformed biobricks K133071, K173003 and I13453. The glycerolstocks are stored at -80 degrees Celsius. If needed, they can be retrieved from this storage to use for experiments.

</p>

02

Assessing Gas Production BioBricks in E.Coli

July 24

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Notebook generator

July 25

Rens Boeser

Automatic generation of entries completed

02

Notebook generator

July 25

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Google Drive API

July 25

Rens Boeser

Used the Google drive REST API to download the entries from drive

01

Google Drive API

July 25

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Automatic uploader

July 25

Rens Boeser

Used the igemwiki API to update pages using software

01

Automatic uploader

July 25

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Transformation

July 27

Loraine Nelson | Elise Grootscholten | Paul Reusink

<p>To be able to always get the necessary biobricks, we made an glycerol stock after every transformation. The glycerol stocks are stored at -80 degrees Celsius. If needed, they can retrieved from this storage to use for experiments.

</p>

02

Transformation

July 27

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Assessing Gas Production BioBricks in E.Coli

July 27

Elise Grootscholten | Randall de Waard

<p>For further experiments there is isolated DNA needed of the biobricks J23100, K133071, K173003 and I134353. The DNA is isolated out of the bacteria with the help of a plasmid purifaction kit. After isolation this DNA can be used for digestion and ligation or other experiments. J23100 (from the glycerolstock): 325,59 ng/ul, K173003: 217,06 ng/ul, K133071: 186,79 ng/ul, I13453: 88,18 ng/ul

</p>

03

Assessing Gas Production BioBricks in E.Coli

July 27

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Automation program

July 29

Rens Boeser

Connected the page uploader to the notebook generator

01

Automation program

July 29

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Automatic uploader

July 29

Rens Boeser

Created a program that uploads all updated pages

02

Automatic uploader

July 29

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Page generator

July 31

Rens Boeser

Built a page builder that automatically adds the header and footer before uploading

01

Page generator

July 31

<style>

#switch-62:checked ~ #card-62 { width: 100%; height: auto; } #switch-62:checked ~ #card-62 .entryform { display: block; } #switch-62:checked ~ #card-62 .cardform, #switch-62:checked ~ #card-62::before, #switch-62:checked ~ #card-62::after { display: none; } </style>

Google Drive API

July 31

Rens Boeser

Redone the google API handler for reusability and readability and made the google API handler generic

02

Google Drive API

July 31

<style>

#switch-63:checked ~ #card-63 { width: 100%; height: auto; } #switch-63:checked ~ #card-63 .entryform { display: block; } #switch-63:checked ~ #card-63 .cardform, #switch-63:checked ~ #card-63::before, #switch-63:checked ~ #card-63::after { display: none; } </style>

Automation program

July 31

Rens Boeser

revamped the main program

02

Automation program

July 31

<style>

#switch-64:checked ~ #card-64 { width: 100%; height: auto; } #switch-64:checked ~ #card-64 .entryform { display: block; } #switch-64:checked ~ #card-64 .cardform, #switch-64:checked ~ #card-64::before, #switch-64:checked ~ #card-64::after { display: none; } </style>

Automation program

August 1

Rens Boeser

Finished redoing the application for generating and uploading pages

03

Automation program

August 1

<style>

#switch-65:checked ~ #card-65 { width: 100%; height: auto; } #switch-65:checked ~ #card-65 .entryform { display: block; } #switch-65:checked ~ #card-65 .cardform, #switch-65:checked ~ #card-65::before, #switch-65:checked ~ #card-65::after { display: none; } </style>

Notebook

August 2

Rens Boeser

Added month categorization to the page

05

Notebook

August 2

<style>

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Transformation

August 9

Loraine Nelson | Elise Grootscholten | Paul Reusink

<p>For further experiments we needed isolated DNA. The DNA is isolated out of the bacteria with the help of a plasmid purifaction kit. After isolation this DNA can be used for digestion and ligation or other experiments.

</p>

03

Transformation

August 9

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Assessing Gas Production BioBricks in E.Coli

August 10

Elise Grootscholten | Randall de Waard

<p>The biobricks J23100, K133071, K173003 and I134353 were sucessfully digested after the second time. After the digestions the biobricks K133071 and K173003 were dephosphorylated and ligated with the inserts J23100 and I13453. This was done in the original backbone of K133071 and K173003, and not another control backbone. To know if the biobricks were right ligated this was done by testing practically. See the experiments: Testing gas production.

</p>

04

Assessing Gas Production BioBricks in E.Coli

August 10

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Urea and sodium pyruvate test for resistance E.coli

August 10

Randall de Waard | Elise Grootscholten

<p>Testing different amounts of urea and sodiumpyruvate to know which concentrations the bacteria survive.

</p>

01

Urea and sodium pyruvate test for resistance E.coli

August 10

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Assessing Gas Production BioBricks in E.Coli

August 13

Elise Grootscholten | Randall de Waard

<p>Transformations of the biobricks (K133071 + J23100), (K13071 + I1345), (K173003 + J23100) and (K173003 + I13453) in NEB10B�ta. There was no grow except for the biobrick combination K133071 + J23100.

</p>

05

Assessing Gas Production BioBricks in E.Coli

August 13

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Assessing Gas Production BioBricks in E.Coli

August 13

Elise Grootscholten | Randall de Waard

<p>A colony PCR is done for the NEB10B�ta E.coli cells with expected the biobrick combination of K133071 with J23100. Nevertheless, on a gel the difference with and without promotor couldn't be seen. So there must be another way of proving the right biobricks are there.

</p>

06

Assessing Gas Production BioBricks in E.Coli

August 13

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Assessing Gas Production BioBricks in E.Coli

August 13

Elise Grootscholten | Randall de Waard

The ligations and transformations of the biobricks K173003 + J23100, K173003 + I13453, and K133071 + I13453 has been performed again. There was a lot of grow on the agar plates. To know if the biobricks were right ligated this was done by testing practically. See the experiments: Testing gas production.

07

Assessing Gas Production BioBricks in E.Coli

August 13

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Testing gas production

August 16

Elise Grootscholten | Paul Reusink

<p>Making a set up for the gas production testing and testing it with NEB10B�ta with the expected biobricks in it (K133071 + J23100) and a negative control.

</p>

01

Testing gas production

August 16

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Testing gas production

August 23

Elise Grootscholten | Paul Reusink

<p>Making a set up for the gas production testing and testing it with NEB10B�ta with the expected biobricks in it (K133071 + I13453), (K173003 + J23100), (K173003 + I13453) and a negative control.

</p>

02

Testing gas production

August 23

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Testing gas production

August 23

Elise Grootscholten | Paul Reusink

<p>Gasproduction testing for the biobricks (K173003 + I13453), (K133071 + I13453) and negative controls (B0015 and K133071 without urea and arabinose).

K173003 + I13453 is tested with sodiumpyruvate and arabinose for gasproduction and K133071 + I13453 is tested with urea and arabinose for gasproduction.

The negative control also produces a little bit gas.

</p>

03

Testing gas production

August 23

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Testing gas production

August 23

Elise Grootscholten | Paul Reusink

<p>Testing the gasproduction of the colonies 9 and 10 of biobricks (K173003 + J23100), colonies 5 and 7 of biobricks (K173003 + I13453) and colony 4 of biobricks (K133071 + I13453) with and without centrifuging the bacteria. There is also a negative control (J04450 pSB1K3) with Kanamycine. The negative contol started with a lot of gas inside the tube. We can not see wether there is produced more after a day or not. This have to be tested later.

</p>

04

Testing gas production

August 23

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Assessing Gas Production BioBricks in E.Coli

August 27

Elise Grootscholten | Randall de Waard

<p>Minipreps are made of colonies 11 and 19 of biobrick combination K133071 + J23100. Results: 11. 270,57 ng/ul 19. 253,59 ng/ul.

</p>

08

Assessing Gas Production BioBricks in E.Coli

August 27

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Assessing Gas Production BioBricks in E.Coli

August 27

Elise Grootscholten | Randall de Waard

<p>A miniprep of the biobrick K352002 is made. The concentration is 69,77 ng/ul.

</p>

09

Assessing Gas Production BioBricks in E.Coli

August 27

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Urea and sodium pyruvate test for resistance E.coli

August 28

Randall de Waard | Elise Grootscholten

<p>Testing different amounts of urea and sodiumpyruvate to know which concentrations the bacteria survive.

</p>

02

Urea and sodium pyruvate test for resistance E.coli

August 28

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Assessing Gas Production BioBricks in E.Coli

September 7

Elise Grootscholten | Randall de Waard

<p>Digestions, gelelectrophoresis, dephosphorylations and ligations of different biobrick combinations. These biobrick combinations are 4 different promotors (J23100, I13453, K352002, K352003) with 4 different gasproduction biobricks (k173003, K173013, K133071, K133116). J23100 is about 1 kb to long. The rest seems likely to be right digested. The ligations will be transformed in NEB10b�ta and digested again as control.

</p>

10

Assessing Gas Production BioBricks in E.Coli

September 7

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Assessing Gas Production BioBricks in E.Coli

September 7

Elise Grootscholten | Randall de Waard

<p>Transformations of the biobrick combinations in NEB10b�ta. The transformations are plated on kanamycine agar plates, because all the ligations were done in pSB1K3 (kanamycine resistence) backbone. Pink and with colonies appeared after incubation by 37 degrees Celcius for about 12h. The white colonies will be used for further experiments.

</p>

11

Assessing Gas Production BioBricks in E.Coli

September 7

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Assessing Gas Production BioBricks in E.Coli

September 11

Elise Grootscholten | Randall de Waard

<p>Plasmid DNA was isolated of 20 different colonies. The first time something went wrong. The second time we had good concentrations of isolated plasmid DNA. After this we will digest the DNA to see if the plasmids all have the required biobricks. The tube have a code from now on, see table 1.

Number	Promotor	Gene	Backbone
A	K352002 (CooF)	K173013	pSB1K3
B	K352002 (CooF)	K173003	pSB1K3
C	K352002 (CooF)	K133071	pSB1K3
D	K352003 (CooM)	K133071	pSB1K3
E	K352003 (CooM)	K173003	pSB1K3
F	K352003 (CooM)	K173013	pSB1K3
H	I13453	K173013	pSB1K3
I	I13453	K173003	pSB1K3
J	II13453	K133071	pSB1K3

Table 1: list of biobricks of abbreviations

</p>

12

Assessing Gas Production BioBricks in E.Coli

September 11

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Assessing Gas Production BioBricks in E.Coli

September 11

Elise Grootscholten | Randall de Waard

<p>The minipreps of experiment 12 are digested with the restriction enzymes: SmaI and ScaI. Only Sca and Sma are both incubated at 37 degrees Celcius. Sma has to be incubated at 25 degrees Celcius. This is done in experiment 15.

</p>

13

Assessing Gas Production BioBricks in E.Coli

September 11

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Assessing Gas Production BioBricks in E.Coli

September 13

Elise Grootscholten | Randall de Waard

<p>Digestions have been done of the biobrickcombinations K352002 +K133116 + pSB1K3 and K352003 + K133116 + pSB1K3 with restriction-enzymes ScaI and SmaI

</p>

15

Assessing Gas Production BioBricks in E.Coli

September 13

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Assessing Gas Production BioBricks in E.Coli

September 14

Elise Grootscholten | Randall de Waard

<p>All the digestions of experiment 13 have digested again with SmaI for an our at 25 degrees Celcius. Because earlier the digestions have been put immediately bt 37 degrees Celcius. It looks like H1, J1 and D2 include the right biobricks.

</p>

16

Assessing Gas Production BioBricks in E.Coli

September 14

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Assessing Gas Production BioBricks in E.Coli

September 17

Elise Grootscholten | Randall de Waard

<p>Minipreps of the biobrick combinations: K352002+K133116+pSB1K3 (1) and K352003+K133116+pSB1K3 (2) are done. The DNA concentration is for 1:189,3 ng/μl and for 2: 355,3 ng/μl.

</p>

14

Assessing Gas Production BioBricks in E.Coli

September 17

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Testing gas production

September 17

Elise Grootscholten | Paul Reusink

<p>Different strains of E.coli are tested as negative control. Those strains were: NEB10B�ta, BL21 (DE3), BL21, HB101, DH5alpha and JM109. NEB10B�ta produced the most gas. BL21, HB101 and JM101 produced none/almost none gas. Because BL21 isn't a K12 strain we can not use that one. That is why we will test further gasproduction in HB101 and JM109. And maybe those will be our final E.coli strains.

</p>

05

Testing gas production

September 17

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Assessing Gas Production BioBricks in E.Coli

September 20

Elise Grootscholten | Randall de Waard

32 minipreps have been performed. A lot of them have a low concentration nucleic acid and/or have a high 260/280 and 260/230 rate. Therefore those will be done again.

17

Assessing Gas Production BioBricks in E.Coli

September 20

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Assessing Gas Production BioBricks in E.Coli

September 26

Elise Grootscholten | Randall de Waard

<p>Making overnight cultures of the numbers: A1, A4, A5, A6, B1, B5, B6 C1, C2, C3, C4, C5, C6, E1, E2, E5, E6, F4, F5 with Kanamycin. These biobrick combinations can be found in experiment 12. Also the first digestions with XbaI, Eco0109I, HindIII and SspI-HF have been done.

</p>

19

Assessing Gas Production BioBricks in E.Coli

September 26

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Assessing Gas Production BioBricks in E.Coli

September 27

Elise Grootscholten | Randall de Waard

<p>Minipreps have been made of the numbers: A1, A4, A5, A6, B1, B5, B6 C1, C2, C3, C4, C5, C6, E1, E2, E5, E6, F4, F5.

</p>

20

Assessing Gas Production BioBricks in E.Coli

September 27

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Assessing Gas Production BioBricks in E.Coli

September 27

Elise Grootscholten | Randall de Waard

<p>From 27-09 until 04-10 more than 200 digestions and 17 gelelectrophoresis have been performed. This was done as a control for our composite parts. We digested with XbaI, Eco01019 and SspI-HF/HindIII. Every restriction-enzyme has an unique place to cut in our constructs. With this we could test if the promoter, backbone and gas production gene was present. However, the digestions didn't show us very good results. After this we started with PCR.

</p>

21

Assessing Gas Production BioBricks in E.Coli

September 27

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Assessing Gas Production BioBricks in E.Coli

October 8

Elise Grootscholten | Randall de Waard

<p>Digestions with EcoRI-HF and PstI are done for the biobrick numbers A2, B1, B5, B6, D1, E1, E3, I1, J1, J1.2, CooA (8) and pSB1C3. This is done because now the Kanamycin backbone can be replaced for the Chloramphenicol backbone. This is done by dephosphorylation and ligation.

</p>

25

Assessing Gas Production BioBricks in E.Coli

October 8

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Testing gas production

October 11

Elise Grootscholten | Paul Reusink

<p>Overnight cultures made of the following strains with the right plasmid:

Number	HB101	JM109
J1	1x	1x
I1	3x	3x
D1	2x	2x
B1	1x	1x
B6	1x	1x

Table 1: Overnight culture scheme.

</p>

06

Testing gas production

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Difference between revisions of "Team:Rotterdam HR/Notebook"

Revision as of 13:41, 15 October 2018

Contents

Notebook

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May 10

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May 21

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May 24

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May 27

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June 9

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June 9

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June 10

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June 10

Construction pages

June 13

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June 13

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June 14

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June 14

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June 14

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June 14

Architecture design [TC]

June 18

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June 18

Human Practices page

June 22

Human Practices page

June 22

Main page

June 23

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June 23

Architecture design [TC]

June 24

Architecture design [TC]

June 24