Skip to content
Open
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
176 commits
Select commit Hold shift + click to select a range
f374fec
Setting up GitHub Classroom Feedback
github-classroom[bot] Sep 26, 2023
6d466e0
Update README.md
s183456-dtu Sep 26, 2023
94cb734
Update README.md
s183456-dtu Sep 26, 2023
6e4065e
Requirements updated
MGSS7 Oct 10, 2023
3611f90
Update .DS_Store
MGSS7 Oct 10, 2023
2b08b1b
Update on name
MGSS7 Oct 10, 2023
8ccf509
Update to requirements after memote install
MGSS7 Oct 22, 2023
13fadab
Merge pull request #2 from 27410/Milles-work
MGSS7 Oct 22, 2023
6dfb050
Memote analysis created
MGSS7 Oct 22, 2023
96fa446
Merge pull request #3 from 27410/Milles-work
MGSS7 Oct 22, 2023
30f7f7a
Updated requirements
MGSS7 Oct 22, 2023
0d21d86
Merge pull request #4 from 27410/Milles-work
MGSS7 Oct 22, 2023
25edc90
Mondays work
MGSS7 Oct 23, 2023
fbd5158
Merge pull request #5 from 27410/Milles-work
MGSS7 Oct 23, 2023
e79d13d
Update of files
MGSS7 Oct 24, 2023
9e32562
Tuesdays work
MGSS7 Oct 31, 2023
a4b4541
Addition of the required reactions to cell factory
MGSS7 Nov 8, 2023
2d26e66
Merge pull request #6 from 27410/Milles-work
MGSS7 Nov 8, 2023
a026baa
Pathway prediction now working
MGSS7 Nov 8, 2023
bcae3c4
Merge pull request #7 from 27410/Milles-work
MGSS7 Nov 8, 2023
7546e5e
Update 1_incoporation_of_heterologous_genes.ipynb
MGSS7 Nov 8, 2023
0ac2fac
Merge pull request #8 from 27410/Milles-work
MGSS7 Nov 8, 2023
e1afc25
Test
annalauemoeller Nov 9, 2023
ab04988
Merge pull request #9 from 27410/anna
MGSS7 Nov 9, 2023
3764bb8
Add files via upload
s183456-dtu Nov 13, 2023
f974e64
Change of name to the 1_ file
MGSS7 Nov 14, 2023
831eb61
Merge pull request #10 from 27410/Milles-work
MGSS7 Nov 14, 2023
4a96a23
Update 7_Co-factor swap #tryingmybest.ipynb
s183456-dtu Nov 14, 2023
aaaef9d
Delete Test.ipynb
MarieFWeinell Nov 14, 2023
c1eca88
Merge pull request #11 from 27410/Marie
MarieFWeinell Nov 14, 2023
5de8aa6
Delete Test.ipynb
MatildeReiff Nov 14, 2023
e5eb92a
Made changes to 7_Co-factor swap
s183456-dtu Nov 14, 2023
81cfc55
Merge pull request #12 from 27410/Nanna
MGSS7 Nov 14, 2023
e782611
Correction of 0_ and 1_ file + creation of 2_ file
MGSS7 Nov 15, 2023
70a4b05
Merge pull request #13 from 27410/Mille_2
MGSS7 Nov 15, 2023
19d18de
Update README.md
MGSS7 Nov 15, 2023
3a1fd4b
Create 5_FSEOF_analysis.ipynb
MarieFWeinell Nov 15, 2023
5ad5d48
Update 5_FSEOF_analysis.ipynb
MarieFWeinell Nov 15, 2023
3e2d83a
Merge pull request #14 from 27410/Marie
MarieFWeinell Nov 15, 2023
560e32b
Deletion of additional requirements
MGSS7 Nov 15, 2023
dbde2cf
Merge pull request #15 from 27410/Mille
MGSS7 Nov 15, 2023
b39f1e6
Made changes to 7_Co-factor swap
s183456-dtu Nov 15, 2023
d06c32d
Merge pull request #16 from 27410/Nanna
s183456-dtu Nov 15, 2023
22ef855
Update 5_FSEOF_analysis.ipynb
MGSS7 Nov 15, 2023
16cad4b
Merge pull request #18 from 27410/Mille_2
MGSS7 Nov 15, 2023
42e7fea
Update 7_Co-factor swap.ipynb
MGSS7 Nov 15, 2023
d70fea3
Changes to 1_, 5_ and 7_ files
MGSS7 Nov 15, 2023
d058b7d
Merge pull request #19 from 27410/Mille_2
MGSS7 Nov 15, 2023
ffe2d27
Update requirements.txt
MGSS7 Nov 15, 2023
57048dd
Merge pull request #20 from 27410/Mille_2
MGSS7 Nov 15, 2023
1dfebc8
Final Changes for Today
MGSS7 Nov 16, 2023
6185b6b
Merge pull request #21 from 27410/Mille_2
MGSS7 Nov 16, 2023
b1ebfce
Removed DS_Store file
MGSS7 Nov 16, 2023
da63f9d
Merge pull request #22 from 27410/Mille_2
MGSS7 Nov 16, 2023
e04d801
2_ file created
annalauemoeller Nov 16, 2023
38936ed
Merge pull request #23 from 27410/anna
annalauemoeller Nov 16, 2023
cd9eb18
Update 2_maximum_theoretical_yield.ipynb
MGSS7 Nov 16, 2023
ce03e81
Merge pull request #24 from 27410/anna_mille
MGSS7 Nov 16, 2023
affac67
5_FSEOF_analysis
MarieFWeinell Nov 16, 2023
a4db0a0
Merge pull request #26 from 27410/MarieNy
MarieFWeinell Nov 16, 2023
3b7d40a
Building on co-factor swap
s183456-dtu Nov 16, 2023
0e23dba
Small 7_co-factor swap changes
s183456-dtu Nov 16, 2023
d660ebb
Merge pull request #27 from 27410/Nanna
s183456-dtu Nov 16, 2023
02e9f6a
Create 5_OptGene_analysis.ipynb
MatildeReiff Nov 16, 2023
7c98d1b
Updates
annalauemoeller Nov 16, 2023
5d92c08
Merge pull request #28 from 27410/anna_3
annalauemoeller Nov 16, 2023
3a2d684
Merge pull request #29 from 27410/Matilde
MatildeReiff Nov 16, 2023
dd08e84
Updates to max. yield
annalauemoeller Nov 16, 2023
159e8e8
Merge pull request #30 from 27410/anna_5
annalauemoeller Nov 16, 2023
4acf619
Update 5_FSEOF_analysis.ipynb
MarieFWeinell Nov 17, 2023
d9541db
Merge pull request #31 from 27410/MarieNy
MarieFWeinell Nov 17, 2023
ccc98f7
Update 2_phenotypic_phase_planes.ipynb
MGSS7 Nov 19, 2023
cb7fb09
Merge pull request #32 from 27410/Mille_3
MGSS7 Nov 19, 2023
751ceaa
Possible solution for OptKnock
MatildeReiff Nov 20, 2023
4f754a8
Merge pull request #33 from 27410/Matilde
MatildeReiff Nov 20, 2023
fb5f9d5
Small updates to most of the files
MGSS7 Nov 21, 2023
64ee894
Merge pull request #34 from 27410/Mille
MGSS7 Nov 21, 2023
6297318
Introducing het_gene co-factor swap
s183456-dtu Nov 21, 2023
1a7416d
Merge pull request #36 from 27410/Nanna
s183456-dtu Nov 21, 2023
3124d8a
OptKnock with different options
MatildeReiff Nov 21, 2023
e71c01b
Merge pull request #37 from 27410/Matilde
MatildeReiff Nov 21, 2023
d372cb2
Update 7_Co-factor swap.ipynb
s183456-dtu Nov 22, 2023
393b473
Dummy-checking the co-factor results
s183456-dtu Nov 22, 2023
a140eb2
Merge pull request #38 from 27410/Nanna_new
s183456-dtu Nov 22, 2023
1dcb600
Update 5_FSEOF_analysis.ipynb
MarieFWeinell Nov 22, 2023
8f9a74d
Update 5_FSEOF_analysis.ipynb
MarieFWeinell Nov 23, 2023
d266277
Updates to medium analysis
annalauemoeller Nov 24, 2023
2f9fda0
Merge pull request #40 from 27410/anna_6
annalauemoeller Nov 24, 2023
d6b1acb
Update 5_FSEOF_analysis.ipynb
MarieFWeinell Nov 24, 2023
31b1e2a
Updates to analysis
annalauemoeller Nov 24, 2023
58ab9d7
Merge pull request #41 from 27410/anna_7
annalauemoeller Nov 24, 2023
a0b1cfc
Merge branch 'main' into MarieNy
MarieFWeinell Nov 27, 2023
5ab003a
Merge pull request #39 from 27410/MarieNy
MarieFWeinell Nov 27, 2023
fe17efd
Changes to PPP
MGSS7 Nov 27, 2023
a763b6f
Merge pull request #42 from 27410/Mille
MGSS7 Nov 27, 2023
44b5542
Final updates and deletion of empty file
annalauemoeller Nov 28, 2023
9231e5b
Merge pull request #43 from 27410/anna_test_pull
annalauemoeller Nov 28, 2023
329b006
Changes made to 1_, 3_, and the data files for our models + requireme…
MGSS7 Nov 28, 2023
eb01a4b
Merge pull request #44 from 27410/Mille
MGSS7 Nov 28, 2023
a745dc4
FSEOF
MarieFWeinell Nov 28, 2023
eda4add
Merge pull request #45 from 27410/MarieNyNy
MarieFWeinell Nov 28, 2023
c6e4a35
Small changes
annalauemoeller Nov 28, 2023
fa2c68c
Introduction of 5_DFBA
s183456-dtu Nov 28, 2023
3b006dc
Fix FSEOF naming
s183456-dtu Nov 28, 2023
2277d0f
Merge branch 'main' into Nanna
s183456-dtu Nov 28, 2023
c9ac3a6
Merge pull request #48 from 27410/Nanna
s183456-dtu Nov 28, 2023
6d65686
Rename 5_FSEOF_analysis.ipynb to 4_FSEOF_analysis.ipynb
s183456-dtu Nov 29, 2023
f18059a
Update 4_FSEOF_analysis.ipynb
MGSS7 Dec 3, 2023
4e467b1
Update 2_maximum_theoretical_yield.ipynb
MGSS7 Dec 3, 2023
371b6e8
Update carbon_sources.png
MGSS7 Dec 3, 2023
6a5d9fa
Merge pull request #46 from 27410/anna_ny_ny
MGSS7 Dec 3, 2023
1a88aff
Merge pull request #50 from 27410/main
MatildeReiff Dec 4, 2023
0aac35a
Merge pull request #51 from 27410/Matilde
MatildeReiff Dec 4, 2023
8464415
Edits to multiple files
MGSS7 Dec 5, 2023
0c9e6a5
Merge pull request #52 from 27410/Mille
MGSS7 Dec 5, 2023
6ac039d
Merge pull request #53 from 27410/main
MatildeReiff Dec 5, 2023
e213e40
Updates to PPP files
MGSS7 Dec 5, 2023
00f62fd
Merge pull request #54 from 27410/Mille
MGSS7 Dec 5, 2023
35d7475
Push for Matilde
MGSS7 Dec 5, 2023
df7302b
Merge pull request #55 from 27410/Mille
MGSS7 Dec 5, 2023
8fae18e
Merge pull request #56 from 27410/main
MatildeReiff Dec 5, 2023
797c259
OptKnock changes
MatildeReiff Dec 5, 2023
09755cf
Merge pull request #57 from 27410/Matilde
MatildeReiff Dec 5, 2023
b9963f8
Change to file2
annalauemoeller Dec 5, 2023
4553088
Merge pull request #58 from 27410/anna_ny_ny
annalauemoeller Dec 5, 2023
15a979b
Changes to 2 and 7 comments
s183456-dtu Dec 5, 2023
f14990a
Edits
MGSS7 Dec 5, 2023
efe78f3
Merge pull request #60 from 27410/Mille
MGSS7 Dec 5, 2023
c10dd19
Merge pull request #59 from 27410/Nanna
s183456-dtu Dec 5, 2023
2fb4895
DFBA working!
MatildeReiff Dec 5, 2023
627b17a
Merge pull request #61 from 27410/Matilde
MatildeReiff Dec 5, 2023
0faa80c
Changes to file 7
MGSS7 Dec 5, 2023
5bad517
Merge pull request #62 from 27410/Mille
MGSS7 Dec 5, 2023
950e8b7
Intro figures
MatildeReiff Dec 5, 2023
faff540
Merge pull request #63 from 27410/Matilde
MatildeReiff Dec 5, 2023
d0f995e
Updating comments to most files
s183456-dtu Dec 5, 2023
8a9302a
Merge pull request #64 from 27410/Nanna
s183456-dtu Dec 5, 2023
f60fd76
Saving figures
MGSS7 Dec 5, 2023
a79e529
Merge pull request #65 from 27410/Mille
MGSS7 Dec 5, 2023
85d3367
Almost last run of the code and deletion of unused files
MGSS7 Dec 5, 2023
21a5b8b
Merge pull request #66 from 27410/Mille
MGSS7 Dec 5, 2023
bc247ef
New figure
MatildeReiff Dec 5, 2023
8e53829
Update Report.ipynb
MatildeReiff Dec 5, 2023
f517b91
Merge pull request #67 from 27410/Matilde
MatildeReiff Dec 5, 2023
476d039
FInal run of all code
MGSS7 Dec 5, 2023
3e9f7e9
Merge pull request #68 from 27410/Mille
MGSS7 Dec 5, 2023
c2c7c35
Small updates
MGSS7 Dec 5, 2023
37b8556
Merge pull request #69 from 27410/Mille
MGSS7 Dec 5, 2023
9a0bf74
Results inserted
MatildeReiff Dec 5, 2023
9c4779a
Merge pull request #70 from 27410/Matilde
MatildeReiff Dec 5, 2023
33c4190
Update README.md
s183456-dtu Dec 5, 2023
ef830ac
Update README.md
s183456-dtu Dec 5, 2023
a4ae276
Update README.md
s183456-dtu Dec 5, 2023
e56e40e
Update Report.ipynb
MGSS7 Dec 5, 2023
ef1a138
Merge pull request #71 from 27410/Mille
MGSS7 Dec 5, 2023
eb531e3
Small changes
MGSS7 Dec 5, 2023
0b1cd5f
Update README.md
s183456-dtu Dec 5, 2023
79fa5ee
Changes to report
MGSS7 Dec 5, 2023
094a3f1
Merge pull request #72 from 27410/Mille
MGSS7 Dec 5, 2023
6db36a6
Deletion work
MGSS7 Dec 5, 2023
0d4e077
Merge pull request #73 from 27410/Mille
MGSS7 Dec 5, 2023
9b561b8
Create 7_Co-factor_swap.ipynb
MGSS7 Dec 5, 2023
ae25046
Merge pull request #74 from 27410/Mille
MGSS7 Dec 5, 2023
bbb9173
Update README.md
MGSS7 Dec 5, 2023
c5ed1fb
Update README.md
MGSS7 Dec 5, 2023
f966214
Update README.md
MGSS7 Dec 5, 2023
171cdf4
Update Report.ipynb
MGSS7 Dec 5, 2023
a32e487
Merge pull request #75 from 27410/Mille
MGSS7 Dec 5, 2023
45a2159
Update README.md
MGSS7 Dec 5, 2023
c852cd6
Update README.md
MGSS7 Dec 5, 2023
5374f21
Update README.md
MGSS7 Dec 5, 2023
a45e320
Update Report.ipynb
MGSS7 Dec 5, 2023
88008b1
Merge pull request #76 from 27410/Mille
MGSS7 Dec 5, 2023
45612aa
LAST PUSH EVER PLEASE
MGSS7 Dec 5, 2023
5c8c778
Seriously the last push
MGSS7 Dec 5, 2023
d0b4098
Merge pull request #77 from 27410/Mille
MGSS7 Dec 5, 2023
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 3 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -127,3 +127,6 @@ dmypy.json

# Pyre type checker
.pyre/

# .DS_Store generated on mac
.DS_Store
452 changes: 452 additions & 0 deletions 0_memote_analysis.ipynb

Large diffs are not rendered by default.

Loading