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1384cce
Updated Model fitting appendix and added new lectures
mhasoba Oct 28, 2019
f601253
Updated Model fitting appendix
mhasoba Oct 28, 2019
202b0e1
Updated Model fitting appendix and lectures
mhasoba Oct 28, 2019
d5c5bbf
Updated Miniproject appendix
mhasoba Oct 29, 2019
c6fffeb
Updated Miniproject appendix and data
mhasoba Oct 29, 2019
3d61be4
Updated Miniproject appendix
mhasoba Oct 29, 2019
45721c3
Updated Miniproject appendix
mhasoba Oct 29, 2019
424c061
Restored Martin Brazeau's C lectures
mhasoba Nov 1, 2019
307654d
Updated Python chapter II
mhasoba Nov 11, 2019
c2e3934
Updated Python chapter II
mhasoba Nov 12, 2019
62c006f
Updated Python chapter II
mhasoba Nov 12, 2019
089d74f
Updated Python chapter II
mhasoba Nov 12, 2019
0185a24
Updated Python chapter II
mhasoba Nov 13, 2019
68afc08
Updated Python chapter II and added missing script
mhasoba Nov 13, 2019
44d043f
Added HTML versions of nbs
mhasoba Nov 14, 2019
5fcfb01
Updated Python chapter II and added missing script
mhasoba Nov 14, 2019
1081627
Updated some appendices
mhasoba Nov 15, 2019
7e16d3e
Updated some appendices
mhasoba Nov 15, 2019
2d441b1
Updated Python II and jupyter intro nb
mhasoba Nov 15, 2019
6dd5a61
Updated miniproject nb
mhasoba Nov 18, 2019
5a0f2ce
Updated miniproject nb and data
mhasoba Nov 18, 2019
0c39ed3
Updated miniproject nb
mhasoba Nov 19, 2019
35c365f
Updated miniproject nb
mhasoba Nov 19, 2019
337f3a5
Updated miniproject nb
mhasoba Nov 19, 2019
2bf3878
Updated miniproject nb
mhasoba Nov 19, 2019
d815795
Updated miniproject nb and gernated htmls of nbs
mhasoba Nov 19, 2019
7df437a
Updated miniproject nb and gernated htmls of nbs
mhasoba Nov 19, 2019
0e79e36
Some edits to stats nbs
mhasoba Dec 2, 2019
a87c618
Updated feedback code and appendix
mhasoba Dec 3, 2019
acb8dbb
Updated stats notebooks
mhasoba Dec 8, 2019
87ef68b
Updated htmlversions of notebooks
mhasoba Dec 9, 2019
fb3a3d8
Updated stats notebooks
mhasoba Dec 9, 2019
85395f5
Updated stats notebooks
mhasoba Dec 10, 2019
6c31cda
Updated stats notebooks
mhasoba Dec 11, 2019
6893542
Updated stats notebooks
mhasoba Dec 12, 2019
cc214b2
Update Q4 in exercises
mbrazeau Jan 6, 2020
e1c130f
Updated NLLS Lecture
mhasoba Jan 23, 2020
d41794a
Merge branch 'master' of github.com:mhasoba/TheMulQuaBio
mhasoba Jan 23, 2020
a39759a
Updated NLLS Lecture and model fitting juyter notebook
mhasoba Jan 24, 2020
85fd9ee
Updated model fitting juyter notebook
mhasoba Jan 27, 2020
4b135b4
Tweaks to some notebooks, and added weekly computing solutions.
mhasoba Mar 8, 2020
64f2489
Edits to Jupyter nbs
mhasoba May 22, 2020
a5a5f6e
Edits to stats Jupyter nbs
mhasoba May 29, 2020
a3196c0
Edits to stats Jupyter nbs
mhasoba May 29, 2020
c761356
Edits to stats Jupyter nbs and re-exported html versions
mhasoba May 29, 2020
6aef36f
Edits to stats Jupyter nbs
mhasoba May 29, 2020
8973634
Edits to stats Jupyter nbs
mhasoba Jun 3, 2020
8e94497
Edits to stats Jupyter nbs, removed solutions directory
mhasoba Jun 5, 2020
a1a7664
Updated Readme
mhasoba Jun 5, 2020
0b42437
Added a missing script file
mhasoba Jun 5, 2020
1c7a612
Merge branch 'master' of github.com:mhasoba/TheMulQuaBio
mhasoba Jun 5, 2020
fd161a3
Edits to stats Jupyter nbs
mhasoba Jun 5, 2020
a6770c9
Edits to stats Jupyter nbs
mhasoba Jun 5, 2020
75810a4
Edits to stats Jupyter nbs
mhasoba Jun 9, 2020
78cafc5
move old code examples
mbrazeau Sep 18, 2020
1dc5d87
initial updates and new exercises
mbrazeau Sep 18, 2020
6ea1b3b
Edits some notebooks
mhasoba Sep 25, 2020
4a30aa4
Edits some notebooks
mhasoba Sep 25, 2020
95ba13e
Merge branch 'master' of github.com:mhasoba/TheMulQuaBio
mhasoba Sep 25, 2020
a1a10fb
Updated main README
mhasoba Sep 30, 2020
e40ce4c
Switched project to a jupyter book
mhasoba Oct 3, 2020
490b4b3
Add extended python notebooks
fwimp Oct 6, 2020
8b5cb3b
Change wget example in grep to reflect new structure
fwimp Oct 6, 2020
d21f513
Merge pull request #15 from mhasoba/issue11fix
mhasoba Oct 6, 2020
8d96036
Merge pull request #14 from mhasoba/francis_logging_and_oop
mhasoba Oct 6, 2020
5c4df93
Updates to fix various errors in noteooks
mhasoba Oct 6, 2020
512a5b7
Updates to fix errors in Unix and Intro noteooks
mhasoba Oct 7, 2020
4ae5029
added a new file that we'll remove later
mhasoba Oct 8, 2020
d55931c
removed the file
mhasoba Oct 8, 2020
cb9a6af
Updated readme, configuration file, and some notebooks
mhasoba Oct 9, 2020
7f301eb
added a new file that we'll remove later
mhasoba Oct 12, 2020
e3c3dc6
removed the file
mhasoba Oct 12, 2020
48d1ec1
Updated some notebooks
mhasoba Oct 12, 2020
482e0b7
Updated some notebooks , added feedback code
mhasoba Oct 13, 2020
803cf96
Updated some practical code
mhasoba Oct 13, 2020
e1c135b
Updated some notebooks and assessment appendix
mhasoba Oct 15, 2020
7a1c65e
Updated Python I notebook and code
mhasoba Oct 16, 2020
3e0e284
Updated some notebooks and feedback script
mhasoba Oct 20, 2020
f4ac9c9
Updated some notebooks
mhasoba Oct 23, 2020
6d4378f
Updated Model Fitting lecture for 2020-21
mhasoba Oct 26, 2020
3612c8d
Updated NLLS Fitting lecture for 2020-21
mhasoba Oct 27, 2020
ec92082
Updated some notebooksand R code
mhasoba Oct 30, 2020
173f736
Updated some notebooks
mhasoba Nov 2, 2020
25d0b33
Updated some readings
mhasoba Nov 10, 2020
8d978dd
Updated some Notebooks, especially Python II
mhasoba Nov 15, 2020
77862f2
Add tmux suggestion to jupyter notebook notebook
fwimp Nov 17, 2020
6b09acc
Add note on using tmux with remote jobs
fwimp Nov 17, 2020
a277f0b
Merge pull request #36 from mhasoba/jupyter_tmux
mhasoba Nov 17, 2020
bf9067f
Updated blackbirds.py practical script
mhasoba Nov 17, 2020
04d24cd
Add `with` statement section to python I
fwimp Nov 17, 2020
f544598
Update csv read example to use `with`
fwimp Nov 17, 2020
dec4d54
Added lmfit tutorial
Nov 18, 2020
f4931a1
Added lmfit tutorial
Nov 18, 2020
fd0688d
Merge pull request #39 from mhasoba/lmfit_tutorial
mhasoba Nov 19, 2020
c20eac2
Added Pablo's Model fitting in Python Appendix
mhasoba Nov 23, 2020
973dba9
Erased exercise solutions
Nov 23, 2020
8d54fc0
Merge pull request #44 from mhasoba/lmfit_tutorial
mhasoba Nov 23, 2020
5ed1d3d
uploaded solutions for exercise
Nov 23, 2020
e338e2d
Merge pull request #45 from mhasoba/lmfit_tutorial
mhasoba Nov 23, 2020
34af6d0
Updated some notebooks
mhasoba Nov 26, 2020
e3a15b4
Merge pull request #38 from mhasoba/python_1_usewith
mhasoba Dec 1, 2020
0d7df6f
Updated some notebooks and the NLLS lecture
mhasoba Dec 7, 2020
88bba63
Merge branch 'master' of github.com:mhasoba/TheMulQuaBio
mhasoba Dec 7, 2020
bb25590
Further updated the NLLS notebook and lecture
mhasoba Dec 7, 2020
19a227d
Updated NLLS lecture
mhasoba Dec 7, 2020
23dd25a
Updated NLLS lecture
mhasoba Dec 7, 2020
d5fd640
update printf and string variables for correct use
mbrazeau Jan 12, 2021
9bf0b7f
Added noGit flag. Fixed Week1/10 issue.
JCur96 Feb 23, 2021
4036426
edits to profiling tools, plus some additions to the feedback script …
JCur96 Mar 1, 2021
4292bd3
Added optional noGit and garbageCollection to the Feedback script
JCur96 Mar 2, 2021
42a451f
Added weekly expected script checking, updated launch.json with addit…
JCur96 Mar 3, 2021
3ce63d4
Double checked all scripts where in the lists for each week
JCur96 Mar 13, 2021
41500d8
Removed extraneous files!
JCur96 Mar 13, 2021
3b3ee1c
Update Feedback.py
JCur96 Mar 13, 2021
3c8e54d
Merge pull request #51 from JCur96/QOLChanges
mhasoba Mar 18, 2021
19461e4
Updated some jupyter Notebooks
mhasoba Oct 7, 2021
31d250c
Updated notebooks
mhasoba Oct 9, 2021
cf9a970
Book Intro
mhasoba Oct 9, 2021
5fe06cb
Updated book's config
mhasoba Oct 9, 2021
acfc26a
Updated book build
mhasoba Oct 9, 2021
f16e665
Updated some Notebooks and Readings
mhasoba Oct 13, 2021
0cec0ac
Updated book's config (fixed issue with inline latex rendering) and u…
mhasoba Oct 18, 2021
e0f1584
Updated model fitting lecture and some notebooks
mhasoba Oct 26, 2021
9bf4c29
Updated model fitting lecture and some notebooks
mhasoba Oct 26, 2021
78b5b65
Updated model fitting lecture
mhasoba Oct 26, 2021
b26edc6
Updated model fitting lecture pdf and Feedback script
mhasoba Oct 29, 2021
c969536
update intro to language
mbrazeau Jan 5, 2022
0615f0f
Merge pull request #66 from mhasoba/mbrazeau-patch-1
mhasoba Jan 5, 2022
b6fd1c6
full update; rewrite
mbrazeau Jan 9, 2022
65c4502
update; rewrite
mbrazeau Jan 9, 2022
9132b37
add a new exercise
mbrazeau Jan 9, 2022
91860c6
add new exercise
mbrazeau Jan 9, 2022
21a55c7
update info on floating points
mbrazeau Jan 9, 2022
ff0b814
Merge pull request #67 from mhasoba/cprog
mhasoba Jan 9, 2022
f3b4dd7
add progs from lectures
mbrazeau Jan 12, 2022
8f7f88c
add pointers examples
mbrazeau Jan 12, 2022
7c616b5
add shiftbyte example code
mbrazeau Jan 12, 2022
9228b50
day 5 morning programs
mbrazeau Jan 14, 2022
9a96fdb
files from afternoon: linking C and python
mbrazeau Jan 14, 2022
48def91
add the calculator program
mbrazeau Jan 14, 2022
ec340bb
ensuring all files up-to-date
mbrazeau Jan 20, 2022
a7d5377
Fix erroneous order of least/most sig bits
mbrazeau Jan 20, 2022
1f84e38
Fix missing float cast and typo
mbrazeau Jan 21, 2022
c1d149e
Note to reader about one of the examples
mbrazeau Jan 21, 2022
e254e66
fix error in variable naming
mbrazeau Jan 21, 2022
a95bac2
fix errors in var names
mbrazeau Jan 21, 2022
3bbf652
Merge pull request #68 from mhasoba/mbrazeau-patch-2
mhasoba Jan 21, 2022
7cea900
Merge pull request #69 from mhasoba/cprog
mhasoba Jan 21, 2022
7b95a3b
single consolidated file with all slides
mbrazeau Jan 31, 2022
f78e2b4
Merge pull request #70 from mhasoba/cprog
mhasoba Jan 31, 2022
37c6898
fixed error on bit significance
mbrazeau Mar 23, 2022
9727732
Merge pull request #72 from mhasoba/cprog
mhasoba Mar 24, 2022
ddbaf10
Fixed various notebook issues, including #59 and 60
mhasoba May 15, 2022
a2ddd9e
Fixed some notebook issues, suppressed two topic chapters
mhasoba Jun 15, 2022
60f9547
Update Python I to fix #22 and #56
fwimp Oct 2, 2022
9631000
Update Python II to fix #22 and #56
fwimp Oct 2, 2022
1345347
Rework git add section to encourage safer practices and add friendly …
fwimp Oct 2, 2022
72cefef
Add gitignore best practices and whitelist paradigm alternative.
fwimp Oct 2, 2022
acb0811
Merge pull request #80 from mhasoba/minor_git_chapter_rework
mhasoba Oct 4, 2022
14763fb
Merge pull request #78 from mhasoba/print_formatting_refactor
mhasoba Oct 4, 2022
d34bc26
Updated jupyter nbs and loops / lict comprehensions python pracs
mhasoba Oct 14, 2022
214199a
Updated Linmods lecture
mhasoba Nov 9, 2022
21d1677
Update current standard.
mbrazeau Jan 6, 2023
16d72f0
Updates on preprocessor text subs; compiling
mbrazeau Jan 6, 2023
3fc184d
Merge pull request #116 from mhasoba/mbrazeau-C-2023
mhasoba Jan 6, 2023
2fd4a0c
Update grammar and complete an example
mbrazeau Jan 13, 2023
e3ae965
Merge pull request #117 from mhasoba/mbrazeau-patch-1
mhasoba Jan 13, 2023
9f04783
Fix error in pre- and post-fix operators.
mbrazeau Mar 30, 2023
235c92f
Merge pull request #118 from mhasoba/mbrazeau-patch-1
mhasoba May 1, 2023
57529ca
Remove accidental colon character
smith558 Oct 4, 2023
8faaecc
Merge pull request #119 from smith558/patch-1
mhasoba Oct 8, 2023
6bc8157
Add missed space
smith558 Oct 9, 2023
3ca8f07
Merge pull request #120 from mhasoba/smith558-patch-1
mhasoba Oct 10, 2023
6efe9b3
Add a guide for word count in LaTex
smith558 Dec 1, 2023
1e6f029
updated C week materials
mhasoba Jan 19, 2024
f737dcc
Added Mathcourse
PBreul Jan 22, 2024
080e90b
Merge pull request #125 from smith558/master
mhasoba Jan 26, 2024
b493590
Merge pull request #126 from mhasoba/mathsforbiologists
mhasoba Jan 26, 2024
d278721
Added missing changes to _toc.yml file
PBreul Jan 26, 2024
56d3213
Merge pull request #127 from mhasoba/mathsforbiologists
mhasoba Jan 26, 2024
4b9c544
Replaced TODOs with a new file to include meeting notes in markdown
mhasoba Sep 25, 2024
a4b1856
removed old TODos
mhasoba Sep 25, 2024
69d51fa
Git ignore JetBrains config
smith558 Sep 25, 2024
54ff004
Lock jupyter-book version to prevent further breaking changes
smith558 Sep 25, 2024
b4bfab6
Temporary fix for layout issue
smith558 Sep 25, 2024
da18ac8
Merge branch 'master' into layout-fix
smith558 Sep 25, 2024
927dd8d
Merge pull request #129 from mhasoba/layout-fix
mhasoba Sep 26, 2024
c62cee6
updated several notebooks and associated code + data
mhasoba Oct 8, 2024
f794020
Added new tip box in Git notebook called Pre-Commit Git Hook
hel0122 Oct 10, 2024
6620c25
Added new tip box in Git notebook called Pre-Commit Git Hook
hel0122 Oct 10, 2024
ec2ca84
Amended typo in Pre-Commit Git Hook tip box
hel0122 Oct 10, 2024
419bf13
Merge pull request #134 from hel0122/development
mhasoba Oct 10, 2024
a5a30d2
Updated README.md
mhasoba Oct 11, 2024
f628daa
Moved out of this project to merge with separate automarker project
mhasoba Oct 15, 2024
9fd255f
Merge branch 'master' of github.com:mhasoba/TheMulQuaBio
mhasoba Oct 15, 2024
a4ca513
Fixed incorrect conditional
hel0122 Oct 21, 2024
96635e2
Fixed bug in foo_3 function of 'cfexercises1.py'
hel0122 Oct 21, 2024
9db4603
Merge pull request #135 from hel0122/development
mhasoba Oct 24, 2024
b20f020
Updated assessment guidelines, including coding and git good/bad prac…
mhasoba Oct 24, 2024
55a0f63
Further updated coding and git good/bad practices in assesssment appe…
mhasoba Oct 24, 2024
22819fb
revisions to git chapter - significant restructuring and new content
mhasoba Oct 25, 2024
70e73e4
revisions to git chapter - significant restructuring and new content
mhasoba Oct 27, 2024
2ac7e88
Merged separate Python chapters into one, and added a section on good…
mhasoba Oct 27, 2024
c66f793
Updated git chapter following first review
mhasoba Oct 28, 2024
268b496
Partial changes to merged python chapter addressing fwimp's review
mhasoba Oct 28, 2024
a0a1091
Final changes to git chapter addressing fwimp's review
mhasoba Oct 28, 2024
8f7e9de
Removed the previous two split python chapters
mhasoba Oct 28, 2024
f344e56
Merge pull request #136 from TheMulQuaBio/git_chapter_revisions
mhasoba Oct 29, 2024
cef10bd
Updated assessment appendix to reflect changes in Git chapter and (up…
mhasoba Oct 29, 2024
b68f89d
Updated .gitignore and rm-ed to stop tracking _build directory
mhasoba Oct 29, 2024
b443d0e
Made changes to pre-commit git hook section in Git notebook
hel0122 Oct 30, 2024
d6c0d05
moved the networks section from main python chapter to test directory…
mhasoba Nov 3, 2024
5093185
several updates for merging into main branch
mhasoba Nov 3, 2024
af951fd
Merge branch 'master' of github.com:TheMulQuaBio/TMQB into python_cha…
mhasoba Nov 3, 2024
094a0e2
Merge pull request #137 from TheMulQuaBio/python_chapter_changes
mhasoba Nov 3, 2024
7fd0fcb
Merge pull request #139 from hel0122/development
mhasoba Nov 3, 2024
0ed5980
Added hpc appendix to test
g-kalogiannis Nov 14, 2024
683f4ce
Added HPC appendix and figures to notebooks
g-kalogiannis Nov 15, 2024
1f2a608
Updated chapter file names, updated Readme, and made some edits to th…
mhasoba Nov 16, 2024
b56cec6
Merge pull request #141 from TheMulQuaBio/hpc_teaching
mhasoba Nov 16, 2024
d9f75eb
Updated (simplified) file names, deleted some extra directories and f…
mhasoba Nov 20, 2024
d248708
Updated Readme and License
mhasoba Nov 29, 2024
49fe6e9
Update Notes_n_TODOs.md
mhasoba Dec 4, 2024
15d9281
Merge pull request #144 from MulQuaBio/mhasoba-patch-1
mhasoba Dec 4, 2024
b71163f
Update README.md
mhasoba Jan 6, 2025
11e53e2
Merge pull request #149 from MulQuaBio/mhasoba-patch-2
mhasoba Jan 6, 2025
940e471
Trimmed Notes_n_TODOs and fixed broken links in README
mhasoba Jan 7, 2025
66b63f0
Fixed broken cross-references and streamlined some file names
mhasoba Jan 7, 2025
bbc506b
test
yanzhu624 Jan 8, 2025
39e919c
combination of math chapters
yanzhu624 Jan 9, 2025
08df4c8
Added Vincent Jansen's Ecoloigical Modelling lecture materials
mhasoba Jan 9, 2025
351539d
Added first draft of EnE Modelling lecture
mhasoba Jan 9, 2025
5d28f80
Renamed and moved combined maths for biologists notebook to `notebook…
mhasoba Jan 9, 2025
c5d4d55
Merge pull request #152 from MulQuaBio/move-chapter
mhasoba Jan 9, 2025
bede6a4
updated TOC
mhasoba Jan 9, 2025
c42ccc9
add info of vectors and fix a small bug
yanzhu624 Jan 12, 2025
d4e77f2
fix a small bug
yanzhu624 Jan 12, 2025
e5ca4b2
Added EnE modelling Lecture 1 - Modelling and Model Fitting in EnE
mhasoba Jan 14, 2025
31c4b8e
Updated Maths for Biologists appendix, and toc & config files
mhasoba Jan 14, 2025
5efd1d5
Renamed stats intro file
mhasoba Jan 14, 2025
067b075
Merge branch 'main' into add-info-vector
yanzhu624 Jan 14, 2025
9e1962c
Delete content/_toc.yml
mhasoba Jan 19, 2025
a46b9ce
Merge pull request #154 from MulQuaBio/add-info-vector
mhasoba Jan 19, 2025
360567a
Merge branch 'main' of github.com:MulQuaBio/MQB
mhasoba Jan 19, 2025
d6399ea
Updates to EnE Modelling lectures
mhasoba Jan 19, 2025
b2d8a1d
Updated three EnE modelling notebooks
mhasoba Jan 20, 2025
f880788
Added modified EnE Interactions chapter back
mhasoba Jan 22, 2025
7c08a2b
Add files via upload
tinyuhui Feb 7, 2025
ecdd07c
Update MLE notebooks into a single chapter and added breif intro
mhasoba Feb 9, 2025
4a7a75b
minor updates to MLE.ipynb
mhasoba Jun 4, 2025
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67 changes: 66 additions & 1 deletion .gitignore
100644 → 100755
Original file line number Diff line number Diff line change
@@ -1 +1,66 @@
*.pyc
*~
*.tmp
content/results/*
content/[Ss]andbox/*
*.code-workspace

# Python
*.py[co]
__pycache__/

# Jupyter
.ipynb_checkpoints/

# Jupyter book (the _build directory contains the output files generated when you build a Jupyter Book, such as HTML pages, PDFs, and other assets. These files are artifacts that can be recreated from your source files at any time.)
content/_build/

# R History files
.Rhistory
.Rapp.history

# R Session Data files
.RData

## Core latex/pdflatex auxiliary files:
*.aux
*.lof
*.log
*.lot
*.fls
*.out
*.toc
*.fmt
*.fot
*.cb
*.cb2
.*.lb

## Intermediate documents:
*.dvi
*.xdv
*-converted-to.*
# these rules might exclude image files for figures etc.
# *.ps
# *.eps
# *.pdf

## Generated if empty string is given at "Please type another file name for output:"
.pdf

## Bibliography auxiliary files (bibtex/biblatex/biber):
*.bbl
*.bcf
*.blg
*-blx.aux
*-blx.bib
*.run.xml

## Build tool auxiliary files:
*.fdb_latexmk
*.synctex
*.synctex(busy)
*.synctex.gz
*.synctex.gz(busy)
*.pdfsync

.idea/
42 changes: 0 additions & 42 deletions BiolStructs_C/Part_00-C_for_biologists.md

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211 changes: 0 additions & 211 deletions BiolStructs_C/Part_01-Compiler_and_basics.md

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