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KMG060 Systems Biology course - repo for students

License: GNU General Public License v3.0

MATLAB 89.50% R 10.50%
rna-seq-analysis metabolic-models flux-balance-analysis systems-biology enzyme-constraints

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christophboerlin avatar ckitti avatar edkerk avatar ivandomenzain avatar johan-gson avatar jonathanrob avatar

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kmg060-systems-biology-course's Issues

model.rxnComps issue

model.rxnComps is a 53x1 array, when it should be 52x1 I think.
I believe the mistake is in the first 8 cells, as they are al 3 (extracellular), when just the first 7 should be.

fix:update_exercise3_files

Update all files for ex3 here in order to be consistent with the files in Canvas.

Also, try to improve documentation (scripts, slides or even report template) according the feedback obtained from student's questions.

  • Excess comment on considering the carbon ratio between ethanol and glucose has caused confusion
  • Update report template (remove references to previous years, clarify what is requested in determined/underdetermined soluitions and also in the reversibility correction)

fix: Improve exercise 1 script

After checking the students reports for exercise#1 in the 2020 KMG060 course we have detected some minor issues with the script, slides and report templates that should be fixed:

  • In the slides it is mentioned that MRN normalization is performed on the readcounts data, whilst the script encodes for RLE type normalization.
  • Ambiguity between the usage of terms differentially expressed genes and significantly differentially expressed genes, which creates some confusion, specially when they are required to work with the top 10 and top 1 DE genes.
  • We need to be more explicit with the required tasks in the report (for example be more specific about asking to include the figures and stuff).

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