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Repository to accompany transcriptomics integration method developed during the third year of my PhD

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59m_final.ipynb
59m_final.ipynb
 
 
59m_no_thresholds.ipynb
59m_no_thresholds.ipynb
 
 
59m_with_thresholds.ipynb
59m_with_thresholds.ipynb
 
 
README.md
README.md
 
 
caov3_final.ipynb
caov3_final.ipynb
 
 
caov3_no_thresholds.ipynb
caov3_no_thresholds.ipynb
 
 
caov3_with_thresholds.ipynb
caov3_with_thresholds.ipynb
 
 
comparison_26102022.py
comparison_26102022.py
 
 
comparison_2610222.ipynb
comparison_2610222.ipynb
 
 
cov318_final.ipynb
cov318_final.ipynb
 
 
cov318_no_thresholds.ipynb
cov318_no_thresholds.ipynb
 
 
cov318_with_thresholds.ipynb
cov318_with_thresholds.ipynb
 
 
dmem_10%FBS.csv
dmem_10%FBS.csv
 
 
dmem_10_FBS_media.ipynb
dmem_10_FBS_media.ipynb
 
 
dmem_extra_glut_10_FBS_media.ipynb
dmem_extra_glut_10_FBS_media.ipynb
 
 
dmem_mem_vitamins_and_aas_media.ipynb
dmem_mem_vitamins_and_aas_media.ipynb
 
 
dmemhams_extra_glutamine_media.ipynb
dmemhams_extra_glutamine_media.ipynb
 
 
growth_plots.ipynb
growth_plots.ipynb
 
 
heya8_final.ipynb
heya8_final.ipynb
 
 
heya8_no_thresholds.ipynb
heya8_no_thresholds.ipynb
 
 
heya8_with_thresholds.ipynb
heya8_with_thresholds.ipynb
 
 
knockdown_simulations.ipynb
knockdown_simulations.ipynb
 
 
knockout_simulations_and_correlation_with_ccle.ipynb
knockout_simulations_and_correlation_with_ccle.ipynb
 
 
oaw28_final.ipynb
oaw28_final.ipynb
 
 
oaw28_no_thresholds.ipynb
oaw28_no_thresholds.ipynb
 
 
oaw28_with_thresholds.ipynb
oaw28_with_thresholds.ipynb
 
 
ov56_final.ipynb
ov56_final.ipynb
 
 
ov56_no_thresholds.ipynb
ov56_no_thresholds.ipynb
 
 
ov56_with_thresholds.ipynb
ov56_with_thresholds.ipynb
 
 
ovcar8_lg_pxt.ipynb
ovcar8_lg_pxt.ipynb
 
 
requirements.txt
requirements.txt
 
 
visualising_datasapread.ipynb
visualising_datasapread.ipynb
 
 

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ovarian_genome_scale_modeling

Repository to accompany transcriptomics integration method developed during the third year of my PhD

Constraint-based modelling performed on the 'Human-GEM-annotated.xml' 2020 version of the Human1 genome-scale model, developed by Robinson et al, 2020 (PMID: 32209698) [(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7331181/)]

Transcriptomics data was used to constrain generic GEM to six cell line-specific ovarian cancer models (CCLE, DepMap Public 22Q2, 'CCLE_expression.csv') [(https://depmap.org/portal/download/all/)]

Six cell line-specific models were constrained: three high-grade (CAOV3, COV318, OAW28), and three low-grade (59M, HEYA8, OV56)

Constraint-based modeling used FBA and own integration code to create reaction constraint dictionaries, which were integrated using COBRApy and MEWpy

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Repository to accompany transcriptomics integration method developed during the third year of my PhD

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