-
Hi,
I just realized that the air compressor's power consumption seems off in the PolarizeFuelCellStack example. It turns out that the air mass provided by the compressor doesn't match the consumpti…
-
First copy [this file](https://github.com/PNNL-CompBio/p3/blob/main/functional/calculate-functional-enrichment.Rmd) to this repo. Then we can run the three tests on the protein data (syn25706561) and …
-
SSAs, at scale, usually represent sparsely connected reaction networks. As such it's often more effective to store and access information on a per-reaction basis rather than storing a full matrix of …
-
Hello,
After spending a significant amount of time going through the various modkit threads on how best to set the mod-thresholds and filter-thresholds values, I am still uncertain as to the under…
-
This simply requires the following:
- `inspect_raw_data` should return all plots with linear x scales;
- a new function is needed to plot the corrected FRET signal with vertical lines at the theor…
-
when I call `r.getFullStoichiometryMatrix()`, the order of the metabolites changes depending on whether the method is called in a class or in a Jupyter notebook. From what I can tell, the order of the…
-
(base) C:\Users\Lenovo\scFEA>python src/scFEA.py --data_dir data --input_dir input --test_file Seurat_geneExpr.csv --moduleGene_file module_gene_glutaminolysis1_m23.csv --stoichiometry_matrix cmMat_gl…
-
Code such as the following triggers a warning in PyCharm: Expected type 'bool', got 'None' instead.
b = balance_stoichiometry({'Fe', 'O2'}, {'FeO', 'Fe2O3'}, underdetermined=None)
I don't know i…
-
Hi all,
I just tried to create some simple stochastic model and reproduce the results in COPASI (see below).
It seems like the roadrunner gillespie integrator is not calculating the particle number i…
-
This script generates a data file based on a given SBML model and then tries to run the LM plugin starting with random parameter values. A model that produces the errors is provided, but other models …