Pinned

1. Minesweeper Minesweeper Public

   Genome Design Algorithm for Minimal Genomes using Whole Cell Models

   Python 1

2. Supercomputer_Simulation_Files_for_Mycoplasma_genitalium_whole-cell_model Supercomputer_Simulation_Files_for_Mycoplasma_genitalium_whole-cell_model Public

   Bash scripts (*.sh), gene knockout (*_ko.list), and experiment name (*_exp.list) files for producing Mycoplasma genitalium whole-cell model simulations on a SLURM controlled supercomputer cluster.

   Shell 1

3. Analysis_Code_for_Mycoplasma_genitalium_whole-cell_model Analysis_Code_for_Mycoplasma_genitalium_whole-cell_model Public

   Matlab scripts that produce an automated analysis of M.genitalium whole-cell model simulations, when run on using bash script locally / on supercomputer clusters. MGGRunner.m is our version of Simu…

   MATLAB 1

4. binom_statistics_for_Designing_Minimal_Genomes_Using_Whole-Cell_Models_paper binom_statistics_for_Designing_Minimal_Genomes_Using_Whole-Cell_Models_paper Public

   Statistics for classifying single gene knockout that show multiple phenotypes. Uses Binom R Package to perform binomial proportion confidence intervals. Graphing with R and Seaborn (python).

   Jupyter Notebook 1

5. Gene_Ontology_Comparison_for_Mycoplasma_genitalium_whole-cell_model Gene_Ontology_Comparison_for_Mycoplasma_genitalium_whole-cell_model Public

   Python notebooks created on Azure Notebooks that compare / melt / select Gene Ontology Biological Process Terms (see Unitprot Mycoplasma genitalium strain G-37 https://www.uniprot.org/uniprot/?quer…

   Jupyter Notebook 1