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An open API service indexing awesome lists of open source software.

Projects in Awesome Lists by SysBioChalmers

A curated list of projects in awesome lists by SysBioChalmers .

https://github.com/sysbiochalmers/dlkcat

Deep learning and Bayesian approach applied to enzyme turnover number for the improvement of enzyme-constrained genome-scale metabolic models (ecGEMs) reconstruction

bayesian deep-learning enzyme-constraints enzyme-turnover-number kcat kinetics

Last synced: 29 Jul 2025

https://github.com/sysbiochalmers/human-gem

The generic genome-scale metabolic model of Homo sapiens

genome-scale-models human-metabolism standard-gem

Last synced: 12 Apr 2025

https://github.com/sysbiochalmers/gecko

Toolbox for including enzyme constraints on a genome-scale model.

data-integration enzyme-constraints kinetics matlab proteomics systems-biology toolbox

Last synced: 24 Oct 2025

https://github.com/sysbiochalmers/hgtphylodetect

HGTphyloDetect is a versatile toolbox to identify horizontal gene transfer (HGT) events combined with phylogenetic analysis.

evolutionary-biology high-throughput-pipeline horizontal-gene-transfer phylogenetics sequence-analysis systems-biology

Last synced: 29 Jul 2025

https://github.com/sysbiochalmers/ecmodels

A container for all enzyme constrained models created by GECKO.

genome-scale-models kinetics metabolism systems-biology

Last synced: 29 Jul 2025

https://github.com/sysbiochalmers/bayesiangem

This repository contains code and data needed to replicate the analysis carried out in the manuscript Li G, et al. 2020.

Last synced: 29 Jul 2025

https://github.com/sysbiochalmers/orthomics

Collection of scripts for gene age sorting and multi-omics data mining and analysis

data-integration data-visualization de-analysis orthology proteomics rnaseq

Last synced: 07 Mar 2026

https://github.com/sysbiochalmers/yeast-species-gems

A universal metabolic model knowledge database (pan-GEM) for current existing yeast species with genome sequence, based on which we will build the GEMs of high quality for each yeast species.

pan-genome-annotation pan-metabolic-model pathway-conservation-analysis strain-specific-metabolic-model yeast-species

Last synced: 05 Jan 2026

https://github.com/sysbiochalmers/ecfactory

A constraint-based method for prediction of metabolic engineering targets using ecModels of metabolism

cell-factory enzyme-constraints metabolic-models microbes

Last synced: 14 Jun 2025

https://github.com/sysbiochalmers/mouse-gem

Genome-scale model for Mus musculus

standard-gem

Last synced: 20 Aug 2025

https://github.com/sysbiochalmers/fruitfly-gem

Genome scale model for Drosophila melanogaster

standard-gem

Last synced: 13 Oct 2025

https://github.com/sysbiochalmers/sybil

Efficient Constrained Based Modelling in R

Last synced: 29 Jul 2025

https://github.com/sysbiochalmers/hanpo-gem

Draft genome-scale model of Hansenula polymorpha (Ogataea polymorpha; Pichia angusta)

Last synced: 29 Jul 2025

https://github.com/sysbiochalmers/zebrafish-gem

Genome-scale model for Danio rerio

standard-gem

Last synced: 21 Jul 2025

https://github.com/sysbiochalmers/muscleatpproductionsimulation

Models and scripts for simulations of ATP production in muscle, the repo contains: A) A small scale enzyme constrained stoichiometric model of metabolism of the single muscle fiber B) A whole body metabolic model incorporating complex I bypass.

Last synced: 29 Jul 2025

https://github.com/sysbiochalmers/multi_scale_evolution

Multi-scale evolution analysis of with aid of protein 3D structures for 332 different yeast species plus 11 fungal species.

332-yeast-species evolution-analysis mutation-cluster-analysis pan-genome-analysis protein-3d-structure

Last synced: 06 Jan 2026

https://github.com/sysbiochalmers/singlecellmodeling

Code for the publication "Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data"

Last synced: 29 Jul 2025

https://github.com/sysbiochalmers/slimer

Collection of scripts for improving lipid constraints in yeast-GEM

data-integration lipidomics systems-biology yeast

Last synced: 29 Jul 2025

https://github.com/sysbiochalmers/worm-gem

Genome-scale model for Caenorhabditis elegans

standard-gem

Last synced: 09 Jul 2025

https://github.com/sysbiochalmers/sybil-sbml

SBML (Systems Biology Markup Language) integration in sybil

Last synced: 29 Jul 2025

https://github.com/sysbiochalmers/streptomyces_coelicolor-gem

Genome-scale model of Streptomyces coelicolor.

genome-scale-models

Last synced: 28 Oct 2025

https://github.com/sysbiochalmers/mlessential

A computational toolbox to predict essential genes using machine learning based on sequence and evolution-based information

evolutionary-information gene-essentiality machine-learning sequence-features

Last synced: 26 Mar 2025

https://github.com/sysbiochalmers/livercellmetabolismsimulation

Simulation of HepG2 and Huh7 cultivations under different nutrient conditions

Last synced: 26 Mar 2025

https://github.com/sysbiochalmers/sco-gem

The consensus GEM for Streptomyces coelicolor -

genome-scale-model standard-gem streptomyces-coelicolor

Last synced: 29 Jul 2025

https://github.com/sysbiochalmers/halo-gem

Genome-scale metabolic model for Halomonas bluephagenesis TD01

Last synced: 26 Mar 2025

https://github.com/sysbiochalmers/dsave-r

R Package DSAVE (Down-SAmpling based Variation Estimation). The package operates on single-cell RNA-Seq data and is useful for finding misclassified cells, comparing the outcome of clustering methods, figuring out minimum clustering sizes to get the same variation as for bulk, and comparing the technical variation across datasets. The package is compatible with Seurat.

Last synced: 26 Mar 2025

https://github.com/sysbiochalmers/brainmetabolismmodeling

Modeling of the energy metabolism of the brain

Last synced: 27 Jul 2025

https://github.com/sysbiochalmers/enzymeconstrained_humanmodels

Collection of scripts for enhancing humanGEM based models with kinetic and proteomics constraints and specialized simulation utilities.

enzyme-constraints genome-scale-models kinetics proteomics-data-integration systems-biology

Last synced: 16 Aug 2025

https://github.com/sysbiochalmers/human-maps

Human1 metabolic maps

Last synced: 06 Jan 2026

https://github.com/sysbiochalmers/proyeast8-gem

Mutation mapping analysis using CLUMPS and hotspot method with aid of protein 3D structures for the metabolic gene from yeast GEM

Last synced: 14 Jun 2025

https://github.com/sysbiochalmers/enzyme-parameters-analysis

Global analysis of kinetic parameters in the BRENDA database, used by the GECKO toolbox

Last synced: 24 Oct 2025

https://github.com/sysbiochalmers/rat-gem

Genome-scale model for Rattus norvegicus

standard-gem

Last synced: 10 Feb 2026

https://github.com/sysbiochalmers/yeastsmodels

Container of computational models of metabolism for different yeast species.

gems metabolic-models metabolism systems-biology yeast-species

Last synced: 19 Mar 2026

https://github.com/sysbiochalmers/kiwi

The Kiwi python package combines gene-set analyses with biological networks to visualize the interactions between genesets that are significant in a given biological system.

Last synced: 10 Jun 2026

https://github.com/sysbiochalmers/childrengutmicrobialgems

58 GEMs for gut bacterial species from microbiota of healthy and malnourished children.

genome-scale-models

Last synced: 19 Mar 2026

https://github.com/sysbiochalmers/cplexapi

R Interface to C API of IBM ILOG CPLEX

Last synced: 26 Mar 2025

https://github.com/sysbiochalmers/mitoyeast-gem

yeast-GEM with an expansion of the mitochondrial compartments

Last synced: 06 Oct 2025

https://github.com/sysbiochalmers/overflow

Supplementary code and results from doi:10.1101/2020.02.20.957662

genome-scale-models metabolism proteomics yeast

Last synced: 26 Mar 2025

https://github.com/sysbiochalmers/enzymeconstrainedsmallyeast

Enzyme constrained model of intermediary metabolism in S. cerevisiae

Last synced: 18 Oct 2025

https://github.com/sysbiochalmers/human-gem-guide

Guide for Human-GEM

Last synced: 19 Mar 2026

https://github.com/sysbiochalmers/yarrowia_multifactor

Data and scripts used for the RNA-seq analysis of Yarrowia lipolytica (fat-free strain and urea utilisation)

Last synced: 20 Oct 2025

https://github.com/sysbiochalmers/yeast-maps

Metabolic maps for the Yeast-8.3 GEM

Last synced: 26 Mar 2025

https://github.com/sysbiochalmers/falconet

The FALCONET R package enables to build and visualise metabolic maps of GEM automatically with aid of cellDesigner 4.4 and R platform

automatic-visualization metabolic-map omics-mapping system-biology

Last synced: 26 Mar 2025

https://github.com/sysbiochalmers/singlecelltoolbox

Contains general code for handling single-cell RNA-Seq data in Matlab. Also contains some functions for bulk data some additional general functions.

Last synced: 11 Jun 2025

https://github.com/sysbiochalmers/ytkprimerdesign

Python gui and shiny app for primer generation

Last synced: 26 Mar 2025

https://github.com/sysbiochalmers/cody

Last synced: 26 Mar 2025

https://github.com/sysbiochalmers/sybil-glpkapi

R Interface to C API of GLPK

Last synced: 14 Jul 2025

https://github.com/sysbiochalmers/reproduce

Assesing the quality and reproducibility of absolute proteomic data

proteomics reproducible-research

Last synced: 19 Mar 2026

https://github.com/sysbiochalmers/pclactis

Proteome-constrained model of Lactococcus lactis

genome-scale-models metabolism proteome-constraint

Last synced: 26 Mar 2025

https://github.com/sysbiochalmers/epo_gfp

Transcriptome analysis of EPO- and GFP-producing HEK293 Cell-lines

Last synced: 26 Mar 2025

https://github.com/sysbiochalmers/workshops

A collection of Sysbio workshops.

Last synced: 29 Jul 2025

https://github.com/sysbiochalmers/sybil-gurobiapi

Gurobi support for sybil

Last synced: 26 Mar 2025

https://github.com/sysbiochalmers/gecko2_simulations

Collection of scripts for reproduction of simulation results in "Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0".

constraint-based-modeling enzyme-constraints metabolism

Last synced: 24 Aug 2025

https://github.com/sysbiochalmers/proteomereallocationforfastgrowth

Collection of data and scripts for analyzing the proteome allocation of yeast grown in rich and minimal medium

Last synced: 08 Jul 2025

https://github.com/sysbiochalmers/energy_metabolism_model

Energy metabolism model

Last synced: 21 Sep 2025

https://github.com/sysbiochalmers/clpapi

R Interface to C API of COIN-OR Clp

Last synced: 29 Jul 2025

https://github.com/sysbiochalmers/trinityrnaseq-hebbe

https://github.com/trinityrnaseq/trinityrnaseq for Hebbe via Singularity Hub

Last synced: 19 Mar 2026

https://github.com/sysbiochalmers/sysbio.se

The sysbio.se source code

Last synced: 22 Jun 2025

https://github.com/sysbiochalmers/salb-gem

GEM for Streptomyces albidoflavus (S.albus J1074)

Last synced: 26 Mar 2025

https://github.com/sysbiochalmers/depcrpaperutils

Some files needed to run kallisto and bustools in Google Colab

Last synced: 06 Jan 2026

https://github.com/sysbiochalmers/comparativestudycrabtreeeffect

Collection of data and scripts for the study "Adaptations in metabolism and protein translation give rise to the Crabtree effect in yeast"

Last synced: 26 Mar 2025

https://github.com/sysbiochalmers/cofactoryeast

Integration of cofactors with proteome-constrained model of Saccharomyces cerevisiae

cofactor genome-scale-models

Last synced: 26 Mar 2025

https://github.com/sysbiochalmers/cellfactory-ecyeastgem

Code and data for in silico strain design for enhanced production of +100 typical bio-products with yeast as a cell-factory. Predictions are based on the ecYeastGEM model avaiable at ecModels.

cell-factory constraint-based-modeling enzyme-constraints yeast

Last synced: 29 Jul 2025

https://github.com/sysbiochalmers/nomenclature-toolbox

Matlab Toolbox for appending external biological database annotation information to Genome-scale Metabolic Models generated from KBase

Last synced: 05 Jan 2026

https://github.com/sysbiochalmers/cancerproteinsecretionml

A collection of scripts to analyze cancer transcriptomics data using various statistical and machine-learning approaches.

Last synced: 26 Mar 2025

https://github.com/sysbiochalmers/hyena

Hybrid promoter design using advanced transcription factor binding predictions

Last synced: 26 Mar 2025

https://github.com/sysbiochalmers/stig-met

Simulation Toolbox for Infant Growth with focus on Metabolism.

Last synced: 26 Mar 2025

https://github.com/sysbiochalmers/papla-gem

Genome-scale metabolic model of Papiliotrema laurentii

Last synced: 26 Mar 2025

https://github.com/sysbiochalmers/preprna-seqforftinit

Code for the publication describing how to prepare RNA-Seq profiles for methods that derive context-specific models from RNA-Seq data

Last synced: 05 Feb 2026

https://github.com/sysbiochalmers/tmemodeling

Modeling of the tumor microenvironment using a diffusion model for upptake constraints.

Last synced: 06 Oct 2025

https://github.com/sysbiochalmers/geckolight

A version of Gecko that produces much smaller models, primarily for human, but doesn't support individual protein constraints from proteomics, only a global protein usage constraint..

Last synced: 12 Oct 2025

https://github.com/sysbiochalmers/rnaseqctprofileeval

Contains code for the paper about RNA-Seq cell type profiles evaluation.

Last synced: 26 Mar 2025

https://github.com/sysbiochalmers/dsave-m

Matlab code for the paper "Dissecting Cell-to-Cell Variation in Single-cell RNA-Seq Data"

Last synced: 26 Mar 2025

https://github.com/sysbiochalmers/chipexo_pipeline

Pipeline for analyzing ChIPexo datasets

Last synced: 19 Mar 2026

https://github.com/sysbiochalmers/ecoli-gem

Genome-scale metabolic model for Escherichia coli

genome-scale-models standard-gem systems-biology

Last synced: 15 Feb 2026

https://github.com/sysbiochalmers/panyeast-gem

Reconstruction of a pan-genome metabolic model for S. cerevisiae - the pan model and scripts to make strain-specific models.

Last synced: 19 Mar 2026

https://github.com/sysbiochalmers/ecm_yeast

Automated pipeline for full kinetic parameterization of a reduced model for Saccharomyces cerevisiae's central carbon metabolism.

Last synced: 25 Jun 2025