Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

GitHub topics: metabolism

Repositories

pub-calculator-io/bmr-calculator

Free WordPress Plugin: Free BMR calculator uses well-known algorithms to calculate the basal metabolic rate. Also, find out more about the factors that influence BMR. www.calculator.io/bmr-calculator/

Language: JavaScript - Size: 4.55 MB - Last synced: about 11 hours ago - Pushed: about 18 hours ago - Stars: 6 - Forks: 0

hanruizhang/zhanglab

Lab website

Language: HTML - Size: 39.1 MB - Last synced: about 14 hours ago - Pushed: 1 day ago - Stars: 0 - Forks: 0

Metaboverse/Metaboverse

Visualization and analysis platform for metabolic data and network pattern recognition

Language: JavaScript - Size: 511 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 38 - Forks: 6

MetaSys-LISBP/PhysioFit

Estimation of extracellular fluxes and growth rate

Language: Python - Size: 3.84 MB - Last synced: about 11 hours ago - Pushed: about 13 hours ago - Stars: 6 - Forks: 4

biosustain/incawrapper

A python wrapper for Metabolic Flux Analysis (MFA) using INCA with additional functionalities

Language: Python - Size: 91.7 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 2 - Forks: 0

Knowledge-Graph-Hub/kg-microbe

Language: Jupyter Notebook - Size: 284 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 14 - Forks: 3

MetExplore/dexom-python

diversity-based enumeration of optimal context-specific metabolic networks using the cobrapy library

Language: Python - Size: 1.61 MB - Last synced: 3 days ago - Pushed: 2 months ago - Stars: 1 - Forks: 0

dBenedek/MetabolicExpressR

Metabolic subtyping of tumors from gene expression data

Language: HTML - Size: 62.2 MB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 0 - Forks: 0

vjz3qz/cancer-metabolic-analysis

Bioinformatics project analyzing cancer metabolism using computational modeling and analysis. The project was awarded the GIDI-UP: Summer Research Award and includes data, models, and scripts.

Language: Jupyter Notebook - Size: 23.4 KB - Last synced: 8 days ago - Pushed: 4 months ago - Stars: 1 - Forks: 0

opencobra/cobrapy

COBRApy is a package for constraint-based modeling of metabolic networks.

Language: Python - Size: 60.6 MB - Last synced: 8 days ago - Pushed: about 1 month ago - Stars: 444 - Forks: 211

fawda123/BASEmetab_script

script only for BASEmetab

Language: R - Size: 1.33 GB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 0 - Forks: 0

fawda123/EBASE

Estuarine Bayesian Single-station Estimation

Language: R - Size: 64.1 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 0 - Forks: 0

PlanesLab/gMCSpy

Efficient calculation of gMCS in python.

Language: Python - Size: 21.8 MB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 3 - Forks: 0

fawda123/nerrs-metabolism

Materials for evaluating metabolism estimates and detiding for NERRS sites

Language: R - Size: 777 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 0 - Forks: 0

zimmmermann-kogadeeva-group/GEMsembler

GEMsembler tool for assembling and comparing several types of Genome-Scale Metabolic Models (GEMs)

Language: Python - Size: 5.45 MB - Last synced: 15 days ago - Pushed: 16 days ago - Stars: 3 - Forks: 0

IVANDOMENZAIN/diverseYeasts_metabolism

Language: MATLAB - Size: 113 MB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 1 - Forks: 1

PistilliLab/CLAMSwrangler-web

Web version of CLAMS Wrangler. Built using Django and bootstrap.

Language: Python - Size: 271 KB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 0 - Forks: 0

yaoguangluo/ChromosomeDNA

《DNA元基催化与肽计算》在进化计算中, 软件函数文件进行 DNA 语义元基索引编码的 PDE 新陈代谢优化方式, 是一种有效的进化方式.

Language: Java - Size: 670 MB - Last synced: 21 days ago - Pushed: 21 days ago - Stars: 7 - Forks: 2

cdanielmachado/carveme

CarveMe: genome-scale metabolic model reconstruction

Language: Python - Size: 121 MB - Last synced: 11 days ago - Pushed: 3 months ago - Stars: 138 - Forks: 49

babessell1/MADRID Fork of HelikarLab/COMO

Metabolic Drug Repurposing Pipeline

Language: Python - Size: 733 MB - Last synced: 23 days ago - Pushed: 24 days ago - Stars: 4 - Forks: 0

biosustain/shu

Multi-dimensional, trans-omics metabolic maps.

Language: Rust - Size: 21.5 MB - Last synced: 13 days ago - Pushed: about 2 months ago - Stars: 37 - Forks: 0

MetaSys-LISBP/KinetX

Supplementary code of Cox et al., 2019

Language: Python - Size: 16.6 KB - Last synced: 28 days ago - Pushed: over 5 years ago - Stars: 0 - Forks: 1

resendislab/corda

An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al

Language: Python - Size: 1.6 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 21 - Forks: 8

roberts-farm-of-ideas/3

Finding thermodynamic cycles in the metabolism

Language: Python - Size: 4.53 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

opentecr/opentecr-data

contains the actual data for the openTECR database

Size: 4.87 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 1

opentecr/opentecr

contains general information about the openTECR database

Size: 5.09 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 5 - Forks: 3

nlnw/ztunes

Language: Jupyter Notebook - Size: 218 KB - Last synced: about 1 month ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 1

PistilliLab/CLAMSwrangler

Python program for cleaning, trimming, binning, and reformatting of data generated by the Columbus Instruments CLAMS for downstream statistical analysis.

Language: Python - Size: 442 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

cdanielmachado/reframed

ReFramed: metabolic modeling package

Language: Python - Size: 1.01 MB - Last synced: 26 days ago - Pushed: 3 months ago - Stars: 51 - Forks: 13

johnjdavisiv/gap-app

Grade-adjusted pace (GAP) calculator for runners

Language: HTML - Size: 1.09 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

PathVisio/FindYourInteraction

PathVisio plugin to find relevant metabolic reactions from Rhea

Language: Java - Size: 13.7 KB - Last synced: about 2 months ago - Pushed: about 6 years ago - Stars: 1 - Forks: 1

biosustain/multitfa

Multivariate thermodynamics-based metabolic flux analysis in Python.

Language: Python - Size: 70.9 MB - Last synced: 17 days ago - Pushed: 5 months ago - Stars: 8 - Forks: 2

BioSystemsUM/BioCatalyzer

BioCatalyzer: a rule-based tool to predict compound metabolism

Language: Python - Size: 58.4 MB - Last synced: 17 days ago - Pushed: about 1 year ago - Stars: 4 - Forks: 0

fawda123/WtRegDO

A simple package to implement weighted regression on dissolved oxygen time series

Language: R - Size: 18.5 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 5 - Forks: 0

rcolpo/pgp_reconstruction

Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models

Language: Python - Size: 4.76 MB - Last synced: 16 days ago - Pushed: 6 months ago - Stars: 11 - Forks: 0

carrascomj/kair

COnstraint-Based Reconstruction and Analysis in Rust

Language: Rust - Size: 140 KB - Last synced: 7 days ago - Pushed: about 3 years ago - Stars: 3 - Forks: 0

jbpauly/fasting

A Python package to interact with fasting logs from apps like Zero.

Language: Python - Size: 721 KB - Last synced: about 2 months ago - Pushed: about 3 years ago - Stars: 8 - Forks: 1

mjenior/riptide

Reaction Inclusion by Parsimony and Transcript Distribution

Language: Python - Size: 4.53 MB - Last synced: 13 days ago - Pushed: about 1 year ago - Stars: 9 - Forks: 3

jrcramos/Hybrid-modeling-of-bioreactor-with-LSTM

Deep hybrid modeling of bioreactor cell culture data using Long Short-Term Memory (LSTM) networks combined with first principles equations

Language: MATLAB - Size: 3.6 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 5 - Forks: 3

SysBioChalmers/overflow

Supplementary code and results from doi:10.1101/2020.02.20.957662

Language: MATLAB - Size: 10.3 MB - Last synced: 3 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0

franciscozorrilla/metaGEM

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

Language: Python - Size: 262 MB - Last synced: 3 months ago - Pushed: 4 months ago - Stars: 160 - Forks: 34

SBRG/cobrame

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)

Language: Python - Size: 1.61 MB - Last synced: about 2 months ago - Pushed: over 5 years ago - Stars: 32 - Forks: 18

fawda123/spam_detiding

quick and dirty eval of metab estimates on SPAM project before/after detiding

Size: 394 KB - Last synced: 3 months ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 0

fawda123/detide_eval

Materials for evaluating DO detiding with weighted regression

Language: R - Size: 2.53 GB - Last synced: 3 months ago - Pushed: almost 3 years ago - Stars: 1 - Forks: 0

fawda123/detiding_cases

case studies for removing tidal signal from DO time series

Language: R - Size: 99.5 MB - Last synced: 3 months ago - Pushed: almost 9 years ago - Stars: 1 - Forks: 0

fawda123/detiding_corrs

shiny app for correlations between tide and metabolism with different windows

Language: R - Size: 4.08 MB - Last synced: 3 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

fawda123/BASEmetab Fork of dgiling/BASEmetab

R package for single-station stream ecosystem metabolism estimation

Size: 2.04 MB - Last synced: 3 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

SCMeTA/SCMeTA

A python library for single-cell metabolism data analysis.

Language: Python - Size: 514 KB - Last synced: 20 days ago - Pushed: 3 months ago - Stars: 12 - Forks: 2

tracykuper/mimics

Multi-scale model of Metabolism In Cellular Systems

Language: Java - Size: 8.66 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

Robaina/BRENDApyrser

A Python parser for the BRENDA database

Language: Python - Size: 702 KB - Last synced: 9 days ago - Pushed: 8 months ago - Stars: 17 - Forks: 4

AHuffmyer/EarlyLifeHistory_Energetics

Ontogenetic shifts in symbiotic and metabolic state in coral early life history

Language: HTML - Size: 407 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 5 - Forks: 1

ethrya/circadianGlucose

Physically Based Modelling of Cirdadian Glucose Dynamics

Language: Matlab - Size: 251 KB - Last synced: 5 months ago - Pushed: over 5 years ago - Stars: 4 - Forks: 2

PiotrTymoszuk/biggrExtra

metabolic pathway modeling based on gene expression

Language: R - Size: 9.34 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

openalea-incubator/WheatFspm

WheatFspm is a Functional Structural Plant Model (FSPM) of wheat based on an innovative modelling framework for a better understanding of grass morphogenesis and C-N economy in interaction with environmental conditions.

Language: Python - Size: 34.2 MB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 10 - Forks: 8

openCONTRABASS/CONTRABASS

Constraint-based model vulnerabilities analysis - Python analysis tool http://contrabass.unizar.es

Language: HTML - Size: 5.61 MB - Last synced: 30 days ago - Pushed: 7 months ago - Stars: 3 - Forks: 0

MetaSys-LISBP/GL_GNT_bypass

13C metabolic flux analysis of the extracellular GL-GNT by-pass of E. coli

Language: Component Pascal - Size: 866 KB - Last synced: 28 days ago - Pushed: 6 months ago - Stars: 1 - Forks: 0

Electrum-app/Electrum

Visualization platform for exploring MIDAS protein-small molecule interaction data

Language: Jupyter Notebook - Size: 59.1 MB - Last synced: about 2 months ago - Pushed: 8 months ago - Stars: 1 - Forks: 0

adalbertobrant/metabolismobasal

Simple metabolic calculator to weight loss

Language: HTML - Size: 257 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 16 - Forks: 27

lrd3uu/COVID19_metabolomics

Pipeline for analyzing metabolomics data, specifically in the context of metabolic shifts related to disease severity

Language: Python - Size: 22.5 KB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

lrd3uu/gardnerella_pangenome

G. vaginalis metabolic model construction and biofilm pathway characterization

Language: Jupyter Notebook - Size: 55.7 KB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

franciscozorrilla/SymbNET

Teaching materials for SymbNET course: from MAGs to GEMs

Language: Jupyter Notebook - Size: 81.9 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 11 - Forks: 3

SysBioChalmers/pcLactis

Proteome-constrained model of Lactococcus lactis

Language: Jupyter Notebook - Size: 107 MB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 1

OSS-Lab/MetQy

Repository for R package MetQy (read related publication here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6247936/)

Language: R - Size: 277 MB - Last synced: 8 months ago - Pushed: over 2 years ago - Stars: 17 - Forks: 9

MetabolicAtlas/MetabolicAtlas

Open source genome-scale metabolic models of human and model animals

Language: Vue - Size: 66 MB - Last synced: 7 months ago - Pushed: 10 months ago - Stars: 18 - Forks: 2

gibbslab/exp2flux

An R package to incorporate in a continuous way the gene-expression data as FBA flux boundaries in a metabolic model. Also, functions to calculate and plot the differences between model fluxes in different metabolic scenarios was included. This is an implementation of the algorithm described by Lee et al. (2012) in DOI: 10.1186/1752-0509-6-73.

Language: R - Size: 1.19 MB - Last synced: 7 months ago - Pushed: about 7 years ago - Stars: 2 - Forks: 0

hahmadima/GaussianProcess_Corn

Gaussian process regression model to predict energy of corn sample for poultry given levels of chemical compositions

Language: MATLAB - Size: 11.7 KB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 1

barberislab/ChIP-exo_Fkh1_Fkh2

ChIP-exo analysis highlights Fkh1 and Fkh2 transcription factors as hubs that integrate multi-scale networks in budding yeast | T.D.G.A. Mondeel, P. Holland, J. Nielsen and M. Barberis | 2019 | https://doi.org/10.1093/nar/gkz603

Language: HTML - Size: 174 MB - Last synced: 7 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

changwn/scFEA

single cell Flux Estimation Analysis (scFEA) Try the below web server!

Language: Jupyter Notebook - Size: 51.2 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 66 - Forks: 27

Wishartlab-openscience/Biotransformer

A computational tool for the prediction and identification of metabolites.

Language: Java - Size: 69.2 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 2 - Forks: 1

DenisTitovLab/Glycolysis.jl

Package for modeling glycolysis activity

Language: Julia - Size: 4.86 MB - Last synced: 4 days ago - Pushed: about 1 month ago - Stars: 6 - Forks: 0

SchlossLab/Jenior_Metatranscriptomics_mSphere_2018

Repository associated with Jenior ML, et al. (2018). mSphere.

Language: R - Size: 261 MB - Last synced: 9 months ago - Pushed: almost 6 years ago - Stars: 4 - Forks: 2

nicholaswunz/old-data

Raw data from older studies.

Size: 218 KB - Last synced: 9 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

SysBioChalmers/ecModels

A container for all enzyme constrained models created by GECKO.

Language: MATLAB - Size: 94.7 MB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 8 - Forks: 6

etheleon/omics-neo4j-container

Dockerfile to set up omics DB and preinitialized databases

Language: Shell - Size: 15.6 KB - Last synced: 9 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

sysbiolux/MelanomaPaper

Consensus models of Bintener et al. 2023

Size: 16.4 MB - Last synced: 9 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 0

cdanielmachado/embl_gems

EMBL GEMs: A collection of GEnome-scale Models for bacterial species

Size: 1.56 GB - Last synced: 9 months ago - Pushed: about 5 years ago - Stars: 23 - Forks: 9

cdanielmachado/cooccurrence

Supplementary data for co-occurrence manuscript

Language: Jupyter Notebook - Size: 11.9 MB - Last synced: 9 months ago - Pushed: over 4 years ago - Stars: 10 - Forks: 3

emunozh/smum

Spatial Microsimulation Urban Metabolism (SMUM)

Language: Shell - Size: 0 Bytes - Last synced: 10 months ago - Pushed: almost 6 years ago - Stars: 1 - Forks: 3

PiotrTymoszuk/simmun

Metabolism of serum neurotransmitter precursors after COVID-19

Language: TeX - Size: 85.1 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 0

AHuffmyer/acropora_larval_metabolism

Metabolism and gene expression in Acropora pulchra larvae under elevated temperature in Moorea - October 2022

Size: 5.85 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 0

stier-lab/Csik-etal-Functional-Ecology

All code and data for the manuscript "TITLE HERE"

Language: R - Size: 47.1 MB - Last synced: 10 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

gibbslab/g2f

An R package to find the gaps in metabolic networks, and fill it from the stoichiometric reactions of a reference metabolic reconstruction using a weighting function. Also include the option to download all the set of gene-associated stoichiometric reactions for a specific organism from the KEGG database.

Language: R - Size: 566 KB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 5 - Forks: 3

GuilleGarciaG/Metabolic_scaling_ectothermic_vertebrates

This repository contains codes and data needed to reproduce the analyses and figures of the manuscript: García-Gómez, G., Hirst A., Spencer, M., and Atkinson, D. (2023). Responses of intraspecific metabolic scaling to temperature and activity differ between water- and air-breathing ectothermic vertebrates.

Language: R - Size: 176 KB - Last synced: 3 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

cdanielmachado/framed

framed: a metabolic modeling package for python

Language: Python - Size: 6.54 MB - Last synced: 21 days ago - Pushed: over 4 years ago - Stars: 26 - Forks: 10

gibbslab/minval

An R package to identify orphan metabolites and evaluate the mass and charge balance of stoichiometric reactions. The package also includes functions to characterize and write models in TSV and SBML formats, extract all reactants, products, metabolite names and compartments from a metabolic reconstruction.

Language: R - Size: 7.1 MB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 1