109 Open source projects that are alternatives of or similar to cobrame

An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!

The consensus GEM for Saccharomyces cerevisiae

📖 Generation and Applications of Knowledge Graphs in Systems and Networks Biology

Spatial alignment of single cell transcriptomic data.

A prediction model for differential gene expression (DE) based on genome-wide regulatory interactions

A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.

The blackbean is a command tool for elasticsearch operations by using cobra. Besides, blackbean is the name of my lovely French bulldog.

CellMLToolkit.jl is a Julia library that connects CellML models to the Scientific Julia ecosystem.

Example application

PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways

A web application to visualize and edit the pathway models represented by SBGN Process Description Notation

Go 服务框架脚手架. 整合 echo、swag、viper、nsq、logrus、fx、xorm、cobra 等第三方库

Tools to generate and study moment equations for any chemical reaction network using various moment closure approximations

CarveMe: genome-scale metabolic model reconstruction

Encrypt your files or notes by your GPG key and save to MinIO or AWS S3 easily!

Fast visualization tool for large-scale and high dimensional single-cell data

Contact map analysis for biomolecules; based on MDTraj

Documentation, models and code relating to the 3rd edition of the textbook Stochastic Modelling for Systems Biology

The SBML Test Suite is a conformance testing system. It allows developers and users to test the degree and correctness of the SBML support provided in a software package.

python Parameter EStimation TOolbox

Towards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.

Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.

A python library for metabolic networks sampling and analysis

SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit

Workshop in omics integration and systems biology

Ultrafast sequence typing and gene detection from NGS raw reads

Collection of scripts for bacterial genomics

A web application to visualize and edit pathway models

KinK is a helper CLI that facilitates to manage KinD clusters as Kubernetes pods. Designed to ease clusters up for fast testing with batteries included in mind.

Parameter estimation for dynamical models using high-performance computing, batch and mini-batch optimizers, and dynamic load balancing.

A simple way to evaluate the security of your Kubernetes deployment against sets of best practices defined by various community sources

Differential Gene Correlation Analysis

CPM implementation in pure JavaScript

Syntax highlighting for computational biology

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

A curated list of awesome computational cryo-EM methods.

TCGA data acquisition and processing for Project Cognoma

🧬 An R package for visualizing molecular data in 3D

Fast Inference of Networks from Directed Regulations

R package to access DoRothEA's regulons

An interactive web portal for exploring immuno-oncology data

Transcripts annotation and GO enrichment Fisher tests

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

This repository contains the tensorflow implementation of "GNE: A deep learning framework for gene network inference by aggregating biological information"

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

A Curated List of Computational Biology Datasets Suitable for Machine Learning

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

A library to build and execute typed scientific workflows

An integrated software environment for multi-algorithm, multi-timescale, multi-spatial-representation simulation of various cellular phenomena

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

The Microbiome Interpretable Temporal Rule Engine

Curation and analysis of metabolic models

StochPy is a versatile stochastic modeling package which is designed for stochastic simulation of molecular control networks

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data

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

💹 SIMON is powerful, flexible, open-source and easy to use machine learning knowledge discovery platform 💻

A pretty CLI to find animes passing images 👉😳👈