101 Open source projects that are alternatives of or similar to doctoral-thesis

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

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

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!

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

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

A Python framework for integrating biological databases and structured data sources in Biological Expression Language (BEL)

An interactive web portal for exploring immuno-oncology data

Web-component for creating & showing VSM-sentences — Visual Syntax Method

Collection of scripts for bacterial genomics

A web application to visualize and edit pathway models

Template to deploy a Data Product for data stream processing into a Data Landing Zone of the Data Management & Analytics Scenario (former Enterprise-Scale Analytics). The Data Product template can be used by cross-functional teams to ingest, provide and create new data assets within the platform.

Transformer-based Memory Networks for Knowledge Graph Embeddings (ACL 2020) (Pytorch and Tensorflow)

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

Fast Inference of Networks from Directed Regulations

A python library for metabolic networks sampling and analysis

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

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

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

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

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

Translator of spreadsheet mappings into R2RML, RML or YARRRML

The Microbiome Interpretable Temporal Rule Engine

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

A library to build and execute typed scientific workflows

Fitness landscape exploration sandbox for biological sequence design.

Spatial alignment of single cell transcriptomic data.

Some of the projects i made when starting to learn R for Data Science at the university

Clustering scRNAseq by genotypes

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

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

python Parameter EStimation TOolbox

CPM implementation in pure JavaScript

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

A Curated List of Computational Biology Datasets Suitable for Machine Learning

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

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.

Workshop in omics integration and systems biology

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

Predicting protein structure through sequence modeling

The Common Core Ontology Repository holds the current released version of the Common Core Ontology suite.

The consensus GEM for Saccharomyces cerevisiae

DeepChem 2017: Deep Learning & NLP for Computational Chemistry, Biology & Nano-materials

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

🧬 An R package for visualizing molecular data in 3D

A research data management plugin for the Git version control system.

A curated list of awesome computational cryo-EM methods.

Streamlining SLAM-seq analysis with ultra-high sensitivity

Framework and command-line tools for integrating FollowTheMoney data streams from multiple sources

A Go package for engineering organisms.

A bioinformatics API and web-app to integrate multi-omics datasets & interface with public databases.

This is the main repository for the HackBio'2020 Virtual Internship Experience ❤️

Syntax highlighting for computational biology

pyQms, generalized, fast and accurate mass spectrometry data quantification

WInte.r is a Java framework for end-to-end data integration. The WInte.r framework implements well-known methods for data pre-processing, schema matching, identity resolution, data fusion, and result evaluation.

Robust and scalable inference of cell lineages from gene expression data.

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

Ultrafast sequence typing and gene detection from NGS raw reads

Powerful RDF Knowledge Graph Generation with [R2]RML Mappings

RSS Reader for Android with article filtering and curation

Keras implementation of path-based link prediction model for knowledge graph completion