65 Open source projects that are alternatives of or similar to ball

Predicting protein structure through sequence modeling

A curated list of awesome computational cryo-EM methods.

Python for chemoinformatics

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.

Differentiable molecular simulation of proteins with a coarse-grained potential

VSCode Extension for interactively visualising protein structure data in the editor

🧬 An R package for visualizing molecular data in 3D

Streamlining SLAM-seq analysis with ultra-high sensitivity

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

A Julia package to view macromolecular structures in the REPL, in a Jupyter notebook/JupyterLab or in Pluto

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

Webpage of the Bonvinlab @ Utrecht University and HADDOCK software

A python package for graph kernels, graph edit distances, and graph pre-image problem.

Rosetta FunFolDes – a general framework for the computational design of functional proteins.

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

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

A library to build and execute typed scientific workflows

A Go package for engineering organisms.

STAPLE (Shared Tools for Automatic Personalised Lower Extremity modelling) consists of a collection of methods for generating skeletal models from three-dimensional bone geometries, usually segmented from medical images. The methods are currently being expanded to create complete musculoskeletal models.

An all-atom protein structure dataset for machine learning.

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

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

screenlamp is a Python toolkit for hypothesis-driven virtual screening

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

Collection of scripts for bacterial genomics

Introduction to Applied Mathematics and Informatics in Drug Discovery (AMIDD)

Tool to build force field input files for molecular simulation.

Ultrafast sequence typing and gene detection from NGS raw reads

Syntax highlighting for computational biology

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

CPM implementation in pure JavaScript

pytoda - PaccMann PyTorch Dataset Classes. Read the docs: https://paccmann.github.io/paccmann_datasets/

An R Package for Geneset Enrichment Workflows

A Docker-based, cloudable platform for the development of chemoinformatics-centric web applications and microservices.

Chemoinformatics toolkit with support for inorganic molecules

The Microbiome Interpretable Temporal Rule Engine

Implementation of the paper - Automatic chemical design using a data-driven continuous representation of molecules

A package for atom-typing as well as applying and disseminating forcefields

Fitness landscape exploration sandbox for biological sequence design.

Spatial alignment of single cell transcriptomic data.

Clustering scRNAseq by genotypes

A Chemical Knowledge Graph of What is Common in the World.

pyQms, generalized, fast and accurate mass spectrometry data quantification

organic chemistry reaction prediction using NMT with Attention

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

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

Code and Data to accompany "Dilated Convolutions for Modeling Long-Distance Genomic Dependencies", presented at the ICML 2017 Workshop on Computational Biology

A Curated List of Computational Biology Datasets Suitable for Machine Learning

Repository for spectral neighbor analysis potential (SNAP) model development.

Bayesian tools for fitting molecular mechanics torsion parameters to quantum chemical data.

CReM: chemically reasonable mutations framework

MolEnc: a molecular encoder using rdkit and OCaml.

Chemoinformatics tool for ligand-based virtual screening

Contact map analysis for biomolecules; based on MDTraj

A dependency-free cross-platform swiss army knife for PDB files.

Myokit: A simple interface to cardiac cellular electrophysiology

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

FreeSASA Python Module

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

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!