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123 search results found

Graphein ⭐ 932

Protein Graph Library

Diffdock ⭐ 686

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

A high-performance, Pythonic language for bioinformatics

Dash Cytoscape ⭐ 555

Interactive network visualization in Python and Dash, powered by Cytoscape.js

Biotite ⭐ 515

A comprehensive library for computational molecular biology

Openchem ⭐ 450

OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research

Cobrapy ⭐ 414

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

A toolbox for integrated information theory.

DANCE: A Deep Learning Library and Benchmark Platform for Single-Cell Analysis

Geodiff ⭐ 211

Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022).

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

Variational Autoencoder for Dimensionality Reduction of Time-Series

Metagem ⭐ 155

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

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

Clairvoyante ⭐ 142

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

Pterasoftware ⭐ 136

Ptera Software is a fast, easy-to-use, and open-source software package for analyzing flapping-wing flight.

Souporcell ⭐ 134

Clustering scRNAseq by genotypes

Python library for reading, writing, and converting computational chemistry file formats and generating input files.

Dna2vec ⭐ 103

dna2vec: Consistent vector representations of variable-length k-mers

Python_biologist ⭐ 101

Python Programming for Biologists

Race and ethnicity Imputation from Disease history with Deep LEarning

Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling

Diffdock Pp ⭐ 73

Implementation of DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models in PyTorch (ICLR 2023 - MLDD Workshop)

A Python-based Effective Feature Generation Tool from DNA, RNA, and Protein Sequences

Cassiopeia ⭐ 67

A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction

Source code for "Molecular Mechanics-Driven Graph Neural Network with Multiplex Graph for Molecular Structures"

Biosimspace ⭐ 64

Code and resources for the EPSRC BioSimSpace project.

Pyscreener ⭐ 56

pythonic interface to virtual screening software

NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions

B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference, and affinity prediction

Biosimspace ⭐ 48

An interoperable Python framework for biomolecular simulation.

C.origami ⭐ 47

C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.

Glycowork ⭐ 46

Package for processing and analyzing glycans and their role in biology.

FABind: Fast and Accurate Protein-Ligand Binding (NeurIPS 2023)

Cell2cell ⭐ 44

User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins

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!

Physics Aware Multiplex Gnn ⭐ 35

Code for our Nature Scientific Reports paper "A universal framework for accurate and efficient geometric deep learning of molecular systems"

Python implementation of Spatial Analysis of Functional Enrichment (SAFE)

Pycontact ⭐ 34

Analysis of non-covalent interactions in MD trajectories

Myokit: A simple interface to cardiac cellular electrophysiology

Python API for the Interactive Tree of Life (iTOL)

Interpretable genotype-phenotype landscape modeling

Contact_map ⭐ 31

Contact map analysis for biomolecules; based on MDTraj

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.

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

An Artificial Neural Network-based discriminator for validating clinically significant genomic variants

BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations (EMNLP 2023)

Im2im Uq ⭐ 29

Image-to-image regression with uncertainty quantification in PyTorch. Take any dataset and train a model to regress images to images with rigorous, distribution-free uncertainty quantification.

Python libraries and utilities for computational biology

Straindesign ⭐ 27

StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy

pyQms, generalized, fast and accurate mass spectrometry data quantification

Create WDL documentation using Markdown.

Regulatory Prediction ⭐ 24

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

A Python Framework for Modeling and Analysis of Signaling Systems

The Microbiome Interpretable Temporal Rule Engine

Patchsim ⭐ 21

Code for simulating the metapopulation SEIR model. Sample network for US national simulation included.

Smart search engine for all bioinformatics databases worldwide

KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.

Screenlamp ⭐ 18

screenlamp is a Python toolkit for hypothesis-driven virtual screening

Slamdunk ⭐ 18

Streamlining SLAM-seq analysis with ultra-high sensitivity

Biosemble ⭐ 17

AI assembly of bioNLP wordnets

A Python toolkit for setting up benchmarking dataset using biomedical networks

SLIP is a sandbox environment for engineering protein sequences with synthetic fitness functions.

MuRaL is a deep learning framework for estimating single-nucleotide mutation rates across the genome.

Diff Evol Tree Search ⭐ 15

We introduce a differentiable approach to phylogenetic tree construction, optimizing tree and ancestral sequences in its original representation itself, thus requiring no prior training data.

Patient-Specific Modeling in Python

Brendapyrser ⭐ 14

A Python parser for the BRENDA database

Hypothesis Bio ⭐ 14

Hypothesis extension for computational biology

pyABC: distributed, likelihood-free inference

Query sequence database by HMMs arranged in predefined synteny structure

Bioinformatics Conf Vids ⭐ 13

List of conferences with talk videos posted online

Toolchest Client Python ⭐ 13

Toolchest Python client

Biosimulators ⭐ 13

Registry of containerized biosimulation tools that support a standard command-line interface

Clair3 Trio ⭐ 12

Clair3-Trio: variant calling in trio using Nanopore long-reads

A Tutorial for Parallelised Scalable Simulations in TensorFlow

Phylotoast ⭐ 12

Tools for phylogenetic data analysis including visualization and cluster-computing support.

Ammolite ⭐ 12

Visualize structure data from Biotite with PyMOL

Keypoint Diffusion ⭐ 12

A diffusion model for structure-based drug design with faster inference from learned representations of protein structure.

Repository for my research on generative modelling of cell images

Isambard ⭐ 11

Intelligent System for Analysis, Model Building And Rational Design of biomolecules.

An implementation of the Locally Scaled Diffusion Map (LDFMap) dimensionality reduction technique.

CONNET: Accurate Genome Consensus in Assembling Nanopore Sequencing Data via Deep Learning

Pgp_reconstruction ⭐ 10

Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models

Zincbinddb ⭐ 10

The database and API backend for ZincBind - the database of zinc binding sites

Codebase of the paper "Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling" (ICLR 2024)

A bare metal Python library for building and manipulating protein molecular structures

Ngsderive ⭐ 10

Forensic analysis tool useful in backwards computing information from next-generation sequencing data.

Discovering de novo shared transcriptional programs in single cancer cells

Py4lifesci ⭐ 9

Code repository for the book "Python for the Life Sciences" by Lancaster & Webster

This python code creates hybrid MD/MC (NAMD/GOMC) simulations for the NVT, NPT, GCMC, and GEMC-NVT ensembles

PCA on Genotypes

Intro_to_wc_modeling ⭐ 9

Whole-cell modeling tutorials

Multi-Atom Structure/Selection Toolkit with Interaction Capabilities

Scripts to prepare and analyze molecular dynamics simulations

Siteinterlock ⭐ 8

A toolkit for predicting the binding mode of small molecules interacting with proteins based on interfacial rigidification, as assessed by graph theoretic constraint counting on the covalent and noncovalent bond network. Raschka et al. (2016) Proteins: Structure, Function, and Bioinformatics

Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics

Embeddings to Network Alignment - align biological networks between two species

Team Greider ⭐ 8

Main repository for the HackBio'2021 Virtual Internship Experience for #Team-Greider ❤️

MD DaVis: A python package to analyze molecular dynamics trajectories of proteins

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