Projects in Awesome Lists tagged with biology

https://github.com/deepchem/deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

biology deep-learning drug-discovery hacktoberfest materials-science quantum-chemistry

Last synced: 29 Sep 2024

https://github.com/openworm/openworm

Repository for the main Dockerfile with the OpenWorm software stack and project-wide issues

biology elegans openworm simulation

Last synced: 01 Oct 2024

https://github.com/Revolutionary-Games/Thrive

The main repository for the development of the evolution game Thrive.

biology csharp evolution game godot godot-engine sandbox science simulation strategy thrive

Last synced: 01 Aug 2024

https://github.com/revolutionary-games/thrive

The main repository for the development of the evolution game Thrive.

biology csharp evolution game godot godot-engine sandbox science simulation strategy thrive

Last synced: 27 Sep 2024

https://github.com/openworm/OpenWorm

Repository for the main Dockerfile with the OpenWorm software stack and project-wide issues

biology elegans openworm simulation

Last synced: 30 Jul 2024

https://github.com/duerrsimon/bioicons

A library of free open source icons for science illustrations in biology and chemistry

biology chemistry graphics illustration science

Last synced: 05 Aug 2024

https://github.com/mims-harvard/TDC

Therapeutics Commons: Artificial Intelligence Foundation for Therapeutic Science

artificial-intelligence benchmarks bioinformatics biology biomedicine biotech cheminformatics chemistry datasets deep-learning drug-discovery machine-learning medicine precision-medicine therapeutics

Last synced: 01 Aug 2024

https://github.com/kblin/ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

bioinformatics biology command-line download-genomes genbank genomics ncbi python

Last synced: 01 Aug 2024

https://github.com/AstraZeneca/chemicalx

A PyTorch and TorchDrug based deep learning library for drug pair scoring. (KDD 2022)

biology chemistry deep-chemistry deep-learning drug drug-discovery drug-interaction drug-pair geometric-deep-learning geometry graph-neural-network machine-learning pharma polypharmacy pytorch smiles smiles-strings torch torchdrug

Last synced: 31 Jul 2024

https://github.com/kyegomez/AlphaFold3

Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch

ai alphafold artificial-intelligence bio biology biology-ai geneml ml

Last synced: 26 Sep 2024

https://github.com/chainer/chainer-chemistry

Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry

biology chainer chemistry deep-learning graph-convolutional-networks neural-network python

Last synced: 01 Aug 2024

https://github.com/pallada-92/dna-3d-engine

3d engine implementation in DNA code!

3d 3d-engine biology chemical-kinetics chemical-reaction-networks chemical-reactions cube dna in-vitro molecular-biology molecular-programming piperine raymarching real-reactive-programming strand-displacement

Last synced: 01 Aug 2024

https://github.com/biojs/biojs

🔬A library of JavaScript components to represent biological data

biojs biology javascript visualisation

Last synced: 02 Aug 2024

https://github.com/GMOD/jbrowse

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.

bioinformatics biology genome-annotation genome-browser genomics protein-annotation

Last synced: 01 Aug 2024

https://github.com/SciML/Catalyst.jl

Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.

biology chemical-reactions differential-equations dsl gillespie-algorithm julia ode rate-laws reaction-network scientific-machine-learning sciml sde simulation systems-biology systems-biology-simulation

Last synced: 01 Aug 2024

https://github.com/tariqdaouda/pyGeno

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

bed bioinformatics biology cancer cancer-genomes cancer-genomics csv-parser ensembl genome genome-annotation genome-browser genome-sequencing genomes genomics gtf medical medicine proteomics snps vcf

Last synced: 01 Aug 2024

https://github.com/ropensci/taxize

A taxonomic toolbelt for R

api api-wrapper biodiversity biology darwincore data nomenclature r r-package rstats taxize taxonomy

Last synced: 03 Aug 2024

https://github.com/intermine/intermine

A powerful open source data warehouse system

api bioinformatics biology clojure clojurescript data-visualisation data-visualization data-warehouse genetics genomics java lgplv3 open-source opensource perl postgresql python tomcat tomcat8 webservices

Last synced: 01 Oct 2024

https://github.com/maayanlab/clustergrammer

An interactive heatmap visualization built using D3.js

biology clustering d3 heatmap jupyter-notebook jupyter-widget python visualization

Last synced: 27 Sep 2024

https://github.com/MaayanLab/clustergrammer

An interactive heatmap visualization built using D3.js

biology clustering d3 heatmap jupyter-notebook jupyter-widget python visualization

Last synced: 28 Aug 2024

https://github.com/Benjamin-Lee/deep-rules

Ten Quick Tips for Deep Learning in Biology

bioinformatics biology computational-biology data-science deep-learning genomics machine-learning manubot manuscript

Last synced: 02 Aug 2024

https://github.com/sorgerlab/indra

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.

bioinformatics biology computational-biology indra modeling nlp pysb sbml systems-biology

Last synced: 30 Sep 2024

https://github.com/peptoneltd/dspp-keras

Protein order and disorder data for Keras, Tensor Flow and Edward frameworks with automated update cycle made for continuous learning applications.

ai amino-acids biology biotechnology database dataset keras machine-learning polymer prediction protein protein-structure tensorflow

Last synced: 26 Sep 2024

https://github.com/ljvmiranda921/seagull

A Python Library for Conway's Game of Life

artificial-life artificial-life-algorithms biology cellular-automata conways-game-of-life game-of-life mathematics simulation-framework

Last synced: 02 Oct 2024

https://github.com/salvatorera/tutorial

Tutorials on machine learning, artificial intelligence, data science with math explanation and reusable code (in python and R)

artificial-intelligence bioinformatics biology computer-vision convolutional-neural-networks data-science deep-learning graph image machine-learning natural-language-processing nlp python r streamlit streamlit-webapp tutorial tutorials vision-transformer

Last synced: 26 Sep 2024

https://github.com/globalbioticinteractions/globalbioticinteractions

Global Biotic Interactions provides access to existing species interaction datasets

biodiversity bioinformatics biology diet diseases ecoinformatics ecology eol etl-framework food-webs globi parasites pollinators species-interactions

Last synced: 03 Aug 2024

https://github.com/ismms-himc/clustergrammer2

"Dimensionality-increasing" data visualization tool and interactive WebGL Jupyter widget built for single-cell data.

binder binder-ready biology hacktoberfest heatmap javascript jupyter-widgets python regl visualization webgl

Last synced: 31 Jul 2024

https://github.com/chao1224/Geom3D

Geom3D: Geometric Modeling on 3D Structures, NeurIPS 2023

3d 3d-structures ai4science biology chemistry crystals drugs equivariance geometry group invariance material molecules physics proteins symmetry

Last synced: 03 Aug 2024

https://github.com/AstraZeneca/onto_merger

OntoMerger is an ontology alignment library for deduplicating knowledge graph nodes that represent the same domain.

algorithm alignment biological-networks biology graph kg knowledge knowledge-graph mapping ontology ontology-alignment

Last synced: 03 Aug 2024

https://github.com/BioDynaMo/biodynamo

BioDynaMo is a high-performance and modular, agent-based simulation platform.

agent-based agent-based-framework agent-based-modelling biology cancer epidemiology high-performance large-scale modular-design neuroscience parallel simulation

Last synced: 08 Aug 2024

https://github.com/BioJulia/BioStructures.jl

A Julia package to read, write and manipulate macromolecular structures (particularly proteins)

bioinformatics biojulia biology julia pdb protein-structure structural-bioinformatics structural-biology

Last synced: 09 Aug 2024

https://github.com/diegozea/mitos.jl

A Julia package to analyze protein sequences, structures, and evolutionary information

bioinformatics biology coevolution conservation julia-language multiple-sequence-alignment mutual-information pdb pfam protein-evolution protein-sequence-analysis protein-structure proteins sifts structural-bioinformatics

Last synced: 29 Sep 2024

https://github.com/betsee/betse

Bio Electric Tissue Simulation Engine: Mark I

bioelectric biology multiphysics-modeling multiphysics-simulation python science-research simulator

Last synced: 09 Aug 2024

https://github.com/petercollingridge/cell-simulation

Python simulation of a single-celled organism

biology evolution python python27

Last synced: 01 Oct 2024

https://github.com/ecojulia/microbiome.jl

For analysis of microbiome and microbial community data

biology ecology julia-language microbiome

Last synced: 29 Sep 2024

https://github.com/katrinleinweber/PhD-thesis

Experimental tech-demo for PhD thesis in Scientific Markdown; official:

biochemistry biofilm biology citer diatom eds electron-microscopy latex latex-document latexmk make makefile markdown markdown-template microscopy pandoc phd-thesis zotero

Last synced: 08 Aug 2024

https://github.com/katrinleinweber/phd-thesis

Experimental tech-demo for PhD thesis in Scientific Markdown; official:

biochemistry biofilm biology citer diatom eds electron-microscopy latex latex-document latexmk make makefile markdown markdown-template microscopy pandoc phd-thesis zotero

Last synced: 28 Sep 2024

https://saezlab.github.io/mistyR/

Multiview Intercellular SpaTial modeling framework

bioconductor biology intercellular machine-learning modular molecular-biology multiview r spatial spatial-transcriptomics

Last synced: 02 Aug 2024

https://saezlab.github.io/misty

Multiview Intercellular SpaTial modeling framework

bioconductor biology intercellular machine-learning modular molecular-biology multiview r spatial spatial-transcriptomics

Last synced: 22 Aug 2024

https://github.com/biosustain/croissance

Tool for estimating growth rates from microbial growth curves

bioinformatics biology curve-fitting growth-curves

Last synced: 26 Sep 2024

https://github.com/ropensci/worrms

World Register of Marine Species R client

api-wrapper biological-data biology fish jerico-relevant marine-biology marine-species r r-package rstats taxize taxonomy

Last synced: 03 Aug 2024

https://github.com/bayer-science-for-a-better-life/topefind-public

Finding the pitfalls of deep learning predictors of interacting residues in antibodies 🦠

antibodies artificial-intelligence biology deep-learning neural-network protein

Last synced: 26 Sep 2024

https://github.com/georgeoshardo/SyMBac

Accurate segmentation of bacterial microscope images using synthetically generated image data.

biology image-processing microscopy segmentation synthetic-biology

Last synced: 03 Aug 2024

https://github.com/incertae-sedis/smof

Explore and analyze biological sequence data

bioinformatics biology fasta genomics sequence sequence-analysis

Last synced: 02 Aug 2024

https://github.com/LUKE-ZZ/thuthesis-biomedical

清华大学生物，医学，药学等相关专业的毕业论文latex模板。也适用于其他专业。适合本硕博毕业论文和博后报告。本模板在tuna协会的thuthesis项目基础上，增补了和生医药相关同学的内容，也增添了对latex新手更加友好的注释。

biology biomedical latex latex-thesis-template medicine pharmacy tex thuthesis tsinghua tsinghua-university

Last synced: 01 Aug 2024

https://github.com/biojulia/genomicannotations.jl

bioinformatics biology genbank genes genome-annotation gff3 julia

Last synced: 30 Sep 2024

https://github.com/dlesl/gb-io

A Rust library for parsing, writing and manipulating Genbank sequence files

biology genbank rust

Last synced: 02 Oct 2024

https://github.com/mertyildiran/plexus

a novel object-oriented approach to the artificial neural networks inspired by synaptic plasticity between biological neurons

architecture-free artificial-neural-networks bio-inspired biology layerless modular neurons

Last synced: 02 Oct 2024

https://github.com/camilogarciabotero/biomarkovchains.jl

Representing biological sequences as Markov chains

bioinformatics biology dna julia julialang markov-chain

Last synced: 29 Sep 2024

https://github.com/EMODnet/EMODnetWFS

Access EMODnet Web Feature Service data through R

biology dataproducts emodnet marine-data rstats wfs

Last synced: 08 Aug 2024

https://github.com/nelson-gon/cytounet

Deep Learning Based Cell Segmentation

annotations biology cell-biology convolutional-neural-networks dataset deep-learning image-processing image-segmentation image-segmentation-tensorflow images keras-tensorflow pypi python3 segmentation unet-tensorflow

Last synced: 26 Sep 2024

https://github.com/SchmidtDSE/afscgap

Python-based tools for NOAA AFSC GAP marine species surveys data

biodiversity biology fish fisheries noaa

Last synced: 03 Aug 2024

https://github.com/alphonsg/rainbow-optical-flow-for-ali

Automated air liquid interface cell culture analysis using deep optical flow.

bioinformatics biology deep-learning image-analysis optical-flow python pytorch

Last synced: 26 Sep 2024

https://github.com/kolibrid/GeneNet-VR

GeneNet VR: visualization tool for large biological networks

3d bioinformatics biology thesis unity virtual-reality visualization vr

Last synced: 29 Jul 2024

https://github.com/unkindpartition/bamcc

bamcc — split SAM/BAM files into connected components

alignment bioinformatics biology dna rna rna-seq

Last synced: 02 Oct 2024

https://github.com/wagad22/abc-laboratory

ABC-Laboratory is a prototypical simulation software calculating the fluorescence or absorption of different 'biomolecules'. It uses the Godot Game Engive (v.3) and is the result of my Bachelor Hands-on / internship.

absorption biochemistry bioinformatics biology biomolecular-simulation biomolecule chemistry fluorescence godot godot-engine godot-game-engine laboratory laboratory-exercises simulation