kyegomez/AlphaFold3

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

Language: Python - Size: 2.21 MB - Last synced: 8 minutes ago - Pushed: about 10 hours ago - Stars: 292 - Forks: 28

zyxue/zyxue.github.io

My technical blog

Language: SCSS - Size: 5.38 MB - Last synced: about 2 hours ago - Pushed: about 3 hours ago - Stars: 1 - Forks: 0

RNAcentral/rnacentral-webcode

RNAcentral website source code

Language: Python - Size: 38.9 MB - Last synced: about 8 hours ago - Pushed: about 9 hours ago - Stars: 29 - Forks: 8

ghosind/biotools

生物/化学计算工具集

Language: TypeScript - Size: 123 KB - Last synced: about 15 hours ago - Pushed: about 16 hours ago - Stars: 0 - Forks: 0

SysBioChalmers/yeast-GEM

The consensus GEM for Saccharomyces cerevisiae

Language: MATLAB - Size: 67.8 MB - Last synced: about 18 hours ago - Pushed: 2 days ago - Stars: 87 - Forks: 43

chanzuckerberg/czid-web

Infectious Disease Sequencing Platform

Language: TypeScript - Size: 265 MB - Last synced: about 20 hours ago - Pushed: 2 days ago - Stars: 77 - Forks: 22

Pioreactor/pioreactor

Hardware and software for accessible, extensible, and scalable bioreactors. Built on Raspberry Pi.

Language: Python - Size: 7.01 MB - Last synced: about 24 hours ago - Pushed: 1 day ago - Stars: 87 - Forks: 6

cbeier-studio/Xolmis

A free, open source, and multi-platform ornithological data manager, written in Lazarus/FPC.

Language: Pascal - Size: 15.8 MB - Last synced: 27 days ago - Pushed: 27 days ago - Stars: 1 - Forks: 0

johndef64/grpm_bertopic

Language: Jupyter Notebook - Size: 60.1 MB - Last synced: about 9 hours ago - Pushed: 1 day ago - Stars: 0 - Forks: 0

johnmeasey/How-to-write-a-PhD-in-Biological-Sciences

Language: TeX - Size: 66.5 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 1 - Forks: 0

duerrsimon/bioicons

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

Language: Vue - Size: 448 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 1,186 - Forks: 67

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.

Language: Python - Size: 362 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 160 - Forks: 60

globalbioticinteractions/globalbioticinteractions

Global Biotic Interactions provides access to existing species interaction datasets

Language: Java - Size: 150 MB - Last synced: 3 days ago - Pushed: 17 days ago - Stars: 118 - Forks: 17

cmzmasek/forester

forester is a collection of open source libraries of Java and Ruby software for phylogenomics and evolutionary biology research

Language: Java - Size: 126 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 34 - Forks: 15

mcneilco/acas

Language: JavaScript - Size: 46.6 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 11 - Forks: 5

Xyaneon/Xyaneon.Bioinformatics.FASTA

A .NET Standard library for working with FASTA genetic sequence files.

Language: C# - Size: 148 KB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 7 - Forks: 0

jonaspleyer/cellular_raza

Agent-Based modeling tool for cellular simulations

Language: Rust - Size: 127 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 3 - Forks: 0

openworm/OpenWorm

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

Language: Python - Size: 114 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 2,266 - Forks: 179

sanger/sequencescape

Web based LIMS

Language: Ruby - Size: 49.1 MB - Last synced: 27 days ago - Pushed: 29 days ago - Stars: 77 - Forks: 32

deepchem/deepchem

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

Language: Python - Size: 538 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 5,144 - Forks: 1,618

BeckResearchLab/llmao

Combining LLMs with Adverse Outcome Pathway data

Language: Python - Size: 2.45 MB - Last synced: about 9 hours ago - Pushed: about 15 hours ago - Stars: 0 - Forks: 0

BrainAnnex/life123

Dynamical modeling of biological systems in 1, 2 and 3D - incl. diffusion, reactions & compartments (Python, JupyterLab, Plotly)

Language: Jupyter Notebook - Size: 134 MB - Last synced: 1 day ago - Pushed: 3 days ago - Stars: 3 - Forks: 1

ericksamera/abi-sauce

A repo for my introductory bioinformatics toolset.

Language: Python - Size: 143 KB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0

QuackenbushLab/matlab-panda

MATLAB implementation of PANDA & LIONESS algorithms

Language: MATLAB - Size: 4.28 MB - Last synced: 3 days ago - Pushed: almost 5 years ago - Stars: 4 - Forks: 3

ReWire-LLC/rewire_pulse_oximeter_firmware

Firmware for the ReWire pulse oximeter

Language: C++ - Size: 4.32 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0

reiserlab/Modular-LED-Display

This repository collects many existing repositories for Modular LED Displays as submodules and generates a consistent documentation from it. Modular LED Displays are customized display systems used in neuroscientific studies. The displays were initially developed for fly vision, where temporal, spatial, and wavelength sensitivity requires specialized stimuli presentation systems.

Language: HTML - Size: 7.32 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 4 - Forks: 2

BgeeDB/bgee_pipeline

Source code of the Bgee pipeline used to build the Bgee database

Language: Perl - Size: 1020 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 11 - Forks: 4

huangwb8/easySCI

A List of Core SCI Journals For Academics

Language: HTML - Size: 8.67 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 3 - Forks: 0

BiologyTools/BioGTK

A cross platform version of Bio library & program. Bio is a library & program for annotating, & editing various microscopy imaging formats using Bioformats supported images. including whole slide, pyramidal & series.

Language: C# - Size: 146 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 8 - Forks: 2

cogent3/cogent3

Comparative Genomics Toolkit 3

Language: Python - Size: 41.6 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 94 - Forks: 52

datasnakes/OrthoEvolution

An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵

Language: Python - Size: 40.6 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 27 - Forks: 4

reddsky51/scinc

Project Hu.Fr. || 1.freem!nd project-philo ^ 2.exp. vit. hum. ent. 3.Asnt.Vis. #informationisnewmedicine #well-being

Size: 8.78 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 1 - Forks: 0

thomased/thomased.github.io

https://tomwhite.io

Language: SCSS - Size: 186 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 1 - Forks: 1

BjornFJohansson/pydna

Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.

Language: Jupyter Notebook - Size: 47.6 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 155 - Forks: 40

dlopezyse/AI-for-Bio

A free and collaborative space for Machine Learning 🤖 applied to Biology 🧬

Language: Jupyter Notebook - Size: 396 KB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 22 - Forks: 3

jonasoh/spiro

SPIRO is a Smart Plate Imaging Robot

Language: Python - Size: 21 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 7 - Forks: 7

antronerds/r2-training-courses

Size: 24.4 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 2 - Forks: 0

superboom12s/DNA_Data_App

Libreria con diferentes herramientas para manipular los datos de un código de ADN o ARNm y sus respectivas proteínas

Language: Python - Size: 36.1 KB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 2 - Forks: 0

mims-harvard/TDC

Therapeutics Commons: Artificial Intelligence Foundation for Therapeutic Science

Language: Jupyter Notebook - Size: 67.6 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 930 - Forks: 167

BgeeDB/bgee-unil

React code of the Bgee frontend

Language: JavaScript - Size: 48.8 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 1 - Forks: 4

chainer/chainer-chemistry

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

Language: Python - Size: 2.28 MB - Last synced: 3 days ago - Pushed: about 1 year ago - Stars: 611 - Forks: 128

histolab/histolab

Library for Digital Pathology Image Processing

Language: Python - Size: 365 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 339 - Forks: 53

SalvatoreRa/tutorial

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

Language: Jupyter Notebook - Size: 163 MB - Last synced: about 2 hours ago - Pushed: about 22 hours ago - Stars: 120 - Forks: 20

pachterlab/poseidon

poseidon system - open source syringe pumps and microscope for laboratories

Language: Jupyter Notebook - Size: 111 MB - Last synced: about 21 hours ago - Pushed: 10 months ago - Stars: 167 - Forks: 52

dukeofhazardz/bio-detect

Biodetect implements UI for the biodetect-api using React, it harnesses the power of Google's Gemini AI technology to provide detailed descriptions of living organisms, including plants, animals, and insects.

Language: JavaScript - Size: 6.93 MB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 0 - Forks: 0

alandolt/LITOS

LITOS - an easy-to-use tool for optogenetic cell stimulation

Language: C - Size: 36.2 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 10 - Forks: 3

stefanospin7/Progetto_Bioinfo_PLP

Progetto analisi dati Covid-19

Language: Python - Size: 2.09 GB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 4 - Forks: 0

linhaowei1/MolRetrieval

This repo implements many methods to retrieve molecules that are similar to a target molecule from a large molecule corpus.

Language: Python - Size: 36.1 KB - Last synced: 5 days ago - Pushed: 6 days ago - Stars: 1 - Forks: 0

Lattice-Automation/seqviz

a JavaScript DNA, RNA, and protein sequence viewer

Language: TypeScript - Size: 112 MB - Last synced: 5 days ago - Pushed: about 1 month ago - Stars: 213 - Forks: 48

georgeoshardo/SyMBac

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

Language: Python - Size: 155 MB - Last synced: 3 days ago - Pushed: about 2 months ago - Stars: 17 - Forks: 8

BgeeDB/bgee_apps

Source code of the Java Bgee applications

Language: Java - Size: 178 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 2 - Forks: 1

wheretrue/biobear

Work with bioinformatic files using Arrow, Polars, and/or DuckDB

Language: Rust - Size: 1020 KB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 122 - Forks: 7

andschar/taxalook

An R Package and Database containing Information on Organisms

Language: R - Size: 18.6 KB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 1 - Forks: 1

datacarpentry/semester-biology

Forkable teaching materials for course on working with data in R

Language: HTML - Size: 384 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 72 - Forks: 111

maxall41/RustSASA

A Rust library for calculating the SASA/ASA for each atom in a protein. Based on the Shrake & Rupley algorithm.

Language: Rust - Size: 218 KB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 3 - Forks: 0

raghurama123/PyLifeS

A graduate-level elective course: Python Programming for Life Science Students

Language: Jupyter Notebook - Size: 14.8 MB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 6 - Forks: 40

bioDS/lab

Biological Data Science Lab website

Language: HTML - Size: 192 MB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 0 - Forks: 0

matisiekpl/cell-detector

Stupid simple cell extractor from peripheral blood smears 🦀

Language: Python - Size: 8.98 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 0 - Forks: 0

sscansan/genomics_and_GWAS_tutorials

Analysis of SNP variants, derived from chip array genotyping and HTS sequencing

Language: HTML - Size: 26.6 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 1 - Forks: 0

PeptoneLtd/dspp-keras

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

Language: Python - Size: 74.2 KB - Last synced: 8 days ago - Pushed: almost 2 years ago - Stars: 166 - Forks: 21

YogiOnBioinformatics/DAME-Destruction-of-Aqueous-Microfibers-Enzymatically

Destruction of Aqueous Microfibers Enzymatically (DAME): A novel Synthetic Biology systems approach to destroying Polyester-based Microplastic fibers

Size: 7.82 MB - Last synced: 9 days ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

FxllenCode/codont

overcomplicated biology project spaghetti code written at 3 am ¯\_(ツ)_/¯

Language: JavaScript - Size: 34.2 KB - Last synced: 9 days ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

Database-Genius/Database-Genius.github.io

:arrow_right: Preston Hunter: world-class database designer and programmer.

Language: HTML - Size: 5.5 MB - Last synced: 9 days ago - Pushed: over 6 years ago - Stars: 3 - Forks: 2

caleb-collar/caleb-collar

Size: 12.1 MB - Last synced: 9 days ago - Pushed: 7 months ago - Stars: 1 - Forks: 0

jonchang/homebrew-biology

Biology formulae for the Homebrew package manager

Language: Ruby - Size: 215 KB - Last synced: 9 days ago - Pushed: over 2 years ago - Stars: 6 - Forks: 1

BerkeleyLab/matcha

T-cell motility simulator

Language: Fortran - Size: 2.72 MB - Last synced: 9 days ago - Pushed: 3 months ago - Stars: 3 - Forks: 1

Gagniuc/Presentations

This section contains all the original presentations from the supplementary materials related to the book entitled: Algorithms in Bioinformatics: Theory and Implementation. The presentations contain original content related to biology, bioinformatics, genetics, genomics, physics, as well as algorithms or software programming implementations.

Size: 93.3 MB - Last synced: 9 days ago - Pushed: about 2 years ago - Stars: 2 - Forks: 0

Gagniuc/Information-content-vs-percentage

This is a scanner that produces two types of signals. The two signals are calculated from the content of a sliding window. One signal is represented by the self-sequence alignment values and the other is represented by the relative frequency values of Cplus G letters.

Language: HTML - Size: 154 KB - Last synced: 9 days ago - Pushed: about 2 years ago - Stars: 2 - Forks: 0

dhrumilp15/TOPS

My experiences and course work at the enriched math and science TOPS program @ Marc Garneau Collegiate Insitute (Class of '21)

Language: Java - Size: 515 MB - Last synced: 9 days ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

AJWurts/CIRA_ML

CIRA Image Processing and ML

Language: Python - Size: 98.1 MB - Last synced: 9 days ago - Pushed: about 5 years ago - Stars: 1 - Forks: 0

ariG23498/soil_moisture_app Fork of royarg02/soil_moisture_app

For Drip Irrigation

Language: Dart - Size: 497 KB - Last synced: 9 days ago - Pushed: over 4 years ago - Stars: 5 - Forks: 0

ammarfaizi2/pembelahan-sel-a0x1

rxi/Materi Biochemistry/

Language: PHP - Size: 1.21 MB - Last synced: 9 days ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

open-genes/open-genes-frontend

Open Genes is a database of human genes associated with aging and lifespan.

Language: TypeScript - Size: 18.2 MB - Last synced: 9 days ago - Pushed: about 2 months ago - Stars: 8 - Forks: 10

latticescipub/Indian-Journal-of-Advanced-Botany-IJAB- 📦

The Indian Journal of Advanced Botany (IJAB) has ISSN 2582-9475 (online) which is an online, open access, peer reviewed, periodical half yearly international journal.

Size: 2.93 KB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 0 - Forks: 0

conorheffron/normalise-fetalh

Min-Max Normalisation of Fetal Health Data

Language: Python - Size: 13.5 MB - Last synced: 8 days ago - Pushed: 10 days ago - Stars: 1 - Forks: 0

scifir/scifir-units

A C++ library of science for creating scalar, vectorial and field units, angles, coordinates and points, lab numbers, special units like pH, zone ids, astro ids, matrices of units, among other features! (under development)

Language: C++ - Size: 4.67 MB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 2 - Forks: 1

moosa-r/rbioapi

rbioapi: User-Friendly R Interface to Biologic Web Services' API

Language: R - Size: 37.8 MB - Last synced: 8 days ago - Pushed: about 1 month ago - Stars: 17 - Forks: 1

YangLab-um/BiologicalOscillations.jl

A package for researchers working with biological oscillations

Language: Julia - Size: 1.21 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 1 - Forks: 2

olezuzu/Mendelian-Inheritance

Language: Python - Size: 4.88 KB - Last synced: 10 days ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 0

olezuzu/Erbschema

Language: Python - Size: 4.88 KB - Last synced: 10 days ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

Opentrons/opentrons

Software for writing protocols and running them on the Opentrons Flex and Opentrons OT-2

Language: Python - Size: 331 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 384 - Forks: 170

hallvaaw/awesome-biological-image-analysis

A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.

Size: 401 KB - Last synced: 1 day ago - Pushed: 10 days ago - Stars: 93 - Forks: 18

ajsteele/ageless

Data, calculations and text relating to my book, Ageless: The new science of getting older without getting old

Language: HTML - Size: 64.8 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 6 - Forks: 1

lbcb-sci/RiNALMo

RiboNucleic Acid (RNA) Language Model

Language: Python - Size: 326 KB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 21 - Forks: 3

bonaert/specio

Explore the tree of life with Specio and learn about Earth's amazing organisms and animals!

Language: JavaScript - Size: 4.5 MB - Last synced: 11 days ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

Ruibin-Liu/pyuniprot

Store the bioinformatic information in a python object given a Uniprot ID

Language: Python - Size: 229 KB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 3 - Forks: 0

joda01/imagec

Image processor for biological images

Language: C++ - Size: 355 MB - Last synced: 27 days ago - Pushed: 27 days ago - Stars: 2 - Forks: 0

GitData-GA/h5n1

The study focuses on modeling and predicting H5N1 bird flu outbreaks in the United States at the county level, utilizing diverse statistical techniques and machine learning models.

Language: CSS - Size: 123 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 0 - Forks: 1

BiologyTools/BioCore

Bio Library in .NET8. Bio is a library & program for annotating, & editing various microscopy imaging formats using Bioformats supported images. including whole slide, pyramidal & series.

Language: C# - Size: 107 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 2 - Forks: 1

thepadguy/SpheroidSnap

Analysis in Python of photographs of Spheroids from the optical microscope.

Language: Jupyter Notebook - Size: 0 Bytes - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 0 - Forks: 0

dbu9/sciencechronicle.org

Language: HTML - Size: 375 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 0 - Forks: 0

dohlee/spliceai-pytorch

Implementation of SpliceAI, Illumina's deep neural network to predict variant effects on splicing, in PyTorch.

Language: Jupyter Notebook - Size: 150 KB - Last synced: 12 days ago - Pushed: about 1 year ago - Stars: 8 - Forks: 1

th0mr/plasmidcanvas

A simple python plasmid map creator

Language: Python - Size: 5.2 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 1 - Forks: 0

sourceduty/Biologically_Engineered

🧫 Biologically engineered systems, organisms and beings.

Size: 373 KB - Last synced: 12 days ago - Pushed: 13 days ago - Stars: 0 - Forks: 0

xindong95/DEAP

Differential Expression Analysis Pipeline

Language: Python - Size: 215 KB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 0 - Forks: 1

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.

Language: Julia - Size: 2.31 GB - Last synced: about 18 hours ago - Pushed: 1 day ago - Stars: 422 - Forks: 71

vansdardy/UBC-Note-Collections

This is a collection of academic notes on courses I have taken at UBC.

Language: HTML - Size: 197 MB - Last synced: 12 days ago - Pushed: 13 days ago - Stars: 1 - Forks: 0

reymond-group/smilesDrawer

A small, highly performant JavaScript component for parsing and drawing SMILES strings. Released under the MIT license.

Language: JavaScript - Size: 18 MB - Last synced: 12 days ago - Pushed: 4 months ago - Stars: 400 - Forks: 63

Francis-B/Kiwi

Fast regex-based protein digestion and unique peptides finder tool

Language: Python - Size: 6.83 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 0 - Forks: 0

sourceduty/Health

⚕️ Anatomy, medicine, and computational science.

Size: 13.3 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 0 - Forks: 0