Biology

Open-source projects categorized as Biology
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Topics: Bioinformatics Genomics Simulation Python Science
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Top 23 Biology Open-Source Projects

  • deepchem

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

  • Thrive

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

    • Project mention: Was, um Himmels willen, ist das? Super aggressiver Käfer. | /r/de | 2023-07-07

  • InfluxDB

    Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

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  • OpenWorm

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

    • Project mention: The baffling intelligence of a single cell: The story of E. coli chemotaxis | news.ycombinator.com | 2024-03-21

    So I have three thoughts about this.

    The first is cell specialization, particularly neurons. It seems like nature really came up with a universal neuron. There aren't neurons for eyesight vs thinking, etc. They've experimented with this on frogs where they've reweired the optic nerve to a different part ofd the brain and the frog seems to see just fine. They've even added an eye and the frog seems to cope and use it just fine.

    The second is the OpenWorm project [1]. This is an attempt to simulate a relatively simple organism with IIRC ~280 neurons. Despite lots of effort, the simulated version just doesn't match up to the real thing. In artificial neural networks we have a stupidly simplified model of neurons that tends to get reduced to a binary signal and an activation function. Thius can do a lot but it's clearly wholly inadequate for any realistic modelling. The protein interactions in a cell are mind-bogglingly complex.

    The third is the three-body problem. To summarize, we have a general solution for the grvity interactions of two bodies. Add one more and we don't. We have classes of solutions but no general solution. This is why JPL needs to use supercomputers to calculate flight plans with a relatively low number of bodies. We see a relatively simple set of interactions lead to massive complexity with protein folding. I imagine that it just won't be computationally viable to simulate even a single realistic cell given all th einteractions that go on. We're simply left to make estimations.

    [1]: https://openworm.org/

  • ncbi-genome-download

    Scripts to download genomes from the NCBI FTP servers

  • chemicalx

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

  • Vcflib

    C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

  • jvarkit

    Java utilities for Bioinformatics

  • WorkOS

    The modern identity platform for B2B SaaS. The APIs are flexible and easy-to-use, supporting authentication, user identity, and complex enterprise features like SSO and SCIM provisioning.

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  • SeqAn

    SeqAn's official repository.

  • 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.

  • BioAmp-EXG-Pill

    BioAmp EXG Pill is a small and elegant Analog Front End (AFE) board for BioPotential signal acquisition.

  • seagull

    A Python Library for Conway's Game of Life

  • pydna

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

  • BioSequences.jl

    Biological sequences for the julia language

  • Sandboxels

    Sandboxels is an in-browser falling sand simulation game, with mechanics such as heat simulation, electricity, density, chemical reactions, fire, and over 500 unique elements to play with.

    • Project mention: R74n | news.ycombinator.com | 2024-04-23

    It may be better to post the project https://sandboxels.r74n.com/ instead of the whole site. Do you want to post it?

  • biobear

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

  • Wham

    Structural variant detection and association testing

  • full_spectrum_bioinformatics

    An open-access bioinformatics text

  • aquarium

    The Aquarium Lab Operating System (by aquariumbio)

  • betse

    Bio Electric Tissue Simulation Engine: Mark I

  • Swate

    Excel Add-In for annotation of experimental data and computational workflows.

  • cas

    Cellular Automata Simulator (by ghjansen)

  • gazelle

    BioTorrents.de’s version of Gazelle (by biotorrents)

  • mosquito-eradication

    Document practical ways of eradicating mosquitoes from open-air areas

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NOTE: The open source projects on this list are ordered by number of github stars. The number of mentions indicates repo mentiontions in the last 12 Months or since we started tracking (Dec 2020).

Biology related posts

Index

What are some of the best open-source Biology projects? This list will help you:

Project Stars
1 deepchem 5,102
2 Thrive 2,580
3 OpenWorm 2,254
4 ncbi-genome-download 887
5 chemicalx 700
6 Vcflib 595
7 jvarkit 467
8 SeqAn 457
9 Catalyst.jl 421
10 BioAmp-EXG-Pill 236
11 seagull 168
12 pydna 152
13 BioSequences.jl 146
14 Sandboxels 133
15 biobear 120
16 Wham 98
17 full_spectrum_bioinformatics 67
18 aquarium 57
19 betse 49
20 Swate 29
21 cas 28
22 gazelle 18
23 mosquito-eradication 17

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