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    39 repositories

    • CBRdb

      Public
      A curated biochemical database that integrates and refines data from KEGG and ATLAS databases to support precise analyses of biochemical reaction data.
      Python
      •
      MIT License
      •2•12•17•0•Updated Apr 22, 2026Apr 22, 2026

    • assemblytheorytools

      Public
      A centralised set of tools for doing assembly theory calculations
      Python
      •
      MIT License
      •1•5•13•1•Updated Apr 13, 2026Apr 13, 2026

    • assemblycfg

      Public
      Directed string assembly index calculator using smallest grammar algorithm re-pair
      Python
      •
      MIT License
      •0•2•2•0•Updated Mar 5, 2026Mar 5, 2026

    • Patents

      Public
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Mar 25, 2025Mar 25, 2025

    • dagviz

      Public
      Visualization for DAGs
      HTML
      •
      Apache License 2.0
      •6•0•0•0•Updated Jan 27, 2025Jan 27, 2025

    • image-registration

      Public
      Julia source code to stabilize and clean up videos
      Jupyter Notebook
      •0•2•0•0•Updated Nov 20, 2024Nov 20, 2024

    • ecg

      Public
      Pulling information from biological databases, and converting it into easy to use gmls for network science.
      Python
      •
      MIT License
      •2•4•14•2•Updated May 6, 2024May 6, 2024

    • HFSP

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Mar 12, 2024Mar 12, 2024

    • INNLab

      Public
      A python/pytorch package for invertible neural networks
      machine-learninginvertible-neural-networks
      machine-learninginvertible-neural-networks
      Python
      •
      GNU General Public License v3.0
      •7•71•4•0•Updated Jun 19, 2023Jun 19, 2023

    • pyphi-spectrum

      Public
      A toolbox for integrated information theory.
      Jupyter Notebook
      •
      Other
      •105•1•0•0•Updated Feb 10, 2023Feb 10, 2023

    • abfjs

      Public
      A package for reading Axon Binary Format (ABF) files
      JavaScript
      •
      MIT License
      •0•4•0•13•Updated Jan 3, 2023Jan 3, 2023

    • caim

      Public
      A toolkit for analyzing time series extracted from fluorescence imaging data
      JavaScript
      •
      MIT License
      •0•6•17•18•Updated Jan 3, 2023Jan 3, 2023

    • InChI

      Public
      InChI library with CMake build system
      C
      •
      Other
      •0•0•0•0•Updated Mar 3, 2022Mar 3, 2022

    • dglmoore

      Public
      Doug's Slush Repository
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Dec 14, 2021Dec 14, 2021

    • Neet

      Public
      Simulating and analyzing dynamical network models
      networkdynamicsneet
      networkdynamicsneetnetworksciencenetworks-biologynetwork-biology
      Python
      •
      Other
      •10•6•23•3•Updated Dec 14, 2021Dec 14, 2021

    • ImageExplorer.jl

      Public
      A simple tool to explore images generated from simulations
      Julia
      •
      MIT License
      •0•0•0•0•Updated Dec 14, 2021Dec 14, 2021

    • Imogen.jl

      Public
      Imogen is a package for estimating information-theoretic quantities from data
      Julia
      •
      MIT License
      •1•1•0•0•Updated Dec 14, 2021Dec 14, 2021

    • Inform

      Public
      A cross platform C library for information analysis of dynamical systems
      entropyinformation-theorymutual-information
      entropyinformation-theorymutual-informationentropy-ratetransfer-entropyactive-information
      C
      •
      MIT License
      •3•28•15•0•Updated Dec 14, 2021Dec 14, 2021

    • gPID

      Public
      Julia
      •1•1•0•0•Updated Dec 14, 2021Dec 14, 2021

    • fastpathways

      Public
      An implementation and generalization of Thurber's algorithm for orderable assembly spaces
      C++
      •1•1•3•0•Updated Dec 14, 2021Dec 14, 2021

    • Pathways.jl

      Public
      Julia
      •
      MIT License
      •0•1•0•0•Updated Oct 2, 2021Oct 2, 2021

    • Gomen.jl

      Public
      Simulating game-playing agents on a graph
      Julia
      •
      MIT License
      •0•0•0•0•Updated Aug 18, 2021Aug 18, 2021

    • chemevolve

      Public
      Tools for simulating chemical evolution
      Python
      •
      MIT License
      •1•3•0•0•Updated Jul 2, 2021Jul 2, 2021

    • CaimCore.jl

      Public
      A toolkit for analyzing time series extracted from fluorescence imaging data
      Julia
      •
      MIT License
      •0•1•0•0•Updated May 12, 2021May 12, 2021

    • yanborandom

      Public
      Yanbo's random projects
      Mathematica
      •0•0•0•0•Updated Jan 31, 2021Jan 31, 2021

    • parallel-programming-mpi

      Public
      A simple "tutorial" on parallel programming with MPI
      Python
      •0•0•0•0•Updated Aug 14, 2020Aug 14, 2020

    • randomneet

      Public
      A development package for Neet network randomizations.
      Python
      •
      Other
      •0•0•0•0•Updated Feb 18, 2020Feb 18, 2020

    • PyInform

      Public
      A Python Wrapper for the Inform Information Analysis Library
      Python
      •
      MIT License
      •11•57•11•0•Updated Dec 2, 2019Dec 2, 2019

    • informjs

      Public
      A node.js wrapper for the Inform information analysis library
      HTML
      •
      MIT License
      •0•0•0•0•Updated Sep 20, 2019Sep 20, 2019

    • gitting-stuff-done

      Public
      Gitting stuff done... maybe?
      0•2•1•4•Updated Aug 21, 2019Aug 21, 2019
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