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@ucl-cssb Computational Systems and Synthetic Biology, UCL

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    24 repositories

    • flopr

      Public
      An R package for the processing of plate reader and flow cytometry data. This includes: normalisation and calibration of plate reader data, and removing debris and doublets and calibration of flow cytometry data.
      calibrationfluorescenceflow-cytometrynormalisationmicroplate-readerplate-reader
      R
      •
      GNU General Public License v3.0
      •6•10•0•0•Updated Aug 12, 2025Aug 12, 2025

    • MIMIC

      Public
      Modelling and Inference of MICrobiomes Project (MIMIC) is a Python package dedicated to simulate, model, and predict microbial communities interactions
      biologysynthetic-biologymodelingcomputational-biologymicrobial-communitiesmicrobiomeregression-modelsconsortiumsynthetic-dataset-generation
      Python
      •
      MIT License
      •0•8•15•0•Updated Jul 21, 2025Jul 21, 2025

    • CIN_SV

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Jul 15, 2025Jul 15, 2025

    • genome_minimizer

      Public
      Python
      •
      Other
      •1•0•0•0•Updated Jul 7, 2025Jul 7, 2025

    • cneta

      Public
      Copy Number Evolutionary Tree Analysis
      C++
      •
      GNU General Public License v3.0
      •0•5•1•0•Updated Apr 24, 2025Apr 24, 2025

    • DeepCNA

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Feb 19, 2025Feb 19, 2025

    • ucl-cssb.github.io

      Public
      CSS
      •
      Other
      •0•0•0•0•Updated Feb 14, 2025Feb 14, 2025

    • colony-com

      Public
      Diffusion model of a system where sender strains produce AHL in the presence of arabinose. AHL diffuses and activates GFP production in receiver strains
      Python
      •
      MIT License
      •7•0•0•0•Updated Nov 20, 2024Nov 20, 2024

    • DODL

      Public
      DODL: digital optimisation of diffusible logic
      Python
      •1•0•0•0•Updated Apr 5, 2023Apr 5, 2023

    • worm_neural_nets

      Public
      Python
      •1•0•0•0•Updated Feb 1, 2023Feb 1, 2023

    • Spatial-Computing

      Public
      Python
      •1•0•0•0•Updated Sep 20, 2022Sep 20, 2022

    • RED

      Public
      Reinforcment learning for Experimental Design
      Python
      •
      MIT License
      •6•3•0•0•Updated Apr 6, 2022Apr 6, 2022

    • CIN_CRC

      Public
      C++
      •1•0•0•0•Updated Dec 8, 2021Dec 8, 2021

    • experimentDB

      Public
      Simple experimental data management
      R
      •0•1•0•0•Updated Oct 27, 2021Oct 27, 2021

    • CIN_PDO

      Public
      Roff
      •
      MIT License
      •0•0•0•0•Updated May 14, 2021May 14, 2021

    • simulate_cell_growth

      Public
      C++
      •
      MIT License
      •0•1•0•0•Updated Apr 27, 2021Apr 27, 2021

    • WCM_plasmid_loss

      Public
      Python
      •0•0•0•0•Updated Mar 29, 2021Mar 29, 2021

    • AutoCD

      Public
      Automated synthetic microbial Community Design
      C++
      •4•13•0•0•Updated Mar 26, 2021Mar 26, 2021

    • ROCC

      Public
      ROCC: Reinforcement learning for the Optimisation of Co-Cultures
      Python
      •
      MIT License
      •3•11•0•0•Updated Nov 17, 2020Nov 17, 2020

    • sv-model

      Public
      A package that generates and models the evolution of structural variation in cancer genomes through multiple cell cycles, aimed at elucidating the mechanisms behind large scale error events such as chromothripsis.
      Python
      •1•0•0•0•Updated Sep 10, 2020Sep 10, 2020

    • synbioweaver

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 1, 2018Sep 1, 2018

    • ABC-Flow

      Public
      Python
      •2•1•0•0•Updated Aug 12, 2018Aug 12, 2018

    • StabilityFinder

      Public
      Main code area
      Python
      •0•1•0•0•Updated Oct 3, 2016Oct 3, 2016

    • wavelength2colour

      Public
      Convert a numeric wavelength to an RGB or Hex colour
      R
      •0•2•0•0•Updated Sep 2, 2016Sep 2, 2016