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@DD-DeCaF Data-Driven Design of Cell Factories and Communities

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    62 repositories

    • caffeine-tombstone

      Public
      Placeholder website with information on what happened to Caffeine
      CSS
      •
      Apache License 2.0
      •0•1•0•0•Updated Aug 7, 2024Aug 7, 2024

    • memote-service-frontend

      Public
      Vue single page application for uploading models and viewing reports.
      Vue
      •
      Apache License 2.0
      •0•2•2•25•Updated Jan 4, 2023Jan 4, 2023

    • caffeine-vue

      Public
      Caffeine frontend, a state-of-the-art web platform which puts model-guided and data-driven design into practice in industrial biotechnology.
      Vue
      •
      Apache License 2.0
      •2•5•15•30•Updated Jan 3, 2023Jan 3, 2023

    • caffeine-vue-upload-mockup

      Public
      Vue
      •
      Apache License 2.0
      •0•0•0•23•Updated Jan 3, 2023Jan 3, 2023

    • tutorials

      Public
      Teaching materials for cobrapy, cameo, escher and DD-DeCaF
      Jupyter Notebook
      •14•28•0•0•Updated Jul 12, 2022Jul 12, 2022

    • escher

      Public
      Build, view, share, and embed pathway maps.
      JavaScript
      •
      Other
      •79•0•5•0•Updated Jul 6, 2022Jul 6, 2022

    • website

      Public
      DD-DeCaF Website
      JavaScript
      •
      MIT License
      •1•0•1•0•Updated Jun 23, 2022Jun 23, 2022

    • memote-webservice

      Public
      The backend for the MEMOTE web service.
      testmodelsuite
      testmodelsuitemetabolic
      Python
      •
      Apache License 2.0
      •3•0•1•0•Updated Oct 23, 2021Oct 23, 2021

    • id-mapper

      Public
      ID mapper for biological entities (metabolites, reactions, genes, etc)
      Python
      •
      Apache License 2.0
      •1•5•5•2•Updated Jul 21, 2021Jul 21, 2021

    • wsgi-base

      Public
      Base Docker image(s) for WSGI microservices in the DD-DeCaF organization
      Makefile
      •
      Apache License 2.0
      •0•0•1•1•Updated Jul 21, 2021Jul 21, 2021

    • design-storage

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•1•Updated Dec 8, 2020Dec 8, 2020

    • map-storage

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•1•Updated Dec 8, 2020Dec 8, 2020

    • model-storage

      Public
      The storage for metabolic models used by the platform
      Python
      •
      Apache License 2.0
      •0•0•0•1•Updated Dec 8, 2020Dec 8, 2020

    • metabolic-ninja

      Public
      Predict heterologous pathways for the given organism and chemical of interest
      Python
      •
      Apache License 2.0
      •1•1•0•1•Updated Dec 8, 2020Dec 8, 2020

    • warehouse

      Public
      The storage for the experimental data used for modeling: omics, strains, media etc
      Python
      •
      Apache License 2.0
      •0•0•1•1•Updated Dec 8, 2020Dec 8, 2020

    • simulations

      Public
      Model service which takes care of adjusting model according to incoming messages and returns information such as fluxes, theoretical maximum yields, etc
      Python
      •
      Apache License 2.0
      •1•0•0•2•Updated Dec 8, 2020Dec 8, 2020

    • iam

      Public
      Identity and access management
      Python
      •
      Apache License 2.0
      •0•1•0•1•Updated Dec 8, 2020Dec 8, 2020

    • caffeine-bootstrap

      Public
      Makefile
      •
      Apache License 2.0
      •1•4•0•0•Updated Aug 18, 2020Aug 18, 2020

    • metanetx

      Public
      Python
      •
      Apache License 2.0
      •0•0•2•0•Updated May 29, 2020May 29, 2020

    • tag-spy-docker

      Public
      Provide the tag-spy tool in a minimal Python 3.7 Docker image.
      Makefile
      •
      Apache License 2.0
      •0•0•0•0•Updated May 29, 2020May 29, 2020

    • tag-spy

      Public
      Identify the latest DD-DeCaF tag on a particular Docker image.
      dockerdocker-imagetag
      dockerdocker-imagetagdocker-tags
      Python
      •
      Apache License 2.0
      •0•0•1•0•Updated May 29, 2020May 29, 2020

    • modeling-base

      Public
      Base Docker image(s) for metabolic modeling with proprietary solvers.
      Dockerfile
      •
      Apache License 2.0
      •0•0•1•0•Updated May 26, 2020May 26, 2020

    • postgres-base

      Public
      Base Docker image for WSGI microservices with postgres dependencies.
      Makefile
      •
      Apache License 2.0
      •0•0•0•0•Updated May 26, 2020May 26, 2020

    • contributions

      Public
      Measure code contributions to a GitHub organization's repositories.
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated May 16, 2020May 16, 2020

    • cookiecutter-flask-microservice

      Public
      A cookiecutter template for creating microservices with Flask-RESTPlus.
      Python
      •
      Apache License 2.0
      •0•2•1•0•Updated Apr 30, 2020Apr 30, 2020

    • cloudsql-proxy

      Public
      Apache License 2.0
      •0•0•0•0•Updated Feb 27, 2020Feb 27, 2020

    • prometheus

      Public
      Shell
      •
      Apache License 2.0
      •0•0•0•0•Updated Jul 5, 2019Jul 5, 2019

    • bigg-proxy

      Public
      Simple nginx proxy in and the corresponding Dockerfile to relay calls securely to the bigg API
      Shell
      •
      Apache License 2.0
      •0•0•0•0•Updated Jul 5, 2019Jul 5, 2019

    • caffeine-angular

      Public archive
      TypeScript
      •
      Apache License 2.0
      •0•1•1•0•Updated May 24, 2019May 24, 2019

    • pip-compile

      Public
      A minimal Docker image that provides pip-tools in order to lock Python dependencies.
      Makefile
      •
      Apache License 2.0
      •0•0•0•0•Updated Apr 25, 2019Apr 25, 2019
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