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@SD2E Synergistic Discovery and Design

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    82 repositories

    • SYNBICT

      Public
      Synthetic Biology Curation Tools
      Python
      •2•5•37•2•Updated Aug 16, 2026Aug 16, 2026

    • cp-request-api

      Public
      A Python package for structured experimental (aka, challenge problem) requests
      Python
      •
      MIT License
      •0•0•0•1•Updated Apr 13, 2026Apr 13, 2026

    • test-harness

      Public
      GitHub mirror of https://gitlab.sd2e.org/sd2program/test-harness
      Python
      •1•0•0•0•Updated Feb 19, 2024Feb 19, 2024

    • experimental-intent-parser

      Public
      A tool that combines a word-processing interface with structured tables and assisted linking to definitions to provide a simple interface for incremental codifi…
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•4•52•1•Updated May 1, 2023May 1, 2023

    • xplan

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Oct 26, 2022Oct 26, 2022

    • pysd2cat

      Public
      Python SD2 Circuit Analysis Tool
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 27, 2022May 27, 2022

    • performance-metrics

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated May 25, 2022May 25, 2022

    • precomputed-data-table

      Public
      Jupyter Notebook
      •0•1•0•0•Updated May 24, 2022May 24, 2022

    • diagnose

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated May 22, 2022May 22, 2022

    • rna-seq-pipeline

      Public
      This is the automated RNA-seq processing pipeline used by the SD2 program
      Python
      •1•0•0•0•Updated Mar 24, 2022Mar 24, 2022

    • python-datacatalog

      Public
      (Mirror) Python package containing core business logic and helper utilities for Data Catalog
      metadatawebservicemongodb
      metadatawebservicemongodbpython3jsonschema
      Python
      •
      Other
      •0•0•0•0•Updated Dec 1, 2021Dec 1, 2021

    • omics_tools

      Public
      Mirror of SD2E omics_tools
      Python
      •
      MIT License
      •0•2•0•0•Updated Nov 17, 2021Nov 17, 2021

    • opil

      Public
      The Open Protocol Interface Language (OPIL) is intended as a standard language for protocol interfaces
      Python
      •1•5•59•1•Updated Oct 22, 2021Oct 22, 2021

    • jupyteruser-sd2e

      Public archive
      Dockerfile (and build/test support) for extending SD2E Jupyter Notebooks base image
      jupyter-notebookagaveapitacc
      jupyter-notebookagaveapitacc
      Jupyter Notebook
      •
      Other
      •4•1•10•0•Updated May 28, 2021May 28, 2021

    • bacanora

      Public archive
      Accelerated, tenacious versions of key Agave operations
      Python
      •0•0•1•0•Updated May 19, 2021May 19, 2021

    • sbh-metrics

      Public
      Metrics gleaned from SynBioHub
      Python
      •
      MIT License
      •0•0•0•0•Updated May 6, 2021May 6, 2021

    • base-images

      Public archive
      Consolidated repository for building and improving SD2E's various Docker base images
      dockerreactoragaveapi
      dockerreactoragaveapi
      Python
      •
      Other
      •0•1•1•1•Updated May 5, 2021May 5, 2021

    • pipelinejobs-indexer

      Public
      (Mirror) Indexes outputs from a PipelineJob so they are discoverable in the Data Catalog
      Python
      •0•0•0•1•Updated May 3, 2021May 3, 2021

    • OPIL-specification

      Public
      Open Protocol Interface Language (OPIL) specification document
      TeX
      •1•0•1•1•Updated Apr 22, 2021Apr 22, 2021

    • rsync-work-app

      Public archive
      Tapis app that uses rsync on a personal executionSystem to migrate your /work directory to /work2
      Shell
      •0•0•0•0•Updated Apr 14, 2021Apr 14, 2021

    • CDM

      Public
      Mirror of SD2E CDM
      Jupyter Notebook
      •0•1•0•0•Updated Apr 14, 2021Apr 14, 2021

    • pipelinejobs-manager

      Public
      (Mirror) Manages creation and management of, as well as updates to, Pipelines system jobs.
      metadataworkflowreactor
      metadataworkflowreactor
      Python
      •0•0•0•1•Updated Mar 25, 2021Mar 25, 2021

    • sd2e-cli

      Public archive
      Command line interface for SD2E-tailored version of TACC Cloud API
      Shell
      •
      Other
      •3•1•13•0•Updated Feb 1, 2021Feb 1, 2021

    • synbiohub_adapter

      Public
      metadatapython3
      metadatapython3
      Python
      •
      MIT License
      •2•1•13•1•Updated Jan 21, 2021Jan 21, 2021

    • app-proteowizard

      Public
      Shell
      •0•0•0•0•Updated Jan 13, 2021Jan 13, 2021

    • app-genomics-pipeline

      Public
      Shell
      •0•0•0•0•Updated Jan 13, 2021Jan 13, 2021

    • app-thermorawfileparser

      Public
      Shell
      •0•0•0•0•Updated Jan 13, 2021Jan 13, 2021

    • app-sipros

      Public
      Shell
      •0•0•0•0•Updated Jan 13, 2021Jan 13, 2021

    • experimental-intent-parser-mw

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jun 22, 2020Jun 22, 2020

    • build_request_parser

      Public
      Python
      •0•1•0•0•Updated May 18, 2020May 18, 2020
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