Synergistic Discovery and Design

SYNBICT

Synthetic Biology Curation Tools

opil

The Open Protocol Interface Language (OPIL) is intended as a standard language for protocol interfaces

experimental-intent-parser

A tool that combines a word-processing interface with structured tables and assisted linking to definitions to provide a simple interface for incremental codification of experiment designs.

omics_tools

Mirror of SD2E omics_tools

base-images

Consolidated repository for building and improving SD2E's various Docker base images

build_request_parser

CDM

Mirror of SD2E CDM

jupyteruser-sd2e

Dockerfile (and build/test support) for extending SD2E Jupyter Notebooks base image

precomputed-data-table

sd2e-cli

Command line interface for SD2E-tailored version of TACC Cloud API

synbiohub_adapter

xplan

experimental-intent-parser-mw

python-datacatalog

(Mirror) Python package containing core business logic and helper utilities for Data Catalog

rna-seq-pipeline

This is the automated RNA-seq processing pipeline used by the SD2 program

test-harness

GitHub mirror of https://gitlab.sd2e.org/sd2program/test-harness

app-genomics-pipeline

app-proteowizard

app-sipros

app-thermorawfileparser

bacanora

Accelerated, tenacious versions of key Agave operations

cp-request-api

A Python package for structured experimental (aka, challenge problem) requests

diagnose

OPIL-specification

Open Protocol Interface Language (OPIL) specification document

performance-metrics

pipelinejobs-indexer

(Mirror) Indexes outputs from a PipelineJob so they are discoverable in the Data Catalog

pipelinejobs-manager

(Mirror) Manages creation and management of, as well as updates to, Pipelines system jobs.

pysd2cat

Python SD2 Circuit Analysis Tool

rsync-work-app

Tapis app that uses rsync on a personal executionSystem to migrate your /work directory to /work2

sbh-metrics

Metrics gleaned from SynBioHub