Data Biosphere (@DataBiosphere)

Top repositories

1

toil

A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.
Python
896
star
2

dsub

Open-source command-line tool to run batch computing tasks and workflows on backend services such as Google Cloud.
Python
262
star
3

terra-ui

Web user interface for the Terra platform
TypeScript
52
star
4

leonardo

Notebook service
Scala
44
star
5

terra-docker

Jupyter Notebook
27
star
6

job-manager

Job Manager API and UI for interacting with asynchronous batch jobs and workflows.
TypeScript
26
star
7

terra-interoperability-model

Common data model proposal for biomedical research intended to facilitate and encourage data sharing and reuse
Python
19
star
8

terra-workspace-manager

Java
14
star
9

jade-data-repo

The Terra Data Repository built by the Jade team.
Java
13
star
10

topmed-workflows

a place for topmed workflows
WDL
12
star
11

terra-cli

Java
11
star
12

data-browser

Jupyter Notebook
11
star
13

data-explorer

JavaScript
10
star
14

consent

Broad Institute Data Use Oversight System
Java
9
star
15

data-portal

TypeScript
9
star
16

duos-ui

Broad Institute Data Use Oversight System
JavaScript
9
star
17

consent-ontology

Broad Institute Data Use Oversight System
Java
7
star
18

terra-notebook-utils

Utilities for the Terra notebook environment.
Python
7
star
19

bgzip

Fast streams for block gzip files.
Python
7
star
20

terra-examples

Examples for use in data analysis.
Jupyter Notebook
7
star
21

azul

Metadata indexer and query service used for AnVIL, HCA, LungMAP, and CGP
Python
6
star
22

getm

Concurrent reads of HTTP URL addressed data
Python
6
star
23

terra-landing-zone-service

Java
6
star
24

analysis_pipeline_WDL

Collection of WDL workflows based off the University of Washington TOPMed DCC Best Practices for GWAS. The WDL structure was based upon CWLs written by the Seven Bridges development team.
WDL
6
star
25

hca-ingest

Python
5
star
26

terra-app

Shell
5
star
27

FHIR

Broad FHIR is a FHIR Server that powers applications for Genomics research.
JavaScript
5
star
28

sync-github-labels

Synchronize Github issue and PR labels between two repositories
Python
5
star
29

terra-cloud-resource-lib

Java
5
star
30

terra-resource-buffer

Terra Resource Buffering Service
Java
4
star
31

terra-external-credentials-manager

Java
4
star
32

terra-axon-examples

Example notebooks and documentation for working with the Terra Axon UI.
4
star
33

terra-billing-profile-manager

Java
4
star
34

terra-workspace-data-service

Java
4
star
35

terra-java-project-template

Java
4
star
36

herzog

Version control, test, and CI/CD your Python Jupyter notebooks.
Python
4
star
37

jade-data-repo-ui

UI for the Jade Data Repo
TypeScript
4
star
38

data-explorer-indexers

Python
4
star
39

bard

Metrics collection service
JavaScript
3
star
40

consent-data-use

Shell
3
star
41

encode-ingest

Batch ETL pipeline to mirror ENCODE data into the Jade Data Repository.
Scala
3
star
42

welder

Scala
3
star
43

clinvar-ingest

Batch ETL pipeline to mirror ClinVar releases into the Jade Data Repository.
Scala
3
star
44

xsamtools

Lightly modified versions of htslib and bcftools to merge VCF streams.
Python
3
star
45

terra-policy-service

Java
3
star
46

data-store

AWS and GCP data storage system for genomic data.
Python
3
star
47

calhoun

Notebook preview service
Jupyter Notebook
3
star
48

terra-azure-relay-listeners

Java
3
star
49

consent-ui

Broad Institute Data Use Oversight System
HTML
3
star
50

commons-sample-data

A repo to track various TOPMed and other datasets
Python
2
star
51

github-actions

Data Biosphere GitHub Actions
Shell
2
star
52

wdl-conformance-tests

WDL
2
star
53

topmed-workflow-variant-calling

WDL
2
star
54

saturn-ui-prod-deploy

Terra UI automated prod deploy service
JavaScript
2
star
55

cbas

Java
2
star
56

biocore-data-model

BioCore Data Model
Jupyter Notebook
2
star
57

tanagra

Repo for the Tanagra service being developed by the All of Us DRC
Java
2
star
58

terra-aws-resource-discovery

Java
2
star
59

firecloud-app

2
star
60

terra-drs-hub

Java
2
star
61

terra-axon-ui

Repository for the Terra "Axon" UI
TypeScript
2
star
62

kernel-service-poc

Java
2
star
63

featured-notebooks

Python
2
star
64

dos-azul-lambda

Provides access to DSS azul-index in the Data Object Service schemas
Jupyter Notebook
2
star
65

rex

Survey response service
JavaScript
2
star
66

terra-gcs-bq-streaming-functions

Java
2
star
67

stairway

Stairway saga transaction processor library
Java
2
star
68

terra-resource-janitor

Janitor service to cleanup resources created by Cloud Resource Library (CRL)
Java
2
star
69

ssds

Simple data storage system for AWS and GCP
Python
2
star
70

example-authz-registry

example of maintaining authorization list via github + travis + s3
Python
1
star
71

transporter

Bulk file-transfer system for data ingest
Scala
1
star
72

newt-transformer

Amphibious new data transformer to prepare various sources for CGP DSS Data Loader
Python
1
star
73

lyle

Test user allocation service
JavaScript
1
star
74

bard-client

JavaScript library for shared client-side analytics across DSP
JavaScript
1
star
75

bond

Account linking service
Python
1
star
76

env-base

Base framework environment k8s resources
1
star
77

hca-metadata-api

A library for processing HCA metadata programmatically
Python
1
star
78

data-store-auth

data-store authentication infra management
Python
1
star
79

java-pfb

Java
1
star
80

terra-azure-arm-templates

Shell
1
star
81

saturn-terraform

Terraform definitions for all Saturn-managed repos and GCS projects
HCL
1
star
82

metadata-serialization

Serializing metadata for use and reuse ✒️📋🗃️💻
1
star
83

hamm

Cloud Cost Management Service
Scala
1
star
84

wdl-parsers

A package that provides the generated ANTLR4 WDL parsers for Python.
Python
1
star
85

saturn-documentation

1
star
86

bdcat-integration-tests

This supports integration testing between components for the biodata catalyst grant.
Python
1
star
87

terra-folder-manager

Java
1
star
88

hca-import-validation

A utility to validate a staging area before it is imported.
Python
1
star
89

terra-test-runner

Java
1
star
90

terra-data-catalog

Java
1
star
91

data-platforms

Components of the Commons Alliance
Jupyter Notebook
1
star
92

cbas-ui

JavaScript
1
star
93

findable-ui

TypeScript
1
star