COINSTAC

COINSTAC: Collaborative Informatics and Neuroimaging Suite Toolkit for Anonymous Computation - Published in JOSS (2020)

https://github.com/trendscenter/coinstac

Science Score: 59.0%

This score indicates how likely this project is to be science-related based on various indicators:

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 4 DOI reference(s) in README
✓
Academic publication links
Links to: frontiersin.org, joss.theoj.org, zenodo.org
✓
Committers with academic emails
7 of 29 committers (24.1%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (15.4%) to scientific vocabulary

Keywords

coinstac coinstac-platform

Keywords from Contributors

bids mesh

Scientific Fields

Computer Science Computer Science - 39% confidence

Last synced: 4 months ago · JSON representation

Repository

Collaborative Informatics and Neuroimaging Suite Toolkit for Anonymous Computation

Basic Info

Host: GitHub
Owner: trendscenter
License: mit
Language: JavaScript
Default Branch: master
Homepage:
Size: 859 MB

Statistics

Stars: 50
Watchers: 19
Forks: 19
Open Issues: 205
Releases: 71

Topics

coinstac coinstac-platform

Created almost 10 years ago · Last pushed 5 months ago

Metadata Files

Readme Contributing License Security

Collaborative Informatics and Neuroimaging Suite Toolkit for Anonymous Computation (COINSTAC)

A federated learning solution by your friends at the Center for Translational Research in Neuroimaging and Data Science (TReNDS).

For more extensive documentation for Researchers, Computation Authors and Developers our documentation wiki can be found here

Introduction
- Deep Dive
Quick Start Guide
Description
- The Problem
- The Solution
For Developers and Contributors
Releases
License

Introduction

COINSTAC is software to foster collaborative research, removing large barriers to traditional data-centric collaboration approaches. It enables groups of users to run common analyses on their own machines over their own datasets with ease. The results of these analyses are synchronized to the cloud, and undergo aggregate analyses processes using all contributor data. Federated (decentralized) pipelines allow for distributed, iterative, and feature rich analyses to be run, opening new and exciting capabilities for collaborative computation. It also offers data anonymity through differentially private algorithms, so members do not need to fear PHI traceback.

Let's do research!

Deep Dive

For a deep dive, you can read the projects paper, COINSTAC: A Privacy Enabled Model and Prototype for Leveraging and Processing Decentralized Brain Imaging Data on Frontiers in Neuroscience.

We also curate a list of conference and journal papers on methods and studies related to federated learning and COINSTAC.

Quick Start Guide

If you want to run COINSTAC as an end user
- Download the latest release for your operating system.
- You can download sample data of volumes of regions of interest in the brain, in a format typically produced by FreeSurfer, which can be used in a federated regression.
- You can also download sample neuroimages (structural MRI preprocessed with voxel-based morphometry (VBM)), which can be used in a federated regression.
For more guidance, please see these detailed instructions on how to install and run COINSTAC.

Description

The Problem

You want to do research, and you want to include data from around the world. Unfortunately, orchestrating such an event is anything but trivial.

Coordinating data-driven research can be difficult. Who's going to collect all of the files? Who is going to actually "run" all of the data?
Ensuring privacy can be difficult. Can I trust other people or institutions with my research participants' data? Am I even allowed to share it?
Large datasets can be expensive to transfer. When file sets are in the GB and TB range, network transfers are not immediately trivial or even practical.
Valuable research data may often not be shared due to privacy or IRB constraints.
"Smart bullies" have demonstrated ability to extract personal information from various aggregated, anonymized datasets. How can we share data without revealing confidential information?

Bottom line--collaborative group research requires a great deal of coordination. Human and business factors can hamper research from happening at a pace that we are able to handle! Constraints may even forbid group research to occur at all.

The Solution

Let's remove these barriers. The best usage of research data is to apply it everywhere it can be useful. Our strategy enables otherwise "locked-down data" to become useful again.

COINSTAC removes the barriers to collaborative analysis by:

decentralizing analyses and computation
- each user performs analyses/pipelines/etc all on their own computers. Bits and pieces of each users' output may be sent to a central compute node
- a central compute node performs a complimentary component of the group analysis, generally a Machine Learning algorithm. This node may trigger adjusted computations on users' machines, generally in effort to improve a model, which the research is trying to predict!
not synchronizing full datasets. instead, synchronizing only resultant analysis metrics
- as previously discussed, central compute nodes aggregate these metrics, and attempt to draw conclusions from the contributor swarm
- because machine learning algorithms can be designed to model outcomes via artifacts of your analysis Pipelines, we keep your data safely and conveniently on your own machine, untouched.
applying differential privacy strategies to truly anonymize private data, whilst still permitting collaboration.

You may wonder why we haven't been doing this before! Us too. Let's get started!

For Developers and Contributors

If you are a developer or scientist and want to design a decentralized computation, please see:
- The algorithm development guide for how to build and test your own Decentralized Computation.
If you would like to run your own COINSTAC remote server or contribute to development, please see the setup instructions.
- Reminder: if you just want to use COINSTAC, please see the Quick Start Guide.
We would love for you to contribute to development. Please see our contribution guidelines.
Developer documentation and system design information may be found over in our technical docs.

Security

If you have questions regarding security, please read our security overview.

Releases

Binary releases for several platforms can be found here, under each version's assets tab.

Acknowledgements

COINSTAC is supported by the following grants: - NSF 1631838/1631819, 1453432, 1539067 - NIH 1R01DA040487, R01MH121246, R01MH121246-02S1, R01DA049238, R01MH120482

License

MIT. See LICENSE for details.

Owner

Name: Center for Translational Research in Neuroimaging and Data Science
Login: trendscenter
Kind: organization
Email: info@trendscenter.org
Location: 55 Park Pl NE, Atlanta, GA 30303

Website: www.trendscenter.org
Twitter: CenterTrends
Repositories: 184
Profile: https://github.com/trendscenter

GitHub Events

Total

Create event: 27
Release event: 10
Issues event: 18
Watch event: 1
Delete event: 23
Member event: 1
Issue comment event: 15
Push event: 65
Pull request review event: 3
Pull request event: 43

Last Year

Create event: 27
Release event: 10
Issues event: 18
Watch event: 1
Delete event: 23
Member event: 1
Issue comment event: 15
Push event: 65
Pull request review event: 3
Pull request event: 43

Committers

Last synced: 8 months ago

All Time

Total Commits: 3,635
Total Committers: 29
Avg Commits per committer: 125.345
Development Distribution Score (DDS): 0.686

Past Year

Commits: 107
Committers: 4
Avg Commits per committer: 26.75
Development Distribution Score (DDS): 0.579

Top Committers

Name	Email	Commits
Ross Kelly	r**y@m**g	1,141
Cory Reed	c**d@m**g	553
kalitopix	k**x@g**m	360
Eduardo Rocha	e**g@g**m	349
Javier Romero	j**o@g**m	295
Dylan Martin	d**n@g**m	276
dependabot[bot]	4****]	251
tkah	t**k@u**u	234
cdaringe	c**r@g**m	43
Alex Ramirez	a**z@M**l	30
Eric Verner	e**r@g**u	29
Torran Kahleck	t**k@t**u	21
Bharath	b**i@m**g	13
Eduardo Rocha	e**a@c**z	8
BluntBSE	3****E	6
spanta28	s**a@g**u	4
Javier Romero	j**o@M**l	4
hvgazula	h**a@u**u	2
Xin You	r**u@g**m	2
Aashis Khanal	s**s@g**m	2
Torran Kahleck	t**k@T**l	2
dlandis	d**s@m**g	2
pprae	p**e@i**m	2
everner-ds	e**r@d**m	1
Ross Kelly	r**y@m**u	1
root	r**t@c**g	1
Jason A. Staph	j**h@s**s	1
Chris Filo Gorgolewski	k**i@g**m	1
Anand Sarwate	a**e@r**u	1

Committer Domains (Top 20 + Academic)

mrn.org: 4 gsu.edu: 2 rutgers.edu: 1 staph.us: 1 coinstac.mrn.org: 1 mind.unm.edu: 1 datalyticsolutions.com: 1 innovativesol.com: 1 umich.edu: 1 clevertech.biz: 1 torrans-mbp.mind.unm.edu: 1 unm.edu: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 169
Total pull requests: 242
Average time to close issues: 3 months
Average time to close pull requests: about 1 month
Total issue authors: 8
Total pull request authors: 5
Average comments per issue: 1.56
Average comments per pull request: 0.21
Merged pull requests: 204
Bot issues: 0
Bot pull requests: 136

Past Year

Issues: 15
Pull requests: 55
Average time to close issues: 15 days
Average time to close pull requests: 15 days
Issue authors: 3
Pull request authors: 3
Average comments per issue: 0.2
Average comments per pull request: 0.33
Merged pull requests: 35
Bot issues: 0
Bot pull requests: 33

View more stats

Top Authors

Issue Authors

spanta28 (62)
praeducer (39)
rssk (38)
kalitopix (10)
dylanmartin (10)
pixelsaurus (5)
hvgazula (1)
eminSerin (1)
dependabot[bot] (1)

Pull Request Authors

dependabot[bot] (195)
kalitopix (84)
rssk (27)
pixelsaurus (10)
dylanmartin (6)

Top Labels

Issue Labels

data or vaults (27) research papers (21) High (12) ui or ux or client (12) computations or algorithms (11) bug (10) Low (8) Medium (7) project management (4) documentation (4) feature (2) core-features (2) containerization-singularity-docker (2) containers (2) security or networking (2) architecture (2) system integration (1) devops (1) ci or cd (1) server (1) api (1) qa testing (1) dependencies (1) javascript (1)

Pull Request Labels

dependencies (195) javascript (176)

Packages

Total packages: 1
Total downloads:
- pypi 20 last-month
Total docker downloads: 326

Total dependent packages: 0
Total dependent repositories: 6
Total versions: 10
Total maintainers: 2

pypi.org: coinstac

Python utility library for coinstac

Homepage: https://github.com/trendscenter/coinstac/coinstac-utilities/coinstac-python
Documentation: https://coinstac.readthedocs.io/
License: MIT
Latest release: 0.3.4
published almost 2 years ago

Versions: 10
Dependent Packages: 0
Dependent Repositories: 6
Downloads: 20 Last month
Docker Downloads: 326

Rankings

Docker downloads count: 2.3%

Dependent repos count: 6.1%

Dependent packages count: 7.3%

Forks count: 8.6%

Stargazers count: 10.3%

Average: 17.3%

Downloads: 69.0%

Maintainers (2)

coinstac rssk

Last synced: 4 months ago

Dependencies

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actions/checkout v3 composite
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coinstac-docs/package-lock.json npm

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coinstac-docs/package.json npm

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packages/coinstac-client-core/package-lock.json npm

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packages/coinstac-client-core/package.json npm

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packages/coinstac-client-server/package.json npm

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packages/coinstac-common/package-lock.json npm

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packages/coinstac-common/package.json npm

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packages/coinstac-container-manager/package-lock.json npm

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packages/coinstac-container-manager/package.json npm

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packages/coinstac-desktop-app/package-lock.json npm

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packages/coinstac-desktop-app/package.json npm

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packages/coinstac-graphql-schema/package.json npm

packages/coinstac-images/coinstac-base/package-lock.json npm

389 dependencies

packages/coinstac-images/coinstac-base/package.json npm

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packages/coinstac-pipeline/package-lock.json npm

450 dependencies

packages/coinstac-pipeline/package.json npm

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packages/coinstac-server/package-lock.json npm

200 dependencies

packages/coinstac-server/package.json npm

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packages/coinstac-simulator/package-lock.json npm

268 dependencies

packages/coinstac-simulator/package.json npm

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winston ^3.0.0

packages/coinstac-vault-client/package-lock.json npm

@apollo/client 3.6.6
@colors/colors 1.5.0
@dabh/diagnostics 2.0.3
@graphql-typed-document-node/core 3.1.1
@wry/context 0.6.1
@wry/equality 0.5.2
@wry/trie 0.3.1
async 3.2.5
asynckit 0.4.0
axios 1.6.0
backo2 1.0.2
color 3.2.1
color-convert 1.9.3
color-name 1.1.3
color-string 1.9.1
colorspace 1.1.4
combined-stream 1.0.8
cross-fetch 3.1.5
csv-reader 1.0.8
delayed-stream 1.0.0
enabled 2.0.0
eventemitter3 3.1.2
fecha 4.2.3
fn.name 1.1.0
follow-redirects 1.15.6
form-data 4.0.0
graphql 15.8.0
graphql-tag 2.12.6
hoist-non-react-statics 3.3.2
inherits 2.0.4
is-arrayish 0.3.2
is-stream 2.0.1
iterall 1.3.0
js-tokens 4.0.0
kuler 2.0.0
lodash 4.17.21
logform 2.4.0
loose-envify 1.4.0
mime-db 1.52.0
mime-types 2.1.35
mkdirp 1.0.4
ms 2.1.2
node-fetch 2.6.7
object-assign 4.1.1
one-time 1.0.0
optimism 0.16.1
prop-types 15.8.1
proxy-from-env 1.1.0
react-is 16.13.1
readable-stream 3.6.0
safe-buffer 5.2.1
safe-stable-stringify 2.3.1
simple-swizzle 0.2.2
stack-trace 0.0.10
string_decoder 1.3.0
subscriptions-transport-ws 0.11.0
symbol-observable 1.2.0
symbol-observable 4.0.0
text-hex 1.0.0
tr46 0.0.3
triple-beam 1.3.0
ts-invariant 0.10.3
tslib 2.4.0
util-deprecate 1.0.2
webidl-conversions 3.0.1
whatwg-url 5.0.0
winston 3.7.2
winston-transport 4.5.0
ws 7.5.8
zen-observable 0.8.15
zen-observable-ts 1.2.5

packages/coinstac-vault-client/package.json npm

@apollo/client ^3.3.20
axios ^1.6.0
coinstac-client-core ^6.8.17
coinstac-graphql-schema ^6.8.6
cross-fetch ^3.0.6
csv-reader ^1.0.7
graphql ^15.5.0
lodash ^4.17.21
mkdirp ^1.0.4
subscriptions-transport-ws ^0.11.0
winston ^3.3.3
ws ^7.5.4

packages/coinstac-images/coinstac-iteration-test/requirements.txt pypi

coinstac >=0.3.1 test

packages/coinstac-utilities/coinstac-python/coinstac/coinstac.egg-info/requires.txt pypi

asyncio *
websockets *

packages/coinstac-utilities/coinstac-python/coinstac.egg-info/requires.txt pypi

asyncio *
websockets *

packages/coinstac-utilities/coinstac-python/setup.py pypi

asyncio *
websockets *

COINSTAC

Science Score: 59.0%

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README.md

Collaborative Informatics and Neuroimaging Suite Toolkit for Anonymous Computation (COINSTAC)

For more extensive documentation for Researchers, Computation Authors and Developers our documentation wiki can be found here

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