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grnsight

Web app and service for modeling and visualizing gene regulatory networks.

https://github.com/dondi/grnsight

Science Score: 77.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    14 of 42 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.1%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Web app and service for modeling and visualizing gene regulatory networks.

Basic Info
Statistics
  • Stars: 17
  • Watchers: 7
  • Forks: 8
  • Open Issues: 31
  • Releases: 23
Created about 12 years ago · Last pushed 6 months ago
Metadata Files
Readme License Code of conduct Citation

README.md

GRNsight

DOI Node.js CI Coverage Status

http://dondi.github.io/GRNsight/

GRNsight is an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks. GRNsight is a joint project of the Loyola Marymount University Bioinformatics and Biomathematics Groups, headed by Dr. Kam Dahlquist, Dr. John David N. Dionisio, and Dr. Ben G. Fitzpatrick. Undergraduate students initiated the development of GRNsight in Spring 2014, including Britain Southwick (Computer Science, ’14) and Nicole Anguiano (Computer Science, ’16), with consultation from Katrina Sherbina (Biomathematics, ’14). For current contributors, please see our People page.

A gene regulatory network (GRN) consists of genes, transcription factors, and the regulatory connections between them, which govern the level of expression of mRNA and protein from those genes. GRNs can be mathematically modeled and simulated by applications such as GRNmap, a MATLAB program that estimates the parameters and performs forward simulations of a differential equations model of a GRN. Computer representations of GRNs, such as the models output by GRNmap, are in the form of a tabular spreadsheet (adjacency matrix) that is not easily interpretable. Ideally, GRNs should be displayed as diagrams (graphs) detailing the regulatory relationships (edges) between each gene (node) in the network. To address this need, we developed GRNsight.

GRNsight allows users to upload Excel workbooks generated by GRNmap (as well as Simple Interaction Format text files and GraphML XML files) and uses the network information to automatically create and display a graph of the GRN model. The application colors the edges and adjusts their thickness based on the sign (activation or repression) and the strength (magnitude) of the regulatory relationship, respectively. Finally, GRNsight then allows the user to modify the graph in order to define the best visual layout for the network. Most of GRNsight is written in JavaScript. HTTP requests are handled using Node.js and the Express framework. Graphs are generated through D3.js, a JavaScript data visualization library.

Although originally designed for gene regulatory networks, we believe that GRNsight has general applicability for displaying any small, unweighted or weighted network with directed edges for systems biology or other application domains.

Most users will want to access GRNsight through the web application at http://dondi.github.io/GRNsight/. The source code is available for developers who wish to run their own instance of the GRNsight web service and/or web client.

Documentation on how to use GRNsight is found at https://github.com/dondi/GRNsight, with additional information on the wiki here: https://github.com/dondi/GRNsight/wiki.

If you use GRNsight in your work, please cite:

Dahlquist, K.D., Dionisio, J.D.N., Fitzpatrick, B.G., Anguiano, N.A., Varshneya, A., Southwick, B.J., Samdarshi, M. (2016) GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks. PeerJ Computer Science 2:e85. DOI: 10.7717/peerj-cs.85.

Owner

  • Login: dondi
  • Kind: user

Citation (CITATION.md) 

If you use GRNsight in your work, please cite:

Dahlquist, K.D., Dionisio, J.D.N., Fitzpatrick, B.G., Anguiano, N.A., Varshneya, A., Southwick, B.J., Samdarshi, M. (2016) GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks. _PeerJ Computer Science_ 2:e85. [DOI: 10.7717/peerj-cs.85](https://doi.org/10.7717/peerj-cs.85).

The DOI for the latest release is:

[![DOI](https://zenodo.org/badge/16195791.svg)](https://zenodo.org/badge/latestdoi/16195791)

GitHub Events

Total
  • Create event: 44
  • Commit comment event: 3
  • Issues event: 82
  • Delete event: 50
  • Member event: 2
  • Issue comment event: 348
  • Push event: 217
  • Pull request review comment event: 49
  • Pull request review event: 105
  • Pull request event: 84
  • Gollum event: 31
Last Year
  • Create event: 44
  • Commit comment event: 3
  • Issues event: 82
  • Delete event: 50
  • Member event: 2
  • Issue comment event: 348
  • Push event: 217
  • Pull request review comment event: 49
  • Pull request review event: 105
  • Pull request event: 84
  • Gollum event: 31

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 2,699
  • Total Committers: 42
  • Avg Commits per committer: 64.262
  • Development Distribution Score (DDS): 0.845
Past Year
  • Commits: 58
  • Committers: 7
  • Avg Commits per committer: 8.286
  • Development Distribution Score (DDS): 0.397
Top Committers
Name Email Commits
Mihir Samdarshi m****i@y****m 418
NAnguiano n****1@l****u 320
dondi d****i@l****u 294
Onariaginosa o****n@g****m 293
Eileen Choe e****e@l****u 210
Anu a****a@g****m 188
John Lopez j****6@g****m 146
yshin4 y****4@l****u 129
Alexia Filler a****1@l****u 110
Britainjs b****i@l****u 83
igreen1 i****0@g****m 80
Kam Dahlquist k****t@l****u 71
Kevin Patterson t****3@g****m 61
Dahlquist k****i@l****u 48
Mihir Samdarshi m****i@u****m 47
bhamilton18 b****m@g****m 33
Onariaginosa o****d@l****u 32
ebachoura e****o@g****m 20
Unknown a****i@l****u 19
cazinge e****e@g****m 11
keckuser k****r@k****l 11
Justin Torres j****9@l****u 9
Eileen E****n@C****l 8
John Lopez j****6 7
Mihir Samdarshi m****r@M****l 7
OnaHairtelligence o****a@h****m 6
ebachoura e****a@g****m 6
Zach z****e@l****u 4
Ahmad Mersaghian 7****m@u****m 3
FSloaner F****r@I****u 3
and 12 more...
Committer Domains (Top 20 + Academic)
lion.lmu.edu: 10 lmu.edu: 2 system76-pc.localdomain: 1 ahmads-mbp.lan: 1 itsloaner7.lmumain.edu: 1 hairtelligence.com: 1 lmumain.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 193
  • Total pull requests: 164
  • Average time to close issues: over 1 year
  • Average time to close pull requests: 16 days
  • Total issue authors: 15
  • Total pull request authors: 12
  • Average comments per issue: 6.89
  • Average comments per pull request: 0.56
  • Merged pull requests: 134
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 41
  • Pull requests: 99
  • Average time to close issues: 20 days
  • Average time to close pull requests: 9 days
  • Issue authors: 5
  • Pull request authors: 6
  • Average comments per issue: 1.73
  • Average comments per pull request: 0.41
  • Merged pull requests: 82
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • kdahlquist (85)
  • dondi (72)
  • Onariaginosa (10)
  • ntran18 (10)
  • ceciliazaragoza (3)
  • ahmad00m (3)
  • Sarronnn (2)
  • nchun2 (1)
  • NAnguiano (1)
  • afiller1 (1)
  • jlopez616 (1)
  • mihirsamdarshi (1)
  • akaiap (1)
  • eileenchoe (1)
  • anuvarsh (1)
Pull Request Authors
  • ntran18 (85)
  • ceciliazaragoza (32)
  • akaiap (15)
  • Onariaginosa (8)
  • Amelie1253 (8)
  • Sarronnn (4)
  • dondi (4)
  • ahmad00m (3)
  • MilkaZek (2)
  • luluriffic (1)
  • mihirsamdarshi (1)
  • igreen1 (1)
Top Labels
Issue Labels
priority 0 (78) bug (54) review requested (51) functionality (40) priority 0.5 (34) backlog (27) for next release (21) logistics (20) database (19) enhancement (18) feature request (15) priority 1 (15) documentation (13) testing (12) node coloring (9) gene page (8) web site (8) network (8) refactor (6) ongoing (4) priority 2 (3) code review (2) CMSI4072 (2) invalid (2) wontfix (2) graph layout (2) question (1)
Pull Request Labels
review requested (12) code review (6) for next release (2) priority 0 (2)

Packages

  • Total packages: 1
  • Total downloads:
    • npm 784 last-month
  • Total dependent packages: 1
  • Total dependent repositories: 1
  • Total versions: 16
  • Total maintainers: 1
npmjs.org: grnsight

Web app and service for visualizing models of gene regulatory networks

  • Versions: 16
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 784 Last month
Rankings
Forks count: 6.7%
Downloads: 7.5%
Stargazers count: 8.4%
Dependent repos count: 10.3%
Average: 10.8%
Dependent packages count: 20.9%
Maintainers (1)
dondi
Last synced: 6 months ago

Dependencies

package-lock.json npm
  • 1403 dependencies
package.json npm
  • browser-env 3.3.0 development
  • chai 4.1.2 development
  • coveralls 2.13.1 development
  • eslint 3.19.0 development
  • isomorphic-fetch 2.2.1 development
  • istanbul 0.4.5 development
  • jquery 3.6.0 development
  • jquery-extend 2.0.3 development
  • jsdom 13.2.0 development
  • markdown-pdf 8.0.0 development
  • mocha 2.5.3 development
  • mocha-lcov-reporter 1.3.0 development
  • nock 10.0.6 development
  • sinon 5.1.1 development
  • w3c-xmlserializer 1.0.1 development
  • webpack-cli 2.0.14 development
  • xmlserializer 0.6.1 development
  • body-parser 1.18.2
  • canvg 2.0.0
  • cors 2.8.1
  • cytoscape 2.7.14
  • d3-v4-grid 2.0.1
  • dotenv 8.2.0
  • errorhandler 1.5.0
  • express 4.16.0
  • fs 0.0.1-security
  • googleapis 1.1.5
  • http 0.0.0
  • jspdf 1.5.3
  • method-override 2.3.10
  • moment 2.24.0
  • morgan 1.9.1
  • multiparty 4.2.2
  • node-xlsx 0.7.2
  • nodemon 1.19.1
  • parallelshell 3.0.1
  • pg 8.0.0
  • pg-hstore 2.3.3
  • pug 3.0.2
  • querystring 0.2.0
  • save-svg-as-png 1.4.14
  • sequelize 5.21.6
  • serve-static 1.13.1
  • should 11.2.0
  • stylus 0.54.5
  • supertest 3.0.0
  • url 0.11.0
  • webpack 4.0.0
  • xml2js 0.4.17
  • xmlbuilder 8.2.2