Science Score: 75.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 2 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
4 of 27 committers (14.8%) from academic institutions -
✓Institutional organization owner
Organization ivis-at-bilkent has institutional domain (www.cs.bilkent.edu.tr) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.2%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
A web application to visualize and edit pathway models
Basic Info
- Host: GitHub
- Owner: iVis-at-Bilkent
- License: lgpl-3.0
- Language: JavaScript
- Default Branch: master
- Homepage: http://newteditor.org
- Size: 52.6 MB
Statistics
- Stars: 57
- Watchers: 10
- Forks: 30
- Open Issues: 37
- Releases: 16
Topics
Metadata Files
README.md
Newt: A Sample Application for ChiSE
Newt is a sample application for the web based library named ChiSE developed to visualize and edit the pathway models represented by process description (PD) and activity flow (AF) languages of SBGN, SBML or simple interaction format (SIF).
ChiSE and this sample application are distributed under GNU Lesser General Public License.
How to Cite Usage
Please cite the following when you use Newt:
H. Balci, M.C. Siper, N. Saleh, I. Safarli, L. Roy, M. Kilicarslan, R. Ozaydin, A. Mazein, C. Auffray, O. Babur, E. Demir and U. Dogrusoz, Newt: a comprehensive web-based tool for viewing,constructing, and analyzing biological maps, Bioinformatics, 37(10), pp.1475-1477, 2021.
Software
A deployment of this sample application along with detailed documentation on its usage can be found here. ChiSE and Newt work on every platform that have JavaScript support including mobile devices.
Running a Local Instance
In order to deploy and run a local instance of the tool, please follow the steps below (we recommend the use of version 14.19.3 of node.js):
Installation
git clone https://github.com/iVis-at-Bilkent/newt.git cd newt npm installRunning the tool (Windows)
npm run debug-buildRunning the tool (MacOS/Linux)
sudo npm run debug-build
Then, open a web browser and navigate to localhost. Please note that the default port is 80 but you might have to run this application in another port such as 8080 in some platforms by setting 'port' environment variable.
Credits
Icons made by Freepik, Daniel Bruce, TutsPlus, Robin Kylander, Catalin Fertu, Yannick, Icon Works, Flaticon and licensed with Creative Commons BY 3.0
Third-party libraries: Cytoscape.js, a-color-picker, Backbone, Bootstrap, FileSaver.js, jQuery, jquery-expander, Konva, libxmljs, lodash, underscore, express, browserify, nodemon, Parallel Shell, Tippyjs, nodemailer, body-parser, jsdom, cypress, multer licensed with MIT; Mousetrap, Request licensed with Apache-2.0, Intro.js licensed with GNU AGPL, and chroma-js licensed with this.
We refer the user to GeneCards for detailed properties of genes. Similarly, we pull properties of simple chemicals from ChEBI. CellDesigner conversion is performed through this library and its associated service. Finally, SBML and GPML conversions are due to this Minerva service.
Team
- Hasan Balci, Selbi Ereshova, Umut Utku Ersahince, Noor Muhammad and Ugur Dogrusoz of i-Vis at Bilkent University, Ozgun Babur of University of Massachusetts at Boston, and Emek Demir of the Demir Lab at OHSU
Alumni
Owner
- Name: i-Vis at Bilkent
- Login: iVis-at-Bilkent
- Kind: organization
- Website: http://www.cs.bilkent.edu.tr/~ivis/
- Twitter: iVisAtBilkent
- Repositories: 50
- Profile: https://github.com/iVis-at-Bilkent
i-Vis Research Lab at Bilkent University
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Balci"
given-names: "Hasan"
orcid: "https://orcid.org/0000-0001-8319-7758"
- family-names: "Siper"
given-names: "Metin Can"
- family-names: "Saleh"
given-names: "Nasim"
orcid: "https://orcid.org/0000-0001-8319-7758"
- family-names: "Safarli"
given-names: "Ilkin"
- family-names: "Roy"
given-names: "Ludovic"
orcid: "https://orcid.org/0000-0001-6940-874X"
- family-names: "Kilicarslan"
given-names: "Merve"
- family-names: "Ozaydin"
given-names: "Rumeysa"
- family-names: "Mazein"
given-names: "Alexander"
orcid: "https://orcid.org/0000-0001-7137-4171"
- family-names: "Aufrey"
given-names: "Charles"
- family-names: "Babur"
given-names: "Ozgun"
orcid: "https://orcid.org/0000-0002-0239-5259"
- family-names: "Demir"
given-names: "Emek"
orcid: "https://orcid.org/0000-0002-3663-7113"
- family-names: "Dogrusoz"
given-names: "Ugur"
orcid: "https://orcid.org/0000-0002-7153-0784"
title: "Newt"
version: 3.0.3
date-released: 2021-04-08
url: "https://github.com/iVis-at-Bilkent/newt"
preferred-citation:
type: article
authors:
- family-names: "Balci"
given-names: "Hasan"
orcid: "https://orcid.org/0000-0001-8319-7758"
- family-names: "Siper"
given-names: "Metin Can"
- family-names: "Saleh"
given-names: "Nasim"
orcid: "https://orcid.org/0000-0001-8319-7758"
- family-names: "Safarli"
given-names: "Ilkin"
- family-names: "Roy"
given-names: "Ludovic"
orcid: "https://orcid.org/0000-0001-6940-874X"
- family-names: "Kilicarslan"
given-names: "Merve"
- family-names: "Ozaydin"
given-names: "Rumeysa"
- family-names: "Mazein"
given-names: "Alexander"
orcid: "https://orcid.org/0000-0001-7137-4171"
- family-names: "Aufrey"
given-names: "Charles"
- family-names: "Babur"
given-names: "Ozgun"
orcid: "https://orcid.org/0000-0002-0239-5259"
- family-names: "Demir"
given-names: "Emek"
orcid: "https://orcid.org/0000-0002-3663-7113"
- family-names: "Dogrusoz"
given-names: "Ugur"
orcid: "https://orcid.org/0000-0002-7153-0784"
doi: "10.1093/bioinformatics/btaa850"
journal: "Bioinformatics"
month: 5
start: 1475 # First page number
end: 1477 # Last page number
title: "Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps"
issue: 10
volume: 37
year: 2021
GitHub Events
Total
- Issues event: 107
- Watch event: 3
- Member event: 1
- Issue comment event: 188
- Push event: 96
- Pull request review event: 3
- Pull request event: 27
- Create event: 4
Last Year
- Issues event: 107
- Watch event: 3
- Member event: 1
- Issue comment event: 188
- Push event: 96
- Pull request review event: 3
- Pull request event: 27
- Create event: 4
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| metincansiper | m****r@g****m | 195 |
| Hasan Balcı | b****9@g****m | 170 |
| kinimesi | k****i | 154 |
| Nasim Saleh | n****h@g****m | 114 |
| ugurdogrusoz | u****z@g****m | 98 |
| Ludovic Roy | l****y@e****g | 95 |
| leonarddrv | l****i@b****r | 70 |
| kaansancak | k****k@g****m | 42 |
| ucalis | c****u@g****m | 40 |
| Ahmet Çandıroğlu | a****u@g****m | 36 |
| kinimesi | i****i@s****r | 27 |
| mervekilicarslan5 | 4****5 | 24 |
| dorukcakmakci | d****7@g****m | 24 |
| meneskaraca | 3****a | 20 |
| Gökberk Karaca | g****5@g****m | 19 |
| canbax | y****z@g****m | 16 |
| Salih Altun | s****n@u****r | 14 |
| istemi-bahceci | i****i@g****m | 10 |
| rumeysa | r****n@h****m | 9 |
| Selbi Ereshova | s****a@u****r | 6 |
| Salih Altun | m****n@g****m | 4 |
| fdurupinar | f****r | 2 |
| MobiZaman | m****n@l****m | 1 |
| Olga Ivanova | i****9@g****m | 1 |
| royludo | r****4@h****m | 1 |
| Apple | a****e@A****l | 1 |
| Apple | a****e@a****t | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 133
- Total pull requests: 24
- Average time to close issues: over 1 year
- Average time to close pull requests: about 1 month
- Total issue authors: 16
- Total pull request authors: 5
- Average comments per issue: 3.25
- Average comments per pull request: 0.5
- Merged pull requests: 11
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 68
- Pull requests: 17
- Average time to close issues: 27 days
- Average time to close pull requests: about 4 hours
- Issue authors: 8
- Pull request authors: 4
- Average comments per issue: 1.18
- Average comments per pull request: 0.18
- Merged pull requests: 7
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- ugurdogrusoz (65)
- hasanbalci (28)
- adrienrougny (9)
- NoorMuhammad1 (8)
- umut-er (7)
- mjostaszewski (5)
- kinimesi (2)
- fbergmann (1)
- piotr-gawron (1)
- okg21 (1)
- msalihaltun (1)
- brb-arraytools (1)
- MathurinD (1)
- royludo (1)
- SelbiEreshova (1)
Pull Request Authors
- umut-er (7)
- AEren46 (6)
- eliflaraoguzhan (4)
- sinanhavus (4)
- hasanbalci (3)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- browserify ^11.2.0 development
- express ^4.14.0 development
- nodemon 1.11.0 development
- parallelshell 3.0.1 development
- a-color-picker ^1.2.0
- backbone 1.3.3
- body-parser ^1.19.0
- bootstrap 3.3.7
- chise ^3.0.0
- chroma-js ^1.3.4
- cytoscape github:iVis-at-Bilkent/cytoscape.js#master
- cytoscape-autopan-on-drag 2.2.1
- cytoscape-clipboard 2.2.1
- cytoscape-context-menus 3.1.0
- cytoscape-edge-editing 2.0.1
- cytoscape-edgehandles ~2.13.1
- cytoscape-expand-collapse 4.0.0
- cytoscape-fcose 1.2.3
- cytoscape-grid-guide 2.3.2
- cytoscape-layout-utilities 1.0.2
- cytoscape-node-resize 3.2.1
- cytoscape-panzoom ~2.5.2
- cytoscape-popper ^1.0.2
- cytoscape-undo-redo 1.3.3
- cytoscape-view-utilities 4.1.0
- file-saver ^2.0.2
- intro.js 2.9.3
- jquery ~3.3.1
- jquery-expander 1.7.0
- konva ^1.6.3
- libxmljs 0.19.7
- lodash.get ^4.4.2
- lodash.set ^4.3.2
- mousetrap ^1.6.0
- multer ^1.4.2
- natives ^1.1.6
- nodemailer 6.4.5
- request ^2.81.0
- sbgnviz ^6.0.6
- tippy.js ^3.4.0