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.
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.
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.
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):
- Local Neo4j Database
If you want to use the local instance of Newt with a local Neo4j database, then follow these additional steps before running
npm install: Create a.envfile in the root of the project directory with the following content
LOCAL_DATABASE=true
NEO4J_PLUGIN_PATH=/path/to/your/neo4j/plugins
Replace the NEO4J_PLUGIN_PATH value with the absolute path of your neo4j database plugin folder.
- Installation
git clone https://github.com/iVis-at-Bilkent/newt.git
cd newt
npm install
- Running the tool (Windows)
npm run debug-build
- Running 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.
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.
- 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