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View Code? Open in Web Editor NEWA Biological Boolean Network Simulator developed for the Web
A Biological Boolean Network Simulator developed for the Web
/* * README * * Copyright 2012 Chaitanya Talnikar <[email protected]> * */ Welcome to the biographer simulator. The simulator uses a Makefile to manage the project. make by default executes the directive 'all' which consists of 'lint', 'doc', 'test' and 'pkg'. The simulator source code does not consist of any external libraries by default and they have to be fetched and installed. Build libs: 1. If you are using Ubuntu, install necessary dependences to test and build the software by typing in the terminal: make deps Otherwise please refer below for a list of dependencies: #required to build bui nodejs npm node-uglify #required to build libSBGN.js ant git-core(git) #required for creating documentation jsdoc-toolkit(jsdoc) #required for the offline app libqtwebkit4 python-qt4 #required for lint code check jshint #required for unit testing selenium python api chromedriver(selenium webdriver) 2. Fetch and build the libs by executing the command: make libs The above commands adds the following libs: biographer-ui d3.js libSBGN.js 3. To support SBML files in the simulator the biographer server needs to be setup. Please read the README in the server folder. 4. For testing purposes if you are using Chrome you need to download the Chrome WebDriver available at the following url: http://code.google.com/p/chromedriver/downloads/list Download the linux zip depending on your architechture and install it using the commands: tar -xvf chromedriver*.zip sudo cp chromedriver /usr/bin Now once you have the necessary libs you are ready to test the simulator or create a deployable package. Offline App(browse): To test the application offline(no SBML support) using the qt webkit engine. Run: make browse Testing(test): To run all the tests for the simulator, run: make test This executes all the tests including the file import/export, SBML server tests and the Simulate, Analyse and Plot features using the selenium browser testing framework along with python's unittest. To run specific tests take a look at the main.py file in the tests directory. The default browser is Chrome and the default URL is the localhost web2py server. To change these settings modify the simulator.py file. Packaging(pkg): To create a package which can be easily deployed on a server execute: make pkg A zip file simulator.zip will be created in the root directory. The following tasks don't really require the libs. Code checking(lint): To perform jshint on the js files execute: make lint Documentation(doc): To generate documentation using jsdoc execute: make doc The docs will reside in the jsdoc directory.
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