In systems biology, it is very important to standardize the model for a given biological phenomenon and analyze the system based on this model. Such a model is most of the time based on ordinary differential equation (ODE).
Such a systems biology model is normally described in a standard format, with Systems Biology Markup Language (SBML) being the de-facto standard in the field. Several software tools exist to create SBML models easily. Regarding the analysis of such models, which is mainly via simulation, steady state analysis, or parameter estimation.
Time course simulationprovides the information of each species in the model over time which enables us to understand the dynamical variation of species in model.
Steady state analysiscan give us the values of model objects after enough time has passed and a steady state is reached.
Parameter estimationfocuses on the identification of unknown parameters in the model based on experimental data.
Time course simulation, steady state simulation and parameter estimation are implemented in multiple libraries and tools for SBML, e.g. COPASI, libroadrunner, or the Simulation Core Library. However, establishing the environment for such analysis is often difficult for biologists and a major obstacle to analyze ODE models easily.
This project is part of Google Summer of Code 2017 with the goal of developing a Web App for SBML models which provides functionality for
time course simulation
steady state analysis
The Web App will provide options for uploading SBML models and experimental data files and run the respective simulations with the models.
This repository includes the following files and directories
docs/SBML example files for analysis
examples/SBML example files for analysis
src/Source code for web app
WebContent/Web content for web app
pom.xmlMaven pom file
This project is created in Java as a Maven project. To run the web app locally one can run the server from within eclipse.
Apache tomcat is not contained in the installation, but must be installed separately. During the development
Apache TomCat v6.0.48 is used which is available as
After download the files should be unpacked in the correct position (e.g. :
Eclipse tomcat plugin installation
When you use Eclipse , eclipse tomcat plugin is needed. This file can be downloaded following Task.
- Select Help - Eclipse Marketplace
- Type "tomcat" in find text box
- Install "Eclipse Tomcat Plugin 9.1.2"
Then you start-up eclipse. When you can see the icon of tomcat in Eclipse , the install is accomplished.
Tomcat installation in Eclipse
After you complete installation of eclipse tomcat plugin, you should choose the
tomcat home from
Environment -> Tomcat. For version, please check version 6.x and select
the aforementioned distribution of
After finishing the tomcat configuration one can run the server in Eclipse via:
- Clone repository
git clone https://github.com/TakahiroYamada/SBMLWebApp.git
File -> Open Projects from File System
- Choose the directory of this project in
Properties -> Java Build Path -> Libraries - add library - Server Runtime - Apache Tomcat v6.0
Run | Edit Configurations | + | Tomcat Server | Local
- Select tomcat:
Configure -> Select apache-tomcat-6.0.48
- Select artifact to deploy:
- Add external libraries to
java.library.pathin VM options i.e.
Docker Image of this application has been already prepared. If you felt annoying when you use this application via our server, installing this image and create the container based on it and executing analysis is better for you.
Docker installation : https://docs.docker.com/engine/installation/
docker pull takahiroyamada/gsoc_sbmlanalysis
docker run -it --rm -p 80:8080 takahiroyamada/gsoc_sbmlanalysis
Then you can execute analysis using your favorite browser with the URL of "http://localhost/GSOC_WebMavenProject-0.0.1-SNAPSHOT/"