SbmlViewer is a tool for fast and easy reading biological models written in SBML format. It allows looking through model components and equations even if you have no modeling software installed. It is as simple as reading a web page in your web browser.

SbmlViewer never uploads your files to the server and all transformations are performed locally in your browser, so it is safe and secure for your code.

SbmlViewer is open project located on GitHub. Any feedback is welcomed on Issues page.

When SbmlViewer is helpful:

• You cannot install you favorite tool to read and check some SBML file right now.
• Your software cannot read some specific SBML versions or elements like event, constraint or functionDefinition etc. but the file includes them.
• You need to share your model in human readable format with someone easily.
• Your have some errors when reading foreign SBML and are trying to check the model code.

Quick start

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For models from your computer:

1. Go to the page http://sv.insysbio.com/online/viewer.xhtml
2. Drug’n’drop your SBML OR click on button “Choose file” and select your sbml model.

For models shared on web:

1. Copy the link of your shared model, for instance http://www.example.com/your_sbml_file.xml
2. Write the line in your browser like this http://sv.insysbio.com/online/viewer.xhtml?http://www.example.com/your_sbml_file.xml

Examples

To look through example just try the links

• test 00001 from SBML Test Suite Database
• BIOMD0000000512 from BioModels Database, model of the month in January 2016
• BIOMD0000000588 from BioModels Database, model of the month in February 2017
• BIOMD0000000439 from BioModels Database, model of the month in October 2016

Features

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Current release

Version: 170622

• reading SBML Level 2 Version 1-5
• creating tabular view of model with: sbml2table transformation
• summary generation for chosen element: sbml2element transformation
• generation of equation corresponding to your model: sbml2math transformation

Known restrictions

• some bugs with local parameters in sbml2element transformation
• ignores annotation elements for presentation

Roadmap

• support for SBML level 3
• sbml2tree transformation
• Transformation to Antimony format: sbml2antimony transformation
• Chrome extension for SbmlViewer

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Team

• Viktoria Tkachenko @vetedde
• Evgeny Metelkin @metelkin

License

Apache 2.0

3d party software used

• MathJax
• W3.CSS

About SBML

SBML is a free and open interchange format for computer models of biological processes maintained by SBML community. It is used in many modeling application and can store model structure, math and annotation of elements. SBML is XML based format and designed basically for machine reading and writing.