SbmlViewer is a tool for fast and easy reading of biological models written in SBML format. It allows you to look through model components and equations even if you have no modeling software installed. It is as simple as reading a web page in your 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 an open project hosted on GitHub. Any feedback is welcome on the Issues page.

SbmlViewer is helpful when:

• You need to share your model in a human-readable and compact format.
• You cannot install your favorite tool to read and check an 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 have got some errors importing SBML and you are trying to check the model code.

Quick start

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Try online

For models from your computer:

1. Open the page https://sv.insysbio.com/online/
2. Drag and drop your SBML file, or click the “Choose file” button and select your SBML model.

For models shared on the web:

Some servers do not allow using shared files in this way. In that case, download the file and use the method above.

1. Copy the link of your shared model, for instance https://www.example.com/your_sbml_file.xml
2. Add the external SBML path to the SbmlViewer URL followed by a ?, like this: https://sv.insysbio.com/online/?https://www.example.com/external_sbml_file.xml
3. The full URL above can be shared, sent, or embedded into a web page if you wish.

Examples

To look through examples, 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 list

• reading SBML Level 2 Version 1-5
• reading SBML Level 3 Version 1-2
• transformation to Heta code using sbml2heta or sbml3heta
• transformation to the Antimony format using sbml2antimony or sbml3antimony
• creating tabular view of model with: sbml2table or sbml3table transformation
• summary generation for a chosen element with sbml2element transformation
• generation of ODE system based on your model: sbml2math or sbml3math transformation
• supports specific SBML format generated by simbiology by transforming MathML and using name instead of id, see options
• supports nice printing of the whole document: Ctrl + P

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Browser support

Tested on:

• Google Chrome
• Opera
• Mozilla Firefox
• MS Internet Explorer
• MS Edge
• Safari

License

Apache 2.0

Team

• Viktoria Tkachenko @vetedde
• Evgeny Metelkin @metelkin

About SBML

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