Systems Biology Markup Language

What Systems Biology Markup Language does

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Name

Systems Biology Markup Language

Legal name

Systems Biology Markup Language (SBML)

Website

https://sbml.org

Company type

Private

Founded year

2000

Operating status

Operating

Headcount range

51–100 employees

Short description

The supplied record does not provide source-attributed information about what Systems Biology Markup Language does, whom it serves, its technology, or its business model, preventing validated descriptive analysis at this time.

Ownership category

akta.pro rank

Headquarters

HQ city

Seattle

HQ country

United States

HQ region

North America

Offices5 records

Markets served

GTM type

B2B

Offering type

Software

Cost components

Personnel, Technology or R&D, Operations, Others

Revenue model

1. No Commercial Revenue: SBML is a free and open data format. There is no commercial revenue model - the project is community-driven and supported by funding agencies. Software libraries (libSBML, JSBML) are also freely available under LGPL terms.

Pricing tiers

Go-to-market motion1 record

Distribution channels4 records

Marketing channels5 records

Core offering

SBML is a free, open, XML-based machine-readable data format standard for representing computational models of biological processes such as biochemical reactions, cell signaling pathways, metabolic pathways, and gene regulation. The format is language-independent and tool-neutral, organized into Levels (1, 2, 3) with Versions and Releases, where Level 3 uses a modular architecture with optional packages that extend core functionality.

Product overview

SBML.org is the portal for the Systems Biology Markup Language (SBML), a free and open data format for computational systems biology. The SBML ecosystem includes multiple software tools and libraries: libSBML (C/C++ library with APIs for 10+ languages) and JSBML (pure Java library) for reading, writing, and validating SBML files; Deviser for developing SBML Level 3 packages; the SBML Test Suite for conformance testing; the online SBML Validator; and format conversion tools including SBFC, MOCCASIN, and SBMLToolbox (for MATLAB/Octave). BioModels Database provides a repository of published models in SBML format. The format exists in three Levels (1, 2, 3) with multiple versions, where Level 3 is the modular current generation with optional packages.

Differentiator

Problem solved

Functional benefit

Products and services

• Systems Biology Markup Language (SBML) A free and open XML-based data format for computational systems biology that enables machine-readable representation of models of biological processes such as biochemical reactions, cell signaling pathways, metabolic pathways, and gene regulation. It is language-independent and tool-neutral, used by thousands of researchers worldwide.
• libSBML A programming library written in ISO standard C++ and C that helps read, write, manipulate, translate, and validate SBML files. Supports all SBML Levels and Versions, provides APIs for C, C++, C#, Java, JavaScript, MATLAB, Perl, PHP, Python, R, and Ruby, and is available under LGPL version 2.1.
• JSBML A pure Java library for reading, writing, and manipulating SBML files that maps all SBML elements to a flexible and extended object hierarchy in Java. Supports all constructs up to SBML Level 3 Version 2 Release 2, including APIs for Level 3 packages, and is licensed under LGPL v. 2.1.
• Deviser A development tool that helps create SBML Level 3 packages by automating the generation of basic specifications, UML diagrams, and libSBML plug-ins for the modular Level 3 architecture.
• SBML Test Suite A conformance testing system for SBML that allows developers to test software implementations of SBML support, consisting of a collection of semantic, stochastic, and syntactic test cases plus a framework for running software through the suite.
• SBML Validator An online validator for checking SBML files for compliance with specifications, implementing all validation rules defined in the SBML specifications.
• SBFC (Systems Biology Format Converter) A Java framework and online service for converting between formats used in systems biology, supporting conversion from SBML to BioPAX Levels 2 and 3, MATLAB, Octave, XPP, GraphViz, and APM; usable as a standalone executable or as an EBI-hosted web service under LGPL terms.
• MOCCASIN A Python tool, available under LGPL, that reads ODE-based models written in MATLAB and translates them into SBML format without requiring MATLAB itself, and offers both GUI and command-line interfaces.
• SBMLToolbox An open-source toolbox built on top of libSBML that provides basic functions allowing SBML models to be used in MATLAB and Octave, including functions for creating and validating models and for manipulating and simulating models with ordinary differential equation solvers, available under LGPL.
• BioModels Database An open and free database of human-curated published mathematical models of biological interest, allowing biologists to store, search, and retrieve models in SBML format, with annotations linked to publications, databases of compounds and pathways, and controlled vocabularies.

Named customers2 records

Segments2 records

Ideal customer profiles2 records

Technology focussed Yes

API detail

Has API

Yes

API docs

API detail

Core technology

AI maturity

App detail

Integration4 records

AI capability2 records

Feature4 records

Partnerships

Nine partnerships are on record, tiered core, major and minor.

• COMBINE (COmputational Modeling in BIology NEtwork)coreStrategic or Co-development PartnerSBML is a founding standard of COMBINE, which coordinates development of standards and formats for computational models in biology. COMBINE organizes annual Forum meetings and HARMONY hackathons.
• BioModels Database (EBI)coreStrategic or Co-development PartnerOpen and free database of curated, published mathematical models of biological interests in SBML format. Models are annotated and linked to relevant data resources, publications, and databases.
• Hucka Group (Caltech)coreStrategic or Co-development PartnerComputing + Mathematical Sciences at California Institute of Technology - primary SBML development center led by Michael Hucka.
• Kummer Group (University of Heidelberg)majorStrategic or Co-development PartnerBioQUANT/COS at University of Heidelberg, Germany - funded partner for SBML development.
• Dräger Group (University of Tuebingen)majorStrategic or Co-development PartnerCenter for Bioinformatics (ZBIT) at University of Tuebingen, Germany - funded partner and JSBML development.
• Hermjakob Team (EMBL-EBI)majorStrategic or Co-development PartnerEMBL European Bioinformatics Institute, Hinxton, Cambridge, UK - funded partner and host of BioModels Database.
• Andrews Group (Babraham Institute)majorStrategic or Co-development PartnerBabraham Institute, Cambridge, UK - funded partner and JSBML development contributor.
• Systems Biology Institute (SBI)majorStrategic or Co-development PartnerPast funded partner; holds SBML trademark on behalf of community. Original home of SBML development.
• Google Summer of CodeminorStrategic or Co-development PartnerMultiple SBML-related student projects supported through Google Summer of Code program annually since at least 2014.

Scale indicators3 records

Broad incumbents

• MATLAB SimBiology: MathWorks' commercial model-building and simulation environment for systems biology. SimBiology supports SBML import/export and is a broader, commercially backed incumbent in the same modeling workflow that SBML serves as the interchange layer for.
• COPASI: A widely used open-source software package for modeling and simulation of biochemical networks. COPASI uses SBML for model exchange and is a broad incumbent in systems biology modeling that depends on SBML as its interchange format.

Emerging players

• OpenCOR: An open-source modeling and simulation environment for physiology and systems biology that supports SBML. OpenCOR is an emerging alternative simulation platform whose adoption depends on the same SBML interoperability standards.
• VCell: The Virtual Cell modeling platform from the Center for Cell Analysis and Modeling at UConn. VCell uses SBML for model exchange and contributes rule-based and multi-package development to the SBML ecosystem, making it a closely overlapping but tool-focused peer.
• Tellurium: An integrated Python-based platform for building, simulating, and analyzing biochemical models. Tellurium wraps SBML, SED-ML, and COMBINE archives and is an emerging developer-facing player in the SBML-consuming ecosystem.

Direct peers

• BioModels Database (EBI): EMBL-EBI-hosted open repository of curated, published mathematical models in SBML format. It is the primary content library for SBML models and is both a downstream consumer and a critical ecosystem component for SBML adoption.
• COMBINE: The COmputational Modeling in BIology NEtwork, which SBML is a founding standard of. COMBINE coordinates development of multiple standards and formats for computational biology and organizes the annual Forum and HARMONY hackathons, making it the closest community-coordination peer.
• BioPAX: Biological Pathways Exchange, an open standard for sharing biological pathway data. It overlaps with SBML's mission of standardizing computational biology exchange and is coordinated alongside SBML within the COMBINE network, making it a direct format-standard peer.
• CellML: An XML-based open standard for representing mathematical models of cellular processes. CellML directly overlaps with SBML in cell-biological modeling and shares the same XML/machine-readable format paradigm, making it the closest competing model interchange standard.
• SED-ML: Simulation Experiment Description Markup Language, a COMBINE-coordinated standard for encoding simulation experiments on models encoded in formats such as SBML and CellML. It is a direct sibling standard in the same COMBINE family that SBML anchors.

Market position

Strengths5 records

Weaknesses5 records

Key risks6 records

Key highlights7 records

Customer concentration

• Xx.com/sbmlnews
• GitHubgithub.com/sbmlteam

Revenue estimate

Valuation estimate

Number of profiles

Profiles10 records

Funding overview

Funding rounds

Investors

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M&A

Investments

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Frequently asked questions about Systems Biology Markup Language