Live briefing
Everything about SBML
XML file format for biological models
The Systems Biology Markup Language (SBML) is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of users and developers. SBML can represent many different classes of biological phenomena, including metabolic networks, cell signaling pathways, regulatory networks, infectious diseases, and many others. It has been proposed as a standard for representing computational models in systems biology today. Wikipedia →
🧭 Start here: a 6-step reading path
- Read the overview: SBMLA 5-minute orientation
- Skim a recent paper: libRoadRunner 2.0: a high performance SBML simulation and analysis libraryInfluential work since 2022
- Pick up a classic book: CellMCThe most-reprinted book on the subject
- Read the landmark paper: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network modelsCited 2,495 times
- Go sideways: Systems Biology OntologyA closely related topic
- Go sideways: LibSBMLA closely related topic
📖 Definitions
No dictionary entry for this exact phrase.
🗂️ The subject at a glance
🏆 Landmark papers (most cited)
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
LibSBML: an API Library for SBML
SBML Level 3: an extensible format for the exchange and reuse of biological models
Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
GNU MCSim: Bayesian statistical inference for SBML-coded systems biology models
libRoadRunner: a high performance SBML simulation and analysis library
GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models
🆕 Influential since 2022
libRoadRunner 2.0: a high performance SBML simulation and analysis library
A General Hybrid Modeling Framework for Systems Biology Applications: Combining Mechanistic Knowledge with Deep Neural Networks under the SBML Standard
Automatic Generation of SBML Kinetic Models from Natural Language Texts Using GPT
SBML level 3 package: spatial processes, version 1, release 1
SBMLKinetics: a tool for annotation-independent classification of reaction kinetics for SBML models
📚 Books worth reading
- 📕CellMCEmmet Caulfield · 2014
Ranked by number of editions on Open Library, a rough measure of how lasting a book is.
🔗 Related topics
- Systems Biology Ontology The Systems Biology Ontology (SBO) is a set of controlled, relational vocabularies of terms commonly used in systems biology, and in particular in computational…
- LibSBML LibSBML is an open-source software library that provides an application programming interface (API) for the SBML (Systems Biology Markup Language ) format…
- JSBML JSBML (Java Systems Biology Markup Language) is an open-source Java (API) for the SBML (Systems Biology Markup Language ) format. Its API strives to attain…
- SBSCL The Systems Biology Simulation Core Library (SBSCL) is an open-source, cross-platform pure Java™ programming library that supports the simulation and analysis…
- Libroadrunner libRoadRunner is a C/C++ software library that supports simulation of SBML based models.. It uses LLVM to generate extremely high-performance code and…
- Multi-state modeling of biomolecules Multi-state modeling of biomolecules refers to a series of techniques used to represent and compute the behaviour of biological molecules or complexes…
- BioModels BioModels is a free and open-source repository for storing, exchanging and retrieving quantitative models of biological interest created in 2006. All the…
- COPASI COPASI (COmplex PAthway SImulator) is an open-source software application for creating and solving mathematical models of biological processes such as…