420:", was released in November 2012. This package provides the ability to include models as submodels inside another model. The goal is to support the ability of modelers and software tools to do such things as (1) decompose larger models into smaller ones, as a way to manage complexity; (2) incorporate multiple instances of a given model within one or more enclosing models, to avoid literal duplication of repeated elements; and (3) create libraries of reusable, tested models, much as is done in software development and other engineering fields. The specification was the culmination of years of discussion by a wide number of people.
331:). An important principle is that models are decomposed into explicitly-labeled constituent elements, the set of which resembles a verbose rendition of chemical reaction equations (if the model uses reactions) together with optional explicit equations (again, if the model uses these); the SBML representation deliberately does not cast the model directly into a set of differential equations or other specific interpretation of the model. This explicit, modeling-framework-agnostic decomposition makes it easier for a software tool to interpret the model and translate the SBML form into whatever internal form the tool actually uses.
448:" package for SBML Level 3 was released in May 2013. This package supports the representation of models where an in-depth knowledge of the biochemical reactions and their kinetics is missing and a qualitative approach must be used. Examples of phenomena that have been modeled in this way include gene regulatory networks and signaling pathways, basing the model structure on the definition of regulatory or influence graphs. The definition and use of some components of this class of models differ from the way that species and reactions are defined and used in
242:, UK. By this time, far more people were involved than the original group of SBML collaborators and the continued evolution of SBML became a larger community effort, with many new tools having been enhanced to support SBML. The workshop participants in 2002 collectively decided to revise the form of SBML in Level 2. The first draft of the Level 2 Version 1 specification was released in August 2002, and the final set of features was finalized in May 2003 at the 7th Workshop on Software Platforms for Systems Biology in
669:: A mathematical expression used in combination with the differential equations constructed based on the set of reactions in a model. It can be used to define how a variable's value can be calculated from other variables or used to define the rate of change of a variable. The set of rules in a model can be used with the reaction rate equations to determine the behavior of the model with respect to time. The set of rules constrains the model for the entire duration of simulated time.
283:
act on entities, this same formalism serves analogously for many other types of processes; moreover, SBML has language features supporting the direct expression of mathematical formulas and discontinuous events separate from reaction processes, allowing SBML to represent much more than solely biochemical reactions. Evidence for SBML's ability to be used for more than merely descriptions of biochemistry can be seen in the variety of models available from
367:: upward-compatible specifications that add features and expressive power. Software tools that do not need or cannot support the complexity of higher Levels can go on using lower Levels; tools that can read higher Levels are assured of also being able to interpret models defined in the lower Levels. Thus new Levels do not supersede previous ones. However, each Level can have multiple Versions within it, and new Versions of a Level
436:" package provides support for constraint-based modeling, frequently used to analyze and study biological networks on both a small and large scale. This SBML package makes use of standard components from the SBML Level 3 core specification, including species and reactions, and extends them with additional attributes and structures to allow modelers to define such things as flux bounds and optimization functions.
355:
example of the value of this is in BioModels
Database, where every model is annotated and linked to relevant data resources such as publications, databases of compounds and pathways, controlled vocabularies, and more. With annotations, a model becomes more than simply a rendition of a mathematical construct—it becomes a semantically-enriched framework for communicating knowledge.
210:. Hamid Bolouri was the leader of the development team, which consisted of Andrew Finney, Herbert Sauro, and Michael Hucka. Bolouri identified the need for a framework to enable interoperability and sharing between the different simulation software systems for biology in existence during the late 1990s, and he organized an informal workshop in December 1999 at the
681:: A statement describing some transformation, transport or binding process that can change the amount of one or more species. For example, a reaction may describe how certain entities (reactants) are transformed into certain other entities (products). Reactions have associated kinetic rate expressions describing how quickly they take place.
946:
as the grammar parser. However, the distribution also includes Python bindings which can be installed using pip to make it easy to use from Python. It is also available via the
Tellurium package. More recently, a JavaScript/WASM version has been generated which allows the Antimony language to be used
716:
SBML shorthand is a specification and associated Python tooling to interconvert SBML and the shorthand notation. The format was developed by the UK Newcastle systems biology group sometime before 2006. Its aim was to enable modelers to more rapidly create models without having to either write raw XML
334:
A software package can read an SBML model description and translate it into its own internal format for model analysis. For example, a package might provide the ability to simulate the model by constructing differential equations and then perform numerical time integration on the equations to explore
282:
SBML is sometimes incorrectly assumed to be limited in scope only to biochemical network models because the original publications and early software focused on this domain. In reality, although the central features of SBML are indeed oriented towards representing chemical reaction-like processes that
265:
SBML Level 3 Version 1 Core was published in final form in 2010, after prolonged discussion and revision by the SBML Editors and the SBML community. It contains numerous significant changes in syntax and constructs from Level 2 Version 4, but also represents a new modular base for continued
249:
The next iteration of SBML took two years in part because software developers requested time to absorb and understand the larger and more complex SBML Level 2. The inevitable discovery of limitations and errors led to the development of SBML Level 2 Version 2, issued in
September 2006.
230:
The
Caltech ERATO team developed a proposal for this XML-based format and circulated the draft definition to the attendees of the 2nd Workshop on Software Platforms for Systems Biology in August 2000. This draft underwent extensive discussion over mailing lists and during the 2nd Workshop on Software
257:
SBML Level 2 Version 4 was published in 2008 after certain changes in Level 2 were requested by popular demand. (For example, an electronic vote by the SBML community in late 2007 indicated a majority preferred not to require strict unit consistency before an SBML model is considered
214:
to discuss the matter. In attendance at that workshop were the groups responsible for the development of DBSolve, E-Cell, Gepasi, Jarnac, StochSim, and The
Virtual Cell. Separately, earlier in 1999, some members of these groups also had discussed the creation of a portable file format for metabolic
1273:; Arkin, A. P.; Bornstein, B. J.; Bray, D; Cornish-Bowden, A.; Cuellar, A. A.; Dronov, S.; Gilles, E.D.; Ginkel, M; Gor, V.; Goryanin, I.I.; Hedley, W.J.; Hodgman, T. C.; Hofmeyr, J. -H.; Hunter, P. J.; Juty, N. S.; Kasberger, J. L.; Kremling, A.; Kummer, U.; Le Novère, N.; Loew, L. M.; Lucio, D.;
1153:
SBML has been and continues to be developed by the community of people making software platforms for systems biology, through active email discussion lists and biannual workshops. The meetings are often held in conjunction with other biology conferences, especially the
International Conference on
354:
In addition to the elements above, another important feature of SBML is that every entity can have machine-readable annotations attached to it. These annotations can be used to express relationships between the entities in a given model and entities in external resources such as databases. A good
469:
The SBML Level 3 Layout package provides a specification for how to represent a reaction network in a graphical form. It is thus better tailored to the task than the use of an arbitrary drawing or graph. The SBML Level 3 package only deals with the information necessary to define the
253:
SBML Level 2 Version 3 was published in 2007 after countless contributions by and discussions with the SBML community. 2007 also saw the election of two more SBML Editors as part of the introduction of the modern SBML Editor organization in the context of the SBML development process.
490:
Development of SBML Level 3 packages is being undertaken such that specifications are reviewed and implementations attempted during the development process. Once a specification is stable and there are two implementations that support it, the package is considered accepted. The packages
452:
SBML models. For example, qualitative models typically associate discrete levels of activities with entity pools; consequently, the processes involving them cannot be described as reactions per se, but rather as transitions between states. These systems can be viewed as reactive systems whose
465:
package originated as a set of annotation conventions usable in SBML Level 2. It was introduced at the SBML Forum in St. Louis in 2004. Ralph Gauges wrote the specification and provided an implementation that was widely used. This original definition was reformulated as an SBML
269:
SBML Level 2 Version 5 was published in 2015. This revision included a number of textual (but not structural) changes in response to user feedback, thereby addressing the list of errata collected over many years for the SBML Level 2 Version 4 specification. In addition,
391:
The SBML Team maintains a public issue tracker where readers may report errors or other issues in the SBML specification documents. Reported issues are eventually put on the list of official errata associated with each specification release. The lists of errata are documented on the
350:
SBML allows models of arbitrary complexity to be represented. Each type of component in a model is described using a specific type of data structure that organizes the relevant information. The data structures determine how the resulting model is encoded in XML.
675:: A mathematical expression that defines a constraint on the values of model variables. The constraint applies at all instants of simulated time. The set of constraints in the model should not be used to determine the behavior of the model with respect to time.
941:
Like SBML-shorthand, Antimony provides a simplified text representation of SBML. It uses a minimum of punctuation characters which renders the text easier to read and understand. It also allows users to add comments. Antimony is implemented using C/C++ and
937:
Antimony is based on an earlier DSL implemented in the Jarnac modeling application. That, in turn, was based on the SCAMP modeling application which ultimately drew inspiration from the DSL language developed by David
Garfinkel for the BIOSIM simulator.
1590:
Finney, A., Hucka, M., Bornstein, B.J., Keating, S.M., Shapiro, B.E., Matthews, J., Kovitz, B.L., Schilstra, M.J., Funahashi, A., Doyle, J.C., Kitano, H. (2006). "Software
Infrastructure for Effective Communication and Reuse of Computational Models".
663:: A mathematical expression used to determine the initial conditions of a model. This type of structure can only be used to define how the value of a variable can be calculated from other values and variables at the start of simulated time.
470:
position and other aspects of a graph's layout; the additional details necessary to complete the graph—namely, how the visual aspects are meant to be rendered— are the purview of the separate SBML Level 3 package called
708:. Since SBML is encoded in XML and in particular uses MathML for representing mathematics, the format is not human-readable. As a result, other groups have developed human-readable formats that can be converted to and from SBML.
235:, Japan, in November 2000 as a satellite workshop of the ICSB 2000 conference. After further revisions, discussions and software implementations, the Caltech team issued a specification for SBML Level 1, Version 1 in March 2001.
633:: A well-stirred container of a particular type and finite-size where species may be located. A model may contain multiple compartments of the same compartment type. Every species in a model must be located in a compartment.
1277:; Minch, E.; Mjolsness, E.D.; Nakayama, Y.; Nelson, M.R.; Nielsen, P. F.; Sakurada, T.; Schaff, J. C.; Shapiro, B.E.; Shimizu, T. S.; Spence, H. D.; Stelling, J.; Takahashi, K.; Tomita, M.; Wagner, J.; Wang, J. (2003).
250:
By this time, the team of SBML Editors (who reconcile proposals for changes and write a coherent final specification document) had changed and now consisted of Andrew Finney, Michael Hucka and
Nicolas Le Novère.
627:(only in SBML Level 2): A type of entity that can participate in reactions. Examples of species types include ions such as Ca, molecules such as glucose or ATP, binding sites on a protein, and more.
951:
uses the
Javascript version. Antimony supports SBML Level 3, version 2. Antimony also supports the following SBML packages: Hierarchical Model Composition, Flux Balance Constraints, and Distributions.
687:: A statement describing an instantaneous, discontinuous change in a set of variables of any type (species concentration, compartment size or parameter value) when a triggering condition is satisfied.
215:
network models in the BioThermoKinetics (BTK) group. The same groups who attended the first Caltech workshop met again on April 28–29, 2000, at the first of a newly created meeting series called
223:
was needed to enable the exchange of models between software tools as part of any functioning interoperability framework, and the workshop attendees decided the format should be encoded in
2433:
453:
dynamics are represented by means of state transition graphs (or other Kripke structures ) in which the nodes are the reachable states and the edges are the state transitions.
166:
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
1154:
Systems Biology (ICSB). The community effort is coordinated by an elected editorial board made up of five members. Each editor is elected for a 3-year non-renewable term.
1366:
Hucka, M.; Finney, A.; Bornstein, B. J.; Keating, S. M.; Shapiro, B. E.; Matthews, J.; Kovitz, B. L.; Schilstra, M. J.; Funahashi, A.; Doyle, J. C.; Kitano, H. (2004).
1947:
1606:
615:: A named definition of a new unit of measure, or a redefinition of an existing SBML default unit. Named units can be used in the expression of quantities in a model.
408:
specification is a complete format that can be used alone. Additional Level 3 packages can be layered on to this core to provide additional, optional features.
2474:
388:
Open-source software infrastructure such as libSBML and JSBML allows developers to support all Levels of SBML their software with a minimum amount of effort.
1368:"Evolving a lingua franca and associated software infrastructure for computational systems biology: The Systems Biology Markup Language (SBML) project"
696:
SBML is primarily a format for the exchange of systems biology models between software modeling tools or for archiving models in repositories such as
491:
detailed above have all reached the acceptance stage. The table below gives a brief summary of packages that are currently in the development phase.
1834:"Validation of qualitative models of genetic regulatory networks by model checking: Analysis of the nutritional stress response in Escherichia coli"
270:
Version 5 introduced a facility to use nested annotations within SBML's annotation format (an annotation format that is based on a subset of
1257:
558:
Object structures for representing entity pools with multiple states and composed of multiple components, and reaction rules involving them
432:") was first released in February, 2013. Import revisions were introduced as part of Version 2, released in September, 2015. The "
302:
enable models to be shared and published in a form that other researchers can use even when working with different software environments;
2402:
1234:
211:
525:
Support for encoding models that sample values from statistical distributions or specify statistics associated with numerical values
2374:
2055:
1431:
1832:
Batt, Gregory; Ropers, Delphine; de Jong, Hidde; Geiselmann, Johannes; Mateescu, Radu; Page, Michel; Schneider, Dominique (2005).
2177:
Choi, Kiri; Medley, J. Kyle; König, Matthias; Stocking, Kaylene; Smith, Lucian; Gu, Stanley; Sauro, Herbert M. (September 2018).
2128:
Garfinkel, David (August 1968). "A machine-independent language for the simulation of complex chemical and biochemical systems".
315:—an exchange format used by different present-day software tools to communicate the essential aspects of a computational model.
299:
enable the use of multiple software tools without having to rewrite models to conform to every tool's idiosyncratic file format;
1547:
1525:
1503:
1252:
Encyclopedia of Systems Biology Dubitzky, W., Wolkenhauer, O., Yokota, H., Cho, K.-H. (Eds.) SBML, pp2057-2062 Springer 2013
271:
1146:
As of February 2020, nearly 300 software systems advertise support for SBML. A current list is available in the form of the
2469:
1174:
721:
package for Python is required to assist in the conversion. Currently, SBML-shorthand supports SBML Level 3, version 1.
657:
is used in a generic sense to refer to named quantities regardless of whether they are constants or variables in a model.
1170:
239:
186:, and many others. It has been proposed as a standard for representing computational models in systems biology today.
78:
1279:"The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models"
569:
Support for defining the graphical symbols and glyphs used in a diagram of the model; adjunct to the layout package
238:
SBML Level 2 was conceived at the 5th Workshop on Software Platforms for Systems Biology, held in July 2002, at the
932:
621:(only in SBML Level 2): A type of location where reacting entities such as chemical substances may be located.
340:
724:
The following code is an example of SBML-shorthand being used to describe the simple enzyme-substrate mechanism.
580:
Support for a fine-grained indication of SBML elements that have been changed by the presence of another package
194:
Late in the year 1999 through early 2000, with funding from the Japan Science and Technology Corporation (JST),
2479:
2438:
1941:
1600:
1229:
309:
SBML is not an attempt to define a universal language for quantitative models. SBML's purpose is to serve as a
179:
374:
There are currently three Levels of SBML defined. The current Versions within those Levels are the following:
1620:
Krause, Falko; Uhlendorf, Jannis; Lubitz, Timo; Schulz, Marvin; Klipp, Edda; Liebermeister, Wolfram (2009).
1290:
1162:
591:
Support for describing processes that involve a spatial component, and describing the geometries involved
2367:
2025:
602:
A model definition in SBML Levels 2 and 3 consists of lists of one or more of the following components:
2093:
Sauro, Herbert M. (1993). "SCAMP: a general-purpose simulator and metabolic control analysis program".
1886:
1713:
1468:
1456:
1274:
167:
1295:
1185:
and other languages are developed partly by the SBML Team and partly by the broader SBML community.
1459:(2008). "The markup is the model: Reasoning about systems biology models in the Semantic Web era".
344:
163:
954:
The following example illustrates Antimony being used to describe a simple enzyme-kinetics model:
1204:
284:
183:
36:
705:
1569:
202:
assembled a small team of researchers to work on developing better software infrastructure for
17:
2342:
2287:
2208:
2179:"Tellurium: An extensible python-based modeling environment for systems and synthetic biology"
2145:
2110:
2051:
2006:
1962:
1914:
1855:
1814:
1765:
1694:
1643:
1484:
1390:
1345:
1310:
1253:
171:
2254:
Rodriguez, Nicolas; Pettit, Jean-Baptiste; Dalle Pezze, Piero; Li, Lu; Henry, Arnaud (2016).
2360:
2277:
2267:
2198:
2190:
2137:
2102:
1996:
1904:
1894:
1845:
1804:
1796:
1755:
1747:
1684:
1674:
1633:
1476:
1382:
1367:
1337:
1300:
378:
Level 3 Version 2 Core, for which the final Release 2 specification was issued 26 April 2019
123:
697:
207:
105:
1661:
Alm, Rebekka; Waltemath, Dagmar; Wolfien, Markus; Wolkenhauer, Olaf; Henkel, Ron (2015).
2072:
1890:
1472:
2282:
2255:
2203:
2178:
1909:
1874:
1809:
1784:
1760:
1735:
1689:
1662:
1270:
243:
203:
195:
175:
335:
the model's dynamic behavior. Or, alternatively, a package might construct a discrete
305:
ensure the survival of models beyond the lifetime of the software used to create them.
2463:
2448:
2194:
2141:
2106:
1850:
1833:
1328:
Finney, A.; Hucka, M. (2003). "Systems biology markup language: Level 2 and beyond".
311:
199:
2024:
Ralph Gauges; Sven Sahle; Katjia Wengler; Frank T. Bergmann & Sarah M. Keating.
2001:
1984:
1638:
1621:
1305:
1278:
1452:
717:
or use GUI tools. Two Python tools are provided, mod2sbml.py and sbml2mod.py. The
2338:
466:
Level 3 package, and a specification was formally released in August, 2013.
1178:
1158:
609:: A named mathematical function that may be used throughout the rest of a model.
1480:
404:
Development of SBML Level 3 has been proceeding in a modular fashion. The
2272:
1679:
336:
259:
48:
2082:. Proceedings of the 9th International Meeting on BioThermoKinetics: 221–228.
2306:
1899:
701:
2291:
2212:
2010:
1918:
1859:
1818:
1769:
1698:
1647:
1488:
1394:
1349:
1314:
393:
2149:
2114:
1386:
258:
valid.) Version 4 was finalized after the SBML Forum meeting held in
1800:
2383:
1341:
718:
2240:
2226:
2163:
1147:
948:
482:" package is available, but it has not yet been officially finalized.
2417:
2412:
2397:
1875:"Emergent decision-making in biological signal transduction networks"
1873:
Helikar, Tomas; Konvalina, John; Heidel, Jack; Rogers, Jim A (2008).
1751:
1224:
1214:
1209:
1182:
266:
expansion of SBML's features and capabilities going into the future.
262:, Sweden, as a satellite workshop of ICSB 2008 in the fall of 2008.
1166:
2443:
1783:
Oberhardt, Matthew A; Palsson, Bernhard O; Papin, Jason A (2009).
1409:
1219:
943:
232:
1593:
Systems Modeling in Cell Biology: From Concepts to Nuts and Bolts
1161:
libraries for incorporating SBML into software programmed in the
536:
Support for creating and destroying entities during a simulation
2307:"MIME Media Type for the Systems Biology Markup Language (SBML)"
1983:
Gauges, Ralph; Rost, Ursula; Sahle, Sven; Wegner, Katja (2006).
1269:
Hucka, M.; Finney, A.; Sauro, H. M.; Bolouri, H.; Doyle, J. C.;
1192:
1189:
2356:
1663:"Annotation-based feature extraction from sets of SBML models"
224:
159:
115:
1714:"SBML Level 3 Package: Flux Balance Constraints ('fbc')"
1548:"The 5th Workshop on Software Platforms for Systems Biology"
1526:"The 2nd Workshop on Software Platforms for Systems Biology"
1504:"The 1st Workshop on Software Platforms for Systems Biology"
1734:
Orth, Jeffrey D; Thiele, Ines; Palsson, Bernhard O (2010).
2352:
2050:(1 ed.). Boca Raton, Fla.: Chapman & Hall / CRC.
1622:"Annotation and merging of SBML models with semanticSBML"
478:"). As of November 2015, a draft specification for the "
1785:"Applications of genome-scale metabolic reconstructions"
2347:
416:
The Hierarchical Model Composition package, known as "
323:
SBML can encode models consisting of entities (called
2073:"JARNAC: a system for interactive metabolic analysis"
653:: A quantity with a symbolic name. In SBML, the term
219:. It became clear during the second workshop that a
2426:
2390:
1157:Tools such as an online model validator as well as
139:
134:
121:
111:
101:
77:
59:
47:
35:
2333:
1432:"ANNOUNCEMENT: Portable Metabolic Binary Standard"
217:Workshop on Software Platforms for Systems Biology
2026:"SBML Level 3 Package: Rendering ('render')"
428:The Flux Balance Constraints package (nicknamed "
1879:Proceedings of the National Academy of Sciences
1932:Clarke, E.M., Grumberg, O., Peled, DA (1999).
1361:
1359:
2368:
8:
1946:: CS1 maint: multiple names: authors list (
1605:: CS1 maint: multiple names: authors list (
514:Support for expressing arrays of components
30:
1985:"A model diagram layout extension for SBML"
371:supersede old Versions of that same Level.
2375:
2361:
2353:
1712:Brett G. Olivier & Frank T. Bergmann.
2348:COmputational Modeling in BIology NEtwork
2281:
2271:
2202:
2000:
1908:
1898:
1849:
1808:
1759:
1688:
1678:
1637:
1304:
1294:
327:in SBML) acted upon by processes (called
2048:Stochastic modelling for systems biology
493:
1245:
231:Platforms for Systems Biology, held in
158:) is a representation format, based on
2339:SBML-related presentations and posters
2256:"The systems biology format converter"
1939:
1598:
339:representation of the model and use a
84:SBML Level 3 Version 2 Core, Release 2
31:Systems Biology Markup Language (SBML)
29:
2475:Industry-specific XML-based standards
552:Multistate and Multicomponent species
27:XML file format for biological models
7:
1235:Systems Biology Graphical Notation
221:common model representation format
212:California Institute of Technology
25:
2130:Computers and Biomedical Research
639:: A pool of entities of the same
2195:10.1016/j.biosystems.2018.07.006
2046:Wilkinson, Darren James (2006).
1736:"What is flux balance analysis?"
1330:Biochemical Society Transactions
162:, for communicating and storing
1667:Journal of Biomedical Semantics
152:Systems Biology Markup Language
18:Systems Biology Markup Language
2311:IETF Request for Comments 3823
2305:Kovitz, Benjamin (June 2004).
2107:10.1093/bioinformatics/9.4.441
1851:10.1093/bioinformatics/bti1048
1595:. MIT Press. pp. 369–378.
1461:Journal of Theoretical Biology
547:A means for grouping elements
412:Hierarchical Model Composition
343:simulation method such as the
295:SBML has three main purposes:
1:
2166:. UW Sauro Lab. 25 June 2023.
2002:10.1093/bioinformatics/btl195
1639:10.1093/bioinformatics/btp642
1306:10.1093/bioinformatics/btg015
1195:type, specified by RFC 3823.
947:on the web. The website tool
933:Antimony biochemical language
2243:. UW Sauro Lab. 6 July 2023.
2229:. UW Sauro Lab. 6 July 2023.
2142:10.1016/0010-4809(68)90006-2
1100:// Variable initializations
444:The Qualitative Models or "
381:Level 2 Version 5 Release 1
240:University of Hertfordshire
2496:
2080:Animating the Cellular Map
1481:10.1016/j.jtbi.2007.10.023
1049:// Species initializations
930:
486:Packages under development
2273:10.1186/s12859-016-1000-2
1789:Molecular Systems Biology
1680:10.1186/s13326-015-0014-4
1230:Systems Biology Ontology
956:
726:
424:Flux Balance Constraints
49:Internet media type
2071:Sauro, Herbert (2001).
1900:10.1073/pnas.0705088105
1430:bionet.metabolic-reg.
1150:, hosted at SBML.org.
643:located in a specific
204:computational modeling
65:; 23 years ago
1570:"The 13th SBML Forum"
400:Level 3 packages
88:; 5 years ago
2470:XML markup languages
1963:"The 8th SBML Forum"
1740:Nature Biotechnology
1188:SBML is an official
692:DSLs Supporting SBML
168:biological phenomena
164:computational models
54:application/sbml+xml
1891:2008PNAS..105.1913H
1801:10.1038/msb.2009.77
1473:2008JThBi.252..538K
1387:10.1049/sb:20045008
1148:SBML Software Guide
607:Function definition
363:SBML is defined in
359:Levels and versions
345:Gillespie algorithm
244:Ft. Lauderdale
184:infectious diseases
180:regulatory networks
32:
2260:BMC Bioinformatics
2241:"MakeSBML website"
2227:"MakeSBML website"
2164:"sys-bio/antimony"
1342:10.1042/BST0311472
1205:BioModels Database
661:Initial Assignment
440:Qualitative Models
396:page of SBML.org.
285:BioModels Database
172:metabolic networks
112:Extended from
86:26 April 2019
37:Filename extension
2457:
2456:
2343:Nature Precedings
1410:"History of SBML"
1258:978-1-4419-9863-7
595:
594:
585:Spatial Processes
574:Required Elements
384:Level 1 Version 2
319:Main capabilities
148:
147:
63:2 March 2001
16:(Redirected from
2487:
2377:
2370:
2363:
2354:
2322:
2321:
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2015:
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1952:
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1929:
1923:
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1885:(6): 1913–1918.
1870:
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1752:10.1038/nbt.1614
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1408:Hucka, Michael.
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2018:
1995:(15): 1879–85.
1982:
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1942:cite conference
1938:
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1375:Systems Biology
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1296:10.1.1.562.1085
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2329:
2328:External links
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2169:
2155:
2120:
2101:(4): 441–450.
2095:Bioinformatics
2085:
2063:
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2038:
2016:
1989:Bioinformatics
1975:
1953:
1934:Modal Checking
1924:
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1838:Bioinformatics
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1726:
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1653:
1626:Bioinformatics
1612:
1582:
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1467:(3): 538–543.
1444:
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1283:Bioinformatics
1261:
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1232:
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928:
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2057:1-58488-540-8
2053:
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2020:
2017:
2012:
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1336:(6): 1472–3.
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729:@compartments
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519:Distributions
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312:lingua franca
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200:John C. Doyle
197:
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133:
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100:
82:
80:
76:
62:
58:
52:
50:
46:
40:
38:
34:
19:
2407:
2314:. Retrieved
2310:
2300:
2263:
2259:
2249:
2235:
2221:
2186:
2182:
2172:
2158:
2136:(1): 31–44.
2133:
2129:
2123:
2098:
2094:
2088:
2079:
2066:
2047:
2041:
2029:. Retrieved
2019:
1992:
1988:
1978:
1966:. Retrieved
1956:
1936:. MIT Press.
1933:
1927:
1882:
1878:
1868:
1841:
1837:
1827:
1792:
1788:
1778:
1746:(3): 245–8.
1743:
1739:
1729:
1717:. Retrieved
1707:
1670:
1666:
1656:
1632:(3): 421–2.
1629:
1625:
1615:
1592:
1585:
1573:. Retrieved
1563:
1551:. Retrieved
1541:
1529:. Retrieved
1519:
1507:. Retrieved
1497:
1464:
1460:
1447:
1435:. Retrieved
1425:
1413:. Retrieved
1403:
1381:(1): 41–53.
1378:
1374:
1333:
1329:
1323:
1286:
1282:
1264:
1248:
1187:
1156:
1152:
1145:
953:
940:
936:
723:
715:
695:
684:
678:
672:
666:
660:
654:
650:
644:
641:species type
640:
636:
630:
625:Species type
624:
618:
612:
606:
601:
503:Description
497:Package name
489:
479:
475:
474:(nicknamed "
471:
468:
462:
460:
449:
445:
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429:
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417:
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403:
390:
387:
373:
368:
364:
362:
353:
349:
333:
328:
324:
322:
310:
308:
294:
281:
278:The language
268:
264:
256:
252:
248:
237:
229:
220:
216:
193:
170:, including
155:
151:
149:
2031:24 November
1961:SBML Team.
1719:24 November
1568:SBML Team.
1546:SBML Team.
1531:13 December
1524:SBML Team.
1502:SBML Team.
1453:Kell, D. B.
1437:13 December
1179:Mathematica
1159:open-source
804:@parameters
645:compartment
631:Compartment
341:Monte Carlo
246:, Florida.
124:Open format
42:.xml, .sbml
2464:Categories
2266:(1): 1–7.
2183:Biosystems
1844:: i19–28.
1509:3 December
1457:Mendes, P.
1275:Mendes, P.
1271:Kitano, H.
1241:References
1013:Conversion
885:Conversion
825:@reactions
706:JWS Online
673:Constraint
337:stochastic
260:Gothenburg
178:pathways,
93:2019-04-26
70:2001-03-02
2427:Standards
2316:3 January
2189:: 74–79.
1968:3 January
1575:3 January
1553:3 January
1415:3 January
1291:CiteSeerX
1142:Community
1052:Substrate
989:Substrate
965:Substrate
858:Substrate
837:Substrate
750:Substrate
702:BioModels
655:parameter
651:Parameter
598:Structure
563:Rendering
472:Rendering
461:The SBML
329:reactions
2292:27044654
2213:30053414
2011:16709586
1919:18250321
1860:15961457
1819:19888215
1770:20212490
1699:25904997
1648:19933161
1489:18054049
1395:17052114
1350:14641091
1315:12611808
1199:See also
949:makesbml
927:Antimony
741:@species
679:Reaction
530:Dynamics
291:Purposes
2391:Formats
2384:COMBINE
2283:4820913
2204:6108935
2150:5743538
2115:8402211
1910:2538858
1887:Bibcode
1810:2795471
1795:: 320.
1761:3108565
1690:4405863
1469:Bibcode
1088:Product
1076:Complex
1043:Complex
1025:Product
1019:Complex
1007:Complex
977:Complex
959:binding
909:Complex
894:Product
888:Complex
876:Complex
849:Complex
834:Binding
795:Product
780:Complex
719:libSBML
637:Species
588:spatial
522:distrib
325:species
190:History
135:Website
91: (
68: (
2434:MIRIAM
2418:CellML
2413:SED-ML
2398:BioPAX
2290:
2280:
2211:
2201:
2148:
2113:
2054:
2009:
1917:
1907:
1858:
1817:
1807:
1768:
1758:
1697:
1687:
1673:: 20.
1646:
1487:
1393:
1348:
1313:
1293:
1256:
1225:MIRIAM
1215:CellML
1210:BioPAX
1183:MATLAB
1175:Python
1064:Enzyme
1031:Enzyme
995:Enzyme
971:Enzyme
900:Enzyme
864:Enzyme
843:Enzyme
765:Enzyme
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