[ { "id": "authors:2s3jq-t6239", "collection": "authors", "collection_id": "2s3jq-t6239", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200827-073238775", "type": "article", "title": "SBML Level 3: an extensible format for the exchange and reuse of biological models", "author": [ { "family_name": "Keating", "given_name": "Sarah M.", "orcid": "0000-0002-3356-3542", "clpid": "Keating-S-M" }, { "family_name": "Waltemath", "given_name": "Dagmar", "orcid": "0000-0002-5886-5563" }, { "family_name": "K\u00f6nig", "given_name": "Matthias", "orcid": "0000-0003-1725-179X" }, { "family_name": "Zhang", "given_name": "Fengkai", "orcid": "0000-0001-7112-9328" }, { "family_name": "Dr\u00e4ger", "given_name": "Andreas", "orcid": "0000-0002-1240-5553" }, { "family_name": "Chaouiya", "given_name": "Claudine", "orcid": "0000-0003-2350-0756" }, { "family_name": "Bergmann", "given_name": "Frank T.", "orcid": "0000-0001-5553-4702" }, { "family_name": "Finney", "given_name": "Andrew" }, { "family_name": "Gillespie", "given_name": "Colin S.", "orcid": "0000-0003-1787-0275" }, { "family_name": "Helikar", "given_name": "Tom\u00e1\u0161", "orcid": "0000-0003-3653-1906" }, { "family_name": "Hoops", "given_name": "Stefan", "orcid": "0000-0001-8503-8371" }, { "family_name": "Malik\u2010Sheriff", "given_name": "Rahuman S.", "orcid": "0000-0003-0705-9809" }, { "family_name": "Moodie", "given_name": "Stuart L.", "orcid": "0000-0001-6191-5595" }, { "family_name": "Moraru", "given_name": "Ion I.", "orcid": "0000-0002-3746-9676" }, { "family_name": "Myers", "given_name": "Chris J.", "orcid": "0000-0002-8762-8444" }, { "family_name": "Naldi", "given_name": "Aur\u00e9lien", "orcid": "0000-0002-6495-2655" }, { "family_name": "Olivier", "given_name": "Brett G.", "orcid": "0000-0002-5293-5321", "clpid": "Olivier-B-G" }, { "family_name": "Sahle", "given_name": "Sven" }, { "family_name": "Schaff", "given_name": "James C.", "orcid": "0000-0003-3286-7736" }, { "family_name": "Smith", "given_name": "Lucian P.", "orcid": "0000-0001-7002-6386", "clpid": "Smith-L-P" }, { "family_name": "Swat", "given_name": "Maciej J." }, { "family_name": "Thieffry", "given_name": "Denis", "orcid": "0000-0003-0271-1757" }, { "family_name": "Watanabe", "given_name": "Leandro", "orcid": "0000-0001-7030-8690" }, { "family_name": "Wilkinson", "given_name": "Darren J.", "orcid": "0000-0003-0736-802X" }, { "family_name": "Blinov", "given_name": "Michael L.", "orcid": "0000-0002-9363-9705" }, { "family_name": "Begley", "given_name": "Kimberly", "orcid": "0000-0002-1642-7493", "clpid": "Begley-K" }, { "family_name": "Faeder", "given_name": "James R.", "orcid": "0000-0001-8127-609X" }, { "family_name": "G\u00f3mez", "given_name": "Harold F." }, { "family_name": "Hamm", "given_name": "Thomas M.", "orcid": "0000-0001-9579-7267" }, { "family_name": "Inagaki", "given_name": "Yuichiro", "orcid": "0000-0003-4011-8487" }, { "family_name": "Liebermeister", "given_name": "Wolfram", "orcid": "0000-0002-2568-2381" }, { "family_name": "Lister", "given_name": "Allyson L.", "orcid": "0000-0002-7702-4495" }, { "family_name": "Lucio", "given_name": "Daniel", "orcid": "0000-0002-8912-7213" }, { "family_name": "Mjolsness", "given_name": "Eric", "orcid": "0000-0002-9085-9171" }, { "family_name": "Proctor", "given_name": "Carole J.", "orcid": "0000-0002-1366-1399" }, { "family_name": "Raman", "given_name": "Karthik", "orcid": "0000-0002-9311-7093" }, { "family_name": "Rodriguez", "given_name": "Nicolas", "orcid": "0000-0002-9290-7894" }, { "family_name": "Shaffer", "given_name": "Clifford A.", "orcid": "0000-0003-0001-0295" }, { "family_name": "Shapiro", "given_name": "Bruce E." }, { "family_name": "Stelling", "given_name": "Joerg", "orcid": "0000-0002-1145-891X" }, { "family_name": "Swainston", "given_name": "Neil", "orcid": "0000-0001-7020-1236" }, { "family_name": "Tanimura", "given_name": "Naoki" }, { "family_name": "Wagner", "given_name": "John" }, { "family_name": "Meier\u2010Schellersheim", "given_name": "Martin", "orcid": "0000-0002-8754-6377" }, { "family_name": "Sauro", "given_name": "Herbert M.", "orcid": "0000-0002-3659-6817" }, { "family_name": "Palsson", "given_name": "Bernhard.", "orcid": "0000-0003-2357-6785" }, { "family_name": "Bolouri", "given_name": "Hamid" }, { "family_name": "Kitano", "given_name": "Hiroaki", "orcid": "0000-0002-3589-1953" }, { "family_name": "Funahashi", "given_name": "Akira", "orcid": "0000-0003-0605-239X" }, { "family_name": "Hermjakob", "given_name": "Henning", "orcid": "0000-0001-8479-0262" }, { "family_name": "Doyle", "given_name": "John C.", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Hucka", "given_name": "Michael", "orcid": "0000-0001-9105-5960", "clpid": "Hucka-M" }, { "family_name": "Adams", "given_name": "Richard R." }, { "family_name": "Allen", "given_name": "Nicholas A." }, { "family_name": "Angermann", "given_name": "Bastian R." }, { "family_name": "Antoniotti", "given_name": "Marco" }, { "family_name": "Bader", "given_name": "Gary D." }, { "family_name": "\u010cerven\u00fd", "given_name": "Jan" }, { "family_name": "Courtot", "given_name": "M\u00e9lanie" }, { "family_name": "Cox", "given_name": "Chris D." }, { "family_name": "Dalle Pezze", "given_name": "Piero" }, { "family_name": "Demir", "given_name": "Emek" }, { "family_name": "Denney", "given_name": "William S." }, { "family_name": "Dharuri", "given_name": "Harish" }, { "family_name": "Dorier", "given_name": "Julien" }, { "family_name": "Drasdo", "given_name": "Dirk" }, { "family_name": "Ebrahim", "given_name": "Ali" }, { "family_name": "Eichner", "given_name": "Johannes" }, { "family_name": "Elf", "given_name": "Johan" }, { "family_name": "Endler", "given_name": "Lukas" }, { "family_name": "Evelo", "given_name": "Chris T." }, { "family_name": "Flamm", "given_name": "Christoph" }, { "family_name": "Fleming", "given_name": "Ronan M. T." }, { "family_name": "Fr\u00f6hlich", "given_name": "Martina" }, { "family_name": "Glont", "given_name": "Mihai" }, { "family_name": "Gon\u00e7alves", "given_name": "Emanuel" }, { "family_name": "Golebiewski", "given_name": "Martin" }, { "family_name": "Grabski", "given_name": "Hovakim" }, { "family_name": "Gutteridge", "given_name": "Alex" }, { "family_name": "Hachmeister", "given_name": "Damon" }, { "family_name": "Harris", "given_name": "Leonard A." }, { "family_name": "Heavner", "given_name": "Benjamin D." }, { "family_name": "Henkel", "given_name": "Ron" }, { "family_name": "Hlavacek", "given_name": "William S." }, { "family_name": "Hu", "given_name": "Bin" }, { "family_name": "Hyduke", "given_name": "Daniel R." }, { "family_name": "Jong", "given_name": "Hidde" }, { "family_name": "Juty", "given_name": "Nick" }, { "family_name": "Karp", "given_name": "Peter D" }, { "family_name": "Karr", "given_name": "Jonathan R." }, { "family_name": "Kell", "given_name": "Douglas B." }, { "family_name": "Keller", "given_name": "Roland" }, { "family_name": "Kiselev", "given_name": "Ilya" }, { "family_name": "Klamt", "given_name": "Steffen" }, { "family_name": "Klipp", "given_name": "Edda" }, { "family_name": "Kn\u00fcpfer", "given_name": "Christian" }, { "family_name": "Kolpakov", "given_name": "Fedor" }, { "family_name": "Krause", "given_name": "Falko" }, { "family_name": "Kutmon", "given_name": "Martina" }, { "family_name": "Laibe", "given_name": "Camille" }, { "family_name": "Lawless", "given_name": "Conor" }, { "family_name": "Li", "given_name": "Lu" }, { "family_name": "Loew", "given_name": "Leslie M." }, { "family_name": "Machne", "given_name": "Rainer" }, { "family_name": "Matsuoka", "given_name": "Yukiko" }, { "family_name": "Mendes", "given_name": "Pedro" }, { "family_name": "Mi", "given_name": "Huaiyu" }, { "family_name": "Mittag", "given_name": "Florian" }, { "family_name": "Monteiro", "given_name": "Pedro T" }, { "family_name": "Natarajan", "given_name": "Kedar Nath", "orcid": "0000-0002-9264-1280" }, { "family_name": "Nielsen", "given_name": "Poul M. F." }, { "family_name": "Nguyen", "given_name": "Tramy" }, { "family_name": "Palmisano", "given_name": "Alida" }, { "family_name": "Pettit", "given_name": "Jean\u2010Baptiste" }, { "family_name": "Pfau", "given_name": "Thomas" }, { "family_name": "Phair", "given_name": "Robert D." }, { "family_name": "Radivoyevitch", "given_name": "Tomas" }, { "family_name": "Rohwer", "given_name": "Johann M." }, { "family_name": "Ruebenacker", "given_name": "Oliver A." }, { "family_name": "Saez\u2010Rodriguez", "given_name": "Julio" }, { "family_name": "Scharm", "given_name": "Martin" }, { "family_name": "Schmidt", "given_name": "Henning" }, { "family_name": "Schreiber", "given_name": "Falk" }, { "family_name": "Schubert", "given_name": "Michael" }, { "family_name": "Schulte", "given_name": "Roman" }, { "family_name": "Sealfon", "given_name": "Stuart C." }, { "family_name": "Smallbone", "given_name": "Kieran" }, { "family_name": "Soliman", "given_name": "Sylvain" }, { "family_name": "Stefan", "given_name": "Melanie I." }, { "family_name": "Sullivan", "given_name": "Devin P." }, { "family_name": "Takahashi", "given_name": "Koichi" }, { "family_name": "Teusink", "given_name": "Bas" }, { "family_name": "Tolnay", "given_name": "David" }, { "family_name": "Vazirabad", "given_name": "Ibrahim" }, { "family_name": "Kamp", "given_name": "Axel" }, { "family_name": "Wittig", "given_name": "Ulrike" }, { "family_name": "Wrzodek", "given_name": "Clemens" }, { "family_name": "Wrzodek", "given_name": "Finja" }, { "family_name": "Xenarios", "given_name": "Ioannis" }, { "family_name": "Zhukova", "given_name": "Anna" }, { "family_name": "Zucker", "given_name": "Jeremy" }, { "literal": "SBML Level 3 Community members" } ], "abstract": "Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction\u2010based models and packages that extend the core with features suited to other model types including constraint\u2010based models, reaction\u2010diffusion models, logical network models, and rule\u2010based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single\u2010cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution.", "doi": "10.15252/msb.20199110", "issn": "1744-4292", "publisher": "European Molecular Biology Organization", "publication": "Molecular Systems Biology", "publication_date": "2020-08", "series_number": "8", "volume": "16", "issue": "8", "pages": "Art. No. e9110" }, { "id": "authors:f7evg-ea529", "collection": "authors", "collection_id": "f7evg-ea529", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200812-071428761", "type": "article", "title": "Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1", "author": [ { "family_name": "Smith", "given_name": "Lucian P.", "orcid": "0000-0001-7002-6386", "clpid": "Smith-L-P" }, { "family_name": "Moodie", "given_name": "Stuart L.", "clpid": "Moodie-S-L" }, { "family_name": "Bergmann", "given_name": "Frank T.", "orcid": "0000-0001-5553-4702", "clpid": "Bergmann-F-T" }, { "family_name": "Gillespie", "given_name": "Colin", "clpid": "Gillespie-C-S" }, { "family_name": "Keating", "given_name": "Sarah M.", "orcid": "0000-0002-3356-3542", "clpid": "Keating-S-M" }, { "family_name": "K\u00f6nig", "given_name": "Matthias", "orcid": "0000-0003-1725-179X", "clpid": "K\u00f6nig-M" }, { "family_name": "Myers", "given_name": "Chris J.", "orcid": "0000-0002-8762-8444", "clpid": "Myers-C-J" }, { "family_name": "Swat", "given_name": "Maciek J.", "clpid": "Swat-M-J" }, { "family_name": "Wilkinson", "given_name": "Darren J.", "orcid": "0000-0003-0736-802X", "clpid": "Wilkinson-D-J" }, { "family_name": "Hucka", "given_name": "Michael", "orcid": "0000-0001-9105-5960", "clpid": "Hucka-M" } ], "abstract": "Biological models often contain elements that have inexact numerical values, since they are based on values that are stochastic in nature or data that contains uncertainty. The Systems Biology Markup Language (SBML) Level 3 Core specification does not include an explicit mechanism to include inexact or stochastic values in a model, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactic constructs. The SBML Distributions package for SBML Level 3 adds the necessary features to allow models to encode information about the distribution and uncertainty of values underlying a quantity.", "doi": "10.1515/jib-2020-0018", "issn": "1613-4516", "publisher": "Informationsmanagement in der Biotechnologie", "publication": "Journal of Integrative Bioinformatics", "publication_date": "2020-06", "series_number": "2-3", "volume": "17", "issue": "2-3", "pages": "Art. No. 20200018" }, { "id": "authors:8ztff-8xy27", "collection": "authors", "collection_id": "8ztff-8xy27", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200708-073700691", "type": "article", "title": "The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)", "author": [ { "family_name": "Waltemath", "given_name": "Dagmar", "orcid": "0000-0002-5886-5563", "clpid": "Waltemath-D" }, { "family_name": "Golebiewski", "given_name": "Martin", "clpid": "Golebiewski-M" }, { "family_name": "Blinov", "given_name": "Michael L.", "clpid": "Blinov-M-L" }, { "family_name": "Gleeson", "given_name": "Padraig", "clpid": "Gleeson-P" }, { "family_name": "Hermjakob", "given_name": "Henning", "clpid": "Hermjakob-H" }, { "family_name": "Hucka", "given_name": "Michael", "orcid": "0000-0001-9105-5960", "clpid": "Hucka-M" }, { "family_name": "Inau", "given_name": "Esther Thea", "clpid": "Inau-E-T" }, { "family_name": "Keating", "given_name": "Sarah M.", "orcid": "0000-0002-3356-3542", "clpid": "Keating-S-M" }, { "family_name": "K\u00f6nig", "given_name": "Matthias", "orcid": "0000-0003-1725-179X", "clpid": "K\u00f6nig-M" }, { "family_name": "Krebs", "given_name": "Olga", "clpid": "Krebs-O" }, { "family_name": "Malik-Sheriff", "given_name": "Rahuman S.", "clpid": "Malik-Sheriff-R-S" }, { "family_name": "Nickerson", "given_name": "David", "orcid": "0000-0003-4667-9779", "clpid": "Nickerson-D-P" }, { "family_name": "Oberortner", "given_name": "Ernst", "clpid": "Oberortner-E" }, { "family_name": "Sauro", "given_name": "Herbert M.", "clpid": "Sauro-H-M" }, { "family_name": "Schreiber", "given_name": "Falk", "clpid": "Schreiber-F" }, { "family_name": "Smith", "given_name": "Lucian", "orcid": "0000-0001-7002-6386", "clpid": "Smith-L-P" }, { "family_name": "Stefan", "given_name": "Melanie I.", "clpid": "Stefan-M-I" }, { "family_name": "Wittig", "given_name": "Ulrike", "clpid": "Wittig-U" }, { "family_name": "Myers", "given_name": "Chris J.", "orcid": "0000-0002-8762-8444", "clpid": "Myers-C-J" } ], "abstract": "This paper presents a report on outcomes of the 10th Computational Modeling in Biology Network (COMBINE) meeting that was held in Heidelberg, Germany, in July of 2019. The annual event brings together researchers, biocurators and software engineers to present recent results and discuss future work in the area of standards for systems and synthetic biology. The COMBINE initiative coordinates the development of various community standards and formats for computational models in the life sciences. Over the past 10 years, COMBINE has brought together standard communities that have further developed and harmonized their standards for better interoperability of models and data. COMBINE 2019 was co-located with a stakeholder workshop of the European EU-STANDS4PM initiative that aims at harmonized data and model standardization for in silico models in the field of personalized medicine, as well as with the FAIRDOM PALs meeting to discuss findable, accessible, interoperable and reusable (FAIR) data sharing. This report briefly describes the work discussed in invited and contributed talks as well as during breakout sessions. It also highlights recent advancements in data, model, and annotation standardization efforts. Finally, this report concludes with some challenges and opportunities that this community will face during the next 10 years.", "doi": "10.1515/jib-2020-0005", "issn": "1613-4516", "publisher": "Informationsmanagement in der Biotechnologie", "publication": "Journal of Integrative Bioinformatics", "publication_date": "2020-06", "series_number": "2-3", "volume": "17", "issue": "2-3", "pages": "Art. No. 20200005" }, { "id": "authors:x9nn4-yvh94", "collection": "authors", "collection_id": "x9nn4-yvh94", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200713-124645293", "type": "article", "title": "Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2", "author": [ { "family_name": "Zhang", "given_name": "Fengkai", "orcid": "0000-0001-7112-9328", "clpid": "Zhang-Fengkai" }, { "family_name": "Smith", "given_name": "Lucian P.", "orcid": "0000-0001-7002-6386", "clpid": "Smith-L-P" }, { "family_name": "Blinov", "given_name": "Michael L.", "orcid": "0000-0002-9363-9705", "clpid": "Blinov-M-L" }, { "family_name": "Faeder", "given_name": "James", "orcid": "0000-0001-8127-609X", "clpid": "Faeder-J-R" }, { "family_name": "Hlavacek", "given_name": "William S.", "orcid": "0000-0003-4383-8711", "clpid": "Hlavacek-W-S" }, { "family_name": "Tapia", "given_name": "Jose Juan", "clpid": "Tapia-J-J" }, { "family_name": "Keating", "given_name": "Sarah M.", "orcid": "0000-0002-3356-3542", "clpid": "Keating-S-M" }, { "family_name": "Rodriguez", "given_name": "Nicolas", "clpid": "Rodriguez-N" }, { "family_name": "Dr\u00e4ger", "given_name": "Andreas", "orcid": "0000-0002-1240-5553", "clpid": "Dr\u00e4ger-A" }, { "family_name": "Harris", "given_name": "Leonard A.", "clpid": "Harris-L-A" }, { "family_name": "Finney", "given_name": "Andrew", "clpid": "Finney-A" }, { "family_name": "Hu", "given_name": "Bin", "clpid": "Hu-Bin" }, { "family_name": "Hucka", "given_name": "Michael", "orcid": "0000-0001-9105-5960", "clpid": "Hucka-M" }, { "family_name": "Meier-Schellersheim", "given_name": "Martin", "orcid": "0000-0002-8754-6377", "clpid": "Meier-Schellersheim-M" } ], "abstract": "Rule-based modeling is an approach that permits constructing reaction networks based on the specification of rules for molecular interactions and transformations. These rules can encompass details such as the interacting sub-molecular domains and the states and binding status of the involved components. \n\nConceptually, fine-grained spatial information such as locations can also be provided. Through \"wildcards\" representing component states, entire families of molecule complexes sharing certain properties can be specified as patterns. This can significantly simplify the definition of models involving species with multiple components, multiple states, and multiple compartments. The systems biology markup language (SBML) Level 3 Multi Package Version 1 extends the SBML Level 3 Version 1 core with the \"type\" concept in the Species and Compartment classes. Therefore, reaction rules may contain species that can be patterns and exist in multiple locations. Multiple software tools such as Simmune and BioNetGen support this standard that thus also becomes amedium for exchanging rule-based models. This document provides the specification for Release 2 of Version 1 of the SBML Level 3 Multi package. No design changes have been made to the description of models between Release 1 and Release 2; changes are restricted to the correction of errata and the addition of clarifications.", "doi": "10.1515/jib-2020-0015", "issn": "1613-4516", "publisher": "Informationsmanagement in der Biotechnologie", "publication": "Journal of Integrative Bioinformatics", "publication_date": "2020-06", "series_number": "2-3", "volume": "17", "issue": "2-3", "pages": "Art. No. 20200015" }, { "id": "authors:1ec8y-qr374", "collection": "authors", "collection_id": "1ec8y-qr374", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200706-133639336", "type": "article", "title": "Specifications of standards in systems and synthetic biology: status and developments in 2020", "author": [ { "family_name": "Schreiber", "given_name": "Falk", "clpid": "Schreiber-F" }, { "family_name": "Sommer", "given_name": "Bj\u00f6rn", "clpid": "Sommer-B" }, { "family_name": "Czauderna", "given_name": "Tobias", "clpid": "Czauderna-T" }, { "family_name": "Golebiewski", "given_name": "Martin", "clpid": "Golebiewski-M" }, { "family_name": "Gorochowski", "given_name": "Thomas E.", "clpid": "Gorochowski-T-E" }, { "family_name": "Hucka", "given_name": "Michael", "orcid": "0000-0001-9105-5960", "clpid": "Hucka-M" }, { "family_name": "Keating", "given_name": "Sarah M.", "orcid": "0000-0002-3356-3542", "clpid": "Keating-S-M" }, { "family_name": "K\u00f6nig", "given_name": "Matthias", "orcid": "0000-0003-1725-179X", "clpid": "K\u00f6nig-M" }, { "family_name": "Myers", "given_name": "Chris", "orcid": "0000-0002-8762-8444", "clpid": "Myers-C-J" }, { "family_name": "Nickerson", "given_name": "David", "orcid": "0000-0003-4667-9779", "clpid": "Nickerson-D-P" }, { "family_name": "Waltemath", "given_name": "Dagmar", "orcid": "0000-0002-5886-5563", "clpid": "Waltemath-D" } ], "abstract": "This special issue of the Journal of Integrative Bioinformatics presents papers related to the 10th COMBINE meeting together with the annual update of COMBINE standards in systems and synthetic biology.", "doi": "10.1515/jib-2020-0022", "issn": "1613-4516", "publisher": "Informationsmanagement in der Biotechnologie", "publication": "Journal of Integrative Bioinformatics", "publication_date": "2020-06", "series_number": "2-3", "volume": "17", "issue": "2-3", "pages": "Art. No. 20200022" }, { "id": "authors:thtjw-gg563", "collection": "authors", "collection_id": "thtjw-gg563", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180430-100901666", "type": "article", "title": "SBML Level 3 package: Render, Version 1, Release 1", "author": [ { "family_name": "Bergmann", "given_name": "Frank T.", "orcid": "0000-0001-5553-4702", "clpid": "Bergmann-F-T" }, { "family_name": "Keating", "given_name": "Sarah M.", "orcid": "0000-0002-3356-3542", "clpid": "Keating-S-M" }, { "family_name": "Gauges", "given_name": "Ralph", "clpid": "Gauges-R" }, { "family_name": "Sahle", "given_name": "Sven", "clpid": "Sahle-S" }, { "family_name": "Wengler", "given_name": "Katja", "clpid": "Wengler-K" } ], "abstract": "Many software tools provide facilities for depicting reaction network diagrams in a visual form. Two aspects of such a visual diagram can be distinguished: the layout (i.e.: the positioning and connections) of the elements in the diagram, and the graphical form of the elements (for example, the glyphs used for symbols, the properties of the lines connecting them, and so on). This document describes the SBML Level 3 Render package that complements the SBML Level 3 Layout package and provides a means of capturing the precise rendering of the elements in a diagram. The SBML Level 3 Render package provides a flexible approach to rendering that is independent of both the underlying SBML model and the Layout information. There can be one block of render information that applies to all layouts or an additional block for each layout. Many of the elements used in the current render specification are based on corresponding elements from the SVG specification. This allows us to easily convert a combination of layout information and render information into a SVG drawing.", "doi": "10.1515/jib-2017-0078", "issn": "1613-4516", "publisher": "Informationsmanagement in der Biotechnologie", "publication": "Journal of Integrative Bioinformatics", "publication_date": "2018-04-02", "series_number": "1", "volume": "15", "issue": "1", "pages": "Art. No. 20170078" }, { "id": "authors:8ghxs-99b69", "collection": "authors", "collection_id": "8ghxs-99b69", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180413-161741220", "type": "article", "title": "Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017", "author": [ { "family_name": "Schreiber", "given_name": "Falk", "clpid": "Schreiber-F" }, { "family_name": "Bader", "given_name": "Gary D.", "clpid": "Bader-G-D" }, { "family_name": "Gleeson", "given_name": "Padraig", "clpid": "Gleeson-P" }, { "family_name": "Golebiewski", "given_name": "Martin", "clpid": "Golebiewski-M" }, { "family_name": "Hucka", "given_name": "Michael", "orcid": "0000-0001-9105-5960", "clpid": "Hucka-M" }, { "family_name": "Keating", "given_name": "Sarah M.", "orcid": "0000-0002-3356-3542", "clpid": "Keating-S-M" }, { "family_name": "Le Nov\u00e8re", "given_name": "Nicolas", "orcid": "0000-0002-6309-7327", "clpid": "Le-Nov\u00e8re-N" }, { "family_name": "Myers", "given_name": "Chris", "orcid": "0000-0002-8762-8444", "clpid": "Myers-C-J" }, { "family_name": "Nickerson", "given_name": "David", "orcid": "0000-0003-4667-9779", "clpid": "Nickerson-D-P" }, { "family_name": "Sommer", "given_name": "Bj\u00f6rn", "clpid": "Sommer-B" }, { "family_name": "Waltemath", "given_name": "Dagmar", "orcid": "0000-0002-5886-5563", "clpid": "Waltemath-D" } ], "abstract": "Standards are essential to the advancement of Systems and Synthetic Biology. COMBINE provides a formal body and a centralised platform to help develop and disseminate relevant standards and related resources. The regular special issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards by providing unified, easily citable access. This paper provides an overview of existing COMBINE standards and presents developments of the last year.", "doi": "10.1515/jib-2018-0013", "issn": "1613-4516", "publisher": "Informationsmanagement in der Biotechnologie", "publication": "Journal of Integrative Bioinformatics", "publication_date": "2018-03-29", "series_number": "1", "volume": "15", "issue": "1", "pages": "Art. No. 20180013" }, { "id": "authors:q306x-4ad80", "collection": "authors", "collection_id": "q306x-4ad80", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140211-103736652", "type": "article", "title": "SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools", "author": [ { "family_name": "Chaouiya", "given_name": "Claudine", "orcid": "0000-0003-2350-0756", "clpid": "Chaouiya-C" }, { "family_name": "Ber\u00e9nguier", "given_name": "Duncan", "clpid": "Ber\u00e9nguier-D" }, { "family_name": "Keating", "given_name": "Sarah M.", "orcid": "0000-0002-3356-3542", "clpid": "Keating-S-M" }, { "family_name": "Naldi", "given_name": "Aur\u00e9lien", "clpid": "Naldi-A" }, { "family_name": "van Iersel", "given_name": "Martijn P.", "clpid": "van-Iersel-M-P" }, { "family_name": "Rodriguez", "given_name": "Nicolas", "clpid": "Rodriguez-N" }, { "family_name": "Dr\u00e4ger", "given_name": "Andreas", "orcid": "0000-0002-1240-5553", "clpid": "Dr\u00e4ger-A" }, { "family_name": "B\u00fcchel", "given_name": "Finja", "clpid": "B\u00fcchel-F" }, { "family_name": "Cokelaer", "given_name": "Thomas", "clpid": "Cokelaer-T" }, { "family_name": "Kowal", "given_name": "Bryan", "clpid": "Kowal-B" }, { "family_name": "Wicks", "given_name": "Benjamin", "clpid": "Wicks-B" }, { "family_name": "Gon\u00e7alves", "given_name": "Emanuel", "clpid": "Gon\u00e7alves-E" }, { "family_name": "Dorier", "given_name": "Julien", "orcid": "0000-0002-6717-2451", "clpid": "Dorier-J" }, { "family_name": "Page", "given_name": "Michel", "clpid": "Page-M" }, { "family_name": "Monteiro", "given_name": "Pedro T.", "clpid": "Monteiro-P-T" }, { "family_name": "von Kamp", "given_name": "Axel", "clpid": "von-Kamp-A" }, { "family_name": "Xenarios", "given_name": "Ioannis", "clpid": "Xenarios-I" }, { "family_name": "de Jong", "given_name": "Hidde", "clpid": "de-Jong-H" }, { "family_name": "Hucka", "given_name": "Michael", "orcid": "0000-0001-9105-5960", "clpid": "Hucka-M" }, { "family_name": "Klamt", "given_name": "Steffen", "clpid": "Klamt-S" }, { "family_name": "Thieffry", "given_name": "Denis", "clpid": "Thieffry-D" }, { "family_name": "Le Nov\u00e8re", "given_name": "Nicolas", "orcid": "0000-0002-6309-7327", "clpid": "Le-Nov\u00e8re-N" }, { "family_name": "Saez-Rodriguez", "given_name": "Julio", "clpid": "Saez-Rodriguez-J" }, { "family_name": "Helikar", "given_name": "Tom\u00e1\u0161", "clpid": "Helikar-T" } ], "abstract": "Background:\nQualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, and that they are well-suited for studies of large networks. While numerous groups have developed specific computational tools that provide original methods to analyse qualitative models, a standard format to exchange qualitative models has been missing.\nResults:\nWe present the Systems Biology Markup Language (SBML) Qualitative Models Package (\"qual\"), an extension of the SBML Level 3 standard designed for computer representation of qualitative models of biological networks. We demonstrate the interoperability of models via SBML qual through the analysis of a specific signalling network by three independent software tools. Furthermore, the collective effort to define the SBML qual format paved the way for the development of LogicalModel, an open-source model library, which will facilitate the adoption of the format as well as the collaborative development of algorithms to analyse qualitative models.\nConclusions:\nSBML qual allows the exchange of qualitative models among a number of complementary software tools. SBML qual has the potential to promote collaborative work on the development of novel computational approaches, as well as on the specification and the analysis of comprehensive qualitative models of regulatory and signalling networks.", "doi": "10.1186/1752-0509-7-135", "pmcid": "PMC3892043", "issn": "1752-0509", "publisher": "BioMed Central", "publication": "BMC Systems Biology", "publication_date": "2013-12-10", "volume": "7", "pages": "Art. No. 135" }, { "id": "authors:6nf3f-w9647", "collection": "authors", "collection_id": "6nf3f-w9647", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130104-135113975", "type": "book_section", "title": "A profile of today's SBML-compatible software", "book_title": "2011 IEEE Seventh International Conference on e-Science Workshops", "author": [ { "family_name": "Hucka", "given_name": "Michael", "orcid": "0000-0001-9105-5960", "clpid": "Hucka-M" }, { "family_name": "Bergmann", "given_name": "Frank T.", "orcid": "0000-0001-5553-4702", "clpid": "Bergmann-F-T" }, { "family_name": "Keating", "given_name": "Sarah M.", "orcid": "0000-0002-3356-3542", "clpid": "Keating-S-M" }, { "family_name": "Smith", "given_name": "Lucian P.", "orcid": "0000-0001-7002-6386", "clpid": "Smith-L-P" } ], "abstract": "Computational systems biologists today have a healthy selection of software resources to help them do research. Many software packages, especially those concerned with computational modeling, have adopted SBML (the Systems Biology Markup Language) as a machine-readable format to permit users to exchange models. Our group has a keen interest in understanding the landscape of SBML support. To help us ascertain the state of modern SBML-compatible software, in mid-2011 we initiated a survey of software packages that support SBML. Here we report the preliminary survey results. Based on 81 packages for which we have data so far, we summarize the trends in six areas: (1) What are the major types of functionality offered by the software systems? (2) What mathematical frameworks do they support? (3) What are their SBML-specific capabilities? (4) What other standards do they support besides SBML? (5) What are their characteristics with respect to run-time environments? And finally, (6) what are the availability and licensing terms?", "doi": "10.1109/eScienceW.2011.28", "isbn": "9781467300261", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2011-12", "pages": "143-150" }, { "id": "authors:aymy7-8y709", "collection": "authors", "collection_id": "aymy7-8y709", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141028-175133969", "type": "monograph", "title": "The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core", "author": [ { "family_name": "Hucka", "given_name": "Michael", "orcid": "0000-0001-9105-5960", "clpid": "Hucka-M" }, { "family_name": "Bergmann", "given_name": "Frank T.", "orcid": "0000-0001-5553-4702", "clpid": "Bergmann-F-T" }, { "family_name": "Hoops", "given_name": "Stefan", "orcid": "0000-0001-8503-8371", "clpid": "Hoops-S" }, { "family_name": "Keating", "given_name": "Sarah M.", "orcid": "0000-0002-3356-3542", "clpid": "Keating-S-M" }, { "family_name": "Sahle", "given_name": "Sven", "clpid": "Sahle-S" }, { "family_name": "Schaff", "given_name": "James C.", "orcid": "0000-0003-3286-7736", "clpid": "Schaff-J-C" }, { "family_name": "Smith", "given_name": "Lucian P.", "orcid": "0000-0001-7002-6386", "clpid": "Smith-L-P" }, { "family_name": "Wilkinson", "given_name": "Darren J.", "orcid": "0000-0003-0736-802X", "clpid": "Wilkinson-D-J" } ], "abstract": "This document defines Version 1 of the Systems Biology Markup Language (SBML) Level 3 Core, an electronic model representation format for systems biology. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. SBML is defined neutrally with respect to programming languages and software encoding; however, it is oriented primarily towards allowing models to be encoded using XML, the eXtensible Markup Language (Bray et al., 2004). This document contains many examples of SBML models written in XML. Formal schemas describing the syntax of SBML, as well as other materials and software, are available from the SBML project web site, http://sbml.org/. \n\nThe SBML project is not an attempt to define a universal language for representing quantitative models. The rapidly evolving views of biological function, coupled with the vigorous rates at which new computational techniques and individual tools are being developed today, are incompatible with a one-size-fits-all idea of a universal language. A more realistic alternative is to acknowledge the diversity of approaches and methods being explored by different software tool developers, and seek a common intermediate format\u2014a lingua franca\u2014enabling communication of the most essential aspects of the models. \n\nThe definition of the model description language presented here does not specify how programs should communicate or read/write SBML. We assume that for a simulation program to communicate a model encoded in SBML, the program will have to translate its internal data structures to and from SBML, use a suitable transmission medium and protocol, etc., but these issues are outside the scope of this document.", "publisher": "Caltech Library", "publication_date": "2010-10-06" }, { "id": "authors:w8330-xf943", "collection": "authors", "collection_id": "w8330-xf943", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130111-154935747", "type": "article", "title": "Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions", "author": [ { "family_name": "Hucka", "given_name": "Michael", "orcid": "0000-0001-9105-5960", "clpid": "Hucka-M" }, { "family_name": "Hoops", "given_name": "Stefan", "orcid": "0000-0001-8503-8371", "clpid": "Hoops-S" }, { "family_name": "Keating", "given_name": "Sarah M.", "orcid": "0000-0002-3356-3542", "clpid": "Keating-S-M" }, { "family_name": "Le Nov\u00e8re", "given_name": "Nicolas", "orcid": "0000-0002-6309-7327", "clpid": "Le-Nov\u00e8re-N" }, { "family_name": "Sahle", "given_name": "Sven", "clpid": "Sahle-S" }, { "family_name": "Wilkinson", "given_name": "Darren J.", "orcid": "0000-0003-0736-802X", "clpid": "Wilkinson-D-J" } ], "abstract": "With the rise of Systems Biology as a new paradigm for understanding biological processes, the development of quantitative models is no longer restricted to a small circle of theoreticians. The dramatic increase in the number of these models precipitates the need to exchange and reuse both existing and newly created models. The Systems Biology Markup Language (SBML) is a free, open, XML-based format for representing quantitative models of biological interest that advocates the consistent specification of such models and thus facilitates both software development and model exchange.\n\n Principally oriented towards describing systems of biochemical reactions, such as cell signalling pathways, metabolic networks and gene regulation etc., SBML can also be used to encode any kinetic model. SBML offers mechanisms to describe biological components by means of compartments and reacting species, as well as their dynamic behaviour, using reactions, events and arbitrary mathematical rules. SBML also offers all the housekeeping structures needed to ensure an unambiguous understanding of quantitative descriptions.\n\n This is Release 1 of the specification for SBML Level 2 Version 4, describing the structures of the language and the rules used to build a valid model. SBML XML Schema and other related documents and software are also available from the SBML project web site, http://sbml.org/.", "doi": "10.1038/npre.2008.2715.1", "issn": "1756-0357", "publisher": "Nature Publishing Group", "publication": "Nature Precedings", "publication_date": "2008-12-24" }, { "id": "authors:bt5z9-0wa74", "collection": "authors", "collection_id": "bt5z9-0wa74", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121025-171520224", "type": "article", "title": "LibSBML: an API library for SBML", "author": [ { "family_name": "Bornstein", "given_name": "Benjamin J.", "clpid": "Bornstein-B-J" }, { "family_name": "Keating", "given_name": "Sarah M.", "orcid": "0000-0002-3356-3542", "clpid": "Keating-S-M" }, { "family_name": "Jouraku", "given_name": "Akiya", "clpid": "Jouraku-Akiya" }, { "family_name": "Hucka", "given_name": "Michael", "orcid": "0000-0001-9105-5960", "clpid": "Hucka-M" } ], "abstract": "LibSBML is an application programming interface library for reading, writing, manipulating and validating content expressed in the Systems Biology Markup Language (SBML) format. It is written in ISO C and C++, provides language bindings for Common Lisp, Java, Python, Perl, MATLAB and Octave, and includes many features that facilitate adoption and use of both SBML and the library. Developers can embed libSBML in their applications, saving themselves the work of implementing their own SBML parsing, manipulation and validation software.", "doi": "10.1093/bioinformatics/btn051", "pmcid": "PMC2517632", "issn": "1367-4803", "publisher": "Oxford University Press", "publication": "Bioinformatics", "publication_date": "2008-03-15", "series_number": "6", "volume": "24", "issue": "6", "pages": "880-881" }, { "id": "authors:bek4y-h2p53", "collection": "authors", "collection_id": "bek4y-h2p53", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130111-164005593", "type": "article", "title": "Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions", "author": [ { "family_name": "Hucka", "given_name": "Michael", "orcid": "0000-0001-9105-5960", "clpid": "Hucka-M" }, { "family_name": "Finney", "given_name": "Andrew M.", "clpid": "Finney-A-M" }, { "family_name": "Hoops", "given_name": "Stefan", "orcid": "0000-0001-8503-8371", "clpid": "Hoops-S" }, { "family_name": "Keating", "given_name": "Sarah M.", "orcid": "0000-0002-3356-3542", "clpid": "Keating-S-M" }, { "family_name": "Le Nov\u00e8re", "given_name": "Nicolas", "orcid": "0000-0002-6309-7327", "clpid": "Le-Nov\u00e8re-N" } ], "abstract": "With the rise of Systems Biology as a new paradigm for understanding biological processes, the development of quantitative models is no longer restricted to a small circle of theoreticians. The dramatic increase in the number of these models precipitates the need to exchange and reuse both existing and newly created models. The Systems Biology Markup Language (SBML) is a free, open, XML-based format for representing quantitative models of biological interest that advocates the consistent specification of such models and thus facilitates both software development and model exchange.\n\n Principally oriented towards describing systems of biochemical reactions, such as cell signalling pathways, metabolic networks and gene regulation etc., SBML can also be used to encode any kinetic model. SBML offers mechanisms to describe biological components by means of compartments and reacting species, as well as their dynamic behaviour, using reactions, events and arbitrary mathematical rules. SBML also offers all the housekeeping structures needed to ensure an unambiguous understanding of quantitative descriptions.\n\n This specification presents the structures of the language and the rules used to build a valid model. SBML XML Schema and other related documents and software are also available from the SBML project web site, http://sbml.org/.", "issn": "1756-0357", "publisher": "Nature Publishing Group", "publication": "Nature Precedings", "publication_date": "2007-11-05" }, { "id": "authors:zgtdr-0kf50", "collection": "authors", "collection_id": "zgtdr-0kf50", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130107-155707023", "type": "book_section", "title": "SBML Models and MathSBML", "book_title": "Introduction to Systems Biology", "author": [ { "family_name": "Shapiro", "given_name": "Bruce E.", "clpid": "Shapiro-B-E" }, { "family_name": "Finney", "given_name": "Andrew", "clpid": "Finney-A" }, { "family_name": "Hucka", "given_name": "Michael", "orcid": "0000-0001-9105-5960", "clpid": "Hucka-M" }, { "family_name": "Bornstein", "given_name": "Benjamin", "clpid": "Bornstein-B-J" }, { "family_name": "Funahashi", "given_name": "Akira", "clpid": "Funahashi-A" }, { "family_name": "Jouraku", "given_name": "Akiya", "clpid": "Jouraku-A" }, { "family_name": "Keating", "given_name": "Sarah M.", "orcid": "0000-0002-3356-3542", "clpid": "Keating-S-M" }, { "family_name": "Le Nov\u00e8re", "given_name": "Nicolas", "orcid": "0000-0002-6309-7327", "clpid": "Le-Nov\u00e8re-N" }, { "family_name": "Matthews", "given_name": "Joanne", "clpid": "Matthews-J" }, { "family_name": "Schilstra", "given_name": "Maria J.", "clpid": "Schilstra-M-J" } ], "contributor": [ { "family_name": "Choi", "given_name": "Sangdun", "clpid": "Choi-Sangdun" } ], "abstract": "MathSBML is an open-source, freely-downloadable Mathematica package that facilitates working with Systems Biology Markup Language (SBML) models. SBML is a tool-neutral,\ncomputer-readable format for representing models of biochemical reaction networks, applicable to metabolic networks, cell-signaling pathways, genomic regulatory\nnetworks, and other modeling problems in systems biology that is widely supported by the systems biology community. SBML is based on XML, a standard medium for representing and transporting data that is widely supported on the internet as well as in computational biology and bioinformatics. Because SBML is tool-independent, it enables model transportability, reuse, publication and survival. In addition to MathSBML, a number of other tools that support SBML model examination and manipulation are provided on the sbml.org website, including libSBML, a C/C++ library for reading SBML models; an SBML Toolbox for MatLab; file conversion programs; an SBML model validator and visualizer; and SBML specifications and schemas. MathSBML enables SBML file import to and export from Mathematica as well as providing an API for model manipulation and simulation.", "isbn": "9781597455312", "publisher": "Humana Press", "place_of_publication": "Totowa, NJ", "publication_date": "2007", "pages": "395-421" }, { "id": "authors:qh6jd-6n577", "collection": "authors", "collection_id": "qh6jd-6n577", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:KEAbioinf06", "type": "article", "title": "SBMLToolbox: an SBML toolbox for MATLAB users", "author": [ { "family_name": "Keating", "given_name": "Sarah M.", "orcid": "0000-0002-3356-3542", "clpid": "Keating-S-M" }, { "family_name": "Bornstein", "given_name": "Benjamin J.", "clpid": "Bornstein-B-J" }, { "family_name": "Finney", "given_name": "Andrew", "clpid": "Finney-A" }, { "family_name": "Hucka", "given_name": "Michael", "orcid": "0000-0001-9105-5960", "clpid": "Hucka-M" } ], "abstract": "We present SBMLToolbox, a toolbox that facilitates importing and exporting models represented in the Systems Biology Markup Language (SBML) in and out of the MATLAB environment and provides functionality that enables an experienced user of either SBML or MATLAB to combine the computing power of MATLAB with the portability and exchangeability of an SBML model. SBMLToolbox supports all levels and versions of SBML.", "doi": "10.1093/bioinformatics/btl111", "issn": "1367-4803", "publisher": "Oxford University Press", "publication": "Bioinformatics", "publication_date": "2006-05-15", "series_number": "10", "volume": "22", "issue": "10", "pages": "1275-1277" }, { "id": "authors:a5xc6-3sw58", "collection": "authors", "collection_id": "a5xc6-3sw58", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130107-161648673", "type": "book_section", "title": "Software Infrastructure for Effective Communication and Reuse of Computational Models", "book_title": "System Modeling in Cell Biology: From Concepts to Nuts & Bolts", "author": [ { "family_name": "Finney", "given_name": "Andrew", "clpid": "Finney-A" }, { "family_name": "Hucka", "given_name": "Michael", "orcid": "0000-0001-9105-5960", "clpid": "Hucka-M" }, { "family_name": "Bornstein", "given_name": "Benjamin J.", "clpid": "Bornstein-B-J" }, { "family_name": "Keating", "given_name": "Sarah M.", "orcid": "0000-0002-3356-3542", "clpid": "Keating-S-M" }, { "family_name": "Shapiro", "given_name": "Bruce E.", "clpid": "Shapiro-B-E" }, { "family_name": "Matthews", "given_name": "Joanne", "clpid": "Matthews-J" }, { "family_name": "Kovitz", "given_name": "Ben L.", "clpid": "Kovitz-B-L" }, { "family_name": "Schilstra", "given_name": "Maria J.", "clpid": "Schilstra-M-J" }, { "family_name": "Funahashi", "given_name": "Akira", "clpid": "Funahashi-Akira" }, { "family_name": "Doyle", "given_name": "John", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Kitano", "given_name": "Hiroaki", "clpid": "Kitano-Hiroaki" } ], "contributor": [ { "family_name": "Szallasi", "given_name": "Zoltan", "clpid": "Szallasi-Z" }, { "family_name": "Stelling", "given_name": "J\u00f6rg", "clpid": "Stelling-J" }, { "family_name": "Periwal", "given_name": "Vipul", "clpid": "Periwal-V" } ], "abstract": "Until recently, the majority of computational models in biology were implemented\nin custom programs and published as statements of the underlying mathematics.\nHowever, to be useful as formal embodiments of our understanding of biological\nsystems, computational models must be put into a consistent form that can be\ncommunicated more directly between the software tools used to work with them.\nIn this chapter, we describe the Systems Biology Markup Language (SBML), a\nformat for representing models in a way that can be used by different software\nsystems to communicate and exchange those models. By supporting SBML as an\ninput and output format, different software tools can all operate on an identical\nrepresentation of a model, removing opportunities for errors in translation and\nassuring a common starting point for analyses and simulations. We also take this\nopportunity to discuss some of the resources available for working with SBML as\nwell as ongoing efforts in SBML's continuing evolution.", "isbn": "9780262195485", "publisher": "MIT Press", "place_of_publication": "Cambridge, MA", "publication_date": "2006", "pages": "355-378" }, { "id": "authors:899kp-y7h26", "collection": "authors", "collection_id": "899kp-y7h26", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:HUCieesb04", "type": "article", "title": "Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project", "author": [ { "family_name": "Hucka", "given_name": "M.", "orcid": "0000-0001-9105-5960", "clpid": "Hucka-M" }, { "family_name": "Finney", "given_name": "A.", "clpid": "Finney-A" }, { "family_name": "Bornstein", "given_name": "B. J.", "clpid": "Bornstein-B-J" }, { "family_name": "Keating", "given_name": "S. M.", "orcid": "0000-0002-3356-3542", "clpid": "Keating-S-M" }, { "family_name": "Shapiro", "given_name": "B. E.", "clpid": "Shapiro-B-E" }, { "family_name": "Matthews", "given_name": "J.", "clpid": "Matthews-J" }, { "family_name": "Kovitz", "given_name": "B. L.", "clpid": "Kovitz-B-L" }, { "family_name": "Schilstra", "given_name": "M. J.", "clpid": "Schilstra-M-J" }, { "family_name": "Funahashi", "given_name": "A.", "clpid": "Funahashi-Akira" }, { "family_name": "Doyle", "given_name": "J. C.", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Kitano", "given_name": "H.", "clpid": "Kitano-Hiroaki" } ], "abstract": "Biologists are increasingly recognising that computational modelling is crucial for making sense of the vast quantities of complex experimental data that are now being collected. The systems biology field needs agreed-upon informationstandards if models are to be shared, evaluated and developed cooperatively. Over the last four years, our team has been developing the Systems Biology Markup Language (SBML) in collaboration with an international community of modellers and software developers. SBML has become a de facto standard format for representing formal, quantitative and qualitative models at the level of biochemical reactions and regulatory networks. In this article, we summarise the current and upcoming versions of SBML and our efforts at developing software infrastructure for supporting and broadening its use. We also provide a brief overview of the many SBML-compatible software tools available today.", "doi": "10.1049/sb:20045008", "issn": "1741-2471", "publisher": "IEE", "publication": "Systems Biology", "publication_date": "2004-06", "series_number": "1", "volume": "1", "issue": "1", "pages": "41-53" } ]