COMBINE, the COmputational Modeling in BIology NEtwork, is an initiative to coordinate the development of the various community standards and formats for computational models, initially in systems biology and related fields. [1]
Systems biology is the computational and mathematical modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological systems, using a holistic approach to biological research.
The COMBINE initiative was started in 2010 in an attempt to start a broader series of scientific meetings in order to replace several smaller and more focused meetings and hackathons, notably the Systems Biology Graphical Notation (SBGN) and Systems Biology Markup Language (SBML) meetings. The first COMBINE meeting was organised by Igor Goryanin and held at the University of Edinburgh School of Informatics in October 2010. The final session of the meeting was followed by an event marking the 10th anniversary of SBML. [2] COMBINE meetings have been held annually since; COMBINE 2014 was organised by the University of Southern California and COMBINE 2015 will be organised by the group of Chris Myers at the University of Utah. [3]
A hackathon is a design sprint-like event in which computer programmers and others involved in software development, including graphic designers, interface designers, project managers, and others, often including domain experts, collaborate intensively on software projects.
The Systems Biology Graphical Notation (SBGN) is a standard graphical representation intended to foster the efficient storage, exchange and reuse of information about signaling pathways, metabolic networks, and gene regulatory networks amongst communities of biochemists, biologists, and theoreticians. The system was created over several years by a community of biochemists, modelers and computer scientists.
Igor Goryanin is a systems biologist, who holds a Henrik Kacser Chair in Computational Systems Biology at the University of Edinburgh, and leads the Computational Systems Biology and Bioinformatics group, School of Informatics. He heads the Biological Systems Unit at Okinawa Institute Science and Technology, Japan.
The COMBINE initiative aims to coordinate the development of community standards and formats for computational modelling, particularly in systems biology. In doing so, it is expected a set of complementary but non-overlapping standards will be developed, covering all aspects of computational modelling in all areas of biology. [1] The major representation formats covered by COMBINE activity are the BioPAX standards language, SBGN, SBML and the SED-ML and CellML markup languages. [4] The associated standardisation efforts are MIRIAM, SBO, KiSAO and the BioModels.net model repository. [4]
BioPAX is a RDF/OWL-based standard language to represent biological pathways at the molecular and cellular level. Its major use is to facilitate the exchange of pathway data. Pathway data captures our understanding of biological processes, but its rapid growth necessitates development of databases and computational tools to aid interpretation. However, the current fragmentation of pathway information across many databases with incompatible formats presents barriers to its effective use. BioPAX solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. BioPAX was created through a community process. Through BioPAX, millions of interactions organized into thousands of pathways across many organisms, from a growing number of sources, are available. Thus, large amounts of pathway data are available in a computable form to support visualization, analysis and biological discovery.
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.
The Simulation Experiment Description Markup Language (SED-ML) is a representation format, based on XML, for the encoding and exchange of simulation descriptions on computational models of biological systems. It is a free and open community development project.
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CellML is an XML based markup language for describing mathematical models. Although it could theoretically describe any mathematical model, it was originally created with the Physiome Project in mind, and hence used primarily to describe models relevant to the field of biology. This is reflected in its name CellML, although this is simply a name, not an abbreviation. CellML is growing in popularity as a portable description format for computational models, and groups throughout the world are using CellML for modelling or developing software tools based on CellML. CellML is similar to Systems Biology Markup Language SBML but provides greater scope for model modularity and reuse, and is not specific to descriptions of biochemistry.
Modelling biological systems is a significant task of systems biology and mathematical biology. Computational systems biology aims to develop and use efficient algorithms, data structures, visualization and communication tools with the goal of computer modelling of biological systems. It involves the use of computer simulations of biological systems, including cellular subsystems, to both analyze and visualize the complex connections of these cellular processes.
RuleML is a global initiative, led by a non-profit organization RuleML Inc., that is devoted to advancing research and industry standards design activities in the technical area of rules that are semantic and highly inter-operable. The standards design takes the form primarily of a markup language, also known as RuleML. The research activities include an annual research conference, the RuleML Symposium, also known as RuleML for short. Founded in fall 2000 by Harold Boley, Benjamin Grosof, and Said Tabet, RuleML was originally devoted purely to standards design, but then quickly branched out into the related activities of coordinating research and organizing an annual research conference starting in 2002. The M in RuleML is sometimes interpreted as standing for Markup and Modeling. The markup language was developed to express both forward (bottom-up) and backward (top-down) rules in XML for deduction, rewriting, and further inferential-transformational tasks. It is defined by the Rule Markup Initiative, an open network of individuals and groups from both industry and academia that was formed to develop a canonical Web language for rules using XML markup and transformations from and to other rule standards/systems.
BioModels is a free and open-source repository for storing, exchanging and retrieving quantitative models of biological interest created in 2006. All the models in the curated section of BioModels Database have been described in peer-reviewed scientific literature.
The Systems Biology Ontology (SBO) is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling. SBO is part of the BioModels.net effort.
MIRIAM is a community-level effort to standardize the annotation and curation processes of quantitative models of biological systems. It consists of a set of guidelines suitable for use with any structured format, allowing different groups to collaborate and share resulting models. Adherence to these guidelines also facilitates the sharing of software and service infrastructures built upon modeling activities.
The Commission for the Management and Application of Geoscience Information (CGI), usually referred to by the unofficial "Commission for Geoscience Information" is subcommittee grade scientific organization that concerns itself with geological standard, information management and interoperability matters on a global scale.
The minimum information about a simulation experiment (MIASE) is a list of the common set of information a modeller needs to enable the execution and reproduction of a numerical simulation experiment, derived from a given set of quantitative models.
NeuroML is an XML based model description language that aims to provide a common data format for defining and exchanging models in computational neuroscience. The focus of NeuroML is on models which are based on the biophysical and anatomical properties of real neurons.
LibSBML is an open-source software library that provides an application programming interface (API) for the SBML format. The libSBML library can be embedded in a software application or used in a web servlet as part of the application or servlet's implementation of support for reading, writing, and manipulating SBML documents and data streams. The core of libSBML is written in ISO standard C++; the library provides API for many programming languages via interfaces generated with the help of SWIG.
JSBML is an open-source Java™ (API) for the SBML format. Its API strives to attain a strong similarity to the Java binding of the corresponding library libSBML, but is entirely implemented in Java and therefore platform independent. JSBML provides an elaborated abstract type hierarchy, whose data types implement or extend many interfaces and abstract classes from the standard Java library. In this way, JSBML integrates smoothly into existing Java projects, and provides methods to read, write, evaluate, and manipulate the content of SBML documents.
Identifiers.org is a project providing stable and perennial identifiers for data records used in the Life Sciences. The identifiers are provided in the form of Uniform Resource Identifiers (URIs). Identifiers.org is also a resolving system, that relies on collections listed in the MIRIAM Registry to provide direct access to different instances of the identified records.
Nicolas Le Novère is a British and French biologist. His research focus on modeling signaling pathways and developing tools to share mathematical models.