A data model is an abstract model that organizes elements of data and standardizes how they relate to one another and to the properties of real-world entities. For instance, a data model may specify that the data element representing a car be composed of a number of other elements which, in turn, represent the color and size of the car and define its owner.
A modeling language is any artificial language that can be used to express data, information or knowledge or systems in a structure that is defined by a consistent set of rules. The rules are used for interpretation of the meaning of components in the structure Programing language.
Object–role modeling (ORM) is used to model the semantics of a universe of discourse. ORM is often used for data modeling and software engineering.
A block diagram is a diagram of a system in which the principal parts or functions are represented by blocks connected by lines that show the relationships of the blocks. They are heavily used in engineering in hardware design, electronic design, software design, and process flow diagrams.
Business Process Model and Notation (BPMN) is a graphical representation for specifying business processes in a business process model.
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 Systems Biology Ontology (SBO) is a set of controlled, relational vocabularies of terms commonly used in systems biology, and in particular in computational modeling.
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 short transient receptor potential channel 4 (TrpC4), also known as Trp-related protein 4, is a protein that in humans is encoded by the TRPC4 gene.
Igor I. Goryanin is a systems biologist, who holds a Henrik Kacser Chair in Computational Systems Biology at the University of Edinburgh. He also heads the Biological Systems Unit at the Okinawa Institute of Science and Technology, Japan.
Chromodomain-helicase-DNA-binding protein 3 is an enzyme that in humans is encoded by the CHD3 gene.
Mediator of RNA polymerase II transcription subunit 15, also known as Gal11, Spt13 in yeast and PCQAP, ARC105, or TIG-1 in humans is a protein encoded by the MED15 gene.
Molecular Interaction Maps, also known as MIMs, is a graphic notation to depict cellular and molecular interactions. It was created by Kurt W. Kohn in 1999. The MIM convention is capable of unambiguous representation of networks containing multi-protein complexes, protein modifications, and enzymes that are substrates of other enzymes. This graphical representation makes it possible to view all of the many interactions in which a given molecule may be involved, and it can portray competing interactions, which are common in bioregulatory networks. In order to facilitate linkage to databases, each molecular species is represented only once in a diagram. The MIM notation forms the basis of, and further development of the MIM notation is coordinated with, the Systems Biology Graphical Notation (SBGN) consortium, an international effort to standardize diagrams depicting biochemical and cellular processes studied in systems biology. An update to the notation was published in 2006.
Memory is commonly referred to as the ability to encode, store, retain and subsequently recall information and past experiences in the human brain. This process involves many proteins, one of which is the Histone-binding protein RbAp48, encoded by the RBBP4 gene in humans.
The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of systems biology models, their characterization and interrelationships. KiSAO is part of the BioModels.net project and of the COMBINE initiative.
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.
Multi-state modeling of biomolecules refers to a series of techniques used to represent and compute the behaviour of biological molecules or complexes that can adopt a large number of possible functional states.
Nicolas Le Novère is a British and French biologist. His research focuses on modeling signaling pathways and developing tools to share mathematical models.
The Synthetic Biology Open Language (SBOL) is a proposed data standard for exchanging synthetic biology designs between software packages. It has been under development by the SBOL Developers Group since 2008. This group aims to develop the standard in a way that is open and democratic in order to include as many interests as possible and to avoid domination by a single company. The group also aims to develop and improve the design standard over time as the field of synthetic biology reflects this development.
Mirit I. Aladjem is an Israeli-American biologist researching cellular signaling pathways that regulate DNA synthesis. She is a senior investigator in the National Cancer Institute's developmental therapeutics branch and head of the DNA replication group.
