glossary

Glossary

Abb. / Name	Long name / Alt. Name	Description	Further Informations
A
B
BioPAX	Biological Pathway Exchange	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.	http://www.biopax.org/
C
cellML		Open standard based on the XML markup language to store and exchange computer-based mathematical models.	https://www.cellml.org/
ChEBI	Chemical Entities of Biological Interest	Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.	https://www.ebi.ac.uk/chebi/
COMBINE	COmputational MOdeling in BIology NEtwork	Initiative to coordinate the development of the various community standards and formats for computational models.	http://co.mbine.org/
COMBINE Archive		A COMBINE archive is a single file containing the various documents (and in the future, references to documents), necessary to reproduce a simulation study, providing a model and all associated data and procedures. The archive is encoded using the Open Modeling EXchange format (OMEX).	http://co.mbine.org/standards/omex
COPASI		Biochemical System Simulator	http://copasi.org/
D
DCMI	Dublin Core Metadata Initiative	The Dublin Core™ Metadata Initiative supports innovation in metadata design and best practices. DCMI is supported by its members and is a project of ASIS&T.	https://www.dublincore.org/specifications/dublin-core/dcmi-terms/
dMod		R package for Dynamic Modeling and Parameter Estimation in ODE Models	https://cran.r-project.org/web/packages/dMod/index.html
E
F
G
GO	Gene Ontology	comprehensive, computational model of biological systems, ranging from the molecular to the organism level, across the multiplicity of species in the tree of life	http://geneontology.org/
H
I
Initial Guess		The initial value for iterative optimization to parametrize
J
JAK2	Janus kinase 2	Non-receptor tyrosine kinase. It participates among others in signaling by single-chain receptors as Epo-R.	https://en.wikipedia.org/wiki/Janus_kinase_2
K
KiSAO	Kinetic Simulation Algorithm Ontology	ontology of algorithms for simulating and analyzing biological models, as well as the characteristics of these algorithms, their input parameters, and their outputs. In addition, KiSAO captures relationships among algorithms, their parameters, and their outputs	https://bioportal.bioontology.org/ontologies/KISAO, https://www.nature.com/articles/npre.2010.5122.1.pdf
L
Likelihood Profile	Profile Likelihood	One-dimensional representation of the likelihood indicating which values of a single parameter component are in statistical agreement with the available measurements	http://jeti.uni-freiburg.de/papers/febs12276.pdf
M
MIBBI	Minimum Information for Biological and Biomedical Investigation	The minimum information standard is a set of guidelines for reporting data derived by relevant methods in biosciences. If followed, it ensures that the data can be easily verified, analysed and clearly interpreted by the wider scientific community. Keeping with these recommendations also facilitates the foundation of structuralized databases, public repositories and development of data analysis tools. The individual minimum information standards are brought by the communities of cross-disciplinary specialists focused on the problematic of the specific method used in experimental biology. The initial set of guidelines collected by the MIBBI portal are listed within this collection. However, since that time, the portal has evolved into the FAIRsharing Information Resource.	https://fairsharing.org/collection/MIBBI
MIRIAM		Minimum information requested in the annotation of biochemical models	https://co.mbine.org/standards/miriam
Motiv
Multistart Optimization		Method to test the performance of the iterative estimation of parameters (whether it works), many fits with random initial values, representation as a 'waterfall plot' - chi2 with (ideally) steps = global optimum and local optima Performance der iterativen Optimierung (Abschätzung ob Parameterschätzung funktioniert)
MWG	Massenwirkungsgesetz = Law of Mass Action	rate of a reaction is proportional to the "active mass" of the reacting species (mass per volume = concentration)	https://en.wikipedia.org/wiki/Law_of_mass_action
N
NeuroML		Project focuses on the development of an XML (eXtensible Markup Language) based description language that provides a common data format for defining and exchanging descriptions of neuronal cell and network models.	http://www.neuroml.org/
Newt	Newt Pathway Viewer & Editor	A web based, open source viewer and editor for pathways in Systems Biological Graphical Notation (SBGN) and Simple Interaction Format (SIF)	http://newteditor.org/
Non-identifiability		no information on parameters in the data, flat line in profile likelihood
O
Observation function	Observation function / Observables
ODE	ordinary differential equation	Differential equation containing one or more functions of one independent variable and the derivatives of those functions.	https://en.wikipedia.org/wiki/Ordinary_differential_equation
OMEX	Open Modeling EXchange format	Open Modeling EXchange format (OMEX), together with the use of other standard formats from the Computational Modeling in Biology Network (COMBINE), is the basis of the COMBINE Archive, a single file that supports the exchange of all the information necessary for a modeling and simulation experiment in biology. An OMEX file is a ZIP container that includes a manifest file, listing the content of the archive, an optional metadata file adding information about the archive and its content, and the files describing the model.	http://co.mbine.org/specifications/omex.version-1, https://fairsharing.org/FAIRsharing.27tnee
OMICS		disciplines in biology whose names end in the suffix -omics, such as genomics, proteomics, metabolomics, metagenomics and transcriptomics	https://en.wikipedia.org/wiki/Omics
P
Q
R
RDF	Resource Description Framework	MIRIAM Annotation in COPASI	http://copasi.org/Support/Technical_Documentation/MIRIAM_Annotation/
S
SBGN	Systems Biology Graphical Notation	standardization of the graphical notation for the representation of biological processes	https://sbgn.github.io/, https://www.nature.com/articles/nbt.1558
SBML	Systems Biology Markup Language	machine-readable data exchange format (XML) to represent biochemial models, e.g. metabolic networks, signal transduction, gene regulation..	http://co.mbine.org/standards/sbml
SBO	Systems Biology Ontology	set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modelling.	http://www.ebi.ac.uk/sbo/main/
SBOL	Synthetic Biology Open Language	language for the description and exchange of synthetic biological parts, devices and systems	https://sbolstandard.org/
SBRML	Systems Biology Results Markup Language	Linking systems biology data to models	https://academic.oup.com/bioinformatics/article/26/7/932/213719
SED-ML	Simulation Experiment Description Markup Language	XML-based format to encode simulation setups; exchange and reproducibility of simulation experiments	http://sed-ml.org/, https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-5-198
T
TEDDY	TErminology for the Description of DYnamics	ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology	https://bioportal.bioontology.org/ontologies/TEDDY, https://www.nature.com/articles/npre.2010.5122.1.pdf
Tellurium		Python-based tool to model, simulate and analyse biological systems	https://tellurium.readthedocs.io/en/latest/
U
UniProt	Universal Protein Resource	The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.	https://www.uniprot.org/
V
W
X
Y
Z