Modelling the Structure and Dynamics of Biological Pathways (original) (raw)

Ten simple rules for creating reusable pathway models for computational analysis and visualization

PLOS Computational Biology, 2021

Pathway models are an effective way to capture and share our current understanding of biological processes. A pathway model is defined here as a set of interactions among biological entities (e.g., proteins and metabolites) relevant to a particular context, curated and organized to illustrate a particular process. Properly modeled pathways can be used in the analysis and visualization of diverse types of omics and other biomedical data [1,2]. The modeling process involves taking our knowledge about biological pathways-however messy and incompleteand encoding it in standardized data formats that can be shared, reused, and synthesized with other knowledge in accordance with the Findable, Accessible, Interoperable, and Reusable (FAIR) principles [3]. The rules presented here serve as an introduction and guide to the pathway modeling process, leveraging freely available tools and resources. Biological pathway information is often conveyed as published figures, and rules for better figures, in general, are also relevant when producing pathway models [4]. However, pathway models are more than just figures. In addition to providing an intuitive depiction of a biological process that is easy to understand for humans, they also provide relevant annotations and metadata to be processed by computers. Similarly, rules for network visualizations can be applied to pathway models [5], but the distinct context, layout, and usage of pathway models necessitate specific guidelines and rules. Pathway models are described with specific languages, such as the Systems Biology Graphical Notation (SBGN) [6], the Systems Biology Markup Language (SBML) [7], the Biological Pathway Exchange (BioPAX) format [8], the Graphical Pathway Markup Language (GPML) [9], and many more. Here, we describe a set of rules for constructing pathway models to optimize their use both as graphical representations for human consumption and as FAIR resources for computational analysis. The rules range from reusability and dissemination (Rules 1, 9, and 10), intuitive visual concepts (Rules 2, 7, and 8), to enabling computational analysis (Rules 3 to 6). We hope that these rules provide a simple framework for pathway model curators who want to create (re)usable resources for the scientific community.

Path2Models: large-scale generation of computational models from biochemical pathway maps

BMC Systems Biology, 2013

Background Systems biology projects and omics technologies have led to a growing number of biochemical pathway models and reconstructions. However, the majority of these models are still created de novo, based on literature mining and the manual processing of pathway data. Results To increase the efficiency of model creation, the Path2Models project has automatically generated mathematical models from pathway representations using a suite of freely available software. Data sources include KEGG, BioCarta, MetaCyc and SABIO-RK. Depending on the source data, three types of models are provided: kinetic, logical and constraint-based. Models from over 2 600 organisms are encoded consistently in SBML, and are made freely available through BioModels Database at http://www.ebi.ac.uk/biomodels-main/path2models. Each model contains the list of participants, their interactions, the relevant mathematical constructs, and initial parameter values. Most models are also available as easy-to-understa...

Biochemical modeling with Systems Biology Graphical Notation

Drug Discovery Today, 2010

The Systems Biology Graphical Notation (SBGN) is an emerging standard for graphical notation developed by an international systems biology community. Standardized graphical notation is crucial for efficient and accurate communication of biological knowledge between researchers with various backgrounds in the expanding field of systems biology. Here, we highlight SBGN from a practical point of view and describe how the user can build and simulate SBGN models from a simple drag-and-drop graphical user interface in PathwayLab.

A graphical notation to describe the logical interactions of biological pathways

2006

The modelling of biological intra-cellular pathways requires the systematic capture and representation of interactions between components that are biologically correct and computationally rigorous. The challenge is two fold, to verify and extend our understanding of such pathways by comparing in silico models to experiments; and to ensure that such models are understandable by biologists and for checking biological validity. In this report we present a graphical notation, the Edinburgh Pathway Notation (EPN), which satisfies the central biologically driven requirements while providing a strict formal framework for analysis. The EPN emphasises the use of a logical representation of pathways, which is particularly suited to pathways were some mechanisms are not known in detail.

Celldesigner: A Modeling Tool for Biochemical Networks

2006

Understanding of logic and dynamics of gene-regulatory and biochemical networks is a major challenge of systems biology. To facilitate this research topic, we have developed CellDesigner, a modeling tool of gene-regulatory and biochemical networks. CellDesigner supports users to easily create such networks using solidly defined and comprehensive graphical representation (SBGN: Systems Biology Graphical Notation). CellDesigner is SBML compliant, and is SBW-enabled software so that it can import/export SBML described documents and can integrate with other SBW-enabled simulation/analysis software packages. CellDesigner also supports simulation and parameter search, which is supported by integration with SBML ODE Solver, enabling us to simulate through our sophisticated graphical user interface. We could also browse and modify existing SBML models with references to existing databases. CellDesigner is implemented in Java, thus it runs on various platforms such as Windows, Linux, and MacOS X. CellDesigner is freely available via the Web.

An Intuitive Automated Modelling Interface for Systems Biology

We introduce a natural language interface for building stochastic pi calculus models of biological systems. In this language, complex constructs describing biochemical events are built from basic primitives of association, dissociation and transformation. This language thus allows us to model biochemical systems modularly by describing their dynamics in a narrative-style language, while making amendments, refinements and extensions on the models easy. We demonstrate the language on a model of Fc-gamma receptor phosphorylation during phagocytosis. We provide a tool implementation of the translation into a stochastic pi calculus language, Microsoft Research's SPiM.