A graphical and computational modeling platform for biological pathways

Abstract

EDITORIAL SUMMARY: This is a biologist-friendly modelling scheme facilitating the capture and 15 visualization of knowledge on biological pathways and how components interact. Moreover, when 16 parameterised, these pathway models can be used directly to run simulations of their activity and test 49a simulation run, even on a large model, typically takes only seconds. Models constructed using this 50 approach provide a means of knowledge management, information exchange, and through the computation simulation of their dynamic activity, a means to generate and test hypotheses, and predict a system's behaviour when perturbed.

A detailed graphical and computational model of the mammalian renal circadian clock

“…Despite its importance, relatively little is known about how the peripheral kidney clock operates. We therefore set out to build model of this system using a recently described graphical and computational modelling approach ( 26, 27 ). First, we examined the literature to define the major clock genes, referencing the CircaDB kidney expression dataset (above) to define their qualitative and quantitative expression in this organ.…”

“…A network model of circadian clock pathway was assembled using information curated from Reactome pathway (ID: R-HSA-400253) and primary literature. The model was constructed using the network editing program, yEd (yWorks, Tubingen, Germany) and assembled according to the rules of the modified Edinburgh Pathway Notation (mEPN) scheme ( 26, 27 ). A full list of publications used in the construction of this model and the individual interactions they describe, can be found in Supp.…”

“…Data 3). For more details on creating mEPN models and running simulations through them see ( 26, 27 ).…”

“…Given the lack of a detailed model for this system, we set out to construct a pathway model of the mammalian circadian clock that reflects the consensus view of all known components of the system in man and the relationships between them. In order to achieve this aim, we undertook an extensive review of the literature, employing the mEPN modelling language ( 26, 27 ) to generate a graphical model of the clock, based on the principles of the process diagram ( 28 ). An advantage of the mEPN scheme over other graphical modelling languages is that it also directly supports the use of models for computational modelling, using a stochastic Petri net-based approach ( 29 ).…”

A genomic analysis and transcriptomic atlas of gene expression inPsoroptes ovisreveals feeding- and stage-specific patterns of allergen expression

“…Kallisto is a novel transcriptome-based quantification package that avoids the considerable bias that can be introduced by a genome alignment step [86]. Kallisto generated read counts (transcripts per million (TPM)) for all RNA-seq samples, which were used as input for the network clustering within the Graphia Professional package (Version 2.0, Kajeka, Edinburgh, UK, formerly BioLayout Express 3D [29,87]). Functional annotation of the P. ovis genome and specific-gene clusters was performed within the Blast2GO package (Version 5) [88].…”