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“Heta compiler” is a framework for the development and management of Quantitative Systems Pharmacology modeling platforms
EP35844
Poster Title: “Heta compiler” is a framework for the development and management of Quantitative Systems Pharmacology modeling platforms
Submitted on 18 Feb 2021
Author(s): Evgeny Metelkin
Affiliations: InSysBio LLC, Moscow
This poster was presented at ACoP11
Poster Views: 376
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Poster Information
Abstract: Objectives Today the pharmacology modeling is evolving towards complex mechanism-based dynamical modeling and involves a large amount of biological and clinical data [1]. A typical QSP project may include thousands of molecular components, several drugs and usually is done by a research group involving people with different expertise. The data management, workflow and co-operation in such projects are the challenges. In many cases, the critical step also is the translation of the modeling results to other modeling formats and frameworks. This study is an effort to resolve the typical problems in a QSP project by creating the software infrastructure based on Heta formats and develop a shared and controllable working environment. The pre-formulated requirements are: (i) storing the QSP models and data in integrated infrastructure, (ii) support iterative platform updates, (iii) support of models written in human-readable text and table formats, (iv) export models and data to different popular formats on the fly. Methods Heta language is a Domain Specific Language (DSL) designed for the development and annotation of dynamical models in QSP projects. Heta standard of version 0.2 is fully supported in the Heta compiler. The core of the Heta compiler was developed in JavaScript language and can be used in Node environment, can be a part of a webbased application or potentially integrated with simulation software. Results Heta compiler is developed and tested based on the series of QSP models and projects. Currently Heta compiler supports the export to the following formats: DBSolve, Simbiology, mrgsolve, Matlab, SBML, etc. It was used in open and commercial QSP projects developed by InSysBio: Alzheimer-consortium platform, Immune Response Template, PK/RO simulator for anti-PD-1 mAbs. Discussion Heta compiler will be developing as free open-source software on GitHub and is expected to be a communitydriven framework (https://hetalang.github.io). A series of additional tools to support Heta and Heta compiler is developed: highlighting syntax in Atom and VSCode, SbmlViewer, slv-utils. Conclusions Heta compiler can be used as the framework for a QSP modeling project of any size and complexity. It allows integrate the dynamical models and data as modules and transform the modeling code to different popular formats. It can be easily integrated with existed infrastructure, workflows or used as a part of the CI/CD strategy. Summary: Heta compiler can be used as the framework for a QSP modeling project of any size and complexity. It allows integrate the dynamical models and data as modules and transform the modeling code to different popular formats. It can be easily integrated with existed infrastructure, workflows or used as a part of the CI/CD strategy. References: 1. Knight-Schrijver et al. Computational and Structural Biotechnology Journal (2016) 14, 363-370 Report abuse »
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