Zasnova translacije bioloških modelov v SBML zapis

OSOLIN, TIMOTEJ (author), Moškon, Miha (mentor), Mraz, Miha (co-mentor)

Sistemska biologija, kot pomemben člen v verigi številnih področij pri raziskovanju v medicini, uporablja poleg ostalih tehnik tudi kreiranje in urejanje raznovrstnih bioloških modelov. Pri tem tudi izkorišča prednosti objektno orientiranega modeliranja in programskih orodij, namenjenih izdelavi takih modelov. Na Univerzi v Ljubljani so tako razvili knjižnico, imenovano SysBio, kot pomoč pri ustvarjanju bioloških modelov. Za izdelavo knjižnice je bil uporabljen objektno orientiran Modelica programski jezik, ki pa je na področju sistemske biologije in njej sorodnih ved sorazmerno redek. Tako je za kompatibilnost z ostalimi, pogosteje uporabljenimi orodji, potrebna pretvorba v zapis, ki ga ta orodja podpirajo. Poznamo več različnih oblik zapisa, toda v sistemski biologiji je najbolj razširjen zapis SBML (angl. Systems Biology Markup Language). V pričujočem delu predstavimo razvoj programa, ki omogoča translacijo iz jezika Modelica v zapis SBML. Translacijo demonstriramo na enostavnem modelu metabolne poti, ki jo uspešno pretvorimo iz Modelica v SBML zapis.

• Language: Slovenian
• Keywords: sistemska biologija, SysBio, SBML zapis, Modelica, translacija, biološki modeli
• Work type: Bachelor thesis/paper
• Organization: FRI - Faculty of Computer and Information Science
• Year: 2016
• PID: 20.500.12556/RUL-85030
• Publication date in RUL: 09.09.2016

Secondary language

• Language: English
• Title: Translation of biological models to an SBML notation

Abstract

Systems biology is one of the important fields of study that is helping medicine with its breakthroughs. Amongst other techniques it uses object oriented modelling and corresponding software tools for creation of such models. University of Ljubljana developed a library, named SysBio, as a vital utility for developing biological models. The library was developed using object oriented Modelica programming language, which is relatively rare in the field of systems biology and its related fields. Therefore a translation to a more known format is necessary to ensure the compatibility with the most popular development tools in this field. There are many different types of formats, however SBML (Systems Biology Markup Language) is the most widespread format in systems biology. In the following work we present the development of software, which enables the translation from Modelica language to a SBML format. We demonstrate such translation on a simple model of metabolic pathway, which is successfully converted from Modelica to SBML format.

• Keywords: systems biology, SysBio, SBML format, Modelica, translation, biologic models