Tutorial for Life Sciences-aimed Audience of Biochemical Space Language

Bc. Lucia Helmeciová

Bachelor's thesis

Abstract:

Táto bakalárska práca sa venuje hlavne jazyku Biochemical Space Language vyvinutému v laboratóriu Systémovej Biológie na fakulte Informatky na Masaryklovej univerzite. Obsahuje stručný úvod do rule-based modelovania dizajnu a implemetácie štandardných procedúr na prezentovanie modelov v BCSL obecenstvu so vzdelaním v oblasti biológie, alebo chémie. Formálna definícia BCSL už existuje, ale nebola zatiaľ publikovaná žiadna priamočiara dokumentácia popisujúca vlastnosti a jednoduché príklady modelov v danom jazyku. V tejto práci sme sa zaoberali hlavne tvorbou tutoriálu pre BCSL, ktorý by sa mal zaobísť bez komplikovaných formalismov a urobiť tak jazyk viac prístupným pre zamýšľanú skupinu. Pridali sme aj test, ktorým sme si overili ako dobre vie tutoriál pripraviť testovaciu skupinu na modelovanie v BCSL.

Abstract:

This thesis targets mainly the language developed at the System Biology Laboratory at the Faculty of Informatics, Masaryk University, Biochemical Space Language. It further focuses on the introduction to rule-based modeling, design, and implementation of standard procedures for presenting modeling in BCSL to biologically or chemically oriented audiences. The formal definition of the BCSL already exists, but there was no straightforward document describing the features of the language or providing some basic examples of them and the models. In this thesis, we created a tutorial for the BCSL language which is supposed to avoid complicated formalism and thus make the language more accessible to the intended audience. We also included a variant of a test to verify the acquired knowledge of the subjects and the usefulness of the tutorial.

Keywords

Biochemical, Space, Language,, tutorial

Language used: English

Date on which the thesis was submitted / produced: 15. 12. 2022

Thesis defence

• Date of defence: 31. 1. 2023
• Supervisor: RNDr. Matej Troják
• Reader: RNDr. Eva Šmijáková

Masaryk University

Faculty of Informatics

Bachelor programme / field:
Informatics / Informatics