E-cyanobacterium.org: A Web-based Platform for Systems Biology
of Cyanobacteria

k 2017

E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria

TROJÁK, Matej, David ŠAFRÁNEK, Jakub HRABEC, Jakub ŠALAGOVIČ, Františka ROMANOVSKÁ et. al.

Základní údaje

Originální název

E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria

Autoři

TROJÁK, Matej, David ŠAFRÁNEK, Jakub HRABEC, Jakub ŠALAGOVIČ, Františka ROMANOVSKÁ, Matej HAJNAL a Jan ČERVENÝ

Vydání

Doctoral Workshop on Mathematical and Engineering Methods in Computer Science, 2017

Další údaje

Jazyk

angličtina

Typ výsledku

Prezentace na konferencích

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Česká republika

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Organizační jednotka

Fakulta informatiky

Klíčová slova anglicky

systems biology; cyanobacteria; online tool; model repository

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 30. 10. 2017 11:21, RNDr. Matej Troják, Ph.D.

Anotace

V originále

The understanding of a complex cellular machinery is a crucial problem in current systems biology, especially for photosynthetic organisms such as cyanobacteria. To challenge this uneasy task we have developed an online platform which consists of three interconnected modules. • Biochemical Space (BCS) allows to formally describe (bio)chemical reactions facilitated by cyanobacteria molecular entities. Such reactions are represented in a generalised form of rules specified in the Biochemical Space Language – a novel rule-based language. The rules form a hierarchy of (bio)chemical processes covering transport, metabolism, circadian clock, photosynthesis, and carbon concentrating mechanism. • Model Repository is a collection of related mathematical models accompanied with simulation and static analysis algorithms. Linkage of model components to BCS determines their exact biological meaning. This feature is also present in models exported to SBML standard format. • Experiments Repository serves to import, store, and plot time-series experiments. The measured variables are connected to BCS in the same manner as in the case of model components. Individual experiments possess additional references to related models. In addition, data annotation is available in all modules of the platform. In consequence, BCS, models, and experiments are well-noted and referenceable. Moreover, the usability of the platform is enhanced with visualisations provided for process hierarchy and reaction networks in BCS, simulations in Model Repository, and time-series plots in Experiment Repository. In conclusion, our platform provides a unique solution based on integrating three different approaches to stimulate collaboration between experimental and computational systems biologists.

Návaznosti

GA15-11089S, projekt VaV

Název: Získávání parametrů biologických modelů pomocí techniky ověřování modelů

Investor: Grantová agentura ČR, Získávání parametrů biologických modelů pomocí techniky ověřování modelů

LM2015055, projekt VaV

Název: Centrum pro systémovou biologii (Akronym: C4SYS)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, The national infrastructure C4SYS - Centre for Systems Biology

MUNI/A/0945/2015, interní kód MU

Název: Rozsáhlé výpočetní systémy: modely, aplikace a verifikace V.

Investor: Masarykova univerzita, Rozsáhlé výpočetní systémy: modely, aplikace a verifikace V., DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

Citovat

TROJÁK, Matej, David ŠAFRÁNEK, Jakub HRABEC, Jakub ŠALAGOVIČ, Františka ROMANOVSKÁ, Matej HAJNAL a Jan ČERVENÝ. E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria. In Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. 2017.

@proceedings{1392807,
   author = {Troják, Matej and Šafránek, David and Hrabec, Jakub and Šalagovič, Jakub and Romanovská, Františka and Hajnal, Matej and Červený, Jan},
   booktitle = {Doctoral Workshop on Mathematical and Engineering Methods in Computer Science},
   keywords = {systems biology; cyanobacteria; online tool; model repository},
   language = {eng},
   title = {E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria},
   url = {http://www.memics.cz/2017/},
   year = {2017}
}

TY  - CONF
ID  - 1392807
AU  - Troják, Matej - Šafránek, David - Hrabec, Jakub - Šalagovič, Jakub - Romanovská, Františka - Hajnal, Matej - Červený, Jan
PY  - 2017
TI  - E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria
KW  - systems biology
KW  - cyanobacteria
KW  - online tool
KW  - model repository
UR  - http://www.memics.cz/2017/
N2  - The understanding of a complex cellular machinery is a crucial problem in current systems biology, especially for photosynthetic organisms such as cyanobacteria. To challenge this uneasy task we have developed an online platform which consists of three interconnected modules. • Biochemical Space (BCS) allows to formally describe (bio)chemical reactions facilitated by cyanobacteria molecular entities. Such reactions are represented in a generalised form of rules specified in the Biochemical Space Language – a novel rule-based language. The rules form a hierarchy of (bio)chemical processes covering transport, metabolism, circadian clock, photosynthesis, and carbon concentrating mechanism. • Model Repository is a collection of related mathematical models accompanied with simulation and static analysis algorithms. Linkage of model components to BCS determines their exact biological meaning. This feature is also present in models exported to SBML standard format. • Experiments Repository serves to import, store, and plot time-series experiments. The measured variables are connected to BCS in the same manner as in the case of model components. Individual experiments possess additional references to related models. In addition, data annotation is available in all modules of the platform. In consequence, BCS, models, and experiments are well-noted and referenceable. Moreover, the usability of the platform is enhanced with visualisations provided for process hierarchy and reaction networks in BCS, simulations in Model Repository, and time-series plots in Experiment Repository. In conclusion, our platform provides a unique solution based on integrating three different approaches to stimulate collaboration between experimental and computational systems biologists.
ER  -

TROJÁK, Matej, David ŠAFRÁNEK, Jakub HRABEC, Jakub ŠALAGOVIČ, Františka ROMANOVSKÁ, Matej HAJNAL a Jan ČERVENÝ. E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria. In \textit{Doctoral Workshop on Mathematical and Engineering Methods in Computer Science}. 2017.

Podrobný výpis o publikaci