Detailed Information on Publication Record
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.Basic information
Original name
E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria
Authors
TROJÁK, Matej, David ŠAFRÁNEK, Jakub HRABEC, Jakub ŠALAGOVIČ, Františka ROMANOVSKÁ, Matej HAJNAL and Jan ČERVENÝ
Edition
Doctoral Workshop on Mathematical and Engineering Methods in Computer Science, 2017
Other information
Language
English
Type of outcome
Prezentace na konferencích
Field of Study
10201 Computer sciences, information science, bioinformatics
Country of publisher
Czech Republic
Confidentiality degree
není předmětem státního či obchodního tajemství
References:
Organization unit
Faculty of Informatics
Keywords in English
systems biology; cyanobacteria; online tool; model repository
Tags
International impact, Reviewed
Změněno: 30/10/2017 11:21, RNDr. Matej Troják, Ph.D.
Abstract
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.
Links
| GA15-11089S, research and development project |
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| LM2015055, research and development project |
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| MUNI/A/0945/2015, interní kód MU |
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