Processes
Navigation
To browse the processes in cyanobacterium use either the graphical scheme below or the navigation panel on the left. The root level is displayed after clicking on the Biochemical Space tab in the main menu at the top of the screen.
The central feature of the ontology view is the graphical scheme representing the projection of cyanobacterium to respective biological processes. The graphical scheme is active, the individual processes implemented in the project are highlighted yellow when moving the mouse over them. After clicking on any implemented part, corresponding scheme of selected process is viewed.
Models Tab
The Models Tab displays all models containing selected process. More information can be obtained by clicking on specific model. After clicking on Details, you will be redirected to selected model.
Entities Tab
The Entities Tab displays all entities contained in selected process. More information can be obtained by unfolding specific entity and clicking on Details.
Rules Tab
Rules Tab contains information regarding the modeled rules in selected process. Individual rules are categorized into rule types and can be unfolded by clicking on desired one. After clicking on selected rule, more details are viewed.
Cyanobacterium in its environment
Ryan L. Clark et al., Insights into the industrial growth of cyanobacteria from a model of the carbon-concentrating mechanism, AIChE Journal, 2014
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Fridlyand L, Kaplan A, Reinhold L (1995) Quantitative evaluation of the role of a putative CO2-scavenging entity in the cyanobacterial CO2-concentrating mechanism. Biosystems 1996;37(3):229-38.
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A dynamical model that describes the daily dynamics of diazotrophy in a unicellular cyanobacterium, Crocosphaera watsonii WH8501, in regard to light limitation and obligate diazotrophy.
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Hertel S, Brettschneider Ch, Ilka Axmann M (2013) Revealing a Two-Loop Transcriptional Feedback
Mechanism in the Cyanobacterial Circadian Clock. PLOS Computational Biology 9(3) e1002966.
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Jablonsky J, Schwarz D, Hagemann M (2014) Multi-Level Kinetic Model Explaining Diverse Roles of Isozymes in Prokaryotes. PLoS ONE 9(8): e105292.
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Miyoshi F, Nakayama Y, Kaizu K, Iwasaki H, Tomita M (2007) A mathematical model for the Kai-protein-based chemical oscillator and clock gene expression rhythms in Cyanobacteria. J Biol Rhythms 22:69-8
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Related Numbers: Number of c-rings in ATPase — 14
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Related Numbers: Number of photosystem I units per cell — 96000 , Number of iron atoms in photosystem I units per cell — 1200000
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modifier: As the recombination is considred as subsequent backward electron transport from Fa- to P700+ through Fx, A1, A0 and aChl, these enities must be in neutral state to accept the electron and hence they are modifiers of the recombination-
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modifier: As the recombination is considred as subsequent backward electron transport from Fx- to P700+ through A1, A0 and aChl, these enities must be in neutral state to accept the electron and hence they are modifiers of the recombination-
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modifier: As the recombination is considred as subsequent backward electron transport from A1- to P700+ through A0 and aChl, these enities must be in neutral state to accept the electron and hence they are modifiers of the recombination.
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modifier: 3-1-3-4
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modifier: 3-1-3-4
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modifier: 3-1-3-4
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M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria. In: Computational Methods in Systems Biology, CMSB 2016, Vol. 9859 of LNCS, pp. 316-322. Springer, 2016. DOI