- HOME

Experiments repository is a tool for storage and presentation of time-series data from wet-lab experiments. Every experiment is well-grounded by precise description (device, medium, organism, etc.) and appropriate annotations. Experiment's variables might be related to Biochemical Space. Moreover, it is possible to visualise the data

in a chart.

- BIOCHEMICAL SPACE

Please use the following reference to cite this web site: M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web

- BIOCHEMICAL SPACE

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

CYANONUMBERS

Please use the following reference to cite this web site: M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web

- MODEL REPOSITORY

Model repository. Models. Miyoshi et al. 2007 - SUPPORT - E-CYANOBACTERIUM.ORG Please use the following reference to cite this web site: M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web

- BIOCHEMICAL SPACE

Navigation Below is displayed the entity view of the selected entity. Entity view is shown in the form of scheme expressing relations part of (green), contains (orange), substrate of rule (red) and product of rule (blue). The navigation panel on the left shows the entity in corresponding model and allows you to browse the biological structure

of the model.

- EXPERIMENTS REPOSITORY This page displays basic information about selected experiment. In case of series of experiments, these can be found below in List of experiments with links

- MODEL REPOSITORY

model: Plyusnina et al. (2016) The specific feature of electron transport on thylakoid membrane of cyanobacteria is a combination of photosynthetic and respiratory pathways in one reaction space. . The linear photosynthetic transport includes reactions for photosystem II (PSII), plastoquinone (PQ), cytochrome b6f (Cyt b6f), plastocyanin (PC

- MODEL REPOSITORY

Model repository. Models. Miyoshi et al. 2007

- HOME

Experiments repository is a tool for storage and presentation of time-series data from wet-lab experiments. Every experiment is well-grounded by precise description (device, medium, organism, etc.) and appropriate annotations. Experiment's variables might be related to Biochemical Space. Moreover, it is possible to visualise the data

in a chart.

- BIOCHEMICAL SPACE

Please use the following reference to cite this web site: M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web

- BIOCHEMICAL SPACE

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

CYANONUMBERS

Please use the following reference to cite this web site: M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web

- MODEL REPOSITORY

Model repository. Models. Miyoshi et al. 2007 - SUPPORT - E-CYANOBACTERIUM.ORG Please use the following reference to cite this web site: M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web

- BIOCHEMICAL SPACE

Navigation Below is displayed the entity view of the selected entity. Entity view is shown in the form of scheme expressing relations part of (green), contains (orange), substrate of rule (red) and product of rule (blue). The navigation panel on the left shows the entity in corresponding model and allows you to browse the biological structure

of the model.

- EXPERIMENTS REPOSITORY This page displays basic information about selected experiment. In case of series of experiments, these can be found below in List of experiments with links

- MODEL REPOSITORY

model: Plyusnina et al. (2016) The specific feature of electron transport on thylakoid membrane of cyanobacteria is a combination of photosynthetic and respiratory pathways in one reaction space. . The linear photosynthetic transport includes reactions for photosystem II (PSII), plastoquinone (PQ), cytochrome b6f (Cyt b6f), plastocyanin (PC

- MODEL REPOSITORY

Model repository. Models. Miyoshi et al. 2007

CYANONUMBERS

Please use the following reference to cite this web site: M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web - SUPPORT - E-CYANOBACTERIUM.ORG Please use the following reference to cite this web site: M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web - EXPERIMENTS REPOSITORY Figure 6 Experimental data of Synechocystis sp. PCC 6803 cultivated in non-buffe. 2019-10-22 08:31:46. Panel A: Panel A: dCO2. Figure 6 Experimental data of Synechocystis sp. PCC 6803 cultivated in non-buffe. 2019-10-22 07:38:44. Panel A. Figure 6 Experimental data of Synechocystis sp. PCC 6803 cultivated in non-buffe. 2019-10-22

07:37:55.

- ABOUT US

Contact. Systems Biology Laboratory. Faculty of Informatics Masaryk University Brno Czech Republic. In case of any questions, please do not hesitate to contact us.. Staff

- MODEL REPOSITORY

model: Plyusnina et al. (2016) The specific feature of electron transport on thylakoid membrane of cyanobacteria is a combination of photosynthetic and respiratory pathways in one reaction space. . The linear photosynthetic transport includes reactions for photosystem II (PSII), plastoquinone (PQ), cytochrome b6f (Cyt b6f), plastocyanin (PC

- BIOCHEMICAL SPACE

Entity . Entity is a cornerstone of space hierarchy and represents an object from a wide range of functions – from individual particles to

huge complexes.

- EXPERIMENTS REPOSITORY Series name: Synechocystis 6803 GT-L Batch, Temperature 35oC: Summary: Systematic experiments performed for detailed characterization of physiological responses and growth of Synechocystis 6803 GT-L strain under varying lights (both spectral quality and

- BIOCHEMICAL SPACE

Navigation Below is displayed the entity view of the selected entity. Entity view is shown in the form of scheme expressing relations part of (green), contains (orange), substrate of rule (red) and product of rule (blue). The navigation panel on the left shows the entity in corresponding model and allows you to browse the biological structure

of the model.

- BIOCHEMICAL SPACE

Navigation Below is displayed the reaction view of the selected reaction. Reaction view is shown in the form of scheme showing corresponding substrates(blue) and - EXPERIMENTS REPOSITORY Series name: Figure 6 Experimental data of Synechocystis sp. PCC 6803 cultivated in non-buffe: Summary: measurements of dCO2 (full blue lines) and pH signals (full black lines) signals (left panels) for initial pH 6.5 (panel A), 7.3 (panel C), 7.7 (panel E), and 8.1 (panel

G).

- HOME

Experiments repository is a tool for storage and presentation of time-series data from wet-lab experiments. Every experiment is well-grounded by precise description (device, medium, organism, etc.) and appropriate annotations. Experiment's variables might be related to Biochemical Space. Moreover, it is possible to visualise the data

in a chart.

- SUPPORT - E-CYANOBACTERIUM.ORG Please use the following reference to cite this web site: M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web

CYANONUMBERS

Please use the following reference to cite this web site: M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web

- MODEL REPOSITORY

Model repository. Models. Miyoshi et al. 2007 E-CYANOBACTERIUM.ORG: TUTORIAL Fig. 3 – home page of e-cyanobacterium.org, login and registration panel After registration, e-cyanobacterium.org platform is fully operational. 3. Biochemical Space Section Biochemical space is located in the Main menu (Fig. 4.1).Navigation is possible

- BIOCHEMICAL SPACE

Navigation Below is displayed the reaction view of the selected reaction. Reaction view is shown in the form of scheme showing corresponding substrates(blue) and

- BIOCHEMICAL SPACE

Navigation Below is displayed the entity view of the selected entity. Entity view is shown in the form of scheme expressing relations part of (green), contains (orange), substrate of rule (red) and product of rule (blue). The navigation panel on the left shows the entity in corresponding model and allows you to browse the biological structure

of the model.

- EXPERIMENTS REPOSITORY Series name: Synechocystis 6803 GT-L Batch, Temperature 35oC: Summary: Systematic experiments performed for detailed characterization of physiological responses and growth of Synechocystis 6803 GT-L strain under varying lights (both spectral quality and

- BIOCHEMICAL SPACE

Entity . Entity is a cornerstone of space hierarchy and represents an object from a wide range of functions – from individual particles to

huge complexes.

- HOME

Experiments repository is a tool for storage and presentation of time-series data from wet-lab experiments. Every experiment is well-grounded by precise description (device, medium, organism, etc.) and appropriate annotations. Experiment's variables might be related to Biochemical Space. Moreover, it is possible to visualise the data

in a chart.

- SUPPORT - E-CYANOBACTERIUM.ORG Please use the following reference to cite this web site: M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web

CYANONUMBERS

Please use the following reference to cite this web site: M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web

- MODEL REPOSITORY

Model repository. Models. Miyoshi et al. 2007 E-CYANOBACTERIUM.ORG: TUTORIAL Fig. 3 – home page of e-cyanobacterium.org, login and registration panel After registration, e-cyanobacterium.org platform is fully operational. 3. Biochemical Space Section Biochemical space is located in the Main menu (Fig. 4.1).Navigation is possible

- BIOCHEMICAL SPACE

Navigation Below is displayed the reaction view of the selected reaction. Reaction view is shown in the form of scheme showing corresponding substrates(blue) and

- BIOCHEMICAL SPACE

Navigation Below is displayed the entity view of the selected entity. Entity view is shown in the form of scheme expressing relations part of (green), contains (orange), substrate of rule (red) and product of rule (blue). The navigation panel on the left shows the entity in corresponding model and allows you to browse the biological structure

of the model.

- EXPERIMENTS REPOSITORY Series name: Synechocystis 6803 GT-L Batch, Temperature 35oC: Summary: Systematic experiments performed for detailed characterization of physiological responses and growth of Synechocystis 6803 GT-L strain under varying lights (both spectral quality and

- BIOCHEMICAL SPACE

Entity . Entity is a cornerstone of space hierarchy and represents an object from a wide range of functions – from individual particles to

huge complexes.

- HOME

E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria.It allows models to be represented at different levels of abstraction — as biochemical reaction networks or

CYANONUMBERS

Please use the following reference to cite this web site: M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web

- MODEL REPOSITORY

Model repository. Models. Miyoshi et al. 2007

- MODEL REPOSITORY

Model repository. Models. Miyoshi et al. 2007 - EXPERIMENTS REPOSITORY Figure 6 Experimental data of Synechocystis sp. PCC 6803 cultivated in non-buffe. 2019-10-22 08:31:46. Panel A: Panel A: dCO2. Figure 6 Experimental data of Synechocystis sp. PCC 6803 cultivated in non-buffe. 2019-10-22 07:38:44. Panel A. Figure 6 Experimental data of Synechocystis sp. PCC 6803 cultivated in non-buffe. 2019-10-22

07:37:55.

- BIOCHEMICAL SPACE

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 E-CYANOBACTERIUM.ORG: TUTORIAL Fig. 3 – home page of e-cyanobacterium.org, login and registration panel After registration, e-cyanobacterium.org platform is fully operational. 3. Biochemical Space Section Biochemical space is located in the Main menu (Fig. 4.1).Navigation is possible

- MODEL REPOSITORY

model: Plyusnina et al. (2016) The specific feature of electron transport on thylakoid membrane of cyanobacteria is a combination of photosynthetic and respiratory pathways in one reaction space. . The linear photosynthetic transport includes reactions for photosystem II (PSII), plastoquinone (PQ), cytochrome b6f (Cyt b6f), plastocyanin (PC

- BIOCHEMICAL SPACE

Navigation Below is displayed the entity view of the selected entity. Entity view is shown in the form of scheme expressing relations part of (green), contains (orange), substrate of rule (red) and product of rule (blue). The navigation panel on the left shows the entity in corresponding model and allows you to browse the biological structure

of the model.

- HOME

Experiments repository is a tool for storage and presentation of time-series data from wet-lab experiments. Every experiment is well-grounded by precise description (device, medium, organism, etc.) and appropriate annotations. Experiment's variables might be related to Biochemical Space. Moreover, it is possible to visualise the data

in a chart.

- SUPPORT - E-CYANOBACTERIUM.ORG Please use the following reference to cite this web site: M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web

CYANONUMBERS

Please use the following reference to cite this web site: M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web

- MODEL REPOSITORY

Model repository. Models. Miyoshi et al. 2007 E-CYANOBACTERIUM.ORG: TUTORIAL Fig. 3 – home page of e-cyanobacterium.org, login and registration panel After registration, e-cyanobacterium.org platform is fully operational. 3. Biochemical Space Section Biochemical space is located in the Main menu (Fig. 4.1).Navigation is possible

- BIOCHEMICAL SPACE

Navigation Below is displayed the reaction view of the selected reaction. Reaction view is shown in the form of scheme showing corresponding substrates(blue) and

- BIOCHEMICAL SPACE

Navigation Below is displayed the entity view of the selected entity. Entity view is shown in the form of scheme expressing relations part of (green), contains (orange), substrate of rule (red) and product of rule (blue). The navigation panel on the left shows the entity in corresponding model and allows you to browse the biological structure

of the model.

- EXPERIMENTS REPOSITORY Series name: Synechocystis 6803 GT-L Batch, Temperature 35oC: Summary: Systematic experiments performed for detailed characterization of physiological responses and growth of Synechocystis 6803 GT-L strain under varying lights (both spectral quality and

- BIOCHEMICAL SPACE

Entity . Entity is a cornerstone of space hierarchy and represents an object from a wide range of functions – from individual particles to

huge complexes.

- HOME

Experiments repository is a tool for storage and presentation of time-series data from wet-lab experiments. Every experiment is well-grounded by precise description (device, medium, organism, etc.) and appropriate annotations. Experiment's variables might be related to Biochemical Space. Moreover, it is possible to visualise the data

in a chart.

- SUPPORT - E-CYANOBACTERIUM.ORG Please use the following reference to cite this web site: M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web

CYANONUMBERS

Please use the following reference to cite this web site: M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web

- MODEL REPOSITORY

Model repository. Models. Miyoshi et al. 2007 E-CYANOBACTERIUM.ORG: TUTORIAL Fig. 3 – home page of e-cyanobacterium.org, login and registration panel After registration, e-cyanobacterium.org platform is fully operational. 3. Biochemical Space Section Biochemical space is located in the Main menu (Fig. 4.1).Navigation is possible

- BIOCHEMICAL SPACE

Navigation Below is displayed the reaction view of the selected reaction. Reaction view is shown in the form of scheme showing corresponding substrates(blue) and

- BIOCHEMICAL SPACE

Navigation Below is displayed the entity view of the selected entity. Entity view is shown in the form of scheme expressing relations part of (green), contains (orange), substrate of rule (red) and product of rule (blue). The navigation panel on the left shows the entity in corresponding model and allows you to browse the biological structure

of the model.

- EXPERIMENTS REPOSITORY Series name: Synechocystis 6803 GT-L Batch, Temperature 35oC: Summary: Systematic experiments performed for detailed characterization of physiological responses and growth of Synechocystis 6803 GT-L strain under varying lights (both spectral quality and

- BIOCHEMICAL SPACE

Entity . Entity is a cornerstone of space hierarchy and represents an object from a wide range of functions – from individual particles to

huge complexes.

- HOME

E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria.It allows models to be represented at different levels of abstraction — as biochemical reaction networks or

CYANONUMBERS

Please use the following reference to cite this web site: M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web

- MODEL REPOSITORY

Model repository. Models. Miyoshi et al. 2007

- MODEL REPOSITORY

Model repository. Models. Miyoshi et al. 2007 - EXPERIMENTS REPOSITORY Figure 6 Experimental data of Synechocystis sp. PCC 6803 cultivated in non-buffe. 2019-10-22 08:31:46. Panel A: Panel A: dCO2. Figure 6 Experimental data of Synechocystis sp. PCC 6803 cultivated in non-buffe. 2019-10-22 07:38:44. Panel A. Figure 6 Experimental data of Synechocystis sp. PCC 6803 cultivated in non-buffe. 2019-10-22

07:37:55.

- BIOCHEMICAL SPACE

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 E-CYANOBACTERIUM.ORG: TUTORIAL Fig. 3 – home page of e-cyanobacterium.org, login and registration panel After registration, e-cyanobacterium.org platform is fully operational. 3. Biochemical Space Section Biochemical space is located in the Main menu (Fig. 4.1).Navigation is possible

- MODEL REPOSITORY

model: Plyusnina et al. (2016) The specific feature of electron transport on thylakoid membrane of cyanobacteria is a combination of photosynthetic and respiratory pathways in one reaction space. . The linear photosynthetic transport includes reactions for photosystem II (PSII), plastoquinone (PQ), cytochrome b6f (Cyt b6f), plastocyanin (PC

- BIOCHEMICAL SPACE

Navigation Below is displayed the entity view of the selected entity. Entity view is shown in the form of scheme expressing relations part of (green), contains (orange), substrate of rule (red) and product of rule (blue). The navigation panel on the left shows the entity in corresponding model and allows you to browse the biological structure

of the model.

- HOME

E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria.It allows models to be represented at different levels of abstraction — as biochemical reaction networks or - SUPPORT - E-CYANOBACTERIUM.ORG Please use the following reference to cite this web site: M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web

- MODEL REPOSITORY

Model repository. Models. Miyoshi et al. 2007

CYANONUMBERS

Please use the following reference to cite this web site: M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web E-CYANOBACTERIUM.ORG: TUTORIAL Fig. 3 – home page of e-cyanobacterium.org, login and registration panel After registration, e-cyanobacterium.org platform is fully operational. 3. Biochemical Space Section Biochemical space is located in the Main menu (Fig. 4.1).Navigation is possible

- BIOCHEMICAL SPACE

Navigation Below is displayed the entity view of the selected entity. Entity view is shown in the form of scheme expressing relations part of (green), contains (orange), substrate of rule (red) and product of rule (blue). The navigation panel on the left shows the entity in corresponding model and allows you to browse the biological structure

of the model.

- BIOCHEMICAL SPACE

Navigation Below is displayed the reaction view of the selected reaction. Reaction view is shown in the form of scheme showing corresponding substrates(blue) and - EXPERIMENTS REPOSITORY Series name: Synechocystis 6803 GT-L Batch, Temperature 35oC: Summary: Systematic experiments performed for detailed characterization of physiological responses and growth of Synechocystis 6803 GT-L strain under varying lights (both spectral quality and

- BIOCHEMICAL SPACE

Entity . Entity is a cornerstone of space hierarchy and represents an object from a wide range of functions – from individual particles to

huge complexes.

- HOME

Experiments repository is a tool for storage and presentation of time-series data from wet-lab experiments. Every experiment is well-grounded by precise description (device, medium, organism, etc.) and appropriate annotations. Experiment's variables might be related to Biochemical Space. Moreover, it is possible to visualise the data

in a chart.

- SUPPORT - E-CYANOBACTERIUM.ORG Please use the following reference to cite this web site: M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web

CYANONUMBERS

Please use the following reference to cite this web site: M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web

- MODEL REPOSITORY

Model repository. Models. Miyoshi et al. 2007 E-CYANOBACTERIUM.ORG: TUTORIAL Fig. 3 – home page of e-cyanobacterium.org, login and registration panel After registration, e-cyanobacterium.org platform is fully operational. 3. Biochemical Space Section Biochemical space is located in the Main menu (Fig. 4.1).Navigation is possible

- BIOCHEMICAL SPACE

Navigation Below is displayed the reaction view of the selected reaction. Reaction view is shown in the form of scheme showing corresponding substrates(blue) and

- BIOCHEMICAL SPACE

Navigation Below is displayed the entity view of the selected entity. Entity view is shown in the form of scheme expressing relations part of (green), contains (orange), substrate of rule (red) and product of rule (blue). The navigation panel on the left shows the entity in corresponding model and allows you to browse the biological structure

of the model.

- EXPERIMENTS REPOSITORY Series name: Synechocystis 6803 GT-L Batch, Temperature 35oC: Summary: Systematic experiments performed for detailed characterization of physiological responses and growth of Synechocystis 6803 GT-L strain under varying lights (both spectral quality and

- BIOCHEMICAL SPACE

Entity . Entity is a cornerstone of space hierarchy and represents an object from a wide range of functions – from individual particles to

huge complexes.

- HOME

E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria.It allows models to be represented at different levels of abstraction — as biochemical reaction networks or

CYANONUMBERS

Please use the following reference to cite this web site: M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web

- MODEL REPOSITORY

Model repository. Models. Miyoshi et al. 2007

- MODEL REPOSITORY

Model repository. Models. Miyoshi et al. 2007 - EXPERIMENTS REPOSITORY Figure 6 Experimental data of Synechocystis sp. PCC 6803 cultivated in non-buffe. 2019-10-22 08:31:46. Panel A: Panel A: dCO2. Figure 6 Experimental data of Synechocystis sp. PCC 6803 cultivated in non-buffe. 2019-10-22 07:38:44. Panel A. Figure 6 Experimental data of Synechocystis sp. PCC 6803 cultivated in non-buffe. 2019-10-22

07:37:55.

- BIOCHEMICAL SPACE

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 E-CYANOBACTERIUM.ORG: TUTORIAL Fig. 3 – home page of e-cyanobacterium.org, login and registration panel After registration, e-cyanobacterium.org platform is fully operational. 3. Biochemical Space Section Biochemical space is located in the Main menu (Fig. 4.1).Navigation is possible

- MODEL REPOSITORY

model: Plyusnina et al. (2016) The specific feature of electron transport on thylakoid membrane of cyanobacteria is a combination of photosynthetic and respiratory pathways in one reaction space. . The linear photosynthetic transport includes reactions for photosystem II (PSII), plastoquinone (PQ), cytochrome b6f (Cyt b6f), plastocyanin (PC

- BIOCHEMICAL SPACE

Navigation Below is displayed the entity view of the selected entity. Entity view is shown in the form of scheme expressing relations part of (green), contains (orange), substrate of rule (red) and product of rule (blue). The navigation panel on the left shows the entity in corresponding model and allows you to browse the biological structure

of the model.

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E-CYANOBACTERIUM.ORG E-CYANOBACTERIUM.ORG is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to CYANOBACTERIA . It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations. The platform is unique in providing concise mapping of mathematical models to the formalised consortium-agreed biochemical description. The main goal of the platform is to connect the world of biological knowledge with benefits of mathematical description of dynamic processes. ------------------------- MODEL REPOSITORY is a collection of mathematical models describing particular parts of biological processes. Each model component (i.e. reactant or reaction) is related to Biochemical Space. The model then includes complete biological annotation of all reactants and reactions. Simulations, static analysis, and SBML export are available. BIOCHEMICAL SPACE is constructed from hierarchy of entities and rules visualised in graphical schemes. It forms the backbone of the platform – the process tree. Each scheme represents chosen biological process of cyanobacteria. For each process, appropriate biochemical entities, rules, and models are attached. EXPERIMENTS REPOSITORY

is a tool for

storage and presentation of time-series data from wet-lab experiments. Every experiment is well-grounded by precise description (device, medium, organism, etc.) and appropriate annotations. Experiment's variables might be related to Biochemical Space. Moreover, it is possible to visualise the data in a chart. ------------------------- The experimental platform supplying data for this website has been partially supported by the Czech research infrastructure for systems biology C4SYS (project no LM2015055). The platform development was partially supported within the activities of EC OP project financed from EU with the support of MEYS CR: Local Team and International Consortium for Computational Modelling of a Cyanobacterial Cell, Reg. No. CZ.1.07/2.3.00/20.0256) ------------------------- Please use the following reference to cite this web site: 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