Limits...
Acorn: a grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface.

Sroka J, Bieniasz-Krzywiec L, Gwóźdź S, Leniowski D, Lącki J, Markowski M, Avignone-Rossa C, Bushell ME, McFadden J, Kierzek AM - BMC Bioinformatics (2011)

Bottom Line: Selected models and simulation results can be shared between different users and made publically available.Pathway maps are then used to visualise numerical results within the web environment.It facilitates shared access to models and creation of publicly available constraint based modelling resources.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Informatics University of Warsaw, Poland.

ABSTRACT

Background: Constraint-based approaches facilitate the prediction of cellular metabolic capabilities, based, in turn on predictions of the repertoire of enzymes encoded in the genome. Recently, genome annotations have been used to reconstruct genome scale metabolic reaction networks for numerous species, including Homo sapiens, which allow simulations that provide valuable insights into topics, including predictions of gene essentiality of pathogens, interpretation of genetic polymorphism in metabolic disease syndromes and suggestions for novel approaches to microbial metabolic engineering. These constraint-based simulations are being integrated with the functional genomics portals, an activity that requires efficient implementation of the constraint-based simulations in the web-based environment.

Results: Here, we present Acorn, an open source (GNU GPL) grid computing system for constraint-based simulations of genome scale metabolic reaction networks within an interactive web environment. The grid-based architecture allows efficient execution of computationally intensive, iterative protocols such as Flux Variability Analysis, which can be readily scaled up as the numbers of models (and users) increase. The web interface uses AJAX, which facilitates efficient model browsing and other search functions, and intuitive implementation of appropriate simulation conditions. Research groups can install Acorn locally and create user accounts. Users can also import models in the familiar SBML format and link reaction formulas to major functional genomics portals of choice. Selected models and simulation results can be shared between different users and made publically available. Users can construct pathway map layouts and import them into the server using a desktop editor integrated within the system. Pathway maps are then used to visualise numerical results within the web environment. To illustrate these features we have deployed Acorn and created a web server allowing constraint based simulations of the genome scale metabolic reaction networks of E. coli, S. cerevisiae and M. tuberculosis.

Conclusions: Acorn is a free software package, which can be installed by research groups to create a web based environment for computer simulations of genome scale metabolic reaction networks. It facilitates shared access to models and creation of publicly available constraint based modelling resources.

Show MeSH

Related in: MedlinePlus

The web page representingt GSMN. The table containing reaction names has been interactively filtered for keyword "alanine" in the reaction name. Reaction bounds are editable. The gene names in the Boolean gene-reaction association formula are linked to the functional genomics portal chosen by the user who created the model.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3116490&req=5

Figure 3: The web page representingt GSMN. The table containing reaction names has been interactively filtered for keyword "alanine" in the reaction name. Reaction bounds are editable. The gene names in the Boolean gene-reaction association formula are linked to the functional genomics portal chosen by the user who created the model.

Mentions: The user logs into the system via web interface and can browse GSMN models in tabular format (Figure 3). The rows of reaction tables contain reaction name, reaction formula and lower and upper flux bounds. The last cell of the reaction entry contains gene-reaction association formula representing genes encoding protein subunits of enzymes catalysing this reaction. The genes encoding components of multisubunit enzymes are linked with AND boolean statement and paralogous genes are represented by OR statements. Gene names are linked to gene pages of selected functional genomics resources integrating GSMN model with literature annotations and comparative sequence analysis results. Reaction bounds are editable and are used to set initial conditions of the constraint-based simulations.


Acorn: a grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface.

Sroka J, Bieniasz-Krzywiec L, Gwóźdź S, Leniowski D, Lącki J, Markowski M, Avignone-Rossa C, Bushell ME, McFadden J, Kierzek AM - BMC Bioinformatics (2011)

The web page representingt GSMN. The table containing reaction names has been interactively filtered for keyword "alanine" in the reaction name. Reaction bounds are editable. The gene names in the Boolean gene-reaction association formula are linked to the functional genomics portal chosen by the user who created the model.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3116490&req=5

Figure 3: The web page representingt GSMN. The table containing reaction names has been interactively filtered for keyword "alanine" in the reaction name. Reaction bounds are editable. The gene names in the Boolean gene-reaction association formula are linked to the functional genomics portal chosen by the user who created the model.
Mentions: The user logs into the system via web interface and can browse GSMN models in tabular format (Figure 3). The rows of reaction tables contain reaction name, reaction formula and lower and upper flux bounds. The last cell of the reaction entry contains gene-reaction association formula representing genes encoding protein subunits of enzymes catalysing this reaction. The genes encoding components of multisubunit enzymes are linked with AND boolean statement and paralogous genes are represented by OR statements. Gene names are linked to gene pages of selected functional genomics resources integrating GSMN model with literature annotations and comparative sequence analysis results. Reaction bounds are editable and are used to set initial conditions of the constraint-based simulations.

Bottom Line: Selected models and simulation results can be shared between different users and made publically available.Pathway maps are then used to visualise numerical results within the web environment.It facilitates shared access to models and creation of publicly available constraint based modelling resources.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Informatics University of Warsaw, Poland.

ABSTRACT

Background: Constraint-based approaches facilitate the prediction of cellular metabolic capabilities, based, in turn on predictions of the repertoire of enzymes encoded in the genome. Recently, genome annotations have been used to reconstruct genome scale metabolic reaction networks for numerous species, including Homo sapiens, which allow simulations that provide valuable insights into topics, including predictions of gene essentiality of pathogens, interpretation of genetic polymorphism in metabolic disease syndromes and suggestions for novel approaches to microbial metabolic engineering. These constraint-based simulations are being integrated with the functional genomics portals, an activity that requires efficient implementation of the constraint-based simulations in the web-based environment.

Results: Here, we present Acorn, an open source (GNU GPL) grid computing system for constraint-based simulations of genome scale metabolic reaction networks within an interactive web environment. The grid-based architecture allows efficient execution of computationally intensive, iterative protocols such as Flux Variability Analysis, which can be readily scaled up as the numbers of models (and users) increase. The web interface uses AJAX, which facilitates efficient model browsing and other search functions, and intuitive implementation of appropriate simulation conditions. Research groups can install Acorn locally and create user accounts. Users can also import models in the familiar SBML format and link reaction formulas to major functional genomics portals of choice. Selected models and simulation results can be shared between different users and made publically available. Users can construct pathway map layouts and import them into the server using a desktop editor integrated within the system. Pathway maps are then used to visualise numerical results within the web environment. To illustrate these features we have deployed Acorn and created a web server allowing constraint based simulations of the genome scale metabolic reaction networks of E. coli, S. cerevisiae and M. tuberculosis.

Conclusions: Acorn is a free software package, which can be installed by research groups to create a web based environment for computer simulations of genome scale metabolic reaction networks. It facilitates shared access to models and creation of publicly available constraint based modelling resources.

Show MeSH
Related in: MedlinePlus