Team:Groningen/modeling cumulus

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Latest revision as of 01:36, 22 September 2011

Cumulus is the Cloud based modelling and data exchange program that we developed. Its purpose is to show, as a proof of concept, that it is possible to integrate both the exchange of data, the production of comprehensive models, and the sharing of computational resources into one platform.

To this end we developed a new collaborative Biology Framework based on Service Oriented Architectures (SOA) and on a Web Services. This approach simplifies and harmonizes the work carried out on the Cloud and Grid platform by geographically dispersed scientists. The new collaborative SOA Cloud Framework (called Cumulus) provides an efficient and easy way to run distributed software.

This capability is put to use in a parameter optimization program, (currently a genetic algorithm) to find the optimal parameters for submitted models. In other words, Cumulus makes it simple to use cloud computing resources to find parameters for models, and at the same time, leads to the sharing of information.

Below are links to look at the different parts of the Cumulus project.

Downloading cumulus

[http://igem.molgenrug.nl/igem2011/Cumulus/setup.exe Download the Cumulus Pbad Demo installer] [http://igem.molgenrug.nl/igem2011/Cumulus/Cumulus.zip Download the full source code]

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 [[File:CumulusLogo.png| centre]]
-Cumulus is the Cloud based, modelling and data exchange program that we developed.
+Cumulus is the Cloud based modelling and data exchange program that we developed. Its purpose is to show, as a proof of concept, that it is possible to integrate both the exchange of data, the production of comprehensive models, and the sharing of computational resources into one platform.
-To this end, a new collaborative Biology Framework based on Service Oriented Architectures (SOA) and on a Web Service approach that simplify and harmonize the work carried out on Cloud and Grid platform by geographically dispersed computational scientists has been designed.
+To this end we developed a new collaborative Biology Framework based on Service Oriented Architectures (SOA) and on a Web Services. This approach simplifies and harmonizes the work carried out on the Cloud and Grid platform by geographically dispersed scientists. The new collaborative SOA Cloud Framework (called Cumulus) provides an efficient and easy way to run distributed software.
-The new collaborative SOA Cloud Framework (called CUMULUS) provides an efficient and easy way to run on the Grid distributed versions of scientific codes and it can be easily generalized and incorporated in any Science Gateways by considering the Grid users at the center of the action as a point of generation, integration, control and evaluation of the computational activities.
+This capability is put to use in a parameter optimization program, (currently a genetic algorithm) to find the optimal parameters for submitted models. In other words, Cumulus makes it simple to use cloud computing resources to find parameters for models, and at the same time, leads to the sharing of information.
-Accordingly, the basic goal of Cumulus is to provide to its users with a user-friendly tool allowing them to exploit the innovative features of biological simulation with no need for mastering related technicalities. In other words, Cumulus makes cloud applications black-box like and, at the same time, leads to better memory usage, reduced cpu and wall times consumption as well as to an optimized distribution of tasks over the platform. This leads also to a more efficient exploitation of available features.
+Below are links to look at the different parts of the Cumulus project.
+*[[Team:Groningen/modeling_vision|Our Cumulus vision]]
+*[[Team:Groningen/modeling_methods|Why we build Cumulus]]
+*[[Team:Groningen/modeling_simulation_engine|The Cumulus simulation engine]]
+*[[Team:Groningen/modeling_genetic_algorithms|How we find parameters]]
+*[[Team:Groningen/modeling_results|Cumulus system results]]
+*[[Team:Groningen/modeling_cumulus2|The next version of the Cumulus system]]
-==Links==
-Here are some quick links to look at the
-*[[Team:Groningen/modeling_vision|Vision]]
+===Downloading cumulus===
-*[[Team:Groningen/modeling_methods|Methods]]
+[http://igem.molgenrug.nl/igem2011/Cumulus/setup.exe Download the Cumulus Pbad Demo installer]
-*[[Team:Groningen/modeling_features|Features]]
+[http://igem.molgenrug.nl/igem2011/Cumulus/Cumulus.zip Download the full source code]
-*[[Team:Groningen/modeling_simulation_engine|Simulator]]
-*[[Team:Groningen/modeling_genetic_algorithms|Genetic algortim]]
-*[[Team:Groningen/modeling_results|Results]]
-*[[Team:Groningen/modeling_cumulus2|Cumulus 2.0]]
-Here are some links that might answer you immediate questions:
-*[[Cloud aren't they the white stuff floating in the sky?]]
-*[[A iGEM application in the cloud, Why would you do that?]]
-*[[I work in a genetics department, but what about the algorithm part?]]
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