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Team:Groningen/modeling vision
From 2011.igem.org
Vision
We imagine a world in which biologist are able to share their data with the click of a button. A world in which thurough reliable measuring procedures exist that help scientist characterise their parts using a reliable user friendly computer environment. A world in which not just data but also the models supporting that data are exchanged. A world in which scientist can not only share the burden of exploration but also the burden of computation.
Cumulus is our way of making the world come a little closer. Cumulus has been developed to run
both on the cloud and on the grid by means of the azure platform. by considering as a study case single and parameter study
applications for our particular project. Its use as a tool of Science Gateways to facilitate massive calculations also to the end of improving scientific collaboration.
How we came to building Cumulus
One of the first things we did when we started to model our circuit was to review the most popular modelling tools in the iGEM competition. You can read the results of this review [here].
We decided
The quest for parameters
Even building a simple model of genetic circuit will give the most experienced modellers pause. This is mainly because the behaviours of the different biobrick parts are poorly characterised especially when it comes to parameters. While trying to model our circuit we quickly discovered that most of the parameters we found in literature where very specific to the situation of publication and did not generalize to other circuits. In our opinion this is because scientist are most used to sharing results and not their raw data. If we could find a way to combine all the data available on a part into a single characterisation maybe we could produce some more dependable results.
Cumulus uses a parameter optimization program that is capable of evaluating a single parameter setting in the context of multiple experiments.
Scaling up the computation
All this simulating and comparing would consume large amounts of computational resources. It is strange to expect from scientists that they We wanted to make cumulus an open platform on which everyone can share data. This is why we paralelised cumulus as a cloud aplication
Advantages of Cumulus
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Advantages of a cloud based application
- General public access, everyone can use everyone data
- Sharing computational resources enables us the reap the economy of scale.
- The flexibility of a cloud application helps to avoid the resource wast of underutilisation.
Share in cheap
and en enjoy
Advantages of our generic modelling approach
- Exchangeable models, Share not only you data but also the model which you think describes the data.
- Simulate your cells using a simple simulation engine
- Fit the parameters of you simulation to experimental data at the click of a button.
- Genetic algorithms allow cumulus to explore very large parameters spaces.
- Reap the benefits of overlapping experiment, our modelling system allows you to use data from two experiments that share some, but not all, biobrick parts to improve the characterisation of all parts in both experiments.
