"
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 thorough 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
Cumulus is our way of making this world come a little closer.
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 modeling tools in the iGEM compitetion. You can read the results of this review [here].
We decided
The quest for paramters
Even building a simpel model of genetic circuit will give the most experienced modelers pause. This is mainly because the behaviors of the different biobrick parts are poorly characterised especially when it comes to paramters. While trying to model our curcuit 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 charackterisation maybe we could produce some more dependable results.
Cumulus uses a parameter optimalisation 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
The ad
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.
