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Parallel computation

COPASI simulation backend

Cloud-COPASI is a web-based tool for running computationally intensive simulation and analysis tasks in parallel on a high-throughput computing pool. Cloud-COPASI can connect to existing computing pools, or provides a simple interface for launching a new computing pool using the Amazon Elastic Compute Cloud (EC2).

Cloud-COPASI can run a number of simulation and analysis tasks, including global sensitivity analyses, stochastic simulations, parameter scans, optimizations, and parameter fitting. Each task is automatically split into a number of smaller jobs, which are executed in parallel, allowing for significant speed-ups in running time.

Models must be prepared using COPASI (COmplex PAthway SImulator), a widely used free, open-source, cross-platform simulation tool.

Cloud-COPASI is developed by Edward Kent in the Computational Systems Biology and Biochemical Networks Modeling Group at the University of Manchester, UK, and is built on the Condor-COPASI software. Cloud-COPASI is written in Python using the Django web application framework. Bosco is used to connect to remote compute pools, and HTCondor is used to manage job allocation on EC2 pools.

Spot price bidding

Spot price bidding can be used to significantly reduce instance costs, depending on EC2 demand. If the market price rises above your bid price, any running instances will be suspended until the market price falls again. This can result in a delay to any running tasks. Note that the spot price does not include VAT or other applicable taxes. All times in the spot price history are in GMT

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Fixed price instances

Fixed price instances run at a set price per hour. While they can be more expensive than using spot price bidding, your instances are guaranteed to run, and will not be terminated unexpectedly. Full instance pricing details are available in the AWS documentation. All instances are launched in the US-East (N. Virginia) AWS region.

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