Cloud-COPASI is a web-based service for running computationally intensive simulation and analysis tasks in parallel on a high-throughput computing pool. Cloud-COPASI connects 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 the desktop version of COPASI (COmplex PAthway SImulator), a widely used free, open-source, cross-platform simulation tool.
We host an implementation of Cloud-COPASI, which is available for use free of charge, at cloud.copasi.org. For new users this is the recommended option. Users create an account in this service and link it to computational pools that they have access to (computer clusters, condor pools, etc.). Cloud-COPASI mediates the necessary partition of the task into subtasks and submission of these to the computational pool(s) the user has access.
For those wishing to deploy their own Cloud-COPASI service, please see the Deployment Guide. This option is recommended for advanced users only and requires some tasks to be carried out by the system administrator of your web server.
Cloud-COPASI was originally developed by Hasan Baig and Edward Kent in the Mendes Research Group and is an extension of the previous Condor-COPASI software. Cloud-COPASI has subsequently been updated by Hasan Baig and other members of the Mendes group, as well as others in the COPASI team. 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.
The files in the /html5up/ directory contain the ZeroFour HTML template
package provided by HTML5 Up!. These files are released under the CCA 3.0
license (/html5up/LICENSE.txt)
All other files, unless otherwise stated, are released under the GNU GENERAL
PUBLIC LICENSE Version 3 (/LICENSE.txt)
They are distributed in the hope that they will be useful
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.