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COVID outbreak simulator example #4
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DSC demonstration of the COVID outbreak simulatorTo install DSC,
To run a test (one paramter combination) to make sure everything works,
To run all analysis on a local computer,
3 steps processed (182 jobs completed) To submit job to the cluster,
To extract results, you need to install the https://github.com/stephenslab/dsc/tree/master/dscrutils
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@lmxy0212 Depending on what you are interested in, I'm thinking of either get your help to improve the DSC syntax parser, or implementing more benchmark like this above using DSC, or perhaps both. We can discuss it in our next meeting. |
I also notice that reticulate package is also needed for extracting result
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Below is a demonstration of DSC running https://github.com/ictr/covid19-outbreak-simulator @BoPeng developed.
issue_3.tar.gz
@BoPeng this bundle contains the DSC script and output. A notebook is included in it, which I'll also paste below for us to see. It would be great if you could try it out :) It is a naive replica of the simulation notebook you provided me so it might not look much more elegant than your original notebook implementation. But at least you see to an end user all they have to provide is a short
dsc
configuration file, and their own Python script; and use a query at the end to load results.@junyanj1 @lmxy0212 : Dr. Peng (@BoPeng ) is associate professor of computational biology and epidemiology at Baylor College of Medicine. He is the creator of SoS and SoS notebook on which DSC is built. Dr. Peng will help us (by providing you instructions and suggestions) to improve the engineering of DSC, and explore more applications of it.
@BoPeng : Junyang and Manxueying are master students of CS at Columbia. They are working with me for the Fall semester (and hopefully beyond!) on DSC. Just here to make an introduction, and looking forward to the collaboration!
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