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Data transfer is done on optical fibres.
The data transfer is done using Enhanced Direct memory Access (EDMA) interface configured with optimal External memory Interface (EMIF) setting to read and write data.
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Wait until the transfer is done.
If two communicating VMs are running on the same physical server, data transfer is actually done through shared memory, which is very fast compared to a real computer network.
We are also developing plugins that allow the user to connect different data servers to the system so that transfers are done directly between the servers (and when possible, skipped altogether).
The problem with UniProt/Swiss-Prot to Pfam data transfer is that UniProt curation does not always reflect the latest functional data, and it annotates proteins rather than domains, making automatic transfer impossible.
Sometimes transfers are done at corporate level.
For those uses, speed of data transfer is important.
And the data transfer is a two-way street.
The data transfer can be done while onsite at CHESS (using one's laptop), or back at one's home institution.
If the VMs are running on separate physical systems, data transfer will be done over a dedicated connection between the servers, not the internet, so it will still be acceptably fast.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com