On Nov 23, 2013, at 8:03 AM, Murphy-Olson, Daniel E. <[email protected]> wrote:

We do have the cs database dumps on the FTP server, if they are just looking for raw data.

Would that be ftp://dtn.chicago.kbase.us/assets/kbase-20131010.vdi.gz ? Or something in ftp://dtn.chicago.kbase.us/assets/build/ ? What format are the dumps in? We have no information on kbase.us that explains what the various files are in the ftp site, where to find the data dumps, and what format they're in. (I realize that we probably don't want to advertise the data dumps prominently, since they are for experts only, and will probably result in our getting a barrage of questions about the data format and how to use it.) Can one of you CLI experts advise on the best way to download all the genome sequences and annotations of metabolic networks? Is there somewhere where this is documented? If they generated a file in Iris containing all the genome sequences, would it be too big to download? Would they need to do it chunks? What would be the best way to do that? These seem like questions we might well get asked again, so it would be great to put the answers somewhere where users can find them. If someone can send me the answers, I'll work with Outreach and the documentation team to find an appropriate place to put the information. Thanks, Nomi

--Dan

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On Nov 22, 2013, at 11:21 PM, "Thomas Brettin" <[email protected]> wrote:

You can tell them what commands to use from the CLI.

That's what I would probably do.

t

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On Nov 22, 2013, at 12:51 PM, Nomi Harris <[email protected]> wrote:

A user asked (in https://atlassian.kbase.us/browse/KBASE-474):

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I noticed that KBase has a lot of genome sequences and annotations of metabolic networks. Is there anyway I can get a hold of these data? If not on KBase, do you have any suggestions for where to get, e.g. SEED annotations? Thanks!

This seems like a pretty basic question, but I wasn’t sure what to tell them. Search is not functional right now, but I’m not sure that would be the right way to bulk-download data anyway. There are probably Iris commands that could do this, but what are they? We have no plan to offer bulk data dumps for people to download, right? (I’m not saying we should.)

Any advice?

Thanks, Nomi