November 2013 - Release-team - mailman3.cels.anl.gov

Re: [Release-team] handle service
by Nomi Harris 27 Nov '13

27 Nov '13

Is this new service for internal use only, or will it be exposed to users (via Iris)? Are we doing an actual release this month, or just (re)deploying some services? Will there be a new dmg? When should the new services (e.g., m5nr) be added to our services page (https://kbase.us/developer-zone/services/)? Can someone provide a list of new user-facing (i.e., not just for internal use) services that should be added to that page? Thanks, Nomi On Nov 27, 2013, at 10:56 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > Please include this in the next deployment. It requires a relational database as a one time setup. Should be on db1/db2. > > Tests are working. > > Documentation at API level is there. > > I'm wrapping up a tutorial of sorts to augment the design documentation. > > Tom > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team

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handle service
by Thomas Brettin 27 Nov '13

27 Nov '13

Please include this in the next deployment. It requires a relational database as a one time setup. Should be on db1/db2. Tests are working. Documentation at API level is there. I'm wrapping up a tutorial of sorts to augment the design documentation. Tom

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Re: [Release-team] What to tell a user who wants to download KBase data
by Nomi Harris 23 Nov '13

23 Nov '13

On Nov 23, 2013, at 8:03 AM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov> 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 > >> On Nov 22, 2013, at 11:21 PM, "Thomas Brettin" <brettin(a)mcs.anl.gov> wrote: >> >> You can tell them what commands to use from the CLI. >> >> That's what I would probably do. >> >> t >>> On Nov 22, 2013, at 12:51 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: >>> >>> A user asked (in https://atlassian.kbase.us/browse/KBASE-474) >>>> 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

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Re: [Release-team] What to tell a user who wants to download KBase data
by Thomas Brettin 23 Nov '13

23 Nov '13

That's a good option too. On Nov 23, 2013, at 10:03 AM, "Murphy-Olson, Daniel E." <dolson(a)mcs.anl.gov> wrote: > We do have the cs database dumps on the FTP server, if they are just looking for raw data. > > --Dan > >> On Nov 22, 2013, at 11:21 PM, "Thomas Brettin" <brettin(a)mcs.anl.gov> wrote: >> >> You can tell them what commands to use from the CLI. >> >> That's what I would probably do. >> >> t >>> On Nov 22, 2013, at 12:51 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: >>> >>> A user asked (in https://atlassian.kbase.us/browse/KBASE-474) >>>> 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 >>> _______________________________________________ >>> Release-team mailing list >>> Release-team(a)lists.kbase.us >>> https://lists.kbase.us/mailman/listinfo/release-team >> >> _______________________________________________ >> Release-team mailing list >> Release-team(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/release-team

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Re: [Release-team] What to tell a user who wants to download KBase data
by Murphy-Olson, Daniel E. 23 Nov '13

23 Nov '13

We do have the cs database dumps on the FTP server, if they are just looking for raw data. --Dan > On Nov 22, 2013, at 11:21 PM, "Thomas Brettin" <brettin(a)mcs.anl.gov> wrote: > > You can tell them what commands to use from the CLI. > > That's what I would probably do. > > t >> On Nov 22, 2013, at 12:51 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: >> >> A user asked (in https://atlassian.kbase.us/browse/KBASE-474) >>> 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 >> _______________________________________________ >> Release-team mailing list >> Release-team(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/release-team > > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team

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Re: [Release-team] What to tell a user who wants to download KBase data
by Thomas Brettin 22 Nov '13

22 Nov '13

You can tell them what commands to use from the CLI. That's what I would probably do. t On Nov 22, 2013, at 12:51 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > A user asked (in https://atlassian.kbase.us/browse/KBASE-474) >> 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 > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team

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What to tell a user who wants to download KBase data
by Nomi Harris 22 Nov '13

22 Nov '13

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

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List of new or deleted services in this release?
by Nomi Harris 22 Nov '13

22 Nov '13

Maybe there’s not a complete list yet for this release, but I need a list of new services that need to be added to our Services web page (e.g., m5nr), and any that need to be removed or commented out (e.g., PROM). There have been various emails from people saying “please add my new service to the release” but I’m not clear on what has made the final cut. What would be the best way to get a list of newly released services (those that are publicly accessible, not just for internal use)? Thanks, Nomi

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Re: [Release-team] [Kbase-devel] need list of deploy targets - please send list of modules that need to be deployed.
by Gang Fang 19 Nov '13

19 Nov '13

Hi all, Sorry for the late response. there are two bugs in my codes i am still working on. one or both are probably due to the R package. I guess it could be fixed by today. On Nov 19, 2013, at 3:51 AM, "Yoo, Shinjae" <sjyoo(a)bnl.gov> wrote: > Hi Dan, > > Sorry for the late updates… > > interlog_projection is in git repo and it should be deployable as a service… > > > gene conservation service still need to talk to Gang… > > Thanks, > -SJ > > > On Nov 18, 2013, at 11:25 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov> wrote: > >> Hi Shinjae, >> >> Both of these repos are currently empty. What is the status of the code for these modules? Are you ready for deployment? >> >> ---- >> Daniel Murphy-Olson >> Systems Administrator >> Mathematics & Computer Science Division >> Argonne National Laboratory >> 630-252-0055 >> >> ________________________________________ >> From: Yoo, Shinjae [sjyoo(a)bnl.gov] >> Sent: Wednesday, November 13, 2013 3:21 PM >> To: Thomas Brettin; Taeyun Oh; Gang Fang >> Cc: release-team(a)kbase.us >> Subject: Re: [Kbase-devel] need list of deploy targets - please send list of modules that need to be deployed. >> >> Tom, >> >> We need two repo: >> >> - interlog_projection >> Owner: Taeyun and Gang >> - gene_conservation >> Owner: Gang >> >> I’m helping them to bring services to KBase. >> >> Thanks, >> -SJ >> >> >> On Nov 13, 2013, at 4:08 PM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: >> >>> >>> Please send the release team a note if your module(s) have changed and should be deployed to prod. >>> >>> Tom >>> _______________________________________________ >>> Kbase-devel mailing list >>> Kbase-devel(a)lists.kbase.us >>> https://lists.kbase.us/mailman/listinfo/kbase-devel >> >

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spread sheet for this build
by Thomas Brettin 19 Nov '13

19 Nov '13

https://docs.google.com/spreadsheet/ccc?key=0AriSbOyynCz1dDdJRHJBcGszaldlUE… Please use the tab "Nov 18 2013 Major. I started the list, but there are probably more.

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