May 2013 - Microbe - mailman3.cels.anl.gov

Re: [Microbe] [Kbase-devel] [Outreach] Comments from users at GLBRC retreat
by Cottingham, Robert W. 28 May '13

28 May '13

Thanks Bob. This sounds like the right solution to me. -Bob -----Original Message----- From: Robert Olson [mailto:[email protected]] Sent: Tuesday, May 28, 2013 12:31 PM To: Cottingham, Robert W. Cc: Tobias Paczian; outreach(a)kbase.us Outreach; Folker Meyer; KBase Microbes List; kbase devel; Shane Canon; Nomi Harris Subject: Re: [Microbe] [Kbase-devel] [Outreach] Comments from users at GLBRC retreat That URL has a nonstandard port. Oak Ridge firewall will cut off access. This needs to go thru the proxy (on the KB end) to work properly for everyone. --bob On May 28, 2013, at 7:47 AM, Cottingham, Robert W. wrote: > OK, the problem may be on my end. I will look into that. Thanks for letting me know. > -Bob > > -----Original Message----- > From: Tobias Paczian [mailto:[email protected]] > Sent: Tuesday, May 28, 2013 2:45 AM > To: Cottingham, Robert W. > Cc: Folker Meyer; Shane Canon; outreach(a)kbase.us Outreach; kbase > devel; KBase Microbes List; Nomi Harris > Subject: Re: [Kbase-devel] [Outreach] Comments from users at GLBRC > retreat > > Hi Bob, > > which part of the uploader is not working for you? I just tried the URL and it seemed to work fine. > > Cheers > Tobi > > On May 27, 2013, at 1:20 PM, "Cottingham, Robert W." <cottinghamrw(a)ornl.gov> wrote: > >> Just tried http://140.221.84.204:7051/ It's not working. >> >> What is the priority for getting metadata support? >> Also for getting documentation for uploader in place? >> Will the interface or documentation make clear what aspects of the data model it does and does not support? >> >> -Bob >> >> -----Original Message----- >> From: outreach-bounces(a)lists.kbase.us >> [mailto:[email protected]] On Behalf Of Folker Meyer >> Sent: Monday, May 27, 2013 9:41 AM >> To: Shane Canon >> Cc: outreach(a)kbase.us Outreach; kbase devel; KBase Microbes List; >> Nomi Harris >> Subject: Re: [Outreach] [Kbase-devel] Comments from users at GLBRC >> retreat >> >> The problem is that the uploader in place does not have any metadata support. >> >> For metagenomes/metatranscriptomes it is thus useless. >> >> best, >> Folker >> >> On May 26, 2013, at 11:01 PM, Shane Canon <scanon(a)lbl.gov> wrote: >> >>> >>> Its linked off the labs page (Data Uploader). >>> >>> Here is the direct link... >>> >>> http://140.221.84.204:7051/ >>> >>> --Shane >>> >>> >>> On May 26, 2013, at 7:55 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: >>> >>>> I couldn't find it. URL? >>>> Nomi >>>> >>>> On May 26, 2013, at 4:05 AM, Thomas Brettin <brettint(a)gmail.com> wrote: >>>> >>>>> Word from Henrick (JGI) is that the button exists now. >>>>> >>>>> t >>>>> >>>>> >>>>> On May 24, 2013, at 5:15 PM, Narayan Desai <desai(a)mcs.anl.gov> wrote: >>>>> >>>>>> The plan for 6) is that JGI has put a button in their user portal to load data into Shock/ADM on demand. >>>>>> -nld >>>>>> >>>>>> On May 24, 2013, at 4:26 PM, Christopher Henry wrote: >>>>>> >>>>>>> Hi all, >>>>>>> >>>>>>> I'm going to do a brain dump of comments from users at the GLBRC retreat. I figure everyone should see these. Doreen, can you add to this list? >>>>>>> >>>>>>> 1.) David Benton said we should do everything in "awk", but I >>>>>>> think he was kidding :) >>>>>>> >>>>>>> 2.) Yury Bukhman said we shouldn't refer to the apps in KBase labs as prototypes, because it scares everyone away from using them. Currently, the KBase slide stack calls them prototypes. >>>>>>> >>>>>>> 3.) Audry Gasch gave some awesome input. She was incredibly supporting and helpful during my demo. Here's a few of her comments: >>>>>>> -She found the "usage" of the current commands confusing (but she did like that it was there). She thinks the command "usage" should always start with a high level sentence explaining what the command do. >>>>>>> >>>>>>> -She found the documentation on the KBase website overwhelming. In particular, she didn't like how the "Command line" documentation and the "Web API" documentation was all mixed together. She would have preferred to see those separated out. But also, she would like to see the same sort of "command links" that you have in IRIS in www.kbase.us as well, where you can go to "Modeling Scripts", then look for your command of interest, and click on it to see detailed descriptions. She also said the command documentation was also too low level. It didn't provide high-level descriptions of what each command was fundamentally meant to do. >>>>>>> >>>>>>> -She wanted ALL the documentation to be available somehow >>>>>>> online within IRIS. For example, could she type >>>>>>> "annnotate_genome --docs" and see the complete documentation of >>>>>>> the command with all detail thats on www.kbase.us instead of >>>>>>> just the command usage >>>>>>> >>>>>>> -She loved the idea of the tutorials being built into IRIS, but there needs to be better descriptions of how to use them there. >>>>>>> >>>>>>> -Audrey said she won't use anything in KBase unless she has a good understanding of the fundamental methods the commands use in the background. In the other words, our command documentation should contain links to the papers describing their methods whenever possible, or detailed descriptions of the entire method when no paper exists (e.g. she wants to know that RAST is the annotation technology behind our annotation commands, and Model SEED is the tech behind our modeling commands). >>>>>>> >>>>>>> 4.) After I ran "fastsa-to-genome" and "annotate-genome", many users asked if they could now go and see their genome in the Workspace Browser and in the Genome Browser. >>>>>>> >>>>>>> 5.) Steven Slater said he wants his agrobacteria community to set up a workspace with snapshots of all the agrobacteria genomes in KBase, then he wanted his community to be able to annotate those genomes there and share them as the best available agrobacteria annotations available. He also ultimately wanted to see these get integrated into the automatically propagated annotations. >>>>>>> >>>>>>> 6.) Generally, there was the question is how JGI data would be available in KBase... do we replicate it, or is it "just there" >>>>>>> >>>>>>> Chris >>>> >>>> _______________________________________________ >>>> Kbase-devel mailing list >>>> Kbase-devel(a)lists.kbase.us >>>> https://lists.kbase.us/mailman/listinfo/kbase-devel >>> >>> _______________________________________________ >>> Kbase-devel mailing list >>> Kbase-devel(a)lists.kbase.us >>> https://lists.kbase.us/mailman/listinfo/kbase-devel >> >> _______________________________________________ >> Outreach mailing list >> Outreach(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/outreach >> _______________________________________________ >> Kbase-devel mailing list >> Kbase-devel(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/kbase-devel > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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Re: [Microbe] [Kbase-devel] [Outreach] Comments from users at GLBRC retreat
by Robert Olson 28 May '13

28 May '13

That URL has a nonstandard port. Oak Ridge firewall will cut off access. This needs to go thru the proxy (on the KB end) to work properly for everyone. --bob On May 28, 2013, at 7:47 AM, Cottingham, Robert W. wrote: > OK, the problem may be on my end. I will look into that. Thanks for letting me know. > -Bob > > -----Original Message----- > From: Tobias Paczian [mailto:[email protected]] > Sent: Tuesday, May 28, 2013 2:45 AM > To: Cottingham, Robert W. > Cc: Folker Meyer; Shane Canon; outreach(a)kbase.us Outreach; kbase devel; KBase Microbes List; Nomi Harris > Subject: Re: [Kbase-devel] [Outreach] Comments from users at GLBRC retreat > > Hi Bob, > > which part of the uploader is not working for you? I just tried the URL and it seemed to work fine. > > Cheers > Tobi > > On May 27, 2013, at 1:20 PM, "Cottingham, Robert W." <cottinghamrw(a)ornl.gov> wrote: > >> Just tried http://140.221.84.204:7051/ It's not working. >> >> What is the priority for getting metadata support? >> Also for getting documentation for uploader in place? >> Will the interface or documentation make clear what aspects of the data model it does and does not support? >> >> -Bob >> >> -----Original Message----- >> From: outreach-bounces(a)lists.kbase.us >> [mailto:[email protected]] On Behalf Of Folker Meyer >> Sent: Monday, May 27, 2013 9:41 AM >> To: Shane Canon >> Cc: outreach(a)kbase.us Outreach; kbase devel; KBase Microbes List; Nomi >> Harris >> Subject: Re: [Outreach] [Kbase-devel] Comments from users at GLBRC >> retreat >> >> The problem is that the uploader in place does not have any metadata support. >> >> For metagenomes/metatranscriptomes it is thus useless. >> >> best, >> Folker >> >> On May 26, 2013, at 11:01 PM, Shane Canon <scanon(a)lbl.gov> wrote: >> >>> >>> Its linked off the labs page (Data Uploader). >>> >>> Here is the direct link... >>> >>> http://140.221.84.204:7051/ >>> >>> --Shane >>> >>> >>> On May 26, 2013, at 7:55 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: >>> >>>> I couldn't find it. URL? >>>> Nomi >>>> >>>> On May 26, 2013, at 4:05 AM, Thomas Brettin <brettint(a)gmail.com> wrote: >>>> >>>>> Word from Henrick (JGI) is that the button exists now. >>>>> >>>>> t >>>>> >>>>> >>>>> On May 24, 2013, at 5:15 PM, Narayan Desai <desai(a)mcs.anl.gov> wrote: >>>>> >>>>>> The plan for 6) is that JGI has put a button in their user portal to load data into Shock/ADM on demand. >>>>>> -nld >>>>>> >>>>>> On May 24, 2013, at 4:26 PM, Christopher Henry wrote: >>>>>> >>>>>>> Hi all, >>>>>>> >>>>>>> I'm going to do a brain dump of comments from users at the GLBRC retreat. I figure everyone should see these. Doreen, can you add to this list? >>>>>>> >>>>>>> 1.) David Benton said we should do everything in "awk", but I >>>>>>> think he was kidding :) >>>>>>> >>>>>>> 2.) Yury Bukhman said we shouldn't refer to the apps in KBase labs as prototypes, because it scares everyone away from using them. Currently, the KBase slide stack calls them prototypes. >>>>>>> >>>>>>> 3.) Audry Gasch gave some awesome input. She was incredibly supporting and helpful during my demo. Here's a few of her comments: >>>>>>> -She found the "usage" of the current commands confusing (but she did like that it was there). She thinks the command "usage" should always start with a high level sentence explaining what the command do. >>>>>>> >>>>>>> -She found the documentation on the KBase website overwhelming. In particular, she didn't like how the "Command line" documentation and the "Web API" documentation was all mixed together. She would have preferred to see those separated out. But also, she would like to see the same sort of "command links" that you have in IRIS in www.kbase.us as well, where you can go to "Modeling Scripts", then look for your command of interest, and click on it to see detailed descriptions. She also said the command documentation was also too low level. It didn't provide high-level descriptions of what each command was fundamentally meant to do. >>>>>>> >>>>>>> -She wanted ALL the documentation to be available somehow online >>>>>>> within IRIS. For example, could she type "annnotate_genome >>>>>>> --docs" and see the complete documentation of the command with >>>>>>> all detail thats on www.kbase.us instead of just the command >>>>>>> usage >>>>>>> >>>>>>> -She loved the idea of the tutorials being built into IRIS, but there needs to be better descriptions of how to use them there. >>>>>>> >>>>>>> -Audrey said she won't use anything in KBase unless she has a good understanding of the fundamental methods the commands use in the background. In the other words, our command documentation should contain links to the papers describing their methods whenever possible, or detailed descriptions of the entire method when no paper exists (e.g. she wants to know that RAST is the annotation technology behind our annotation commands, and Model SEED is the tech behind our modeling commands). >>>>>>> >>>>>>> 4.) After I ran "fastsa-to-genome" and "annotate-genome", many users asked if they could now go and see their genome in the Workspace Browser and in the Genome Browser. >>>>>>> >>>>>>> 5.) Steven Slater said he wants his agrobacteria community to set up a workspace with snapshots of all the agrobacteria genomes in KBase, then he wanted his community to be able to annotate those genomes there and share them as the best available agrobacteria annotations available. He also ultimately wanted to see these get integrated into the automatically propagated annotations. >>>>>>> >>>>>>> 6.) Generally, there was the question is how JGI data would be available in KBase... do we replicate it, or is it "just there" >>>>>>> >>>>>>> Chris >>>> >>>> _______________________________________________ >>>> Kbase-devel mailing list >>>> Kbase-devel(a)lists.kbase.us >>>> https://lists.kbase.us/mailman/listinfo/kbase-devel >>> >>> _______________________________________________ >>> Kbase-devel mailing list >>> Kbase-devel(a)lists.kbase.us >>> https://lists.kbase.us/mailman/listinfo/kbase-devel >> >> _______________________________________________ >> Outreach mailing list >> Outreach(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/outreach >> _______________________________________________ >> Kbase-devel mailing list >> Kbase-devel(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/kbase-devel > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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Re: [Microbe] workspace browser - choose workspace service?
by Matt DeJongh 28 May '13

28 May '13

Right, that's what I had in mind. On Fri, May 24, 2013 at 11:16 PM, Christopher Henry <chrisshenry(a)gmail.com>wrote: > Another option is to host a copy of the workspace browser that's pointing > at the other workspace. > Still, setting the URL as an input parameter would be cool. > > On May 22, 2013, at 2:35 PM, Neal Conrad <nconrad(a)mcs.anl.gov> wrote: > > > Hi Matt, > > > > Do you mean use a different workspace via something like > "/browser.html/workspace/<workspace_name>"? If so, no, there's no url > routing right now. > > > > I've been learning the ws browser code and working on some new features, > so I'll append this to the list. > > > > Thanks, > > Neal > > > > > > > > On May 22, 2013, at 8:05 AM, Matt DeJongh wrote: > > > >> Is there a way to configure the workspace browser to use a different > workspace service by specifying the URL? > >> > >> -- > >> Matt DeJongh, Ph.D. > >> Computer Science Department > >> Hope College, Holland, MI 49423 > >> (616) 395-7429 > >> _______________________________________________ > >> Microbe mailing list > >> Microbe(a)lists.kbase.us > >> https://lists.kbase.us/mailman/listinfo/microbe > > > > _______________________________________________ > > Microbe mailing list > > Microbe(a)lists.kbase.us > > https://lists.kbase.us/mailman/listinfo/microbe > > -- Matt DeJongh, Ph.D. Computer Science Department Hope College, Holland, MI 49423 (616) 395-7429

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Re: [Microbe] [Kbase-devel] [Outreach] Comments from users at GLBRC retreat
by Cottingham, Robert W. 28 May '13

28 May '13

OK, the problem may be on my end. I will look into that. Thanks for letting me know. -Bob -----Original Message----- From: Tobias Paczian [mailto:[email protected]] Sent: Tuesday, May 28, 2013 2:45 AM To: Cottingham, Robert W. Cc: Folker Meyer; Shane Canon; outreach(a)kbase.us Outreach; kbase devel; KBase Microbes List; Nomi Harris Subject: Re: [Kbase-devel] [Outreach] Comments from users at GLBRC retreat Hi Bob, which part of the uploader is not working for you? I just tried the URL and it seemed to work fine. Cheers Tobi On May 27, 2013, at 1:20 PM, "Cottingham, Robert W." <cottinghamrw(a)ornl.gov> wrote: > Just tried http://140.221.84.204:7051/ It's not working. > > What is the priority for getting metadata support? > Also for getting documentation for uploader in place? > Will the interface or documentation make clear what aspects of the data model it does and does not support? > > -Bob > > -----Original Message----- > From: outreach-bounces(a)lists.kbase.us > [mailto:[email protected]] On Behalf Of Folker Meyer > Sent: Monday, May 27, 2013 9:41 AM > To: Shane Canon > Cc: outreach(a)kbase.us Outreach; kbase devel; KBase Microbes List; Nomi > Harris > Subject: Re: [Outreach] [Kbase-devel] Comments from users at GLBRC > retreat > > The problem is that the uploader in place does not have any metadata support. > > For metagenomes/metatranscriptomes it is thus useless. > > best, > Folker > > On May 26, 2013, at 11:01 PM, Shane Canon <scanon(a)lbl.gov> wrote: > >> >> Its linked off the labs page (Data Uploader). >> >> Here is the direct link... >> >> http://140.221.84.204:7051/ >> >> --Shane >> >> >> On May 26, 2013, at 7:55 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: >> >>> I couldn't find it. URL? >>> Nomi >>> >>> On May 26, 2013, at 4:05 AM, Thomas Brettin <brettint(a)gmail.com> wrote: >>> >>>> Word from Henrick (JGI) is that the button exists now. >>>> >>>> t >>>> >>>> >>>> On May 24, 2013, at 5:15 PM, Narayan Desai <desai(a)mcs.anl.gov> wrote: >>>> >>>>> The plan for 6) is that JGI has put a button in their user portal to load data into Shock/ADM on demand. >>>>> -nld >>>>> >>>>> On May 24, 2013, at 4:26 PM, Christopher Henry wrote: >>>>> >>>>>> Hi all, >>>>>> >>>>>> I'm going to do a brain dump of comments from users at the GLBRC retreat. I figure everyone should see these. Doreen, can you add to this list? >>>>>> >>>>>> 1.) David Benton said we should do everything in "awk", but I >>>>>> think he was kidding :) >>>>>> >>>>>> 2.) Yury Bukhman said we shouldn't refer to the apps in KBase labs as prototypes, because it scares everyone away from using them. Currently, the KBase slide stack calls them prototypes. >>>>>> >>>>>> 3.) Audry Gasch gave some awesome input. She was incredibly supporting and helpful during my demo. Here's a few of her comments: >>>>>> -She found the "usage" of the current commands confusing (but she did like that it was there). She thinks the command "usage" should always start with a high level sentence explaining what the command do. >>>>>> >>>>>> -She found the documentation on the KBase website overwhelming. In particular, she didn't like how the "Command line" documentation and the "Web API" documentation was all mixed together. She would have preferred to see those separated out. But also, she would like to see the same sort of "command links" that you have in IRIS in www.kbase.us as well, where you can go to "Modeling Scripts", then look for your command of interest, and click on it to see detailed descriptions. She also said the command documentation was also too low level. It didn't provide high-level descriptions of what each command was fundamentally meant to do. >>>>>> >>>>>> -She wanted ALL the documentation to be available somehow online >>>>>> within IRIS. For example, could she type "annnotate_genome >>>>>> --docs" and see the complete documentation of the command with >>>>>> all detail thats on www.kbase.us instead of just the command >>>>>> usage >>>>>> >>>>>> -She loved the idea of the tutorials being built into IRIS, but there needs to be better descriptions of how to use them there. >>>>>> >>>>>> -Audrey said she won't use anything in KBase unless she has a good understanding of the fundamental methods the commands use in the background. In the other words, our command documentation should contain links to the papers describing their methods whenever possible, or detailed descriptions of the entire method when no paper exists (e.g. she wants to know that RAST is the annotation technology behind our annotation commands, and Model SEED is the tech behind our modeling commands). >>>>>> >>>>>> 4.) After I ran "fastsa-to-genome" and "annotate-genome", many users asked if they could now go and see their genome in the Workspace Browser and in the Genome Browser. >>>>>> >>>>>> 5.) Steven Slater said he wants his agrobacteria community to set up a workspace with snapshots of all the agrobacteria genomes in KBase, then he wanted his community to be able to annotate those genomes there and share them as the best available agrobacteria annotations available. He also ultimately wanted to see these get integrated into the automatically propagated annotations. >>>>>> >>>>>> 6.) Generally, there was the question is how JGI data would be available in KBase... do we replicate it, or is it "just there" >>>>>> >>>>>> Chris >>> >>> _______________________________________________ >>> Kbase-devel mailing list >>> Kbase-devel(a)lists.kbase.us >>> https://lists.kbase.us/mailman/listinfo/kbase-devel >> >> _______________________________________________ >> Kbase-devel mailing list >> Kbase-devel(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/kbase-devel > > _______________________________________________ > Outreach mailing list > Outreach(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/outreach > _______________________________________________ > Kbase-devel mailing list > Kbase-devel(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-devel

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Re: [Microbe] [Kbase-devel] [Outreach] Comments from users at GLBRC retreat
by Tobias Paczian 28 May '13

28 May '13

Hi Bob, which part of the uploader is not working for you? I just tried the URL and it seemed to work fine. Cheers Tobi On May 27, 2013, at 1:20 PM, "Cottingham, Robert W." <cottinghamrw(a)ornl.gov> wrote: > Just tried http://140.221.84.204:7051/ > It's not working. > > What is the priority for getting metadata support? > Also for getting documentation for uploader in place? > Will the interface or documentation make clear what aspects of the data model it does and does not support? > > -Bob > > -----Original Message----- > From: outreach-bounces(a)lists.kbase.us [mailto:[email protected]] On Behalf Of Folker Meyer > Sent: Monday, May 27, 2013 9:41 AM > To: Shane Canon > Cc: outreach(a)kbase.us Outreach; kbase devel; KBase Microbes List; Nomi Harris > Subject: Re: [Outreach] [Kbase-devel] Comments from users at GLBRC retreat > > The problem is that the uploader in place does not have any metadata support. > > For metagenomes/metatranscriptomes it is thus useless. > > best, > Folker > > On May 26, 2013, at 11:01 PM, Shane Canon <scanon(a)lbl.gov> wrote: > >> >> Its linked off the labs page (Data Uploader). >> >> Here is the direct link... >> >> http://140.221.84.204:7051/ >> >> --Shane >> >> >> On May 26, 2013, at 7:55 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: >> >>> I couldn't find it. URL? >>> Nomi >>> >>> On May 26, 2013, at 4:05 AM, Thomas Brettin <brettint(a)gmail.com> wrote: >>> >>>> Word from Henrick (JGI) is that the button exists now. >>>> >>>> t >>>> >>>> >>>> On May 24, 2013, at 5:15 PM, Narayan Desai <desai(a)mcs.anl.gov> wrote: >>>> >>>>> The plan for 6) is that JGI has put a button in their user portal to load data into Shock/ADM on demand. >>>>> -nld >>>>> >>>>> On May 24, 2013, at 4:26 PM, Christopher Henry wrote: >>>>> >>>>>> Hi all, >>>>>> >>>>>> I'm going to do a brain dump of comments from users at the GLBRC retreat. I figure everyone should see these. Doreen, can you add to this list? >>>>>> >>>>>> 1.) David Benton said we should do everything in "awk", but I think he was kidding :) >>>>>> >>>>>> 2.) Yury Bukhman said we shouldn't refer to the apps in KBase labs as prototypes, because it scares everyone away from using them. Currently, the KBase slide stack calls them prototypes. >>>>>> >>>>>> 3.) Audry Gasch gave some awesome input. She was incredibly supporting and helpful during my demo. Here's a few of her comments: >>>>>> -She found the "usage" of the current commands confusing (but she did like that it was there). She thinks the command "usage" should always start with a high level sentence explaining what the command do. >>>>>> >>>>>> -She found the documentation on the KBase website overwhelming. In particular, she didn't like how the "Command line" documentation and the "Web API" documentation was all mixed together. She would have preferred to see those separated out. But also, she would like to see the same sort of "command links" that you have in IRIS in www.kbase.us as well, where you can go to "Modeling Scripts", then look for your command of interest, and click on it to see detailed descriptions. She also said the command documentation was also too low level. It didn't provide high-level descriptions of what each command was fundamentally meant to do. >>>>>> >>>>>> -She wanted ALL the documentation to be available somehow online within IRIS. For example, could she type "annnotate_genome --docs" and see the complete documentation of the command with all detail thats on www.kbase.us instead of just the command usage >>>>>> >>>>>> -She loved the idea of the tutorials being built into IRIS, but there needs to be better descriptions of how to use them there. >>>>>> >>>>>> -Audrey said she won't use anything in KBase unless she has a good understanding of the fundamental methods the commands use in the background. In the other words, our command documentation should contain links to the papers describing their methods whenever possible, or detailed descriptions of the entire method when no paper exists (e.g. she wants to know that RAST is the annotation technology behind our annotation commands, and Model SEED is the tech behind our modeling commands). >>>>>> >>>>>> 4.) After I ran "fastsa-to-genome" and "annotate-genome", many users asked if they could now go and see their genome in the Workspace Browser and in the Genome Browser. >>>>>> >>>>>> 5.) Steven Slater said he wants his agrobacteria community to set up a workspace with snapshots of all the agrobacteria genomes in KBase, then he wanted his community to be able to annotate those genomes there and share them as the best available agrobacteria annotations available. He also ultimately wanted to see these get integrated into the automatically propagated annotations. >>>>>> >>>>>> 6.) Generally, there was the question is how JGI data would be available in KBase... do we replicate it, or is it "just there" >>>>>> >>>>>> Chris >>> >>> _______________________________________________ >>> Kbase-devel mailing list >>> Kbase-devel(a)lists.kbase.us >>> https://lists.kbase.us/mailman/listinfo/kbase-devel >> >> _______________________________________________ >> Kbase-devel mailing list >> Kbase-devel(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/kbase-devel > > _______________________________________________ > Outreach mailing list > Outreach(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/outreach > _______________________________________________ > Kbase-devel mailing list > Kbase-devel(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-devel

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Re: [Microbe] [Outreach] [Kbase-devel] Comments from users at GLBRC retreat
by Cottingham, Robert W. 27 May '13

27 May '13

Just tried http://140.221.84.204:7051/ It's not working. What is the priority for getting metadata support? Also for getting documentation for uploader in place? Will the interface or documentation make clear what aspects of the data model it does and does not support? -Bob -----Original Message----- From: outreach-bounces(a)lists.kbase.us [mailto:[email protected]] On Behalf Of Folker Meyer Sent: Monday, May 27, 2013 9:41 AM To: Shane Canon Cc: outreach(a)kbase.us Outreach; kbase devel; KBase Microbes List; Nomi Harris Subject: Re: [Outreach] [Kbase-devel] Comments from users at GLBRC retreat The problem is that the uploader in place does not have any metadata support. For metagenomes/metatranscriptomes it is thus useless. best, Folker On May 26, 2013, at 11:01 PM, Shane Canon <scanon(a)lbl.gov> wrote: > > Its linked off the labs page (Data Uploader). > > Here is the direct link... > > http://140.221.84.204:7051/ > > --Shane > > > On May 26, 2013, at 7:55 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > >> I couldn't find it. URL? >> Nomi >> >> On May 26, 2013, at 4:05 AM, Thomas Brettin <brettint(a)gmail.com> wrote: >> >>> Word from Henrick (JGI) is that the button exists now. >>> >>> t >>> >>> >>> On May 24, 2013, at 5:15 PM, Narayan Desai <desai(a)mcs.anl.gov> wrote: >>> >>>> The plan for 6) is that JGI has put a button in their user portal to load data into Shock/ADM on demand. >>>> -nld >>>> >>>> On May 24, 2013, at 4:26 PM, Christopher Henry wrote: >>>> >>>>> Hi all, >>>>> >>>>> I'm going to do a brain dump of comments from users at the GLBRC retreat. I figure everyone should see these. Doreen, can you add to this list? >>>>> >>>>> 1.) David Benton said we should do everything in "awk", but I think he was kidding :) >>>>> >>>>> 2.) Yury Bukhman said we shouldn't refer to the apps in KBase labs as prototypes, because it scares everyone away from using them. Currently, the KBase slide stack calls them prototypes. >>>>> >>>>> 3.) Audry Gasch gave some awesome input. She was incredibly supporting and helpful during my demo. Here's a few of her comments: >>>>> -She found the "usage" of the current commands confusing (but she did like that it was there). She thinks the command "usage" should always start with a high level sentence explaining what the command do. >>>>> >>>>> -She found the documentation on the KBase website overwhelming. In particular, she didn't like how the "Command line" documentation and the "Web API" documentation was all mixed together. She would have preferred to see those separated out. But also, she would like to see the same sort of "command links" that you have in IRIS in www.kbase.us as well, where you can go to "Modeling Scripts", then look for your command of interest, and click on it to see detailed descriptions. She also said the command documentation was also too low level. It didn't provide high-level descriptions of what each command was fundamentally meant to do. >>>>> >>>>> -She wanted ALL the documentation to be available somehow online within IRIS. For example, could she type "annnotate_genome --docs" and see the complete documentation of the command with all detail thats on www.kbase.us instead of just the command usage >>>>> >>>>> -She loved the idea of the tutorials being built into IRIS, but there needs to be better descriptions of how to use them there. >>>>> >>>>> -Audrey said she won't use anything in KBase unless she has a good understanding of the fundamental methods the commands use in the background. In the other words, our command documentation should contain links to the papers describing their methods whenever possible, or detailed descriptions of the entire method when no paper exists (e.g. she wants to know that RAST is the annotation technology behind our annotation commands, and Model SEED is the tech behind our modeling commands). >>>>> >>>>> 4.) After I ran "fastsa-to-genome" and "annotate-genome", many users asked if they could now go and see their genome in the Workspace Browser and in the Genome Browser. >>>>> >>>>> 5.) Steven Slater said he wants his agrobacteria community to set up a workspace with snapshots of all the agrobacteria genomes in KBase, then he wanted his community to be able to annotate those genomes there and share them as the best available agrobacteria annotations available. He also ultimately wanted to see these get integrated into the automatically propagated annotations. >>>>> >>>>> 6.) Generally, there was the question is how JGI data would be available in KBase... do we replicate it, or is it "just there" >>>>> >>>>> Chris >> >> _______________________________________________ >> Kbase-devel mailing list >> Kbase-devel(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/kbase-devel > > _______________________________________________ > Kbase-devel mailing list > Kbase-devel(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-devel _______________________________________________ Outreach mailing list Outreach(a)lists.kbase.us https://lists.kbase.us/mailman/listinfo/outreach

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Re: [Microbe] [Kbase-devel] [Outreach] Comments from users at GLBRC retreat
by Folker Meyer 27 May '13

27 May '13

The problem is that the uploader in place does not have any metadata support. For metagenomes/metatranscriptomes it is thus useless. best, Folker On May 26, 2013, at 11:01 PM, Shane Canon <scanon(a)lbl.gov> wrote: > > Its linked off the labs page (Data Uploader). > > Here is the direct link… > > http://140.221.84.204:7051/ > > --Shane > > > On May 26, 2013, at 7:55 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > >> I couldn't find it. URL? >> Nomi >> >> On May 26, 2013, at 4:05 AM, Thomas Brettin <brettint(a)gmail.com> wrote: >> >>> Word from Henrick (JGI) is that the button exists now. >>> >>> t >>> >>> >>> On May 24, 2013, at 5:15 PM, Narayan Desai <desai(a)mcs.anl.gov> wrote: >>> >>>> The plan for 6) is that JGI has put a button in their user portal to load data into Shock/ADM on demand. >>>> -nld >>>> >>>> On May 24, 2013, at 4:26 PM, Christopher Henry wrote: >>>> >>>>> Hi all, >>>>> >>>>> I'm going to do a brain dump of comments from users at the GLBRC retreat. I figure everyone should see these. Doreen, can you add to this list? >>>>> >>>>> 1.) David Benton said we should do everything in "awk", but I think he was kidding :) >>>>> >>>>> 2.) Yury Bukhman said we shouldn't refer to the apps in KBase labs as prototypes, because it scares everyone away from using them. Currently, the KBase slide stack calls them prototypes. >>>>> >>>>> 3.) Audry Gasch gave some awesome input. She was incredibly supporting and helpful during my demo. Here's a few of her comments: >>>>> -She found the "usage" of the current commands confusing (but she did like that it was there). She thinks the command "usage" should always start with a high level sentence explaining what the command do. >>>>> >>>>> -She found the documentation on the KBase website overwhelming. In particular, she didn't like how the "Command line" documentation and the "Web API" documentation was all mixed together. She would have preferred to see those separated out. But also, she would like to see the same sort of "command links" that you have in IRIS in www.kbase.us as well, where you can go to "Modeling Scripts", then look for your command of interest, and click on it to see detailed descriptions. She also said the command documentation was also too low level. It didn't provide high-level descriptions of what each command was fundamentally meant to do. >>>>> >>>>> -She wanted ALL the documentation to be available somehow online within IRIS. For example, could she type "annnotate_genome --docs" and see the complete documentation of the command with all detail thats on www.kbase.us instead of just the command usage >>>>> >>>>> -She loved the idea of the tutorials being built into IRIS, but there needs to be better descriptions of how to use them there. >>>>> >>>>> -Audrey said she won't use anything in KBase unless she has a good understanding of the fundamental methods the commands use in the background. In the other words, our command documentation should contain links to the papers describing their methods whenever possible, or detailed descriptions of the entire method when no paper exists (e.g. she wants to know that RAST is the annotation technology behind our annotation commands, and Model SEED is the tech behind our modeling commands). >>>>> >>>>> 4.) After I ran "fastsa-to-genome" and "annotate-genome", many users asked if they could now go and see their genome in the Workspace Browser and in the Genome Browser. >>>>> >>>>> 5.) Steven Slater said he wants his agrobacteria community to set up a workspace with snapshots of all the agrobacteria genomes in KBase, then he wanted his community to be able to annotate those genomes there and share them as the best available agrobacteria annotations available. He also ultimately wanted to see these get integrated into the automatically propagated annotations. >>>>> >>>>> 6.) Generally, there was the question is how JGI data would be available in KBase… do we replicate it, or is it "just there" >>>>> >>>>> Chris >> >> _______________________________________________ >> Kbase-devel mailing list >> Kbase-devel(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/kbase-devel > > _______________________________________________ > Kbase-devel mailing list > Kbase-devel(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-devel

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Re: [Microbe] [Kbase-devel] [Outreach] Comments from users at GLBRC retreat
by Shane Canon 26 May '13

26 May '13

Its linked off the labs page (Data Uploader). Here is the direct link… http://140.221.84.204:7051/ --Shane On May 26, 2013, at 7:55 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > I couldn't find it. URL? > Nomi > > On May 26, 2013, at 4:05 AM, Thomas Brettin <brettint(a)gmail.com> wrote: > >> Word from Henrick (JGI) is that the button exists now. >> >> t >> >> >> On May 24, 2013, at 5:15 PM, Narayan Desai <desai(a)mcs.anl.gov> wrote: >> >>> The plan for 6) is that JGI has put a button in their user portal to load data into Shock/ADM on demand. >>> -nld >>> >>> On May 24, 2013, at 4:26 PM, Christopher Henry wrote: >>> >>>> Hi all, >>>> >>>> I'm going to do a brain dump of comments from users at the GLBRC retreat. I figure everyone should see these. Doreen, can you add to this list? >>>> >>>> 1.) David Benton said we should do everything in "awk", but I think he was kidding :) >>>> >>>> 2.) Yury Bukhman said we shouldn't refer to the apps in KBase labs as prototypes, because it scares everyone away from using them. Currently, the KBase slide stack calls them prototypes. >>>> >>>> 3.) Audry Gasch gave some awesome input. She was incredibly supporting and helpful during my demo. Here's a few of her comments: >>>> -She found the "usage" of the current commands confusing (but she did like that it was there). She thinks the command "usage" should always start with a high level sentence explaining what the command do. >>>> >>>> -She found the documentation on the KBase website overwhelming. In particular, she didn't like how the "Command line" documentation and the "Web API" documentation was all mixed together. She would have preferred to see those separated out. But also, she would like to see the same sort of "command links" that you have in IRIS in www.kbase.us as well, where you can go to "Modeling Scripts", then look for your command of interest, and click on it to see detailed descriptions. She also said the command documentation was also too low level. It didn't provide high-level descriptions of what each command was fundamentally meant to do. >>>> >>>> -She wanted ALL the documentation to be available somehow online within IRIS. For example, could she type "annnotate_genome --docs" and see the complete documentation of the command with all detail thats on www.kbase.us instead of just the command usage >>>> >>>> -She loved the idea of the tutorials being built into IRIS, but there needs to be better descriptions of how to use them there. >>>> >>>> -Audrey said she won't use anything in KBase unless she has a good understanding of the fundamental methods the commands use in the background. In the other words, our command documentation should contain links to the papers describing their methods whenever possible, or detailed descriptions of the entire method when no paper exists (e.g. she wants to know that RAST is the annotation technology behind our annotation commands, and Model SEED is the tech behind our modeling commands). >>>> >>>> 4.) After I ran "fastsa-to-genome" and "annotate-genome", many users asked if they could now go and see their genome in the Workspace Browser and in the Genome Browser. >>>> >>>> 5.) Steven Slater said he wants his agrobacteria community to set up a workspace with snapshots of all the agrobacteria genomes in KBase, then he wanted his community to be able to annotate those genomes there and share them as the best available agrobacteria annotations available. He also ultimately wanted to see these get integrated into the automatically propagated annotations. >>>> >>>> 6.) Generally, there was the question is how JGI data would be available in KBase… do we replicate it, or is it "just there" >>>> >>>> Chris > > _______________________________________________ > Kbase-devel mailing list > Kbase-devel(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-devel

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Re: [Microbe] [Outreach] [Kbase-devel] Comments from users at GLBRC retreat
by Nomi Harris 26 May '13

26 May '13

I couldn't find it. URL? Nomi On May 26, 2013, at 4:05 AM, Thomas Brettin <brettint(a)gmail.com> wrote: > Word from Henrick (JGI) is that the button exists now. > > t > > > On May 24, 2013, at 5:15 PM, Narayan Desai <desai(a)mcs.anl.gov> wrote: > >> The plan for 6) is that JGI has put a button in their user portal to load data into Shock/ADM on demand. >> -nld >> >> On May 24, 2013, at 4:26 PM, Christopher Henry wrote: >> >>> Hi all, >>> >>> I'm going to do a brain dump of comments from users at the GLBRC retreat. I figure everyone should see these. Doreen, can you add to this list? >>> >>> 1.) David Benton said we should do everything in "awk", but I think he was kidding :) >>> >>> 2.) Yury Bukhman said we shouldn't refer to the apps in KBase labs as prototypes, because it scares everyone away from using them. Currently, the KBase slide stack calls them prototypes. >>> >>> 3.) Audry Gasch gave some awesome input. She was incredibly supporting and helpful during my demo. Here's a few of her comments: >>> -She found the "usage" of the current commands confusing (but she did like that it was there). She thinks the command "usage" should always start with a high level sentence explaining what the command do. >>> >>> -She found the documentation on the KBase website overwhelming. In particular, she didn't like how the "Command line" documentation and the "Web API" documentation was all mixed together. She would have preferred to see those separated out. But also, she would like to see the same sort of "command links" that you have in IRIS in www.kbase.us as well, where you can go to "Modeling Scripts", then look for your command of interest, and click on it to see detailed descriptions. She also said the command documentation was also too low level. It didn't provide high-level descriptions of what each command was fundamentally meant to do. >>> >>> -She wanted ALL the documentation to be available somehow online within IRIS. For example, could she type "annnotate_genome --docs" and see the complete documentation of the command with all detail thats on www.kbase.us instead of just the command usage >>> >>> -She loved the idea of the tutorials being built into IRIS, but there needs to be better descriptions of how to use them there. >>> >>> -Audrey said she won't use anything in KBase unless she has a good understanding of the fundamental methods the commands use in the background. In the other words, our command documentation should contain links to the papers describing their methods whenever possible, or detailed descriptions of the entire method when no paper exists (e.g. she wants to know that RAST is the annotation technology behind our annotation commands, and Model SEED is the tech behind our modeling commands). >>> >>> 4.) After I ran "fastsa-to-genome" and "annotate-genome", many users asked if they could now go and see their genome in the Workspace Browser and in the Genome Browser. >>> >>> 5.) Steven Slater said he wants his agrobacteria community to set up a workspace with snapshots of all the agrobacteria genomes in KBase, then he wanted his community to be able to annotate those genomes there and share them as the best available agrobacteria annotations available. He also ultimately wanted to see these get integrated into the automatically propagated annotations. >>> >>> 6.) Generally, there was the question is how JGI data would be available in KBase… do we replicate it, or is it "just there" >>> >>> Chris

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Re: [Microbe] [Kbase-devel] Comments from users at GLBRC retreat
by Christopher Henry 26 May '13

26 May '13

BTW, last week Folker was showing me the very nice data upload web app for MGRAST. I strongly suggested that he create a KBase lab with that data uploader, putting the data in Shock. I personally think this will unlock a whole bunch of workflows that we just can't do right now: -assembly -RNA seq -variation analysis -metagenome modeling Those workflows come up again and again when I demo KBase, because those are some of the most prevalent data types right now, and they're tough to do. The JGI button is great, but a "Data Upload" lab would be really useful too. On May 26, 2013, at 6:05 AM, Thomas Brettin <brettint(a)gmail.com> wrote: > Word from Henrick (JGI) is that the button exists now. > > t > > > On May 24, 2013, at 5:15 PM, Narayan Desai <desai(a)mcs.anl.gov> wrote: > >> The plan for 6) is that JGI has put a button in their user portal to load data into Shock/ADM on demand. >> -nld >> >> On May 24, 2013, at 4:26 PM, Christopher Henry wrote: >> >>> Hi all, >>> >>> I'm going to do a brain dump of comments from users at the GLBRC retreat. I figure everyone should see these. Doreen, can you add to this list? >>> >>> 1.) David Benton said we should do everything in "awk", but I think he was kidding :) >>> >>> 2.) Yury Bukhman said we shouldn't refer to the apps in KBase labs as prototypes, because it scares everyone away from using them. Currently, the KBase slide stack calls them prototypes. >>> >>> 3.) Audry Gasch gave some awesome input. She was incredibly supporting and helpful during my demo. Here's a few of her comments: >>> -She found the "usage" of the current commands confusing (but she did like that it was there). She thinks the command "usage" should always start with a high level sentence explaining what the command do. >>> >>> -She found the documentation on the KBase website overwhelming. In particular, she didn't like how the "Command line" documentation and the "Web API" documentation was all mixed together. She would have preferred to see those separated out. But also, she would like to see the same sort of "command links" that you have in IRIS in www.kbase.us as well, where you can go to "Modeling Scripts", then look for your command of interest, and click on it to see detailed descriptions. She also said the command documentation was also too low level. It didn't provide high-level descriptions of what each command was fundamentally meant to do. >>> >>> -She wanted ALL the documentation to be available somehow online within IRIS. For example, could she type "annnotate_genome --docs" and see the complete documentation of the command with all detail thats on www.kbase.us instead of just the command usage >>> >>> -She loved the idea of the tutorials being built into IRIS, but there needs to be better descriptions of how to use them there. >>> >>> -Audrey said she won't use anything in KBase unless she has a good understanding of the fundamental methods the commands use in the background. In the other words, our command documentation should contain links to the papers describing their methods whenever possible, or detailed descriptions of the entire method when no paper exists (e.g. she wants to know that RAST is the annotation technology behind our annotation commands, and Model SEED is the tech behind our modeling commands). >>> >>> 4.) After I ran "fastsa-to-genome" and "annotate-genome", many users asked if they could now go and see their genome in the Workspace Browser and in the Genome Browser. >>> >>> 5.) Steven Slater said he wants his agrobacteria community to set up a workspace with snapshots of all the agrobacteria genomes in KBase, then he wanted his community to be able to annotate those genomes there and share them as the best available agrobacteria annotations available. He also ultimately wanted to see these get integrated into the automatically propagated annotations. >>> >>> 6.) Generally, there was the question is how JGI data would be available in KBase… do we replicate it, or is it "just there" >>> >>> Chris >>> >>> _______________________________________________ >>> Kbase-devel mailing list >>> Kbase-devel(a)lists.kbase.us >>> https://lists.kbase.us/mailman/listinfo/kbase-devel >> >> _______________________________________________ >> Kbase-devel mailing list >> Kbase-devel(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/kbase-devel >

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