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

26 May '13

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] workspace browser - choose workspace service?
by Christopher Henry 24 May '13

24 May '13

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

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Re: [Microbe] Comments from users at GLBRC retreat
by Adam Arkin 24 May '13

24 May '13

Hey Chris, Thanks for the great summary! Comments inline below. > > ----- Original Message ----- > From: Christopher Henry <chrisshenry(a)gmail.com> > > > 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. > > Well-- I think I we need to have prototypes and beta and clear route to identifying and hardening the things called apps. These are the "attractors" we discussed. This is one of the things we need to work on. Prototypes are an important part of our culture I think! > 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. > > Excellent. > -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. > > Yup. It's on the 3 month list. . > -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). > > This is REALLY important and there is some hints at tasks to that on the 3 month list.... but it is definitely something we need to work. > 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 > > _______________________________________________ > 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 > -- Adam Paul Arkin Dean A. Richard Newton Memorial Chair ------------------------------------- Director, Physical Biosciences Division E.O. Lawrence Berkeley National Laboratory Professor, Department of Bioengineering University of California Berkeley, CA, 94720 CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu PI and Co-Director, ENIGMA SFA, http://enigma.lbl.gov <http://vimss.lbl.gov> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org Office: 512C Energy Biosciences Building (Berkeley Campus) Mailing address: E.O. Lawrence Berkeley National Laboratory 1 Cyclotron Road, MS 955-512L Berkeley, CA 94720 Contact: W: http://genomics.lbl.gov V: 510-495-2366 C: 510-206-1389 F: 510-486-6219 Assistant: Gwyneth A. Terry V: 510-495-2116 E: GATerry(a)lbl.gov -------------------------------------

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Re: [Microbe] [Kbase-devel] Comments from users at GLBRC retreat
by Narayan Desai 24 May '13

24 May '13

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] Comments from users at GLBRC retreat
by Chris Henry 24 May '13

24 May '13

Labeling all of the currently functioning tools in kbase as prototypes seems a little problematic to me. But fair enough. And you're right, I don't think even yury said "everyone". He probably said "some". Sorry to hypobolize. Also, the word beta seems preferable to me than the word prototype. On May 24, 2013 4:43 PM, "Matthew Henderson" <mhenderson(a)lbl.gov> wrote: > On 2), Adam has made it clear that labs are not supposed to be considered > "production quality", so I think using prototypes or beta is an accurate > description of what the labs are supposed to represent. Currently there is > not a roadmap to go from lab to application, which would be considered > production quality. Ultimately many of the current labs will be absorbed > in one way or another into the narrative. > > So you had someone comment that "everyone" was scared away from the labs > pages. I would be extremely doubtful of that statement. I would even be > doubtful if you replaced "everyone" with "most" people. The fact that > Chris is actively promoting the use of certain labs as part of his > tutorials suggest that people are in fact using them despite the > "prototypes" label. > > So I would ask that we not completely remove either a "Beta" or > "prototypes" disclaimer from the labs landing area. > Google has beta plastered all over things and that doesn't stop people > from using them. If prototypes is the problem, then let's change it to > Beta. > > > On Fri, May 24, 2013 at 2:33 PM, Elizabeth M. Glass <marland(a)mcs.anl.gov>wrote: > >> Thanks Chris! >> >> Just as FYI - >> >> 2. Good comment and easily fixed. >> 3. Lynn and I are reviewing the command-line help and a command summary >> is an item we would like to see added along with a usage example for each, >> as most end users will still have trouble deciphering how to use it. >> >> We are reorging the tutorials site as we speak - it is too confusing with >> it all mixed together. >> >> Elizabeth >> >> >> >> ----- Original Message ----- >> From: Christopher Henry <chrisshenry(a)gmail.com> >> To: kbase devel <kbase-devel(a)lists.kbase.us>, outreach(a)kbase.us Outreach >> <outreach(a)kbase.us>, KBase Microbes List <microbe(a)lists.kbase.us> >> Cc: Doreen Ware <ware(a)cshl.edu> >> Sent: Fri, 24 May 2013 16:26:59 -0500 (CDT) >> Subject: [Microbe] Comments from users at GLBRC retreat >> >> 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 >> >> _______________________________________________ >> 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 >> > >

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Re: [Microbe] Comments from users at GLBRC retreat
by Matthew Henderson 24 May '13

24 May '13

On 2), Adam has made it clear that labs are not supposed to be considered "production quality", so I think using prototypes or beta is an accurate description of what the labs are supposed to represent. Currently there is not a roadmap to go from lab to application, which would be considered production quality. Ultimately many of the current labs will be absorbed in one way or another into the narrative. So you had someone comment that "everyone" was scared away from the labs pages. I would be extremely doubtful of that statement. I would even be doubtful if you replaced "everyone" with "most" people. The fact that Chris is actively promoting the use of certain labs as part of his tutorials suggest that people are in fact using them despite the "prototypes" label. So I would ask that we not completely remove either a "Beta" or "prototypes" disclaimer from the labs landing area. Google has beta plastered all over things and that doesn't stop people from using them. If prototypes is the problem, then let's change it to Beta. On Fri, May 24, 2013 at 2:33 PM, Elizabeth M. Glass <marland(a)mcs.anl.gov>wrote: > Thanks Chris! > > Just as FYI - > > 2. Good comment and easily fixed. > 3. Lynn and I are reviewing the command-line help and a command summary is > an item we would like to see added along with a usage example for each, as > most end users will still have trouble deciphering how to use it. > > We are reorging the tutorials site as we speak - it is too confusing with > it all mixed together. > > Elizabeth > > > > ----- Original Message ----- > From: Christopher Henry <chrisshenry(a)gmail.com> > To: kbase devel <kbase-devel(a)lists.kbase.us>, outreach(a)kbase.us Outreach < > outreach(a)kbase.us>, KBase Microbes List <microbe(a)lists.kbase.us> > Cc: Doreen Ware <ware(a)cshl.edu> > Sent: Fri, 24 May 2013 16:26:59 -0500 (CDT) > Subject: [Microbe] Comments from users at GLBRC retreat > > 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 > > _______________________________________________ > 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 >

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