Hey Chris, Thanks for the great summary! Comments inline below.

----- Original Message ----- From: Christopher Henry <[email protected]>

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

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-- 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: [email protected] -------------------------------------