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Re: [Microbe] [Kbase-devel] Phenotype data format proposal
by Adam Paul Arkin 04 Apr '12

04 Apr '12

Hi Guys, Looking really good. Two quick questions on a skim 1) Are you not going to include point mutations/replacements along with insertions/deletions (given the increasing use of MAGE, etc), 2) In the data file info on media would seem to need to be quantitative so the amount of glucose, etc. should be noted. If there is a time series this might be measured in time. This would seem to be important to the analysis where will that data be kept? Adam From: Christopher Henry <chrisshenry(a)gmail.com> Date: Wed, 4 Apr 2012 16:49:37 -0500 To: 'KBase Microbes List' <Microbe(a)lists.kbase.us>, <kbase-devel(a)lists.kbase.us> Subject: [Kbase-devel] Phenotype data format proposal > Hello all, > > Attached is the proposal for phenotype data in KBase that was discussed in the > developers call today. This is geared towards microbes, but probably works for > other cases as well. > This is a draft, so modification can certainly be made. > > Also, after discussing this with Paramvir and Ben, it¹s been decided that we > will also introduce a data format for ³growth phenotypes², which Ben is in > charge of formulating. ³Growth Phenotypes² will be highly derived datasets > (basically knockouts/fitness pairs). ³Growth Phenotypes² will ultimately be > computed from the experimental data-structure described in the attached file, > and ³Growth phenotypes² will be used as direct inputs into FBA and Growmatch > algorithms. > > Chris > _______________________________________________ Kbase-devel mailing list > Kbase-devel(a)lists.kbase.us https://lists.kbase.us/mailman/listinfo/kbase-devel

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Phenotype data format proposal
by Christopher Henry 04 Apr '12

04 Apr '12

Hello all, Attached is the proposal for phenotype data in KBase that was discussed in the developers call today. This is geared towards microbes, but probably works for other cases as well. This is a draft, so modification can certainly be made. Also, after discussing this with Paramvir and Ben, it's been decided that we will also introduce a data format for "growth phenotypes", which Ben is in charge of formulating. "Growth Phenotypes" will be highly derived datasets (basically knockouts/fitness pairs). "Growth Phenotypes" will ultimately be computed from the experimental data-structure described in the attached file, and "Growth phenotypes" will be used as direct inputs into FBA and Growmatch algorithms. Chris

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meetings notes
by Paramvir Dehal 26 Mar '12

26 Mar '12

We had a great discussion today and made a lot of headway on our Phenotype specification on the google doc.03/26/2012: Microbes CallParamvir, John-Marc, Bill, Ben, Tom, Matt, Chris, Ross, Brian Agenda: - May Release - Phenotype CDM - ModelSEED updates - ? Phenotype CDM - ModelSEED data tree has multiple domains adding an experimental domain - build tree of interconnected objects - what are the objects and how are they related - Tom: Collaborative specification with Ross & Microbes - Build the tree with all attributes then have discussion with infrastructure team - CDM is a framework - Will need to have a discussion about strains with Ross - Ben will take MR-1 data and represent it - Chris will do the same with B. subtilis ModelSEED - two weeks new version - code written against data objects - separated from underlying database - data tree will be sent to microbes list - ModelSEED data objects not in CDM will get migrated to KBase space eventually - Chris will email location in GIT repository

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Re: [Microbe] FW: Telecon Today 11am Pacific / 1pm Central / 2pm Eastern
by Matt DeJongh 26 Mar '12

26 Mar '12

https://git.kbase.us/models_api.git/blob/HEAD:/moduleSpecifications/Phenoty… On Mon, Mar 26, 2012 at 3:06 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: > KBase repository folder with phenotype hypothesis spec: > models_api/moduleSpecifications/PhenotypeDataAccess.spec > > -----Original Message----- > From: microbe-bounces(a)lists.kbase.us [mailto:[email protected]] > On Behalf Of Paramvir Dehal > Sent: Monday, March 26, 2012 12:31 PM > To: KBase Microbes List > Subject: [Microbe] Telecon Today 11am Pacific / 1pm Central / 2pm Eastern > > 866-740-1260 Code: 4958182 > > Agenda: > > 1) May Release > > 2) Phenotype CDM > > 3) ModelSEED 2.0 > > Send me anything else you'd like to add to the Agenda > _______________________________________________ > 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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FW: Telecon Today 11am Pacific / 1pm Central / 2pm Eastern
by Christopher Henry 26 Mar '12

26 Mar '12

KBase repository folder with phenotype hypothesis spec: models_api/moduleSpecifications/PhenotypeDataAccess.spec -----Original Message----- From: microbe-bounces(a)lists.kbase.us [mailto:[email protected]] On Behalf Of Paramvir Dehal Sent: Monday, March 26, 2012 12:31 PM To: KBase Microbes List Subject: [Microbe] Telecon Today 11am Pacific / 1pm Central / 2pm Eastern 866-740-1260 Code: 4958182 Agenda: 1) May Release 2) Phenotype CDM 3) ModelSEED 2.0 Send me anything else you'd like to add to the Agenda _______________________________________________ Microbe mailing list Microbe(a)lists.kbase.us https://lists.kbase.us/mailman/listinfo/microbe

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Telecon Today 11am Pacific / 1pm Central / 2pm Eastern
by Paramvir Dehal 26 Mar '12

26 Mar '12

866-740-1260 Code: 4958182 Agenda: 1) May Release 2) Phenotype CDM 3) ModelSEED 2.0 Send me anything else you'd like to add to the Agenda

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microbes call is on
by Paramvir Dehal 12 Mar '12

12 Mar '12

The microbes call is on now, call in if you haven't already

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Microbes Call Meeting Notes
by Paramvir Dehal 05 Mar '12

05 Mar '12

*03/05/2012: Microbes callParamvir, Keith, Bill, John-Marc, Chris, Tom, Matt, Agenda: - Discuss process for realistic KBase timeline for Microbes Demo & Determine unmet needs from Infrastructure - Discuss upcoming Datatypes - Discuss collaborations - Debrief on KBase workshop Discussion 1. KBase Debrief 1. notes from ben 2. access to repository for Nathan and collaborators 3. reconciling annotations 1. MO vs SEED equivalence based on sequence exists now 2. what are all the KBase ID services APIs? 2. Collaborations 1. Chris is going to give typedef to Nathan’s group 2. Tom thinks giving access to repository will be okay 3. Develop some training material before adding new people 4. Assess the level of enthusiasm and understanding/patience 5. Talk to collaborators about needs for datatypes 3. Datatypes 1. Infrastructure datatype registry on the wiki? trac wiki developer link 2. Tom will send link 3. Everyone should check if what they are working on is in there 4. Tom is trying to determine what will be in the next deployment 1. what will be good to have in CDM 2.5months from today 2. what methods as well? data access & analysis 5. Brainstorming for CDM 4. Microbes Timeline 1. Core dune by June? 2. Setup Google Doc for timeline 3. ETA 3/12 Chris will make the docs 5. Microbes Developer list with interests and active projects 1. Reach out to other groups to find out what they’re doing 2. Developers log? 3 column table name - new function - link 3. Tutorials by each science domain 6. Design Review Status? 1. Tom brought it up to Adam & Rick 2. Time hasn’t been set 3. meeting is being scoped 7. Tiny Store walk through on Wednesday Developer call by Bob Olsen *

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Current Entities in the CDM
by Brettin, Thomas S. 05 Mar '12

05 Mar '12

Go to track.kbase.us On the home page, follow the "Authenticated Wiki" link. Follow the "API Documentation" link Look at these two links. Get-entity / Get-relationship API<http://www.mcs.anl.gov/~olson/ksapling.html> Entitiy-Relationship Model Documentation<http://pubseed.theseed.org/ErdbDocWidget.cgi?xmlFileName=/home/parrello/FIG…>

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Microbes Call Today 3/5
by Paramvir Dehal 05 Mar '12

05 Mar '12

We'll have our call today at 11am P / 1pm C / 2pm E 866-740-1260 Code: 4958182

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