- Microbe - mailman3.cels.anl.gov

notes from microbes meeting
by Paramvir Dehal 16 Jul '12

16 Jul '12

*07/16/2012: Microbes CallAttendees: Mike, Jason, Gavin, Matt, Bill, Tom Agenda 1) Demo update 2) Phenotype update 3) Microarrays 4) Tree update 5) Other issues 1) Demo update - On track for building core functionality by mid-August - Two major services need to be built - Phenotype reconciliation services - Tree services - Invite Steven Brenner’s Grad Student Mike Souza to KBase 2) Tree update by Mike Sneddon - Working with Fangfang, Terry and Bruce on exchange format - Common use cases - have some basic ones - please contact Mike - Haven’t heard back from Plants, sent an email to Shiran - will email Jerming and David Westen 3) Phenotype update from Gavin - Pulling data from Shewanella for all public and data ok’d by Duetschbauer - Excel worksheet that Ben Bowen put together that lists all environments associated with data - Waiting on Bruce et al to create loaders - Still some open questions on the data, working with Duestschbauer: - Strains with insertions in intergenic areas currently indistinguishable from wild type in our ER - Motility experiements - Missing data - Stereochemistry for compounds - Have come up with a couple changes to ER - add table to allow grouping by plate 4) Microarrays - Jason Baumohl working on Structured Microarray data - Matt will discuss some issues with Jason that he’d like to see 5) Other topics - UI work - KBase Labs - Python library location? Email dev list - August Build! *

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Microbes Call now
by Paramvir Dehal 16 Jul '12

16 Jul '12

Sorry for not emailing earlier: 866-740-1260 Code: 4958182 Agenda 1) Demo update 2) Phenotype update 3) Microarrays 4) Tree update 5) Other issues

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Re: [Microbe] Microbes call today
by gaprice＠lbl.gov 16 Jul '12

16 Jul '12

Is the call # the same for today? -g On 7/2/2012 10:35 AM, Paramvir Dehal wrote: > Our call starts at 11am Pacific / 1pm Central > > *866-740-1260* > *Code: 4958182* > * > * > *We have two agenda items, email me if there's anything you'd like to > add:* > * > * > *1) KBase Microbes tutorial/walkthrough in September* > * > * > *2) Phenotype use cases * > * > * > * > * > * > * > *Paramvir* > > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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Re: [Microbe] Microbes call today
by gaprice＠lbl.gov 02 Jul '12

02 Jul '12

On 7/2/2012 10:35 AM, Paramvir Dehal wrote: > Our call starts at 11am Pacific / 1pm Central > > *866-740-1260* > *Code: 4958182* > * > * > *We have two agenda items, email me if there's anything you'd like to > add:* > * > * > *1) KBase Microbes tutorial/walkthrough in September* > * > * > *2) Phenotype use cases * > * > * > * > * > * > * > *Paramvir* > > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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Re: [Microbe] Microbes call today
by John-Marc Chandonia 02 Jul '12

02 Jul '12

I'm on... any update on getting a local copy of the CDM (as we discussed with Pavel last week)? JMC -- John-Marc Chandonia (JMChandonia(a)lbl.gov) We're everywhere... Physical Biosciences Division, Berkeley National Lab for your convenience. http://www.strgen.org/~jmc/ -- Psi Corps <*>

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Microbes call today
by Paramvir Dehal 02 Jul '12

02 Jul '12

Our call starts at 11am Pacific / 1pm Central *866-740-1260 * *Code: 4958182* * * *We have two agenda items, email me if there's anything you'd like to add:* * * *1) KBase Microbes tutorial/walkthrough in September* * * *2) Phenotype use cases * * * * * * * *Paramvir*

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Re: [Microbe] extract bulk data from cs
by Robert Olson 21 Jun '12

21 Jun '12

Hi - I put together a similar script the other day that pulls a central store genome out to a typed-object file (as used by the annotate_genome script in the tutorial). It should be a straightforward exercise to modify it to create the exchange format instead. Script attached. Note that it does a reallocation of IDs; you wouldn't need to do this. --bob On Jun 18, 2012, at 1:50 PM, Keith Keller wrote: > Hi all, > > Of course I thought of this just a few minutes after our call ended! > > Is there an easy way to extract data out of the CS in the > tab-delimited exchange format? I want to try to load KBase genomes > into MO so that we can have more agreement between our genomes and > genes. > > --keith > > -- > Keith Keller > kkeller(a)lbl.gov > Physical Biosciences Division, Lawrence Berkeley National Lab > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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extract bulk data from cs
by Keith Keller 18 Jun '12

18 Jun '12

Hi all, Of course I thought of this just a few minutes after our call ended! Is there an easy way to extract data out of the CS in the tab-delimited exchange format? I want to try to load KBase genomes into MO so that we can have more agreement between our genomes and genes. --keith -- Keith Keller kkeller(a)lbl.gov Physical Biosciences Division, Lawrence Berkeley National Lab

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Microbes Call today!
by Paramvir Dehal 18 Jun '12

18 Jun '12

We have a call in about an hour, 11AM Pacific / 1PM Central 866-740-1260 Code: 4958182 Agenda: 1. KBase Tutorial Meeting 2. IRIS framework 3. Datatypes for demo Let me know if you have anything to add. Paramvir

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Mon. microbes meeting conflicts with arkin group
by Gavin A Price 15 Jun '12

15 Jun '12

Does the microbes meeting take priority? -g

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