June 2012 - Microbe - mailman3.cels.anl.gov

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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Re: [Microbe] boolean growth server running
by Gavin Price 05 Jun '12

05 Jun '12

I just switched from the django server to nginx and fastcgi, and as a consequence the service docs link is now: http://140.221.92.10/services/booleangrowth/api/v1/docs -g On 5/19/2012 10:51 PM, Gavin A Price wrote: > Hi all, > > I have a basic version of the boolean growth service running on > Magellan. I'm hoping to get some feedback on the direction I'm going > and the features I have, as well as what I'm planning. > > First rule: Do not share this link outside KBase. The server is > running on the Django test server which is not production worthy. > Also, the server makes parts of the Microbes Online fitness database > visible to the world, and that data is private. That being said, Keith > has blessed me running the server as is, so I take no responsibility > whatsoever for the disaster that will undoubtedly happen (hi Keith!). > > Some rudimentary documentation is here: > http://140.221.92.10:8000/booleangrowth/api/v1/docs > > I recommend you read it and the Tastypie link before you interact with > the server. There are also some development notes linked that include > my to do list and some musings on how to make the service better. > Finally, there's a link to the entry point of the server. > > Any feedback regarding bugs, requested features, the direction I'm > planning, etc. are welcomed and, indeed, strongly encouraged. I don't > want to to write a bunch of code and then find out no one wants to use > it. > > Thanks, Gavin

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Re: [Microbe] KBase Microbes conference call this week?
by Steven E. Brenner 05 Jun '12

05 Jun '12

Sorry I couldn't join -- I was traveling. I would have given advance notice but didn't know it was happening. On Mon, 4 Jun 2012, Paramvir Dehal wrote: > Sorry I haven't sent out an agenda. The meeting is in 20min, maybe > we'll keep it short. > > 866-740-1260 Code: 4958182 > > Paramvir > > On Mon, Jun 4, 2012 at 10:35 AM, Gavin A Price <gavinaprice(a)gmail.com> wrote: >> It's on my calendar but I haven't seen a conference call #, so not sure if >> it's happening. >> >> -g >> _______________________________________________ >> 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] KBase Microbes conference call this week?
by Paramvir Dehal 04 Jun '12

04 Jun '12

Sorry I haven't sent out an agenda. The meeting is in 20min, maybe we'll keep it short. 866-740-1260 Code: 4958182 Paramvir On Mon, Jun 4, 2012 at 10:35 AM, Gavin A Price <gavinaprice(a)gmail.com> wrote: > It's on my calendar but I haven't seen a conference call #, so not sure if > it's happening. > > -g > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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KBase Microbes conference call this week?
by Gavin A Price 04 Jun '12

04 Jun '12

It's on my calendar but I haven't seen a conference call #, so not sure if it's happening. -g

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