- Microbe - mailman3.cels.anl.gov

conference call on Monday
by Pavel Novichkov 26 Jan '12

26 Jan '12

Hi All, The upcoming microbes con call is scheduled for Monday, and I would suggest to discuss in details what should be accomplished by Feb 13. I am still puzzled even about my data... Several strategies have been discussed during the ANL meeting, but still there are more questions than answers. What is going to CDM? What is going to GIT? If CDM has new structure, then the existing API of each core should be rewritten => if existing API will not work, then, once again, what should be submitted to GIT? P.

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RegPrecise web services
by Pavel Novichkov 26 Jan '12

26 Jan '12

Hi everyone, We have released the alpha-version of web services (with help and examples) to get access to the whole content of RegPrecise. http://regprecise.lbl.gov/RegPrecise/services.jsp Please look at it and comment... Accordingly, I am going to shutdown the web server that I used before for the initial test version of web services (http://hazelton.lbl.gov/RegPrecise_test/rest/) Recently we have found several miss-annotations in our data which are in particular caused by changes of the gene coordinates in new versions of genomes... so now we are working on this issue.. Will let you know once it is solved. P.

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Meeting today
by Christopher Henry 16 Jan '12

16 Jan '12

Hi all, Are we having a meeting today? I called in, but the chair person isn't there. It would be a good time to discuss the breakdown of the microbes demo into sub-project and to discuss the plans for the integration meeting. Regardless, I'll send my presentation for the integration meeting out to the microbes list today. Chris

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GTL Microbes Abstract ([email protected])
by Paramvir Dehal (Google Docs) 14 Dec '11

14 Dec '11

I've shared an item with you: GTL Microbes Abstract https://docs.google.com/document/d/1a-fOgYmMPqMI1gqaco8x1p0hHVToE_yMVG_5WnC… It's not an attachment -- it's stored online at Google Docs. To open this document, just click the link above. Hi everyone, Chris started a google doc for the GTL Microbes abstract that is due COB today. Please take a look, feel free to make edits and comments.

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RegPrecise web services presentation
by Pavel Novichkov 06 Dec '11

06 Dec '11

Hi All, Paramvir asked me to send my yesterday presentation to everybody (attached). P.

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Re: [Microbe] Reminder: KBase Microbes Call tomorrow
by Robert Olson 05 Dec '11

05 Dec '11

OK, thank you. See you all then. --bob On Dec 5, 2011, at 11:55 AM, John-Marc Chandonia wrote: > On Mon, Dec 05, 2011 at 11:52:43AM -0600, Robert Olson wrote: >> Is this call at Noon CST or 1pm CST? I have conflicting times in my notes > > It's on my calendar starting an hour from now (1pm CST). > > 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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Re: [Microbe] Reminder: KBase Microbes Call tomorrow
by John-Marc Chandonia 05 Dec '11

05 Dec '11

On Mon, Dec 05, 2011 at 11:52:43AM -0600, Robert Olson wrote: > Is this call at Noon CST or 1pm CST? I have conflicting times in my notes It's on my calendar starting an hour from now (1pm CST). 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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Re: [Microbe] Reminder: KBase Microbes Call tomorrow
by Robert Olson 05 Dec '11

05 Dec '11

Is this call at Noon CST or 1pm CST? I have conflicting times in my notes thanks, --bob On Dec 5, 2011, at 1:52 AM, Paramvir Dehal wrote: > Hi everyone, > > Just a reminder that we're having the KBase Microbes call tomorrow. > Pavel is going to talk about the webservices he's setting up for the > RegFam tools. We will try and use Readytalk.com to share slides. > > 1-866-740-1260 > Code: 4958182# > > slides: > www.readytalk.com > passcode: 4958182 > > Paramvir > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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Reminder: KBase Microbes Call tomorrow
by Paramvir Dehal 05 Dec '11

05 Dec '11

Hi everyone, Just a reminder that we're having the KBase Microbes call tomorrow. Pavel is going to talk about the webservices he's setting up for the RegFam tools. We will try and use Readytalk.com to share slides. 1-866-740-1260 Code: 4958182# slides: www.readytalk.com passcode: 4958182 Paramvir

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Re: [Microbe] February Users meeting
by Adam Paul Arkin 29 Nov '11

29 Nov '11

Sure...but board members can be vision folk.. Stakeholders need to have skin in the game. Please excuse any terseness or errors. This is sent from my mobile. On Nov 29, 2011, at 12:26 PM, "Elizabeth M. Glass" <marland(a)mcs.anl.gov> wrote: > From email chats with Bob and Brian, we would say yes, but would encourage folks to branch out to others. > > Adam - your thoughts? > > Elizabeth > > ----- Original Message ----- > From: Dylan Chivian <dcchivian(a)lbl.gov> > To: Elizabeth M. Glass <marland(a)mcs.anl.gov> > Cc: Paramvir Dehal <psdehal(a)lbl.gov>, Adam Arkin <aparkin(a)lbl.gov>, kbase-microcomm(a)lists.kbase.us, KBase Microbes List <Microbe(a)lists.kbase.us> > Sent: Tue, 29 Nov 2011 14:20:17 -0600 (CST) > Subject: Re: [Microbe] February Users meeting > > Can there be overlap between governance board and stakeholders? > > - dylan > > > On Tue, Nov 29, 2011 at 12:18 PM, Elizabeth M. Glass <marland(a)mcs.anl.gov>wrote: > >> Hi Dylan, >> >> We have a Google document in the Outreach collection that has a listing. >> Sadly, people have been very slow in providing this list. >> >> What was asked, was rather than us inviting arbitrary people from the BRCs >> and U Kbase projects, you as lead/co-lead provide a list of individuals >> that you think will form good collaborative power users/developers for >> KBase .... and are folks that will be enthusiastic about coming to the >> users meeting in February. >> >> I will inform the rest of the Outreach group of your invitations to >> Patrick and Steve. >> >> Elizabeth >> >> ----- Original Message ----- >> From: Dylan Chivian <dcchivian(a)lbl.gov> >> To: Paramvir Dehal <psdehal(a)lbl.gov>, Adam Arkin <aparkin(a)lbl.gov> >> Cc: kbase-microcomm(a)lists.kbase.us, KBase Microbes List < >> Microbe(a)lists.kbase.us> >> Sent: Tue, 29 Nov 2011 13:47:58 -0600 (CST) >> Subject: Re: [Microbe] February Users meeting >> >> Who is already on the list of targeted stakeholders? Where is it being >> maintained? How many stakeholders of each type should attend? I've >> invited Patrik D'haeseleer and Steve Singer, so that's 2 for Microbial >> Communities. >> >> Thanks, >> - Dylan >> >> >> On Tue, Nov 29, 2011 at 11:11 AM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: >> >>> Hi guys, >>> >>> Kbase is planning on having a Users/Targeted Stakeholder Workshop on >>> Sunday, Feb 26th noon- 5pm. This is the day before the DOE 2012 >>> Genomic Science Meeting (26-29). Right now, the plan is to have about >>> 40 attendees and, at this point, I'm not sure how many Kbase Microbes >>> members will be asked to attend. >>> >>> Please let me know if you are planning on attending the DOE Genomics >>> Science meeting and hold off on making your travel arrangements until >>> I find out from Bob how many people from the Microbes group can come. >>> >>> Also, if you have any more suggestions of Targeted Stakeholders, today >>> is the last day to send them to me. >>> >>> Paramvir >>> _______________________________________________ >>> Microbe mailing list >>> Microbe(a)lists.kbase.us >>> https://lists.kbase.us/mailman/listinfo/microbe >>> >> >> >

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