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Microbes Call Reminder
by Paramvir Dehal 28 Nov '11

28 Nov '11

We have our weekly call in 15min. 1-866-740-1260 Code: 4958182# The call should be short, I don't have any urgent agenda items. Agenda: 1) Milestones: Gene & Organism pages 2) Key Collaborators for Feb Meeting 3) New personnel 4) Other items?

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Re: [Microbe] Reminder: Microbes call today
by Keith Keller 14 Nov '11

14 Nov '11

On Mon, Nov 14, 2011 at 12:01 PM, John-Marc Chandonia <JMChandonia(a)lbl.gov> wrote: > Here are my slides from today. Testing it out live requires the > generic MO development password, which Paramvir can give out if > he wants. You can use these credentials: username: kbase password: KBase (note this is case-sensitive) All of our *.tst.microbesonline.org sites are developer sandboxes (which all use the same htpasswd file), so please be patient if it's not always working quickly. Also, please don't share these credentials outside kbase folks. --keith -- Keith Keller kkeller(a)lbl.gov Physical Biosciences Division, Lawrence Berkeley National Lab

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Re: [Microbe] Reminder: Microbes call today
by John-Marc Chandonia 14 Nov '11

14 Nov '11

Here are my slides from today. Testing it out live requires the generic MO development password, which Paramvir can give out if he wants. 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: Microbes call today
by Matt DeJongh 14 Nov '11

14 Nov '11

Here is the link to the CytoSEED screen shots: http://www.cs.hope.edu/cytoseed/ Matt On Mon, Nov 14, 2011 at 1:03 PM, Steven E. Brenner <brenner(a)compbio.berkeley.edu> wrote: > Sorry, got the time wrong. > > On Mon, 14 Nov 2011, Steven E. Brenner wrote: > >> No chairperson? I'm getting hold music and the web site is not loading. >> Is this the right passcode? >> >> On Mon, 14 Nov 2011, Paramvir Dehal wrote: >> >>> John-Marc and Matt are going to talk about Cytoscape and CytoScape Web >>> today. Be sure to login to www.readytalk.com >>> to see the slides. The pass code is: 4958182 >>> >>> >>> 1-866-740-1260 >>> Code: 4958182# > > _______________________________________________ > 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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Re: [Microbe] Reminder: Microbes call today
by Steven E. Brenner 14 Nov '11

14 Nov '11

Sorry, got the time wrong. On Mon, 14 Nov 2011, Steven E. Brenner wrote: > No chairperson? I'm getting hold music and the web site is not loading. Is > this the right passcode? > > On Mon, 14 Nov 2011, Paramvir Dehal wrote: > >> John-Marc and Matt are going to talk about Cytoscape and CytoScape Web >> today. Be sure to login to www.readytalk.com >> to see the slides. The pass code is:ï¿½4958182 >> >> >> 1-866-740-1260 >> Code: 4958182# >

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Re: [Microbe] Reminder: Microbes call today
by Steven E. Brenner 14 Nov '11

14 Nov '11

No chairperson? I'm getting hold music and the web site is not loading. Is this the right passcode? On Mon, 14 Nov 2011, Paramvir Dehal wrote: > John-Marc and Matt are going to talk about Cytoscape and CytoScape Web today. Be sure to login to www.readytalk.com > to see the slides. The pass code is:ï¿½4958182 > > > 1-866-740-1260 > Code: 4958182# >

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Reminder: Microbes call today
by Paramvir Dehal 14 Nov '11

14 Nov '11

John-Marc and Matt are going to talk about Cytoscape and CytoScape Web today. Be sure to login to www.readytalk.com to see the slides. The pass code is: 4958182 1-866-740-1260 Code: 4958182#

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10/17 Microbes Follow up
by Paramvir Dehal 17 Oct '11

17 Oct '11

Hi All, Thanks for joining the Microbes Call today. I've pasted the notes I took at the end of this email. Here's the list of things that I'm expecting from you guys: 1) Bob/Chris: Check with Ross and/or Veronica about coming up with a list of data types that could be useful for checking the consistency of biclustering results. Possibly the subsystems or the Scenarios. 2) Chris: A list of data types from ModelSEED that we can use for checking biclustering results. 3) Chris: Output of the Argonne UI meeting 4) All: Concerns, needs, thoughts on UI issues. 5) All: take a look at our Work Breakdown Structure that was sent around a couple weeks ago, and find the Infrastructure independent tasks that you can work on now. Work on defining data types, clarifying workflow and objectives if enough developer resources are not available. Paramvir 10/17/2011: 11am Microbes callBob is giving an overview of the CDM - move data that makes sense into CDM at Kbase level - import from cores - relational model - API layed across that model - CDM specs still in development Biclustering demo - SEED post-processing data consistency - GO, Subsystems - Veronica and Ross to discuss for SEED - Senarios? possibly better to use than subsystems - Model SEED - coupled reactions - Chris will make a list - Biclusters as a generic putative regulon/subsystem - repository? - comparison/stats with generic tools - consistency check with network + phylogenetic trees - cross check functional and evolutionary consistency UI Meeting - People should send me their input - UI docs from Chris on Thursday Work break down structures - Everyone should take a look at the boxes - Assign people to boxes - Need to start work on the Infrastructure independent tasks Other issues - Timeline for resources

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Re: [Microbe] Microbes Telecon 10/17 11am P / 1pm C
by Brettin, Thomas S. 17 Oct '11

17 Oct '11

Hi All, I apologize for calling in late. I had an early flight to ANL that was cancelled and spent the better half of the morning in the airport before giving up and rescheduling that flight for tomorrow am. Thanks Bob for stepping up. Tom -----Original Message----- From: microbe-bounces(a)lists.kbase.us [mailto:[email protected]] On Behalf Of Paramvir Dehal Sent: Monday, October 17, 2011 1:10 PM To: KBase Microbes List Subject: Re: [Microbe] Microbes Telecon 10/17 11am P / 1pm C Todays agenda: I. Quick review on Infrastructure (Tom) II. Biclustering demo (Paramvir) III. API status IV. Identification of API independent tasks V. Anything else On Wed, Oct 12, 2011 at 11:43 AM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: > This a reminder that we have a Microbes Telecon next monday at 11am P > / 1pm C. Are there any agenda items people would like to bring up? > > 1-866-740-1260 > Code: 4958182# > > Paramvir > _______________________________________________ Microbe mailing list Microbe(a)lists.kbase.us hxxps://lists.kbase.us/mailman/listinfo/microbe

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Re: [Microbe] Microbes Telecon 10/17 11am P / 1pm C
by Paramvir Dehal 17 Oct '11

17 Oct '11

Todays agenda: I. Quick review on Infrastructure (Tom) II. Biclustering demo (Paramvir) III. API status IV. Identification of API independent tasks V. Anything else On Wed, Oct 12, 2011 at 11:43 AM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: > This a reminder that we have a Microbes Telecon next monday at 11am P > / 1pm C. Are there any agenda items people would like to bring up? > > 1-866-740-1260 > Code: 4958182# > > Paramvir >

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