- Microbe - mailman3.cels.anl.gov

Re: [Microbe] Microbes mtg today?
by Paramvir Dehal 10 Sep '12

10 Sep '12

We should still have one. Gavin, can you collect agenda items and send out the reminder email? Pavel, John-Marc and Bill are also at this conference. On Mon, Sep 10, 2012 at 7:46 AM, Gavin Price <gaprice(a)lbl.gov> wrote: > Not sure if we're having one since paramvir is at a conference. > > -g > > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe >

1 0

Re: [Microbe] Microbes mtg today?
by Christopher Henry 10 Sep '12

10 Sep '12

Let's do a meeting. They're only every other week, and with the demo coming up fast, we can't afford to keep canceling them. Chris On Sep 10, 2012, at 9:46 AM, Gavin Price wrote: > Not sure if we're having one since paramvir is at a conference. > > -g > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

1 0

Microbes mtg today?
by Gavin Price 10 Sep '12

10 Sep '12

Not sure if we're having one since paramvir is at a conference. -g

1 0

Microbes report
by Christopher Henry 01 Sep '12

01 Sep '12

FYI: This is the report I send out. I tried to CC the list on the email, but the message got rejected. Hello all, So I've got a draft of the microbes report attached. Note, Paramvir has not approved this yet, and he should do so before it goes out to DOE. Comments and modifications welcome. Also, I didn't get feedback on all the future milestones yet, so I'm waiting for those to be filled in. I admit, I do have one more file to integrate... so some of them may be in there. Comments welcome. I'm not spending a huge amount of time editing section 4, because I'm sure there will be feedback on this. If you edit, I recommend editing the version on googledocs. It's in the microbes collection under KBase project, or you can just follow this link: https://docs.google.com/document/d/1bIWb1tJQ4no3jgWm2-99adTjFm5CILRqoL3Ix3o… In the process of doing this, I found some issues I will list here: 1.) The scheme for the CDM on the KBase website seems out of date: http://pubseed.theseed.org/ErdbDocWidget.cgi?xmlFileName=/home/parrello/Cdm… The microbial phenotype data isn't there. 2.) That URL above is absolutely awful, and in my opinion, that diagram is one of the most critical portions of our documentation. I suggest a simpler URL. 3.) At one point, we had summary stats on the website regarding information in our database (e.g. number of genomes etc). It's gone. It was good. Why was it removed? Best, Chris

1 0

Microbes report
by Christopher Henry 01 Sep '12

01 Sep '12

Hello all, So I've got a draft of the microbes report attached. Note, Paramvir has not approved this yet, and he should do so before it goes out to DOE. Comments and modifications welcome. Also, I didn't get feedback on all the future milestones yet, so I'm waiting for those to be filled in. I admit, I do have one more file to integrate... so some of them may be in there. Comments welcome. I'm not spending a huge amount of time editing section 4, because I'm sure there will be feedback on this. If you edit, I recommend editing the version on googledocs. It's in the microbes collection under KBase project, or you can just follow this link: https://docs.google.com/document/d/1bIWb1tJQ4no3jgWm2-99adTjFm5CILRqoL3Ix3o… In the process of doing this, I found some issues I will list here: 1.) The scheme for the CDM on the KBase website seems out of date: http://pubseed.theseed.org/ErdbDocWidget.cgi?xmlFileName=/home/parrello/Cdm… The microbial phenotype data isn't there. 2.) That URL above is absolutely awful, and in my opinion, that diagram is one of the most critical portions of our documentation. I suggest a simpler URL. 3.) At one point, we had summary stats on the website regarding information in our database (e.g. number of genomes etc). It's gone. It was good. Why was it removed? Best, Chris

1 0

Re: [Microbe] KBase 36 month milestones and KBase 1 year project report
by Christopher Henry 29 Aug '12

29 Aug '12

Nice work Ben. I very much agree with this sentiment. We need to sell these milestones, and we need to sell our progress thus far in the project. The key thing is we need to demonstrate that what we are doing is "transformative", not incremental. Try and emphasize how and why proposed milestones and accomplished work is transformative. On Aug 29, 2012, at 1:19 PM, Ben Bowen wrote: > Hi All, > > I've added some bullet points (purple text) for the 36 month milestones to: > https://docs.google.com/document/d/1nYqaptd630MGjHOIUaDnt9WaW72yKgIxt5vrEqz… > > Paramvir requested that I try and convey the urgency that we move towards showing how to best utilize the information the Microbes Team has put into KBase: in terms of propagation across the entire system and integration across diverse data types. This will require development of analysis approaches for assigning linkages across the system in a tractable way, visualization to convey meaningful understanding of complex content, and user interfaces to capture highly-structured narratives and workflows which are meant to be shared. > > The 36 month deliverables are fantastic! so please don't see the "purple text" as immutable, but do take a second to consider (and write about) how your 36 month deliverables will tie into some form of narrative and have positive impact on the whole scientific community (not just a single post-doc with a genome and some growth-data). > > I like to state the obvious so here goes: as a group we all have to buy into this vision or it will be unreachable. > > Ben > > > > > > > -------------- > Email: BPBowen(a)lbl.gov > Phone: (510) 214-6683 > MS 977-221, Lawrence Berkeley Lab > Web: ms.lbl.gov > > > On Tue, Aug 28, 2012 at 1:51 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: > > > > Hello all, > > > > So as discussed in the conference call, I've created two google docs related to the 1 year DOE reporting. Both documents are in the "KBase Project/Microbes/" collection on GoogleDocs, but I put the links below as well. > > > > The 36 month milestone document is here, and I'm already pasting in the milestones I got from Bob and Terry. I'll be writing my milestones in here as well. > > https://docs.google.com/document/d/1nYqaptd630MGjHOIUaDnt9WaW72yKgIxt5vrEqz… > > > > The 1 year progress report in here, Please put your paragraphs in this documents. I will post my paragraphs as an example. > > https://docs.google.com/document/d/1bIWb1tJQ4no3jgWm2-99adTjFm5CILRqoL3Ix3o… > > > > Questions welcome. Let me know if you have trouble accessing or editing the document. > > > > Best, > > Chris > > _______________________________________________ > > Microbe mailing list > > Microbe(a)lists.kbase.us > > https://lists.kbase.us/mailman/listinfo/microbe >

1 0

Re: [Microbe] KBase 36 month milestones and KBase 1 year project report
by Ben Bowen 29 Aug '12

29 Aug '12

Hi All, I've added some bullet points *(purple text)* for the 36 month milestones to: https://docs.google.com/document/d/1nYqaptd630MGjHOIUaDnt9WaW72yKgIxt5vrEqz… Paramvir requested that I try and convey the urgency that we move towards showing how to best utilize the information the Microbes Team has put into KBase: in terms of propagation across the entire system and integration across diverse data types. This will require development of analysis approaches for assigning linkages across the system in a tractable way, visualization to convey meaningful understanding of complex content, and user interfaces to capture highly-structured narratives and workflows which are meant to be shared. The 36 month deliverables are fantastic! so please don't see the* "purple text" *as immutable, but do take a second to consider (and write about) how your 36 month deliverables will tie into some form of narrative and have positive impact on the whole scientific community (not just a single post-doc with a genome and some growth-data). I like to state the obvious so here goes: as a group we all have to buy into this vision or it will be unreachable. Ben -------------- Email: BPBowen(a)lbl.gov Phone: (510) 214-6683 MS 977-221, Lawrence Berkeley Lab Web: ms.lbl.gov On Tue, Aug 28, 2012 at 1:51 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: > > Hello all, > > So as discussed in the conference call, I've created two google docs related to the 1 year DOE reporting. Both documents are in the "KBase Project/Microbes/" collection on GoogleDocs, but I put the links below as well. > > The 36 month milestone document is here, and I'm already pasting in the milestones I got from Bob and Terry. I'll be writing my milestones in here as well. > https://docs.google.com/document/d/1nYqaptd630MGjHOIUaDnt9WaW72yKgIxt5vrEqz… > > The 1 year progress report in here, Please put your paragraphs in this documents. I will post my paragraphs as an example. > https://docs.google.com/document/d/1bIWb1tJQ4no3jgWm2-99adTjFm5CILRqoL3Ix3o… > > Questions welcome. Let me know if you have trouble accessing or editing the document. > > Best, > Chris > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

1 0

KBase 36 month milestones and KBase 1 year project report
by Christopher Henry 28 Aug '12

28 Aug '12

Hello all, So as discussed in the conference call, I've created two google docs related to the 1 year DOE reporting. Both documents are in the "KBase Project/Microbes/" collection on GoogleDocs, but I put the links below as well. The 36 month milestone document is here, and I'm already pasting in the milestones I got from Bob and Terry. I'll be writing my milestones in here as well. https://docs.google.com/document/d/1nYqaptd630MGjHOIUaDnt9WaW72yKgIxt5vrEqz… The 1 year progress report in here, Please put your paragraphs in this documents. I will post my paragraphs as an example. https://docs.google.com/document/d/1bIWb1tJQ4no3jgWm2-99adTjFm5CILRqoL3Ix3o… Questions welcome. Let me know if you have trouble accessing or editing the document. Best, Chris

1 0

Re: [Microbe] Microbes Call now
by Christopher Henry 28 Aug '12

28 Aug '12

Sorry all. It was stuck in my outbox. The call info is out. Let me know if you don't get it. Chris On Aug 28, 2012, at 12:08 PM, Gavin Price wrote: > Has the call in info been sent out? I don't think I've seen it. > > -g > > On Aug 27, 2012 11:48 AM, "Christopher Henry" <chrisshenry(a)gmail.com> wrote: > Sorry Steven, but I'm going to be decisive. It looks like everyone I need can make the call tomorrow, so we're going to reschedule for tomorrow. > > Again, the agenda will be: > 1.) Overview of the progress of the build and discussion of next steps > 2.) Writing for the DOE annual report this week > > If you have questions or concerns about the DOE report, then let's discuss tomorrow. But I want to emphasize, that report is due this week, so "not contributing until Paramvir gets back" really isn't an option. I'm pretty confident Paramvir and I will have the opportunity to make revisions before the final letter is submitted, so please do not worry about that. > > I'm not sure how the Berkley system works, so I will be sending out my own conference call number shortly. > > Thanks, > Chris > > On Aug 27, 2012, at 1:31 PM, Steven E. Brenner wrote: > > > I am call in right now but still getting hold music. > > Sorry I can't make it tomorrow. > > I am available next Monday if need be. > > > > Steven > > > > On Mon, 27 Aug 2012, Christopher Henry wrote: > > > >> Hey guys, > >> > >> We really really need to have a call this week, given the milestones and the annual report that's due. > >> Logistically, I think today's meeting is dead, and I apologize for that. I had no idea about Paramvir's vacation. I might have his admin code, but I don't think I do. > >> Anyhow, I would like to host a meeting tomorrow, with the following agenda items: > >> > >> 1.) Overview of the progress of the build and discussion of next steps > >> 2.) Writing for the DOE annual report this week > >> > >> I would like to host this meeting at the usual time (2 PM eastern, 1 PM central, 11 AM pacific, except on Tuesday instead of Monday, but it is critically important that the following people be able to attend: > >> Mike, Gavin, Ben, Sam, Scott, Bill, Paval. > >> > >> Sorry if you're not on that list... nothing personal... I still greatly value your work in KBase. Its just those are the people with writing assignments for the DOE annual report. > >> > >> So guys, can you make that time tomorrow? > >> You guys should already have received an email about what you need to do for the report, and if the time is good, I'll send out details on the call shortly. > >> > >> Chris > >> > >> On Aug 27, 2012, at 1:11 PM, Christopher Henry wrote: > >> > >>> Paramvir is on vacation this week, and I don't have the admin key on the conference call number. > >>> I'm thinking we need to switch to a system with no admin key, so we can have meetings without Paramvir. > >>> I'm thinking of having my admin set up weekly calls using Argonne's system. > >>> But it's too late to start with that this week. I propose we have a call one week from today to get back on track, sense we haven't has a call in a while. > >>> > >>> On Aug 27, 2012, at 1:00 PM, John-Marc Chandonia wrote: > >>> > >>>> On Mon, Jul 16, 2012 at 11:07:31AM -0700, Paramvir Dehal wrote: > >>>>> Sorry for not emailing earlier: > >>>>> > >>>>> 866-740-1260 Code: 4958182 > >>>> > >>>> Are we on for today? I'm dialed in but it hasn't started yet. > >>>> > >>>> 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 <*> > >>>> _______________________________________________ > >>>> 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 > >> > > _______________________________________________ > 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

1 0

Re: [Microbe] Microbes Call now
by Gavin Price 28 Aug '12

28 Aug '12

Has the call in info been sent out? I don't think I've seen it. -g On Aug 27, 2012 11:48 AM, "Christopher Henry" <chrisshenry(a)gmail.com> wrote: > Sorry Steven, but I'm going to be decisive. It looks like everyone I need > can make the call tomorrow, so we're going to reschedule for tomorrow. > > Again, the agenda will be: > 1.) Overview of the progress of the build and discussion of next steps > 2.) Writing for the DOE annual report this week > > If you have questions or concerns about the DOE report, then let's discuss > tomorrow. But I want to emphasize, that report is due this week, so "not > contributing until Paramvir gets back" really isn't an option. I'm pretty > confident Paramvir and I will have the opportunity to make revisions before > the final letter is submitted, so please do not worry about that. > > I'm not sure how the Berkley system works, so I will be sending out my own > conference call number shortly. > > Thanks, > Chris > > On Aug 27, 2012, at 1:31 PM, Steven E. Brenner wrote: > > > I am call in right now but still getting hold music. > > Sorry I can't make it tomorrow. > > I am available next Monday if need be. > > > > Steven > > > > On Mon, 27 Aug 2012, Christopher Henry wrote: > > > >> Hey guys, > >> > >> We really really need to have a call this week, given the milestones > and the annual report that's due. > >> Logistically, I think today's meeting is dead, and I apologize for > that. I had no idea about Paramvir's vacation. I might have his admin code, > but I don't think I do. > >> Anyhow, I would like to host a meeting tomorrow, with the following > agenda items: > >> > >> 1.) Overview of the progress of the build and discussion of next steps > >> 2.) Writing for the DOE annual report this week > >> > >> I would like to host this meeting at the usual time (2 PM eastern, 1 PM > central, 11 AM pacific, except on Tuesday instead of Monday, but it is > critically important that the following people be able to attend: > >> Mike, Gavin, Ben, Sam, Scott, Bill, Paval. > >> > >> Sorry if you're not on that list... nothing personal... I still greatly > value your work in KBase. Its just those are the people with writing > assignments for the DOE annual report. > >> > >> So guys, can you make that time tomorrow? > >> You guys should already have received an email about what you need to > do for the report, and if the time is good, I'll send out details on the > call shortly. > >> > >> Chris > >> > >> On Aug 27, 2012, at 1:11 PM, Christopher Henry wrote: > >> > >>> Paramvir is on vacation this week, and I don't have the admin key on > the conference call number. > >>> I'm thinking we need to switch to a system with no admin key, so we > can have meetings without Paramvir. > >>> I'm thinking of having my admin set up weekly calls using Argonne's > system. > >>> But it's too late to start with that this week. I propose we have a > call one week from today to get back on track, sense we haven't has a call > in a while. > >>> > >>> On Aug 27, 2012, at 1:00 PM, John-Marc Chandonia wrote: > >>> > >>>> On Mon, Jul 16, 2012 at 11:07:31AM -0700, Paramvir Dehal wrote: > >>>>> Sorry for not emailing earlier: > >>>>> > >>>>> 866-740-1260 Code: 4958182 > >>>> > >>>> Are we on for today? I'm dialed in but it hasn't started yet. > >>>> > >>>> 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 <*> > >>>> _______________________________________________ > >>>> 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 > >> > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe >

1 0