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Re: [Microbe] DOE Report
by Michael Sneddon 28 Aug '12

28 Aug '12

Sounds good. On Tue, Aug 28, 2012 at 9:40 AM, Fangfang Xia <fangfang.xia(a)gmail.com>wrote: > Sure. Michael, I'm not able to attend the call today as I'm meeting with > Gary in Champaign to go over your comments on the trees. I'll have time to > work on the document tonight. Please send/share anything you have. Thanks. > > On Aug 28, 2012, at 11:33 AM, Christopher Henry <chrisshenry(a)gmail.com> > wrote: > > > Absolutely it does Mike. Can you and fangfang put something in on trees > and assembly? > > Chris > > > > On Aug 28, 2012, at 10:21 AM, Michael Sneddon wrote: > > > >> Hi Chris, > >> I'm not sure if this requires its own section, but I've been working on > getting support for alignments and phylogenetic trees into kbase, which > will help support a variety of other functionality (for both microbes and > communities teams). For instance, Sifter and other tree-based annotation > propagation will require having trees. Let me know if you would like me to > write specifically on this or help with other sections. We can discuss > more during the call. > >> > >> -michael > >> > >> > >> On Mon, Aug 27, 2012 at 11:24 PM, Christopher Henry < > chrisshenry(a)gmail.com> wrote: > >> Hi guys, > >> > >> So the DOE report is due this week. I will write it, but I need your > help. > >> > >> We have to fill in the outline below. Sections 1-3 provide an overview > of work done up to this point. Section 4 outlines work that still needs to > be done. > >> > >> I'm splitting this up into sections 1-3 and sections 4. > >> > >> Now, for most of you, I need guidance for sections 1-3. Try and write > at least a paragraph for each section that attempts to answer the questions > in the outline. I'm fine with bullets if necessary. > >> These are the people I want content from: > >> > >> 1.) Gavin and Ben: phenotype ERD and data load > >> 2.) Bill: GLAMM > >> 3.) Paval: regulon services (and anything else you're working on) > >> 4.) Matt and Aaron: PROM integration, cytoseed (and anything else > you're working on) > >> 5.) Chris (me): metabolic modeling > >> 6.) Steven Brenner: sifter? > >> 7.) Ross/Gordon/Bob: Genome annotation > >> > >> If I left a section of the project, I apologize. Please let me know and > send the appropriate content anyway. > >> > >> I need the content by Wednesday afternoon, but the sooner the better. I > will integrate everything together. Note the length restrictions on each > section of the outline, but don't hold back. I'd rather cut than have to > make stuff up. > >> > >> For section 4, see the attached document entitled "36 month milestone > guidance". Fill in any sections with your name on it. The document has good > guidance on what we need from you. Just follow the instructions. > >> Do your best! If you don't know what to write, then just say so... Also > note, I already sent people this document and instructions earlier. I'm > just sending it again to the whole list so there are no mysteries during > the conference call tomorrow. > >> > >> Best, > >> Chris > >> > >> > >> > >> > >> > >> 1. Description of what is currently being built/done in each area (~1 > page per team) > >> a. What is the overall capability being developed and why is it > needed > >> b. How does it use the KBase infrastructure > >> c. How is this capability unique in the community > >> d. What are the key science drivers > >> e. How does it address DOE mission needs > >> f. How is this capability being made available to the community > >> g. High-level sketch of the functions available in the API to > this capability > >> h. Contributions to crosscutting capabilities > >> i. Relationship to other systems available to the community > (iPlant, IMG, etc.) > >> > >> 2. Development plan and accomplishments to date for the capability (~2 > pages, address on the order of 8-10 major milestones) > >> a. The overall strategy for achieving the capability goals > >> b. Details of the first 18 month milestones (these should be > revised versions of our original plan elements) > >> c. Description of accomplishments in achieving these milestones > >> d. Description of what has been deployed, tested and documented. > >> e. Description of accomplishments beyond the plan of record (new > things that needed to be developed) > >> f. Description of performance, throughput, or other measure of > the progress on meeting the goals. > >> > >> 3. Approach to developing collaborations, acquiring datasets and > partners in this area (~1 page) > >> a. Discussion of contributors and collaborators and what value > they are adding to KBase > >> b. Description of tools and systems we are leveraging from > partners not directly funded by KBase > >> c. Discussion of the major data types and data sources that have > been loaded into KBase and plans for curation and updates > >> d. Discussion of future partnerships that should be established > and steps taken to engage partners > >> e. Discussion of key users or user groups for this areas and plans > for engagement (how outreach is being leveraged) > >> > >> 4. Future work and major milestones for next 18 months (~2 pages) > >> a. Assuming successful completion of existing milestones for Feb > release, what are the top 6-10 next step tasks in this area > >> b. What additional capabilities will these new tasks bring to KBase > >> c. How will these capabilities leverage infrastructure and other > domain tools in KBase > >> d. Highlight the new functions that contribute to crosscutting > (multi-domain) capabilities > >> e. Provide use case examples for these new capabilities and > identify collaborators and partners > >> f. Describe how these capabilities will be integrated into the > KBase API > >> g. Timeline and major dependencies for the milestones (I think we > can rough resource fit, but since we already know what the budgets and > split are, its mostly shifting existing things around). > >> > >> > >> > >> _______________________________________________ > >> Microbe mailing list > >> Microbe(a)lists.kbase.us > >> https://lists.kbase.us/mailman/listinfo/microbe > >> > >> > > > >

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Re: [Microbe] DOE Report
by Fangfang Xia 28 Aug '12

28 Aug '12

Sure. Michael, I'm not able to attend the call today as I'm meeting with Gary in Champaign to go over your comments on the trees. I'll have time to work on the document tonight. Please send/share anything you have. Thanks. On Aug 28, 2012, at 11:33 AM, Christopher Henry <chrisshenry(a)gmail.com> wrote: > Absolutely it does Mike. Can you and fangfang put something in on trees and assembly? > Chris > > On Aug 28, 2012, at 10:21 AM, Michael Sneddon wrote: > >> Hi Chris, >> I'm not sure if this requires its own section, but I've been working on getting support for alignments and phylogenetic trees into kbase, which will help support a variety of other functionality (for both microbes and communities teams). For instance, Sifter and other tree-based annotation propagation will require having trees. Let me know if you would like me to write specifically on this or help with other sections. We can discuss more during the call. >> >> -michael >> >> >> On Mon, Aug 27, 2012 at 11:24 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: >> Hi guys, >> >> So the DOE report is due this week. I will write it, but I need your help. >> >> We have to fill in the outline below. Sections 1-3 provide an overview of work done up to this point. Section 4 outlines work that still needs to be done. >> >> I'm splitting this up into sections 1-3 and sections 4. >> >> Now, for most of you, I need guidance for sections 1-3. Try and write at least a paragraph for each section that attempts to answer the questions in the outline. I'm fine with bullets if necessary. >> These are the people I want content from: >> >> 1.) Gavin and Ben: phenotype ERD and data load >> 2.) Bill: GLAMM >> 3.) Paval: regulon services (and anything else you're working on) >> 4.) Matt and Aaron: PROM integration, cytoseed (and anything else you're working on) >> 5.) Chris (me): metabolic modeling >> 6.) Steven Brenner: sifter? >> 7.) Ross/Gordon/Bob: Genome annotation >> >> If I left a section of the project, I apologize. Please let me know and send the appropriate content anyway. >> >> I need the content by Wednesday afternoon, but the sooner the better. I will integrate everything together. Note the length restrictions on each section of the outline, but don't hold back. I'd rather cut than have to make stuff up. >> >> For section 4, see the attached document entitled "36 month milestone guidance". Fill in any sections with your name on it. The document has good guidance on what we need from you. Just follow the instructions. >> Do your best! If you don't know what to write, then just say so... Also note, I already sent people this document and instructions earlier. I'm just sending it again to the whole list so there are no mysteries during the conference call tomorrow. >> >> Best, >> Chris >> >> >> >> >> >> 1. Description of what is currently being built/done in each area (~1 page per team) >> a. What is the overall capability being developed and why is it needed >> b. How does it use the KBase infrastructure >> c. How is this capability unique in the community >> d. What are the key science drivers >> e. How does it address DOE mission needs >> f. How is this capability being made available to the community >> g. High-level sketch of the functions available in the API to this capability >> h. Contributions to crosscutting capabilities >> i. Relationship to other systems available to the community (iPlant, IMG, etc.) >> >> 2. Development plan and accomplishments to date for the capability (~2 pages, address on the order of 8-10 major milestones) >> a. The overall strategy for achieving the capability goals >> b. Details of the first 18 month milestones (these should be revised versions of our original plan elements) >> c. Description of accomplishments in achieving these milestones >> d. Description of what has been deployed, tested and documented. >> e. Description of accomplishments beyond the plan of record (new things that needed to be developed) >> f. Description of performance, throughput, or other measure of the progress on meeting the goals. >> >> 3. Approach to developing collaborations, acquiring datasets and partners in this area (~1 page) >> a. Discussion of contributors and collaborators and what value they are adding to KBase >> b. Description of tools and systems we are leveraging from partners not directly funded by KBase >> c. Discussion of the major data types and data sources that have been loaded into KBase and plans for curation and updates >> d. Discussion of future partnerships that should be established and steps taken to engage partners >> e. Discussion of key users or user groups for this areas and plans for engagement (how outreach is being leveraged) >> >> 4. Future work and major milestones for next 18 months (~2 pages) >> a. Assuming successful completion of existing milestones for Feb release, what are the top 6-10 next step tasks in this area >> b. What additional capabilities will these new tasks bring to KBase >> c. How will these capabilities leverage infrastructure and other domain tools in KBase >> d. Highlight the new functions that contribute to crosscutting (multi-domain) capabilities >> e. Provide use case examples for these new capabilities and identify collaborators and partners >> f. Describe how these capabilities will be integrated into the KBase API >> g. Timeline and major dependencies for the milestones (I think we can rough resource fit, but since we already know what the budgets and split are, its mostly shifting existing things around). >> >> >> >> _______________________________________________ >> Microbe mailing list >> Microbe(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/microbe >> >> >

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Call TODAY
by Christopher Henry 28 Aug '12

28 Aug '12

Hello all, Microbes call today at 1:00 p.m. CT // 2:00 p.m. ET // 11 a.m. PT. 1-888-850-4523 Participant Passcode: 913601 Best, Chris

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Re: [Microbe] DOE Report
by Christopher Henry 28 Aug '12

28 Aug '12

Absolutely it does Mike. Can you and fangfang put something in on trees and assembly? Chris On Aug 28, 2012, at 10:21 AM, Michael Sneddon wrote: > Hi Chris, > I'm not sure if this requires its own section, but I've been working on getting support for alignments and phylogenetic trees into kbase, which will help support a variety of other functionality (for both microbes and communities teams). For instance, Sifter and other tree-based annotation propagation will require having trees. Let me know if you would like me to write specifically on this or help with other sections. We can discuss more during the call. > > -michael > > > On Mon, Aug 27, 2012 at 11:24 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: > Hi guys, > > So the DOE report is due this week. I will write it, but I need your help. > > We have to fill in the outline below. Sections 1-3 provide an overview of work done up to this point. Section 4 outlines work that still needs to be done. > > I'm splitting this up into sections 1-3 and sections 4. > > Now, for most of you, I need guidance for sections 1-3. Try and write at least a paragraph for each section that attempts to answer the questions in the outline. I'm fine with bullets if necessary. > These are the people I want content from: > > 1.) Gavin and Ben: phenotype ERD and data load > 2.) Bill: GLAMM > 3.) Paval: regulon services (and anything else you're working on) > 4.) Matt and Aaron: PROM integration, cytoseed (and anything else you're working on) > 5.) Chris (me): metabolic modeling > 6.) Steven Brenner: sifter? > 7.) Ross/Gordon/Bob: Genome annotation > > If I left a section of the project, I apologize. Please let me know and send the appropriate content anyway. > > I need the content by Wednesday afternoon, but the sooner the better. I will integrate everything together. Note the length restrictions on each section of the outline, but don't hold back. I'd rather cut than have to make stuff up. > > For section 4, see the attached document entitled "36 month milestone guidance". Fill in any sections with your name on it. The document has good guidance on what we need from you. Just follow the instructions. > Do your best! If you don't know what to write, then just say so... Also note, I already sent people this document and instructions earlier. I'm just sending it again to the whole list so there are no mysteries during the conference call tomorrow. > > Best, > Chris > > > > > > 1. Description of what is currently being built/done in each area (~1 page per team) > a. What is the overall capability being developed and why is it needed > b. How does it use the KBase infrastructure > c. How is this capability unique in the community > d. What are the key science drivers > e. How does it address DOE mission needs > f. How is this capability being made available to the community > g. High-level sketch of the functions available in the API to this capability > h. Contributions to crosscutting capabilities > i. Relationship to other systems available to the community (iPlant, IMG, etc.) > > 2. Development plan and accomplishments to date for the capability (~2 pages, address on the order of 8-10 major milestones) > a. The overall strategy for achieving the capability goals > b. Details of the first 18 month milestones (these should be revised versions of our original plan elements) > c. Description of accomplishments in achieving these milestones > d. Description of what has been deployed, tested and documented. > e. Description of accomplishments beyond the plan of record (new things that needed to be developed) > f. Description of performance, throughput, or other measure of the progress on meeting the goals. > > 3. Approach to developing collaborations, acquiring datasets and partners in this area (~1 page) > a. Discussion of contributors and collaborators and what value they are adding to KBase > b. Description of tools and systems we are leveraging from partners not directly funded by KBase > c. Discussion of the major data types and data sources that have been loaded into KBase and plans for curation and updates > d. Discussion of future partnerships that should be established and steps taken to engage partners > e. Discussion of key users or user groups for this areas and plans for engagement (how outreach is being leveraged) > > 4. Future work and major milestones for next 18 months (~2 pages) > a. Assuming successful completion of existing milestones for Feb release, what are the top 6-10 next step tasks in this area > b. What additional capabilities will these new tasks bring to KBase > c. How will these capabilities leverage infrastructure and other domain tools in KBase > d. Highlight the new functions that contribute to crosscutting (multi-domain) capabilities > e. Provide use case examples for these new capabilities and identify collaborators and partners > f. Describe how these capabilities will be integrated into the KBase API > g. Timeline and major dependencies for the milestones (I think we can rough resource fit, but since we already know what the budgets and split are, its mostly shifting existing things around). > > > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe > >

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Call TODAY
by Silvia Mulligan 28 Aug '12

28 Aug '12

All, At Chris Henry's request, there will be a Microbes call today at 1:00 p.m. CT // 2:00 p.m. ET // 11 a.m. PT. The call in information is below: 1-888-850-4523 Participant Passcode: 913601 Host (Chris Henry only) Passcode: 9136013 Regards, Silvia *********************** Silvia Mulligan Executive Secretary Computing, Environment and Life Sciences Argonne National Laboratory 9700 S. Cass Avenue Argonne, IL 60439 Phone: 630-252-6188 Fax: 630-252-6333

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Re: [Microbe] DOE Report
by Michael Sneddon 28 Aug '12

28 Aug '12

Hi Chris, I'm not sure if this requires its own section, but I've been working on getting support for alignments and phylogenetic trees into kbase, which will help support a variety of other functionality (for both microbes and communities teams). For instance, Sifter and other tree-based annotation propagation will require having trees. Let me know if you would like me to write specifically on this or help with other sections. We can discuss more during the call. -michael On Mon, Aug 27, 2012 at 11:24 PM, Christopher Henry <chrisshenry(a)gmail.com>wrote: > Hi guys, > > So the DOE report is due this week. I will write it, but I need your help. > > We have to fill in the outline below. Sections 1-3 provide an overview of > work done up to this point. Section 4 outlines work that still needs to be > done. > > I'm splitting this up into sections 1-3 and sections 4. > > Now, for most of you, I need guidance for sections 1-3. Try and write at > least a paragraph for each section that attempts to answer the questions in > the outline. I'm fine with bullets if necessary. > These are the people I want content from: > > 1.) Gavin and Ben: phenotype ERD and data load > 2.) Bill: GLAMM > 3.) Paval: regulon services (and anything else you're working on) > 4.) Matt and Aaron: PROM integration, cytoseed (and anything else you're > working on) > 5.) Chris (me): metabolic modeling > 6.) Steven Brenner: sifter? > 7.) Ross/Gordon/Bob: Genome annotation > > If I left a section of the project, I apologize. Please let me know and > send the appropriate content anyway. > > I need the content by Wednesday afternoon, but the sooner the better. I > will integrate everything together. Note the length restrictions on each > section of the outline, but don't hold back. I'd rather cut than have to > make stuff up. > > For section 4, see the attached document entitled "36 month milestone > guidance". Fill in any sections with your name on it. The document has good > guidance on what we need from you. Just follow the instructions. > Do your best! If you don't know what to write, then just say so... Also > note, I already sent people this document and instructions earlier. I'm > just sending it again to the whole list so there are no mysteries during > the conference call tomorrow. > > Best, > Chris > > > > > > 1. Description of what is currently being built/done in each area (~1 page > per team) > a. What is the overall capability being developed and why is it > needed > b. How does it use the KBase infrastructure > c. How is this capability unique in the community > d. What are the key science drivers > e. How does it address DOE mission needs > f. How is this capability being made available to the community > g. High-level sketch of the functions available in the API to this > capability > h. Contributions to crosscutting capabilities > i. Relationship to other systems available to the community > (iPlant, IMG, etc.) > > 2. Development plan and accomplishments to date for the capability (~2 > pages, address on the order of 8-10 major milestones) > a. The overall strategy for achieving the capability goals > b. Details of the first 18 month milestones (these should be revised > versions of our original plan elements) > c. Description of accomplishments in achieving these milestones > d. Description of what has been deployed, tested and documented. > e. Description of accomplishments beyond the plan of record (new > things that needed to be developed) > f. Description of performance, throughput, or other measure of the > progress on meeting the goals. > > 3. Approach to developing collaborations, acquiring datasets and partners > in this area (~1 page) > a. Discussion of contributors and collaborators and what value they > are adding to KBase > b. Description of tools and systems we are leveraging from partners > not directly funded by KBase > c. Discussion of the major data types and data sources that have > been loaded into KBase and plans for curation and updates > d. Discussion of future partnerships that should be established and > steps taken to engage partners > e. Discussion of key users or user groups for this areas and plans > for engagement (how outreach is being leveraged) > > 4. Future work and major milestones for next 18 months (~2 pages) > a. Assuming successful completion of existing milestones for Feb > release, what are the top 6-10 next step tasks in this area > b. What additional capabilities will these new tasks bring to KBase > c. How will these capabilities leverage infrastructure and other > domain tools in KBase > d. Highlight the new functions that contribute to crosscutting > (multi-domain) capabilities > e. Provide use case examples for these new capabilities and identify > collaborators and partners > f. Describe how these capabilities will be integrated into the > KBase API > g. Timeline and major dependencies for the milestones (I think we > can rough resource fit, but since we already know what the budgets and > split are, its mostly shifting existing things around). > > > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe > >

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

28 Aug '12

Ben, The google doc is nice, and you should use it as a reference where possible while you're fleshing out your assigned milestones in the document I sent out earlier (attached as well). The attached word document was created by the KBase PIs (Adam, Rick, and Bob). As such, that is the official document we need to be working from for the DOE reporting. Thanks! Chris On Aug 27, 2012, at 5:59 PM, Ben Bowen wrote: > I'm not sure if you all have looked at this: > https://docs.google.com/document/d/1IurQF9tumhdDYJRYsTJ8SIfNO9WLlxP1BfM8Mgm… > > Skip to the last page. The first couple paragraphs are just some attempts at capturing a mission statement for the microbes team; eventually it should be dumped into a different document. On the last page, you will find aims outlined in broad strokes for the 36 month goals. > > If you feel the need to make major changes to them, please use a different color or something so that when Paramvir gets back he can see the old vs new versions. > > Ben > > > -------------- > Email: BPBowen(a)lbl.gov > Phone: (510) 214-6683 > MS 977-221, Lawrence Berkeley Lab > Web: ms.lbl.gov > > > On Mon, Aug 27, 2012 at 12:37 PM, Ben Bowen <ben.bowen(a)gmail.com> wrote: > I can't make tomorrow's call either. I can get the notes from Gavin. > > -------------- > Email: BPBowen(a)lbl.gov > Phone: (510) 214-6683 > MS 977-221, Lawrence Berkeley Lab > Web: ms.lbl.gov > > > On Mon, Aug 27, 2012 at 11:47 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 > >

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DOE Report
by Christopher Henry 28 Aug '12

28 Aug '12

Hi guys, So the DOE report is due this week. I will write it, but I need your help. We have to fill in the outline below. Sections 1-3 provide an overview of work done up to this point. Section 4 outlines work that still needs to be done. I'm splitting this up into sections 1-3 and sections 4. Now, for most of you, I need guidance for sections 1-3. Try and write at least a paragraph for each section that attempts to answer the questions in the outline. I'm fine with bullets if necessary. These are the people I want content from: 1.) Gavin and Ben: phenotype ERD and data load 2.) Bill: GLAMM 3.) Paval: regulon services (and anything else you're working on) 4.) Matt and Aaron: PROM integration, cytoseed (and anything else you're working on) 5.) Chris (me): metabolic modeling 6.) Steven Brenner: sifter? 7.) Ross/Gordon/Bob: Genome annotation If I left a section of the project, I apologize. Please let me know and send the appropriate content anyway. I need the content by Wednesday afternoon, but the sooner the better. I will integrate everything together. Note the length restrictions on each section of the outline, but don't hold back. I'd rather cut than have to make stuff up. For section 4, see the attached document entitled "36 month milestone guidance". Fill in any sections with your name on it. The document has good guidance on what we need from you. Just follow the instructions. Do your best! If you don't know what to write, then just say so... Also note, I already sent people this document and instructions earlier. I'm just sending it again to the whole list so there are no mysteries during the conference call tomorrow. Best, Chris 1. Description of what is currently being built/done in each area (~1 page per team) a. What is the overall capability being developed and why is it needed b. How does it use the KBase infrastructure c. How is this capability unique in the community d. What are the key science drivers e. How does it address DOE mission needs f. How is this capability being made available to the community g. High-level sketch of the functions available in the API to this capability h. Contributions to crosscutting capabilities i. Relationship to other systems available to the community (iPlant, IMG, etc.) 2. Development plan and accomplishments to date for the capability (~2 pages, address on the order of 8-10 major milestones) a. The overall strategy for achieving the capability goals b. Details of the first 18 month milestones (these should be revised versions of our original plan elements) c. Description of accomplishments in achieving these milestones d. Description of what has been deployed, tested and documented. e. Description of accomplishments beyond the plan of record (new things that needed to be developed) f. Description of performance, throughput, or other measure of the progress on meeting the goals. 3. Approach to developing collaborations, acquiring datasets and partners in this area (~1 page) a. Discussion of contributors and collaborators and what value they are adding to KBase b. Description of tools and systems we are leveraging from partners not directly funded by KBase c. Discussion of the major data types and data sources that have been loaded into KBase and plans for curation and updates d. Discussion of future partnerships that should be established and steps taken to engage partners e. Discussion of key users or user groups for this areas and plans for engagement (how outreach is being leveraged) 4. Future work and major milestones for next 18 months (~2 pages) a. Assuming successful completion of existing milestones for Feb release, what are the top 6-10 next step tasks in this area b. What additional capabilities will these new tasks bring to KBase c. How will these capabilities leverage infrastructure and other domain tools in KBase d. Highlight the new functions that contribute to crosscutting (multi-domain) capabilities e. Provide use case examples for these new capabilities and identify collaborators and partners f. Describe how these capabilities will be integrated into the KBase API g. Timeline and major dependencies for the milestones (I think we can rough resource fit, but since we already know what the budgets and split are, its mostly shifting existing things around).

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Re: [Microbe] Microbes Call now
by Ben Bowen 27 Aug '12

27 Aug '12

I'm not sure if you all have looked at this: https://docs.google.com/document/d/1IurQF9tumhdDYJRYsTJ8SIfNO9WLlxP1BfM8Mgm… Skip to the last page. The first couple paragraphs are just some attempts at capturing a mission statement for the microbes team; eventually it should be dumped into a different document. On the last page, you will find aims outlined in broad strokes for the 36 month goals. If you feel the need to make major changes to them, please use a different color or something so that when Paramvir gets back he can see the old vs new versions. Ben -------------- Email: BPBowen(a)lbl.gov Phone: (510) 214-6683 MS 977-221, Lawrence Berkeley Lab Web: ms.lbl.gov On Mon, Aug 27, 2012 at 12:37 PM, Ben Bowen <ben.bowen(a)gmail.com> wrote: > I can't make tomorrow's call either. I can get the notes from Gavin. > > -------------- > Email: BPBowen(a)lbl.gov > Phone: (510) 214-6683 > MS 977-221, Lawrence Berkeley Lab > Web: ms.lbl.gov > > > On Mon, Aug 27, 2012 at 11:47 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 >> > >

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Re: [Microbe] Microbes Call now
by Ben Bowen 27 Aug '12

27 Aug '12

I can't make tomorrow's call either. I can get the notes from Gavin. -------------- Email: BPBowen(a)lbl.gov Phone: (510) 214-6683 MS 977-221, Lawrence Berkeley Lab Web: ms.lbl.gov On Mon, Aug 27, 2012 at 11:47 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 >

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