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 <[email protected]> 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).
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