AToL: Collaborative Research to resolve major radiations in Nematoda with multigene and other datasets

proposal details and draft writing & assembly page, updated at 10 pm pacific time on March 11th 2008

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The executive summary - version 0 Paul is asking for comments & help no updates yet

Results from prior support: Dave's paragraphs more updates needed from all of us

we will have to demonstrate in some detail what was achieved by Nematol1 (we are allowed up to 5 pages within the 15 page project description, each of us only needs to address his/her single most relevant prior award which is for most of us Nematol1)
- 18S & 28S trees
- multigene data from genome projects (not really our own achievement), cDNA libs, solexa testing, ESTs? Can we come up with a first multigene-like tree before March 14th?
- Nematol database infrastructure
- network of collaborators & experts
- lists of prioritized taxa & identified sources for those taxa across phylum
- toolkit of optimized/innovative methods (solexa, primer pairs, DESS, multifocal databasing, other Nematol tools, ...)
- training of students and postdocs
- publications

Plan of work:

- Generating multigene data PART 1: Nemalog Kelley is asking for comments & help no updates yet (this file is 600Kb in size)

- Generating multigene data PART 2: Solexa Kelley is asking for comments & help no updates yet

- Analyzing multigene data open

- Generating & analyzing mitochondrial gene seqs & gene order data; comparing phylogenetic signal in mitochondrial vs nuclear loci Brad is asking for comments & help no updates yet

- The role of mophology Jim is asking for comments & help this update March 11 8.30pm

  • references for the morphology section NEW
  • - Developmental data: P-granules and axis determination Eyualem is asking for comments & help no updates yet

    - Developmental data: male genital sensilla Dave is working on it

    - Synthesis of phylogenies open

    - Implifications for classification open

    Outreach and impact: open

    - involvement and training of undergrads & high schools, minorities
    - will provide a complete suite of tools and data in a standardized environment, will potentially set the stage revolutionary changes to nematode diagnostics and phylogenetics and genomics and ecology
    -...?Direct involvement of international colleagues
    - We are allowed to budget $ for inviting & visiting non-US collaborators, this is a mechanism for rewarding non-US partners and listing them as senior collaborators. Draft a list of names & schedule their visits to our labs as well as our visits to theirs (aim for 2 week – 2 month durations?)
    - New series of workshops (at CIPRES?) If 3 years then partition the workshops by data types and methods rather than by taxa? Eg year 1 = morphology, ultra & development; year 2 = multigene & mitogenomes; year 3 = the grand synthesis

    Management plan: Paul is asking for comments & help Dave's update 8.30pm March 11

    workshops & travel this is updated, the other parts are 6 years old!
    database & online tools
    more outreach
    division of work & assignment of taskmasters please update or add your roles/profiles!


    Timeline: January 1st 2009 till December 31st 2011 (3 years)

    Total budget: Aim for a $2 million total including overheads. Please inform Krys of your budget before it gets set in stone, so as to allow her to keep track of our collective total.
    Budget slices processing through research offices so far:


    Unincorporated bits and straw men dealing with overall project purpose and structure

    Major objective: In order to complete the framework for the nematode branch of life we need to add, compare and integrate
    - multigene data to be obtained via solexa and multigene catalog of universal primer pairs, for 100-200 species from our already compiled priority lists
    Q: how many species? estimated technology cost $2000/species
    Q: all at UNH or do we need to train one other lab to carry out a third of this work?
    - mitochondrial genomes for a large subset (or all?) of those species, to be obtained via solexa data comvbined with rolling circle)
    - morphological and ultrastructural matrices for respectively all and small subset of those species
    - early development data for a (smnall?) subset of those species
    - a classification built on community-wide consensus, by resolving discussions on e.g. linnean versus phylocode-like system. Probably not genuinely attainable but Nematol2 will be the forum to see how close we can get.

    Minor objective: Major flash/java upgrades to Nematol database & tools to allow online multigene phylogenetics, data mining in all assembled types of data, direct online uploads, more efficient image browsing, phylobiogeography, online MOTU analyses,...?