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Release Notes   Installation Instructions     DownloadImage Modified   press '[' to toggle the sidebar

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Scalable Framework for Importance Sampling (infinite-sites model) in Population Genetics  Dec 10the Linkage Analysis in Neurospora crassa,  May 23, 2013  

a Reproducible Research as Championed by Victoria Stodden

cumulative Features:

  1. Importance Sampling using Multiple Proposals
    1. run sampler by size or time
    2. compute likelihood
    3. compute MLE
    4. multi-core ready

Release Summary:

Importance Sampling (IS)

  •  Likelihood
  •  MLE
  •  Proposals-MultiThreaded
  •  Computational efficiency for IS (via SD vs HAW)

General

  •  Marker for new/improved jobs
  •  

    XML editor w/ Schema support;

  •  Model based Data (API)
  •  nb701 (platform-ide) from src

Phylogeny

  •  gene tree diagram improvements:
  •  save layout (automatically)
  •  no scrollpane; key bindings for mode; help on right-click
  •  drawing code refactored

 

 

 

 

 

 

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 Importance Sampling (IS)

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 New Features

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New Features:

  1. Model ID for TAB08 & KSA00
  2. Data Statistics for TAB08, KSA00 & OrganismData
  3. Repeats Tests
  4. Barratt Mapping Function

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Data Statistics: OrganismData

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Data Statistics: TAB08

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 Phylogeny

 Repeats Tests

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 General

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Related Publications

  • Coalescent: An open-source and scalable framework for Importance Sampling in coalescent theory (under review)
  • Coalescent: An open-source and scalable framework for Exact Calculations in coalescent theory  BMC Bioinformatics (2012) 13:257
  • Release Notes

  • Road Map

    • Project Stat [Ohloh]

    Repeats Tests

    Results from the legacy application have been incorporated into the framework, but the results are not reliable. The theory need to be revisited.

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    Model ID: TAB08

    Results show that models TAB08 and KSA00 can be recovered via MLE.

    TAB08

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    Barratt Mapping Function

    Results from the legacy application have been incorporated into the framework, but the results are not reliable. The theory need to be revisited.

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    Info
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    © 2009-2013 2014 Susanta Tewari. All rights reserved | Have you encountered a bug in CoalescentGenomemap? Want to suggest a new feature? Use Contact Support

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