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  1. Dec 12, 2016
  2. Oct 05, 2016
  3. Sep 17, 2016
  4. Sep 16, 2016
  5. Sep 15, 2016
    • Tim O'Donnell's avatar
      Fix failing test test_class1_allele_specific_cv_and_train_command and switch... · 37b0585f
      Tim O'Donnell authored
      Fix failing test test_class1_allele_specific_cv_and_train_command and switch downloads.yml to point to models without imputation for now
      37b0585f
    • Tim O'Donnell's avatar
    • Tim O'Donnell's avatar
      Big refactor to prepare for release · 942601b3
      Tim O'Donnell authored
      Lazily putting this all in one commit.
      
      * infrastructure for downloading datasets and published trained models (the `mhcflurry-downloads` command)
      * docs and scripts (in `downloads-generation`) to generate the pubilshed datsets and trained models
      * parallelized cross validation and model training implementation, including support for imputation (based on the old mhcflurry-cloud repo, which is now gone)
      * a single front-end script for class1 allele-specific cross validation and model training / testing (`mhcflurry-class1-allele-specific-cv-and-train`)
      * refactor how we deal with hyper-parameters and how we instantiate Class1BindingPredictors
      * make Class1BindingPredictor pickleable and remove old serialization code
      * move code particular to class 1 allele-specific predictors into its own submodule
      * remove unused code including arg parsing, plotting, and ensembles
      * had to bump the binding prediction threshold for the Titin1 epitope from 500 to 700, as this test was sporadically failing for me (see test_known_class1_epitopes.py)
      * Attempt to make tests involving randomness somewhat more reproducible by setting numpy random seed
      * update README
      942601b3
    • Tim O'Donnell's avatar
      Merge pull request #48 from hammerlab/remove-experiements-and-notebooks · 473fe899
      Tim O'Donnell authored
      Remove experiements and notebooks
      473fe899
    • Tim O'Donnell's avatar
      Remove experiements and notebooks · 81697fe0
      Tim O'Donnell authored
      81697fe0
  6. Sep 01, 2016
  7. Aug 30, 2016
    • Tim O'Donnell's avatar
      Merge pull request #45 from hammerlab/dockerize · c440acb0
      Tim O'Donnell authored
      dockerize take 2
      c440acb0
    • Tim O'Donnell's avatar
      small fixes to Dockerfile · c1c38dbd
      Tim O'Donnell authored
      c1c38dbd
    • Tim O'Donnell's avatar
      This is an attempt to have a single docker image that can be used as a base... · 2893567b
      Tim O'Donnell authored
      This is an attempt to have a single docker image that can be used as a base for cloud runs (with mhcflurry-cloud) and also eventually as a way for users to experiment with mhcflurry. Plan is to have this built automatically at https://hub.docker.com/r/hammerlab/mhcflurry/
      
       * supports cpu and theoretically gpu (not tested though)
       * supports python 2 and 3
       * putting Dockerfile in the root of our repo lets us just copy the current checkout of the mhcflurry repo into the image instead of pulling it from github, so it works with branches and non-released versions
       * by default this runs a python 3 jupyter notebook on port 8888 with mhcflurry and some convenience packages installed
       * does not try to train any models or run tests. Models will eventually be downloaded from google cloud storage once we have that working
       * it’s pretty hefty unfortunately, around 2 gig
      
      Also: removed the pin on keras<1.0 in requirements.txt
      2893567b
  8. Aug 03, 2016
  9. Aug 01, 2016
  10. Jul 12, 2016
  11. Jun 24, 2016
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