Changesets - Effects of cost in protein evolution

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Converted alignment spec to use fixtu... was committed by Michael Barton

Tuesday Sep 02

Commit [bef284df1b44dcfecf8be35fed2db498a2f65b57]

Added model and migration for amino a... was committed by Michael Barton 01:44 PM

Commit [2107ac64ea1bb0a1165e7ca06db41b36dc4d9a13]

Added code to load amino acid data ht... was committed by Michael Barton 01:34 PM

Commit [27a4d7f01a2484bcec3c768507614b45c9a5ee89]

Created model and migration for amino... was committed by Michael Barton 01:32 PM

Commit [d8f7f22cfe138c9a13d9a6a74ea5e590aa810888]

Updated evolutionary rate estimation ... was committed by Michael Barton

Monday Sep 01

Commit [0ed2170d5d5795bdd1c053481d06ea10c2b45083]

Updated specing for adding unrooted t... was committed by Michael Barton 04:13 PM

Commit [60e80449ea071ca2fe512b59af9d9fde9fb326d8]

Updated alignment to return an unroot... was committed by Michael Barton 04:12 PM

Commit [db10dd6265063364d292f01e1a5a34fcae50af74]

Added method in evolutionary rate to ... was committed by Michael Barton 04:11 PM

Commit [4852cefae25bbe2a6e5f4287847e0c72c7e7253c]

Added column in gene mutations table ... was committed by Michael Barton 04:11 PM

Commit [6b1cebd45208e0f8f0be5595e0c63ddb69910b89]

Added new version of bioruby http://g... was committed by Michael Barton 03:01 PM

Commit [a22450610a0f33a9be1d96ca07a8a4ec0e79342f]

Added tasks for loading and clearing ... was committed by Michael Barton

Thursday Aug 21

Commit [45f50f60dc1e55501b370707ca00170a5bdb6c92]

Updated tasks for clearing site and g... was committed by Michael Barton 05:53 PM

Commit [a7730d75b7d34f03db0c792b9639c27fa24df7fc]

Updated loading of gene wise mutation... was committed by Michael Barton 05:52 PM

Commit [fdbb4b28d623992ccf08746fa4fe5d9d13696b10]

Updated table columns names for gene ... was committed by Michael Barton 05:41 PM

Commit [1141f1153c9ee34b4b8e1bb6352c05bebb0abcf0]

Added fastercsv gem to environment ht... was committed by Michael Barton 05:21 PM

Commit [4758f8bbb3b0205fb2238cfa29428843e448994b]

Added task to load rate estimations f... was committed by Michael Barton 03:07 PM

Commit [77984cf023d06eda38aa38b65b117d3a818910fe]

Updated foreign key associations for ... was committed by Michael Barton 02:47 PM

Commit [91f98590187350219cb0af918ad0b22b4914cab5]

Updated analysis.rake for 002 to use ... was committed by Michael Barton 11:57 AM

Commit [0bc27a8fd178ba4680352d9fca342d25c0b7d58c]

Updated starfish loader to include th... was committed by Michael Barton 11:56 AM

Commit [b30666a73a31111652fbbaab28268d08bcebeb83]

Updated migration for gene table to a... was committed by Michael Barton 11:29 AM

Commit [55ae5149b72954d18e82c2b238bfe2d69f408fed]

Updated sitewise analysis specing for... was committed by Michael Barton

Tuesday Aug 19

Commit [5b16c21b6b87ee76f2e6757cfb45b5c47fd20595]

Switched site mutation to use a map, ... was committed by Michael Barton 06:26 PM

Commit [e8e8702c47191b323f24f7df0404a1c24a4e3d41]

Updated alignment codon specing for n... was committed by Michael Barton 05:58 PM

Commit [330b26610ee79e38c0c01ce7b20a3f8c590e5197]

Updated loading of alignment codons t... was committed by Michael Barton 05:57 PM

Commit [2170c0775d7e4044d5d2dd2a14c9bd913ab08e1e]

Added index and column for whether al... was committed by Michael Barton 05:56 PM

Commit [6421673d144724d2a35e318c294d992f15649b0d]

EvolutionaryRate.tree_length is now s... was committed by Michael Barton 03:31 PM

Commit [1611beb4280bdb628beb3cd97327bba42937d77d]

Updated bioruby code to include parsi... was committed by Michael Barton 03:30 PM

Commit [59d2a3d55b875836b9c07820d750620e24aac8ad]

Updated module reference from Bio::Co... was committed by Michael Barton 02:08 PM

Commit [068a826370915772500c72f27bafe56e0e98b8b6]

Updated codeml requirement in environ... was committed by Michael Barton 02:06 PM

Commit [66b7826ef4f900a6a5aa2ef96d3c5160495481c2]

Added Codeml option to include data w... was committed by Michael Barton 02:02 PM

Commit [f90297f678aa00cac82adcd4b8600f893d5fc200]

Added new version of bioruby with cod... was committed by Michael Barton 02:01 PM

Commit [bc95b56fc5e2bf1907508463c4b1f58dd2b9fa00]

Updated specing data for alignment YD... was committed by Michael Barton 01:47 PM

Commit [bb3ecb3ee772b504fd987c9a9be2513545d2d2e7]

Updated specing to check that alignme... was committed by Michael Barton 12:09 PM

Commit [f0e9719ba081fa84cd3c1afc7c5d7b95062be868]

Added specing to check that alignment... was committed by Michael Barton 12:05 PM

Commit [2c43279703ac5b254f5c83294b2412818177bf46]

Updated specing to check error messag... was committed by Michael Barton 12:04 PM

Commit [6c7484805eaaf9229306c87f0f89a5c90a804433]

Added spec to ensure that alignments ... was committed by Michael Barton 11:20 AM

Commit [b954d6e560dc4a82677c161fefc798e92b1deb9a]

Added sequence files for YDL177C http... was committed by Michael Barton

Monday Aug 18

Commit [9fb0e62d0c5cfc3ec37cc4cf61132aafecab4136]

Changed data in alignment specing for... was committed by Michael Barton 08:11 PM

Commit [9f548d723f37ba57317c266675bbf76a17e56f40]

Updated method to check what the name... was committed by Michael Barton 08:10 PM

Commit [8c00d8be53511993703c7f5e327a68f862b0d806]

Added chunk of code at the start of t... was committed by Michael Barton 08:10 PM

Commit [189fbe3b191ef19e0d1b44dc50cbb028f7761123]

Updated tree method for the alignment... was committed by Michael Barton 08:07 PM

Commit [90214bad7f15ec966a3fa2d0fb743c9e4dc62bfa]

Added additional validations for alig... was committed by Michael Barton 08:06 PM

Commit [26d2c3d8d3c7ee174ffe34af9ba7e9b883ea4309]

Added method to gene model to strip l... was committed by Michael Barton 08:03 PM

Commit [f98cf651f9df106dac67bea00cc682f4a757198c]

Switched test case gene being used, n... was committed by Michael Barton 08:01 PM

Commit [0f7a9f3a237fc85a27964b105ccc6b6e785144ab]

Gene loading now removes line breaks.... was committed by Michael Barton 04:11 PM

Commit [5678778689dcb33b68dca56f66b1f4a7d94df70b]

Updated alignment to return only one ... was committed by Michael Barton 04:09 PM

Commit [c8a2df6b43054c0496226e5cad2f58965eaeadf4]

Gene loading now removes line breaks.... was committed by Michael Barton 03:58 PM

Commit [16a75fecd4459e86b21a83de646f7a95507205d4]

Added validation to ensure that the y... was committed by Michael Barton 03:47 PM

Commit [b46fb75a2d220595c9df0927cabe28aa2e106ea9]

Reordered validations to execute in o... was committed by Michael Barton 03:45 PM

Commit [7f264c9e69eb6b56b4a5894bedb7f97379923acc]

Set validates_presence_of to be first... was committed by Michael Barton 03:37 PM

Commit [1afdcdc090b5007eb30ebe4a4a509c4377d6534a]

Added profiling for loading site muta... was committed by Michael Barton

Wednesday Aug 13

Commit [bfbd9c342806aa0bfce393c73a6b9494f616fe57]

Updated alignment codon profiling to ... was committed by Michael Barton 03:08 PM

Commit [09613385bc50a7fcb2a761df3e45d6f1659400ad]

Updated all specs to use helper data ... was committed by Michael Barton 03:04 PM

Commit [10aa7b7fce8bba5ccc6b7db8ae81d5ef0bb3a42d]

Created helper methods for specing to... was committed by Michael Barton 03:04 PM

Commit [a750287bccb921071c276495ffb864cb8f9c0891]

Added more specs for site mutation ra... was committed by Michael Barton 12:05 PM

Commit [84eac78c800d475dc7003fdff90b52e95dcbfb8a]

Fixed evolutionary rate method call i... was committed by Michael Barton 11:56 AM

Commit [7575edd2d8644eb605d32b8851668e370f937861]

Updated starfish method to use alignm... was committed by Michael Barton 11:55 AM

Commit [a4bddb436fd1d6ac2bde53330ffa87e360c5eaea]

Swapped which enumerable was being in... was committed by Michael Barton 11:53 AM

Commit [f6870768ef548e4bf5c9d17b09a66e4f444f33d5]

Merge branch 'master' into gene_rate ... was committed by Michael Barton 11:49 AM

Commit [9508948e23d2379bbdb1f434b5c9c15040904ddd]

Change private method calls not to ca... was committed by Michael Barton 11:49 AM

Commit [edf4727cee39efe8de3a044ae92ee39b73a5c3a6]

Michaelbarton Effects of cost in protein evolution

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