284e95a4eccf4eaba722ab8d53f1296b0ead8007 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/f3bc3444fccf14a52fb64e17c5c1e87333597005 f3bc3444fccf14a52fb64e17c5c1e87333597005 2008-12-04T09:16:41-08:00 2008-12-04T09:16:41-08:00 Updated plotting of gene cost density. More pretty. 4d941431368a19aba5427e1008231311d63e07c0 Michael Barton mail@michaelbarton.me.uk cea75c10de3fa8ad82e88196dcf2fd8a674b2ce8 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/284e95a4eccf4eaba722ab8d53f1296b0ead8007 284e95a4eccf4eaba722ab8d53f1296b0ead8007 2008-12-03T08:29:10-08:00 2008-12-03T08:29:10-08:00 Created script to plot gene cost densities 34fbef0895e9b3b4a084ea084517453232a23ee2 Michael Barton mail@michaelbarton.me.uk 1cc18d17d56d0d41d3acd0ccfa2c38470e2cbfaf Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/cea75c10de3fa8ad82e88196dcf2fd8a674b2ce8 cea75c10de3fa8ad82e88196dcf2fd8a674b2ce8 2008-12-03T07:05:37-08:00 2008-12-03T07:05:37-08:00 Created task to print average gene cost 518307d9d91ddac6918512fd3990716b1ead04cf Michael Barton mail@michaelbarton.me.uk b1dcdd2ce0469b4f7b2fdc6e0da3a218f553be3e Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/1cc18d17d56d0d41d3acd0ccfa2c38470e2cbfaf 1cc18d17d56d0d41d3acd0ccfa2c38470e2cbfaf 2008-12-03T06:59:28-08:00 2008-12-03T06:59:28-08:00 Created gene methods for total and average molecular weight 43864dc21db05a0e9affb69c09a6623f4b15e766 Michael Barton mail@michaelbarton.me.uk 0cf839bf87d9dd76f3a5c94a095b46ac9f2f6165 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/b1dcdd2ce0469b4f7b2fdc6e0da3a218f553be3e b1dcdd2ce0469b4f7b2fdc6e0da3a218f553be3e 2008-12-03T06:58:55-08:00 2008-12-03T06:58:55-08:00 Create gene specs for average and total molecular weight 27e5223347c364a943642be8d924f0713b18ee6c Michael Barton mail@michaelbarton.me.uk e7623fcc1e93359809a3d88281bb4b024713af38 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/0cf839bf87d9dd76f3a5c94a095b46ac9f2f6165 0cf839bf87d9dd76f3a5c94a095b46ac9f2f6165 2008-12-03T06:58:05-08:00 2008-12-03T06:58:05-08:00 Created gene factory 74ba68c1ee0e300051354ba2f4506265a8989705 Michael Barton mail@michaelbarton.me.uk e70d0a3ad494d7c8901f70ae71b2b4a1c9752bdd Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/e7623fcc1e93359809a3d88281bb4b024713af38 e7623fcc1e93359809a3d88281bb4b024713af38 2008-12-03T04:29:10-08:00 2008-12-03T04:29:10-08:00 Moved descriptions of average gene costs to average alignment costs fa50ced1270472d2b0b05905b6538931ba9fb616 Michael Barton mail@michaelbarton.me.uk 71101c3907ac2daa4ecee635241438c887dd9b93 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/e70d0a3ad494d7c8901f70ae71b2b4a1c9752bdd e70d0a3ad494d7c8901f70ae71b2b4a1c9752bdd 2008-12-03T04:11:36-08:00 2008-12-03T04:11:36-08:00 Moved plot flux sensitivity to plot directory d7dc251c1862e1dba56a6f8145944ea53a2dfe10 Michael Barton mail@michaelbarton.me.uk 7408c070cbed6f6563dcb43c9716149650d85054 028bd408042e46f87cbe4be8b5fb49cdf9c749bc Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/71101c3907ac2daa4ecee635241438c887dd9b93 71101c3907ac2daa4ecee635241438c887dd9b93 2008-12-03T04:09:53-08:00 2008-12-03T04:09:53-08:00 Merge branch 'master' into flux_analysis 3b0bd3ddc3d3d9aedab31be88333f812c28c4e20 Michael Barton mail@michaelbarton.me.uk dfe344afac4016bd7e862a445970ae6edeae69d9 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/028bd408042e46f87cbe4be8b5fb49cdf9c749bc 028bd408042e46f87cbe4be8b5fb49cdf9c749bc 2008-12-03T04:08:39-08:00 2008-12-03T04:08:39-08:00 R script to plot flux estimation vs gene cost ebc8e6e0bc58000a48aad4c7b2ef8364340bc7ca Michael Barton mail@michaelbarton.me.uk cd615a4b696f37ed53d9d470040c0c08c95c76b3 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/dfe344afac4016bd7e862a445970ae6edeae69d9 dfe344afac4016bd7e862a445970ae6edeae69d9 2008-12-03T03:58:31-08:00 2008-12-03T03:58:31-08:00 Updated rake method for plotting of flux sensitivity data bf218e930191d57cbb1e5ba39266080bdae428dd Michael Barton mail@michaelbarton.me.uk cd615a4b696f37ed53d9d470040c0c08c95c76b3 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/7408c070cbed6f6563dcb43c9716149650d85054 7408c070cbed6f6563dcb43c9716149650d85054 2008-10-21T03:44:28-07:00 2008-10-21T03:44:28-07:00 Created R script to plot distribution of flux sensitivities f210fee85bf4dcefaf0d2cd63901b15f96ce84af Michael Barton mail@michaelbarton.me.uk 1b3819b22c64e222a712e4bee883fbae78065159 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/cd615a4b696f37ed53d9d470040c0c08c95c76b3 cd615a4b696f37ed53d9d470040c0c08c95c76b3 2008-10-20T09:00:36-07:00 2008-10-20T09:00:36-07:00 Pretty-fication 2fdb38cbf09fa0d82710605607c68e050242dbd9 Michael Barton mail@michaelbarton.me.uk 65f694fb76b445668fa2e624da35d5a4d8ce16f4 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/1b3819b22c64e222a712e4bee883fbae78065159 1b3819b22c64e222a712e4bee883fbae78065159 2008-10-20T07:34:19-07:00 2008-10-20T07:34:19-07:00 Created task to print all flux sensitivity data 6f9565ac4864b127e67a11391ca57977e9fcc3fb Michael Barton mail@michaelbarton.me.uk e9822082b6a24b6ee4f097037c00a0e25eb27801 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/65f694fb76b445668fa2e624da35d5a4d8ce16f4 65f694fb76b445668fa2e624da35d5a4d8ce16f4 2008-10-20T07:33:42-07:00 2008-10-20T07:33:42-07:00 Updated flux sensitivity data loading so that nil value may created gene column 42bf86332ecb78f450b343fbaa3abf0f1a01958d Michael Barton mail@michaelbarton.me.uk be8afb13480dd02d901312654add2ce5d9181bac Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/e9822082b6a24b6ee4f097037c00a0e25eb27801 e9822082b6a24b6ee4f097037c00a0e25eb27801 2008-10-20T07:33:00-07:00 2008-10-20T07:33:00-07:00 Added dependency for flux sensitivity data loading 318eb572dfe2aa946e35a511e166883573aa85aa Michael Barton mail@michaelbarton.me.uk 166ef584d1eed1e6db58b2d7ee852ee8ea5a1e73 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/be8afb13480dd02d901312654add2ce5d9181bac be8afb13480dd02d901312654add2ce5d9181bac 2008-10-20T07:31:03-07:00 2008-10-20T07:31:03-07:00 Removed validation for gene_id to be present. May be nil if no corresponding verified ORF c011a5cc3c77b2fbd55af3a81d5242bbcc525884 Michael Barton mail@michaelbarton.me.uk ae47e4e0a66ba214a32ec6607132924b39e08a3f 1db148c092889192a55b4b0638a2bcd72e4bb1de Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/166ef584d1eed1e6db58b2d7ee852ee8ea5a1e73 166ef584d1eed1e6db58b2d7ee852ee8ea5a1e73 2008-10-16T08:33:20-07:00 2008-10-16T08:33:20-07:00 Merge branch 'flux' 9648c474053b30b2b4a0f2c4079ded15e30cb0b3 Michael Barton mail@michaelbarton.me.uk 19021252f9d55abe054cfe2724f83c831aa0d2bd Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/ae47e4e0a66ba214a32ec6607132924b39e08a3f ae47e4e0a66ba214a32ec6607132924b39e08a3f 2008-10-16T08:32:51-07:00 2008-10-16T08:32:51-07:00 Created r script to plot correlation between cost and rate, factored by tree length 4709425a98bb9b76f10bf4f0dd686af3c9c187ab Michael Barton mail@michaelbarton.me.uk 8c3b4bd9105ef8ecb754b3956c5ebd2715cbe302 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/19021252f9d55abe054cfe2724f83c831aa0d2bd 19021252f9d55abe054cfe2724f83c831aa0d2bd 2008-10-16T08:32:13-07:00 2008-10-16T08:32:13-07:00 Added r script to plot gene cost vs tree length 3b665905ad5064c06659fcad7bb2f68ee528dcc3 Michael Barton mail@michaelbarton.me.uk 88954c41ce4b1f9b45eb261ec8989ce0677021a4 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/8c3b4bd9105ef8ecb754b3956c5ebd2715cbe302 8c3b4bd9105ef8ecb754b3956c5ebd2715cbe302 2008-10-16T08:31:34-07:00 2008-10-16T08:31:34-07:00 Added r script to plot all sites vs rates 3175a62bba6f55ad3c50beeeb5785c7b2def3f54 Michael Barton mail@michaelbarton.me.uk e534eb1af798135d027f767c532035d2af7cf658 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/88954c41ce4b1f9b45eb261ec8989ce0677021a4 88954c41ce4b1f9b45eb261ec8989ce0677021a4 2008-10-16T06:44:02-07:00 2008-10-16T06:44:02-07:00 Ignore r result files 56b70065f647fabda446e8f1ea4da9e510b2cd4e Michael Barton mail@michaelbarton.me.uk ecdadf08e6c797b8ab48667619bf1dcbd03d4afa Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/e534eb1af798135d027f767c532035d2af7cf658 e534eb1af798135d027f767c532035d2af7cf658 2008-10-16T06:43:03-07:00 2008-10-16T06:43:03-07:00 Created task to print all site and cost rates f32361f2624605be46aa0d2bb71b790f812041df Michael Barton mail@michaelbarton.me.uk 9b1a0db42a0cbd3210e6144bd9385c7a7c86fb75 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/ecdadf08e6c797b8ab48667619bf1dcbd03d4afa ecdadf08e6c797b8ab48667619bf1dcbd03d4afa 2008-10-16T06:28:58-07:00 2008-10-16T06:28:58-07:00 Created rake task to print gene per-residue cost vs alignment tree length 04dc6c17949c66b6654b192309462a612291590b Michael Barton mail@michaelbarton.me.uk 44887c59df819baf154c1c632146f26ecdbb6ac0 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/1db148c092889192a55b4b0638a2bcd72e4bb1de 1db148c092889192a55b4b0638a2bcd72e4bb1de 2008-10-16T04:23:31-07:00 2008-10-16T04:23:31-07:00 Created rake task to plot gene cost vs gene flux sensitivity edd01fa2cace381395d90ed97081ee0c8034febd Michael Barton mail@michaelbarton.me.uk 3557489b002b715b3e767026fea936efa6a98496 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/44887c59df819baf154c1c632146f26ecdbb6ac0 44887c59df819baf154c1c632146f26ecdbb6ac0 2008-10-16T04:22:40-07:00 2008-10-16T04:22:40-07:00 Created rake tasks to drop and create flux sensitivities table c154426510258a562087048e756fde1a09b9e4a9 Michael Barton mail@michaelbarton.me.uk ce078745b67b22f048dc80c6f50eab875c02d68b Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/3557489b002b715b3e767026fea936efa6a98496 3557489b002b715b3e767026fea936efa6a98496 2008-10-16T04:13:42-07:00 2008-10-16T04:13:42-07:00 Added flux sensitivity data b22b0463959f837b03aeb20ca9e1fd76e60b7caa Michael Barton mail@michaelbarton.me.uk 840c5e593440983678427333d34149008056fdbc Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/ce078745b67b22f048dc80c6f50eab875c02d68b ce078745b67b22f048dc80c6f50eab875c02d68b 2008-10-16T04:13:05-07:00 2008-10-16T04:13:05-07:00 Added flux sensitivity association to gene class 7661e4670cc4954a3bd69a7f60bd71ad45612f33 Michael Barton mail@michaelbarton.me.uk e4aaba6985427d8ea8e87654ab381f61a99c233a Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/840c5e593440983678427333d34149008056fdbc 840c5e593440983678427333d34149008056fdbc 2008-10-16T04:12:24-07:00 2008-10-16T04:12:24-07:00 Created flux sensitivity model 88c5839f6801fae6de5826ff27bf31022ab10916 Michael Barton mail@michaelbarton.me.uk 9b1a0db42a0cbd3210e6144bd9385c7a7c86fb75 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/cost_in_evolution/commit/e4aaba6985427d8ea8e87654ab381f61a99c233a e4aaba6985427d8ea8e87654ab381f61a99c233a 2008-10-16T04:11:37-07:00 2008-10-16T04:11:37-07:00 Created migration to make flux_sensitivities table 825edca3773374dcc767d07a96ec52b73682d2a5 Michael Barton mail@michaelbarton.me.uk