d24cba1736eee9f5cdfe400eb16d83fba59d440f Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/organised_experiments/commit/824f1a043831fcce9fee8ea47c319c19020971a9 824f1a043831fcce9fee8ea47c319c19020971a9

2008-07-25T10:11:59-07:00

Updated analysis rake for new datamapper compatability. 3082169b898f6a2552a71281b998a64c4fbeca87 Michael Barton mail@michaelbarton.me.uk 47bfcfb397190e69caf3da26be03327edd4967e7 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/organised_experiments/commit/d24cba1736eee9f5cdfe400eb16d83fba59d440f d24cba1736eee9f5cdfe400eb16d83fba59d440f

2008-07-25T10:11:31-07:00

Updated gene model for new DataMapper compatability. 3f3f31caef00d69e96423b8f64bc1dd7b75b105d Michael Barton mail@michaelbarton.me.uk 226bbc7fc23e4fdd9b14f1a825c0365e8571126d Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/organised_experiments/commit/47bfcfb397190e69caf3da26be03327edd4967e7 47bfcfb397190e69caf3da26be03327edd4967e7

2008-07-25T10:10:52-07:00

Updated drop and create methods for new DataMapper API. Implemented hideous drop method, as DM removed drop_all_tables! a1e332904500e0367b7a09a669bb0cbb4f720e8b Michael Barton mail@michaelbarton.me.uk 935a9d015dc951ec3edf41aa62077d3babd72d21 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/organised_experiments/commit/226bbc7fc23e4fdd9b14f1a825c0365e8571126d 226bbc7fc23e4fdd9b14f1a825c0365e8571126d

2008-07-25T10:09:17-07:00

Added new (ridiculous!) gem requirements for datamapper. ee7448c0f5d0daf083a8be6d05fa00f7d59f2f37 Michael Barton mail@michaelbarton.me.uk 91c0f6c439126729fd16f8fe03adb5c21c212fd1 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/organised_experiments/commit/935a9d015dc951ec3edf41aa62077d3babd72d21 935a9d015dc951ec3edf41aa62077d3babd72d21

2008-07-25T10:07:55-07:00

Updated example database file for DataMapper compatability * Explicity uses symbols for keys in key-value pairs. * Datamapper complains otherwise. Looks for a gem by that name, if is a string istead of a symbol. 4f872b67137c078321d27028e3d05f41912e80fd Michael Barton mail@michaelbarton.me.uk 6d89cfde84619536f4aa745835a46a9b23289d8a Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/organised_experiments/commit/91c0f6c439126729fd16f8fe03adb5c21c212fd1 91c0f6c439126729fd16f8fe03adb5c21c212fd1

2008-05-27T06:41:35-07:00

Added Jan Aerts code for managing hard and soft dependencies between tasks. 001:sequence_stats and 001:length_histo now cause the database to be populated if there are no sequences in it. This is done via Jan's :check_load_sequence task. 8084172858dfbe88729597366a831e3b05946010 Michael Barton mail@michaelbarton.me.uk 39d182397126d31333f08d9a828a1af480927f39 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/organised_experiments/commit/6d89cfde84619536f4aa745835a46a9b23289d8a 6d89cfde84619536f4aa745835a46a9b23289d8a

2008-05-27T06:41:00-07:00

Fixed typo in gene property seqences => sequence 827168f8504aeb652764174e58446a94b44108cd Michael Barton mail@michaelbarton.me.uk 367043f5f7e9371c528b232f0c3bdd4d0cbe3939 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/organised_experiments/commit/39d182397126d31333f08d9a828a1af480927f39 39d182397126d31333f08d9a828a1af480927f39

2008-05-24T12:03:44-07:00

Removed notes file. Contains nothing relevent. 06d9cc256060893a53808d87dc0cbaa812a1f788 Michael Barton mail@michaelbarton.me.uk cf74f28a1a1eeec422eb8ad6b49880d787875401 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/organised_experiments/commit/367043f5f7e9371c528b232f0c3bdd4d0cbe3939 367043f5f7e9371c528b232f0c3bdd4d0cbe3939

2008-05-24T12:00:33-07:00

Updated gitignore to include sqlite3 databases, and database configuration files. 2dc3a99600bafaeb01830b1f813e6819d3dc5b40 Michael Barton mail@michaelbarton.me.uk 371a50b342d652da402a9fbfd9ad78acb4e417c8 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/organised_experiments/commit/cf74f28a1a1eeec422eb8ad6b49880d787875401 cf74f28a1a1eeec422eb8ad6b49880d787875401

2008-05-24T11:58:27-07:00

Added validation check to gene object creation 479e1d659f1a8f47e7d3c19106fd035188456053 Michael Barton mail@michaelbarton.me.uk 636d6f1abc175585988258e149989768552cc4f8 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/organised_experiments/commit/371a50b342d652da402a9fbfd9ad78acb4e417c8 371a50b342d652da402a9fbfd9ad78acb4e417c8

2008-05-24T11:57:51-07:00

Fixed sequence validation for gene model 737e305144a865389933270defd5541494994c30 Michael Barton mail@michaelbarton.me.uk ade4c9c3d3641e0f6690206893cb29dd0fa6d938 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/organised_experiments/commit/636d6f1abc175585988258e149989768552cc4f8 636d6f1abc175585988258e149989768552cc4f8

2008-05-24T11:56:49-07:00

Switch ActiveRecord find methods to DataMapper b91ca9fd724efc6662d15d6a5de788407e335658 Michael Barton mail@michaelbarton.me.uk 56079e6fd0174910d98cf6fe9c8090b5d729460a Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/organised_experiments/commit/ade4c9c3d3641e0f6690206893cb29dd0fa6d938 ade4c9c3d3641e0f6690206893cb29dd0fa6d938

2008-05-24T11:56:20-07:00

Added complete rebuild task to main Rakefile 10412c725e27d94ee874dcff7bd16797ffe621b7 Michael Barton mail@michaelbarton.me.uk 35980e619782f665591cc63bda60ea5022ae919d Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/organised_experiments/commit/56079e6fd0174910d98cf6fe9c8090b5d729460a 56079e6fd0174910d98cf6fe9c8090b5d729460a

2008-05-22T10:40:52-07:00

Added validation to gene model. 50214717fbcfc49671509791a178d4be2d8dc9a1 Michael Barton mail@michaelbarton.me.uk 2b3fd57b6d1795057022564cf3313f3e5e9cbc08 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/organised_experiments/commit/35980e619782f665591cc63bda60ea5022ae919d 35980e619782f665591cc63bda60ea5022ae919d

2008-05-09T10:12:21-07:00

Removed active record migration. Updated gene model with DataMapper properties. 530f33a9588b4bb985a43d1c7262c468d26b7cb7 Michael Barton mail@michaelbarton.me.uk 9e5354f74fe712e0aa749eef8bfdd400781bff5d Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/organised_experiments/commit/2b3fd57b6d1795057022564cf3313f3e5e9cbc08 2b3fd57b6d1795057022564cf3313f3e5e9cbc08

2008-05-09T10:10:34-07:00

Removed database configuration file. Created example file instead. df6bc7b58331096cec49c63485705306cc229f84 Michael Barton mail@michaelbarton.me.uk 289fa58968d83d8ef1a0bcc173159094e969f8a1 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/organised_experiments/commit/9e5354f74fe712e0aa749eef8bfdd400781bff5d 9e5354f74fe712e0aa749eef8bfdd400781bff5d

2008-05-09T10:09:05-07:00

Added DataMapper migrate tasks to Rakefile d1714225b28e7f3af96aee0f981e4f4f423dac4c Michael Barton mail@michaelbarton.me.uk 704047794755412c236a54fe32fbe7b07a646130 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/organised_experiments/commit/289fa58968d83d8ef1a0bcc173159094e969f8a1 289fa58968d83d8ef1a0bcc173159094e969f8a1

2008-05-09T10:08:39-07:00

Created environment config file. Switched to DataMapper instead of ActiveRecord Models loaded in config file Rake tasks still loaded in main Rakefile Changed gem from active_record to data_mapper Changed database loading to Datamapper 432ea5da042a688d26fd88d9468dc1400d668735 Michael Barton mail@michaelbarton.me.uk 27e8728bf4766115a3fb0e6ec9533fa90780492f Michael Barton mail@bioinformaticszen.com http://github.com/michaelbarton/organised_experiments/commit/704047794755412c236a54fe32fbe7b07a646130 704047794755412c236a54fe32fbe7b07a646130

2008-04-26T13:07:09-07:00

Added task to plot histogram of binned result data 8d102dddcd5689e8a808cba62d6bdb7acd82fac9 Michael Barton mail@bioinformaticszen.com 654f540e94983d70bd4518922258e72066b4b6df Michael Barton mail@bioinformaticszen.com http://github.com/michaelbarton/organised_experiments/commit/27e8728bf4766115a3fb0e6ec9533fa90780492f 27e8728bf4766115a3fb0e6ec9533fa90780492f

2008-04-26T12:17:10-07:00

Added method to bin gene length into frequency table 4452b2e367b4383f4c8145e47542fc5f53b43ebd Michael Barton mail@bioinformaticszen.com aa26304841bc823353309374bd82ca8eb564904a Michael Barton mail@bioinformaticszen.com http://github.com/michaelbarton/organised_experiments/commit/654f540e94983d70bd4518922258e72066b4b6df 654f540e94983d70bd4518922258e72066b4b6df

2008-04-26T11:07:02-07:00

Updated taks dependency for statistics for analysis 001 rebuild 8521decd8ac6871e5df9140cf843db890144068a Michael Barton mail@bioinformaticszen.com fb206a39bf9de48b32cdd8ed640a06b433eab790 Michael Barton mail@bioinformaticszen.com http://github.com/michaelbarton/organised_experiments/commit/aa26304841bc823353309374bd82ca8eb564904a aa26304841bc823353309374bd82ca8eb564904a

2008-04-26T11:05:52-07:00

Added gitignore to not included results in version control fa8a514098502f5cb34bd3f6018648848c60c36b Michael Barton mail@bioinformaticszen.com 33978c3af6c1e08c7f0720b33da2dc23a9a383dc Michael Barton mail@bioinformaticszen.com http://github.com/michaelbarton/organised_experiments/commit/fb206a39bf9de48b32cdd8ed640a06b433eab790 fb206a39bf9de48b32cdd8ed640a06b433eab790

2008-04-26T11:04:18-07:00

Updated project notes 28c0c33a61b86b773edd2156eb92b90e41d4a3c9 Michael Barton mail@bioinformaticszen.com 7b241b15a53e7e17d4d4a1e4cef881046d2772a9 Michael Barton mail@bioinformaticszen.com http://github.com/michaelbarton/organised_experiments/commit/33978c3af6c1e08c7f0720b33da2dc23a9a383dc 33978c3af6c1e08c7f0720b33da2dc23a9a383dc

2008-04-26T11:04:05-07:00

Added new statistics task 4d41060cc6d04e480e63a5e04e945fba368c717e Michael Barton mail@bioinformaticszen.com 6d4f67f50ba37507787a97f1132417fbef539775 Michael Barton mail@bioinformaticszen.com http://github.com/michaelbarton/organised_experiments/commit/7b241b15a53e7e17d4d4a1e4cef881046d2772a9 7b241b15a53e7e17d4d4a1e4cef881046d2772a9

2008-04-26T11:03:13-07:00

Added mean and standard deviation methods for Gene class 1bfcf9980f270e5226b34d8fecc2d9d204a9f55e Michael Barton mail@bioinformaticszen.com e3a3139394707b6219c700f24535f5b619756fe9 Michael Barton mail@bioinformaticszen.com http://github.com/michaelbarton/organised_experiments/commit/6d4f67f50ba37507787a97f1132417fbef539775 6d4f67f50ba37507787a97f1132417fbef539775

2008-04-26T10:19:41-07:00

Removed activerecord logger 1d3bc16a23dac6c5bd29015709601d675e1bfa41 Michael Barton mail@bioinformaticszen.com c2894583706f7806a1e7eb4d683bd085e3e0ff1c Michael Barton mail@bioinformaticszen.com http://github.com/michaelbarton/organised_experiments/commit/e3a3139394707b6219c700f24535f5b619756fe9 e3a3139394707b6219c700f24535f5b619756fe9

2008-04-26T10:16:13-07:00

Created method to load data into database from Bio::FlatFile entry. 7736a2eb459244b14e4da2e38de618237780891c Michael Barton mail@bioinformaticszen.com 41872022a1c0763d0e811fbd188659807e618bb1 Michael Barton mail@bioinformaticszen.com http://github.com/michaelbarton/organised_experiments/commit/c2894583706f7806a1e7eb4d683bd085e3e0ff1c c2894583706f7806a1e7eb4d683bd085e3e0ff1c

2008-04-26T09:38:55-07:00

Fixed typo in first analysis rake file. b24f4723a3791c1d95d5961c7b2169d9eeacbc42 Michael Barton mail@bioinformaticszen.com a80054f72c43222a09a0329ceecf5ababa3d2afd Michael Barton mail@bioinformaticszen.com http://github.com/michaelbarton/organised_experiments/commit/41872022a1c0763d0e811fbd188659807e618bb1 41872022a1c0763d0e811fbd188659807e618bb1

2008-04-26T09:38:19-07:00

Reorganised Rake file. Removed environment task, as is required everytime a task is run 4f59901169010a18ea4bed75991bc3ee6af3114d Michael Barton mail@bioinformaticszen.com e8ef55948f767629d8ed618d2ebca5e202059b8a Michael Barton mail@bioinformaticszen.com http://github.com/michaelbarton/organised_experiments/commit/a80054f72c43222a09a0329ceecf5ababa3d2afd a80054f72c43222a09a0329ceecf5ababa3d2afd

2008-04-26T09:29:22-07:00

Created database loading and deleting tasks 32049bda608fa1ef44abaaaade42884619059dba Michael Barton mail@bioinformaticszen.com