Timeline
Sep 9, 2010:
- 3:19 PM Changeset [234] by
- Updated TODO to reflect proper architecture for efficient cataloging, …
- 3:19 PM Changeset [233] by
- Added indexing by path and max_score
- 3:18 PM Changeset [232] by
- Commented out catalog search for proteins, to be implemented later
- 3:18 PM Changeset [231] by
- Don't track minimal dataset
- 3:18 PM Changeset [230] by
- Don't track anything in db
Sep 8, 2010:
- 5:08 PM Changeset [229] by
- Indexing maximum score of each peptide in a catalog
- 5:07 PM Changeset [228] by
- Added zeo.conf to use zeo with the application
- 5:07 PM Changeset [227] by
- Updated dependencies in order to use ZEO
- 5:07 PM Changeset [226] by
- Cosmetic changes
- 3:19 PM Changeset [225] by
- TODO revamped
- 3:18 PM Changeset [224] by
- Added score filter form to experiment template
- 3:18 PM Changeset [223] by
- Fixed protein batch
- 3:18 PM Changeset [222] by
- Removed awful function to filter proteins by maximum score and instead …
- 3:17 PM Changeset [221] by
- Assign maximum protein score to the object instead of returning
- 3:17 PM Changeset [220] by
- Included max_score in Peptide instantiation
- 3:17 PM Changeset [219] by
- Added function to protein model to get the maximum score of all the …
- 3:17 PM Changeset [218] by
- Quick and dirty filtering of proteins by maximum score of its petides
- 3:16 PM Changeset [217] by
- Better arrangment of imports for views
- 3:16 PM Changeset [216] by
- Experiment view filters by maximum score of all the peptides …
Sep 7, 2010:
- 3:51 PM Changeset [215] by
- Removed completed tasks from TODO
- 3:50 PM Changeset [214] by
- Updated protein template to show protein ratios
- 3:50 PM Changeset [213] by
- Better rounding of numbers for PSM data
- 3:50 PM Changeset [212] by
- Added update method for protein ratios, update of psm ratios done …
- 3:49 PM Changeset [211] by
- TODO updated
- 3:49 PM Changeset [210] by
- Added calculation of quant ratios at for psms, updated template to …
- 3:49 PM Changeset [209] by
- Parsing XIC integration for MsQuant?
- 3:48 PM Changeset [208] by
- TODO updated
Sep 6, 2010:
- 5:15 PM Changeset [207] by
- Added a line to show the PSM scan in the XICs
- 5:15 PM Changeset [206] by
- Removed few tasks from TODO
- 5:14 PM Changeset [205] by
- Added drawing of scans taken for quantitation in psm template
- 5:14 PM Changeset [204] by
- Added method to PSM to check whether it was quantified, updated …
- 5:14 PM Changeset [203] by
- Added method to peptide to check if it has any peptides quantified, …
- 5:13 PM Changeset [202] by
- Fixed points and lines for XIC and spectrum plots
Sep 2, 2010:
- 5:30 PM Changeset [201] by
- More tasks after naive XIC drawing
- 5:30 PM Changeset [200] by
- Added canvas plotting of XIC
- 5:30 PM Changeset [199] by
- JSON coordinates for XIC plotting accessible from psm view
- 5:29 PM Changeset [198] by
- Minor cosmetic changes
- 5:29 PM Changeset [197] by
- TODO updated: more granular tasks for quantitation
- 5:29 PM Changeset [196] by
- Added function to find out psm id by spectrum id and completed MsQuant? …
- 5:28 PM Changeset [195] by
- Fixed bug that was assigning psm_refs to spectra wrongly
- 5:28 PM Changeset [194] by
- Added psm references to spectrum and updated mascot parser
- 5:28 PM Changeset [193] by
- Added repoze.catalog to distribute dependencies
- 5:28 PM Changeset [192] by
- Added MsQuant? parser to appmaker
- 5:27 PM Changeset [191] by
- Itergroup like parsing iterator for MsQuant? parser. It alternates …
- 5:27 PM Changeset [190] by
- Deleted sequence parsing for MsQuant? output (not possible to parse …
- 5:27 PM Changeset [189] by
- Explained modification position issue with MsQuant? output in TODO.
- 5:27 PM Changeset [188] by
- Obtaining spec id from msquant files
- 5:26 PM Changeset [187] by
- Parsing msquant psm data
- 5:26 PM Changeset [186] by
- Added dummy msquant module to parse msquant output, added the msquant …
- 5:26 PM Changeset [185] by
- Removed brackets from the formatted peptide sequence
- 5:25 PM Changeset [184] by
- Deleted unnecessary folders variable in appmaker
- 5:25 PM Changeset [183] by
- TODO updated
- 5:25 PM Changeset [182] by
- Readable URLs for psms and peptide models
- 5:25 PM Changeset [181] by
- Updated templates to show MME
- 5:24 PM Changeset [180] by
- Calculate MME for all Psms
- 5:24 PM Changeset [179] by
- Renamed functions to update proteins and peptides
- 5:24 PM Changeset [178] by
- TODO updated
Aug 30, 2010:
- 3:44 PM Changeset [177] by
- 1 px width for peaks in spectrum graph
- 3:44 PM Changeset [176] by
- Better xs limits for spectrum graph
- 3:43 PM Changeset [175] by
- Added flot.js resource and drawing the spectra from psm view
- 3:43 PM Changeset [174] by
- Proper JSON output of MS/MS peaks for PSM view
- 3:43 PM Changeset [173] by
- Added psm view with its template and link from peptide view
- 3:42 PM Changeset [172] by
- TODO updated
Aug 26, 2010:
- 5:23 PM Changeset [171] by
- Parsing MS/MS peaks
- 5:23 PM Changeset [170] by
- TODO updated
- 5:23 PM Changeset [169] by
- Added peptide template
- 5:22 PM Changeset [168] by
- Added psm view, template and links from peptive view
- 5:22 PM Changeset [167] by
- Renamed views like Python functions
- 5:22 PM Changeset [166] by
- Added link to home to the master template
- 5:21 PM Changeset [165] by
- TODO updated
- 5:21 PM Changeset [164] by
- Added protein sequence formatting and updated protein template to show …
- 5:21 PM Changeset [163] by
- Updated protein template to show number of PSMs and score
- 5:21 PM Changeset [162] by
- Added method to update the maximum score of the psms of a peptide
- 5:20 PM Changeset [161] by
- TODO updated
Aug 25, 2010:
- 4:48 PM Changeset [160] by
- Coverage is stored as a protein attribute, added sorting by coverage too
- 4:47 PM Changeset [159] by
- Added naked_seq attribute constructor to peptide and sequence coverage …
- 2:37 PM Changeset [158] by
- TODO updated
- 2:37 PM Changeset [157] by
- Storing psms and peptide counts as attributes of peptides and proteins …
- 2:36 PM Changeset [156] by
- TODO updated
- 2:36 PM Changeset [155] by
- Fixed bug that was skipping first 100 proteins in sorting
- 2:36 PM Changeset [154] by
- Fixed batch size issue
- 2:36 PM Changeset [153] by
- Fixed sorting by psms in ajax loader
- 2:35 PM Changeset [152] by
- Simplified experiment view
- 2:35 PM Changeset [151] by
- Cleaned up endless scrolling for protein batch, now the batch is …
- 2:35 PM Changeset [150] by
- Protein template now using master template
- 2:34 PM Changeset [149] by
- Extracted master template from experiment template, now the experiment …
- 2:34 PM Changeset [148] by
- Fixed sort by PSM link
- 2:34 PM Changeset [147] by
- TODO updated
- 2:33 PM Changeset [146] by
- TODO updated
Aug 24, 2010:
- 6:21 PM Changeset [145] by
- TODO updated
- 6:20 PM Changeset [144] by
- Added link for sorting by psms or peptides to the experiment template
- 5:40 PM Changeset [143] by
- Added sorting by psms per protein as a subpath of experiment view
- 5:40 PM Changeset [142] by
- Added app_view, redirect to experiment (necessary to handle subpath …
- 4:55 PM Changeset [141] by
- Added method to protein model for number of psms per protein, also …
- 4:55 PM Changeset [140] by
- Added psm_refs to peptide and updated the parser
- 4:54 PM Changeset [139] by
- TODO updated
- 4:54 PM Changeset [138] by
- Added SWISS-PROT links to proteins in experiment view
- 4:54 PM Changeset [137] by
- Added Gene entrez links to batch view
- 4:53 PM Changeset [136] by
- Sorting proteins in experiment by number of peptides
- 4:53 PM Changeset [135] by
- Added the number of peptides for each protein to the experiment view
- 4:53 PM Changeset [134] by
- Added protein method to get the number of peptide references. Added …
- 4:52 PM Changeset [133] by
- Added external links to Gene Entrez
- 4:52 PM Changeset [132] by
- TODO updated
- 4:52 PM Changeset [131] by
- Pick first Gene Symbol when multiple ids
- 4:51 PM Changeset [130] by
- Updated experiment view with SWISS-PROT ID, fixed template when there …
- 4:51 PM Changeset [129] by
- Updated models and templates to display ext_ids, Gene symbol as example
- 4:51 PM Changeset [128] by
- Parsing description of proteins and external databases ids properly
- 4:50 PM Changeset [127] by
- Added home link to protein view
- 4:50 PM Changeset [126] by
- Updated TODO
- 4:50 PM Changeset [125] by
- Adjusted endless scroll parameters for smoother
- 4:50 PM Changeset [124] by
- Updated TODO
- 4:49 PM Changeset [123] by
- Comment to not forget some tests
- 4:49 PM Changeset [122] by
- Batch loader now loads next 100 proteins
- 4:49 PM Changeset [121] by
- Batch view loads the next 100 proteins, hardcoded
- 4:48 PM Changeset [120] by
- tal expression for batch_view lodader
- 4:48 PM Changeset [119] by
- Test Ajax call upon reaching the bottom of the page
- 4:48 PM Changeset [118] by
- Updated TODO
- 4:47 PM Changeset [117] by
- Updated experiment template and css to show protein description
- 4:47 PM Changeset [116] by
- Parsing description of proteins
- 4:47 PM Changeset [115] by
- Added extra attributes to protein model
- 4:47 PM Changeset [114] by
- Updated TODO
- 4:46 PM Changeset [113] by
- Printing modification symbols before Aa in peptides
- 4:46 PM Changeset [112] by
- Using the mascot_ptm to user ptm map while parsing
- 4:46 PM Changeset [111] by
- Added map for mascot ptms to user desired terms
- 4:45 PM Changeset [110] by
- Added sequence formatting method to peptide model. It's the human …
- 4:45 PM Changeset [109] by
- Deactivated template debugger (start up too slow)
- 4:45 PM Changeset [108] by
- Updated TODO.
Aug 18, 2010:
- 5:29 PM Changeset [107] by
- Added real links to proteins in experiment view
- 5:29 PM Changeset [106] by
- Added test view for protein
- 5:28 PM Changeset [105] by
- Updated Experiment view with dummy links
- 5:28 PM Changeset [104] by
- Updated TODO
- 5:28 PM Changeset [103] by
- Experiment view showing protein ids only. Deleted old apply_mods function
- 5:27 PM Changeset [102] by
- Added function to apply modifications to a peptide sequence from …
- 5:27 PM Changeset [101] by
- Added parsing for Mascot masses
- 5:27 PM Changeset [100] by
- Updated TODO
Aug 17, 2010:
- 5:11 PM Changeset [99] by
- Parsing SER paramaters and adding them to each PSM
- 5:11 PM Changeset [98] by
- Updated TODO
- 5:11 PM Changeset [97] by
- Fixed stripping bug, added parsing of fragmentation type
- 5:11 PM Changeset [96] by
- Parsing quantitation mode
- 5:10 PM Changeset [95] by
- Deleted charges parameter
- 5:10 PM Changeset [94] by
- Parsing peak list file name from dat file
- 5:10 PM Changeset [93] by
- Parses enzyme type
- 5:09 PM Changeset [92] by
- Parsed Fasta database name
- 5:09 PM Changeset [91] by
- Merged parsing parameters method in 1 method
- 5:09 PM Changeset [90] by
- Added reference to SER parameter for every PSM
- 5:08 PM Changeset [89] by
- Rearranged priorities
Aug 16, 2010:
- 5:28 PM Changeset [88] by
- Better formatting for experiment template
- 5:27 PM Changeset [87] by
- Added parse method for fragment tolerance
- 5:27 PM Changeset [86] by
- Deleted unnecessary TODO
- 5:27 PM Changeset [85] by
- Cosmetic changes to parsers module
- 5:27 PM Changeset [84] by
- Added TODO for parsers module
- 5:26 PM Changeset [83] by
- Added parser for precursor tolerance
- 5:26 PM Changeset [82] by
- Docstring for Experiment model
- 5:26 PM Changeset [81] by
- Added SerParameters? model
- 5:25 PM Changeset [80] by
- Fixed attribute assignment in Ptms
- 5:25 PM Changeset [79] by
- Added Ptm model
- 5:25 PM Changeset [78] by
- Updated TODO
- 12:58 PM Changeset [77] by
- Added test function for jQuery endless scrolling. Didn't work with …
- 12:56 PM Changeset [76] by
- Tried to implement endless scrolling, not working
Aug 13, 2010:
- 1:45 PM Changeset [75] by
- Dummy view for proteins
- 1:45 PM Changeset [74] by
- Activated template debugger
- 1:45 PM Changeset [73] by
- Updated setup.py for new document file extension
- 1:45 PM Changeset [72] by
- Added table to master template
- 9:57 AM Changeset [71] by
- Updated TODO with hints about parsing dat files directly to the database
Aug 12, 2010:
- 5:21 PM Changeset [70] by
- Updated TODO
- 4:47 PM Changeset [69] by
- Merged from traunk because repository couldn't be pushed
- 2:28 PM Changeset [68] by
- This is a test commit without authentication
- 12:08 PM Changeset [67] by
- Replaced messy fasta parser with a much better implementation
- 11:36 AM Changeset [66] by
- Renamed the .txt files to .rst
- 11:36 AM Changeset [65] by
- Converted TODO to proper reST fromat
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