Timeline


and

Sep 9, 2010:

3:19 PM Changeset [234] by j@…
Updated TODO to reflect proper architecture for efficient cataloging, …
3:19 PM Changeset [233] by j@…
Added indexing by path and max_score
3:18 PM Changeset [232] by j@…
Commented out catalog search for proteins, to be implemented later
3:18 PM Changeset [231] by j@…
Don't track minimal dataset
3:18 PM Changeset [230] by j@…
Don't track anything in db

Sep 8, 2010:

5:08 PM Changeset [229] by j@…
Indexing maximum score of each peptide in a catalog
5:07 PM Changeset [228] by j@…
Added zeo.conf to use zeo with the application
5:07 PM Changeset [227] by j@…
Updated dependencies in order to use ZEO
5:07 PM Changeset [226] by j@…
Cosmetic changes
3:19 PM Changeset [225] by j@…
TODO revamped
3:18 PM Changeset [224] by j@…
Added score filter form to experiment template
3:18 PM Changeset [223] by j@…
Fixed protein batch
3:18 PM Changeset [222] by j@…
Removed awful function to filter proteins by maximum score and instead …
3:17 PM Changeset [221] by j@…
Assign maximum protein score to the object instead of returning
3:17 PM Changeset [220] by j@…
Included max_score in Peptide instantiation
3:17 PM Changeset [219] by j@…
Added function to protein model to get the maximum score of all the …
3:17 PM Changeset [218] by j@…
Quick and dirty filtering of proteins by maximum score of its petides
3:16 PM Changeset [217] by j@…
Better arrangment of imports for views
3:16 PM Changeset [216] by j@…
Experiment view filters by maximum score of all the peptides …

Sep 7, 2010:

3:51 PM Changeset [215] by j@…
Removed completed tasks from TODO
3:50 PM Changeset [214] by j@…
Updated protein template to show protein ratios
3:50 PM Changeset [213] by j@…
Better rounding of numbers for PSM data
3:50 PM Changeset [212] by j@…
Added update method for protein ratios, update of psm ratios done …
3:49 PM Changeset [211] by j@…
TODO updated
3:49 PM Changeset [210] by j@…
Added calculation of quant ratios at for psms, updated template to …
3:49 PM Changeset [209] by j@…
Parsing XIC integration for MsQuant?
3:48 PM Changeset [208] by j@…
TODO updated

Sep 6, 2010:

5:15 PM Changeset [207] by j@…
Added a line to show the PSM scan in the XICs
5:15 PM Changeset [206] by j@…
Removed few tasks from TODO
5:14 PM Changeset [205] by j@…
Added drawing of scans taken for quantitation in psm template
5:14 PM Changeset [204] by j@…
Added method to PSM to check whether it was quantified, updated …
5:14 PM Changeset [203] by j@…
Added method to peptide to check if it has any peptides quantified, …
5:13 PM Changeset [202] by j@…
Fixed points and lines for XIC and spectrum plots

Sep 2, 2010:

5:30 PM Changeset [201] by j@…
More tasks after naive XIC drawing
5:30 PM Changeset [200] by j@…
Added canvas plotting of XIC
5:30 PM Changeset [199] by j@…
JSON coordinates for XIC plotting accessible from psm view
5:29 PM Changeset [198] by j@…
Minor cosmetic changes
5:29 PM Changeset [197] by j@…
TODO updated: more granular tasks for quantitation
5:29 PM Changeset [196] by j@…
Added function to find out psm id by spectrum id and completed MsQuant?
5:28 PM Changeset [195] by j@…
Fixed bug that was assigning psm_refs to spectra wrongly
5:28 PM Changeset [194] by j@…
Added psm references to spectrum and updated mascot parser
5:28 PM Changeset [193] by j@…
Added repoze.catalog to distribute dependencies
5:28 PM Changeset [192] by j@…
Added MsQuant? parser to appmaker
5:27 PM Changeset [191] by j@…
Itergroup like parsing iterator for MsQuant? parser. It alternates …
5:27 PM Changeset [190] by j@…
Deleted sequence parsing for MsQuant? output (not possible to parse …
5:27 PM Changeset [189] by j@…
Explained modification position issue with MsQuant? output in TODO.
5:27 PM Changeset [188] by j@…
Obtaining spec id from msquant files
5:26 PM Changeset [187] by j@…
Parsing msquant psm data
5:26 PM Changeset [186] by j@…
Added dummy msquant module to parse msquant output, added the msquant …
5:26 PM Changeset [185] by j@…
Removed brackets from the formatted peptide sequence
5:25 PM Changeset [184] by j@…
Deleted unnecessary folders variable in appmaker
5:25 PM Changeset [183] by j@…
TODO updated
5:25 PM Changeset [182] by j@…
Readable URLs for psms and peptide models
5:25 PM Changeset [181] by j@…
Updated templates to show MME
5:24 PM Changeset [180] by j@…
Calculate MME for all Psms
5:24 PM Changeset [179] by j@…
Renamed functions to update proteins and peptides
5:24 PM Changeset [178] by j@…
TODO updated

Aug 30, 2010:

3:44 PM Changeset [177] by j@…
1 px width for peaks in spectrum graph
3:44 PM Changeset [176] by j@…
Better xs limits for spectrum graph
3:43 PM Changeset [175] by j@…
Added flot.js resource and drawing the spectra from psm view
3:43 PM Changeset [174] by j@…
Proper JSON output of MS/MS peaks for PSM view
3:43 PM Changeset [173] by j@…
Added psm view with its template and link from peptide view
3:42 PM Changeset [172] by j@…
TODO updated

Aug 26, 2010:

5:23 PM Changeset [171] by j@…
Parsing MS/MS peaks
5:23 PM Changeset [170] by j@…
TODO updated
5:23 PM Changeset [169] by j@…
Added peptide template
5:22 PM Changeset [168] by j@…
Added psm view, template and links from peptive view
5:22 PM Changeset [167] by j@…
Renamed views like Python functions
5:22 PM Changeset [166] by j@…
Added link to home to the master template
5:21 PM Changeset [165] by j@…
TODO updated
5:21 PM Changeset [164] by j@…
Added protein sequence formatting and updated protein template to show …
5:21 PM Changeset [163] by j@…
Updated protein template to show number of PSMs and score
5:21 PM Changeset [162] by j@…
Added method to update the maximum score of the psms of a peptide
5:20 PM Changeset [161] by j@…
TODO updated

Aug 25, 2010:

4:48 PM Changeset [160] by j@…
Coverage is stored as a protein attribute, added sorting by coverage too
4:47 PM Changeset [159] by j@…
Added naked_seq attribute constructor to peptide and sequence coverage …
2:37 PM Changeset [158] by j@…
TODO updated
2:37 PM Changeset [157] by j@…
Storing psms and peptide counts as attributes of peptides and proteins …
2:36 PM Changeset [156] by j@…
TODO updated
2:36 PM Changeset [155] by j@…
Fixed bug that was skipping first 100 proteins in sorting
2:36 PM Changeset [154] by j@…
Fixed batch size issue
2:36 PM Changeset [153] by j@…
Fixed sorting by psms in ajax loader
2:35 PM Changeset [152] by j@…
Simplified experiment view
2:35 PM Changeset [151] by j@…
Cleaned up endless scrolling for protein batch, now the batch is …
2:35 PM Changeset [150] by j@…
Protein template now using master template
2:34 PM Changeset [149] by j@…
Extracted master template from experiment template, now the experiment …
2:34 PM Changeset [148] by j@…
Fixed sort by PSM link
2:34 PM Changeset [147] by j@…
TODO updated
2:33 PM Changeset [146] by j@…
TODO updated

Aug 24, 2010:

6:21 PM Changeset [145] by j@…
TODO updated
6:20 PM Changeset [144] by j@…
Added link for sorting by psms or peptides to the experiment template
5:40 PM Changeset [143] by j@…
Added sorting by psms per protein as a subpath of experiment view
5:40 PM Changeset [142] by j@…
Added app_view, redirect to experiment (necessary to handle subpath …
4:55 PM Changeset [141] by j@…
Added method to protein model for number of psms per protein, also …
4:55 PM Changeset [140] by j@…
Added psm_refs to peptide and updated the parser
4:54 PM Changeset [139] by j@…
TODO updated
4:54 PM Changeset [138] by j@…
Added SWISS-PROT links to proteins in experiment view
4:54 PM Changeset [137] by j@…
Added Gene entrez links to batch view
4:53 PM Changeset [136] by j@…
Sorting proteins in experiment by number of peptides
4:53 PM Changeset [135] by j@…
Added the number of peptides for each protein to the experiment view
4:53 PM Changeset [134] by j@…
Added protein method to get the number of peptide references. Added …
4:52 PM Changeset [133] by j@…
Added external links to Gene Entrez
4:52 PM Changeset [132] by j@…
TODO updated
4:52 PM Changeset [131] by j@…
Pick first Gene Symbol when multiple ids
4:51 PM Changeset [130] by j@…
Updated experiment view with SWISS-PROT ID, fixed template when there …
4:51 PM Changeset [129] by j@…
Updated models and templates to display ext_ids, Gene symbol as example
4:51 PM Changeset [128] by j@…
Parsing description of proteins and external databases ids properly
4:50 PM Changeset [127] by j@…
Added home link to protein view
4:50 PM Changeset [126] by j@…
Updated TODO
4:50 PM Changeset [125] by j@…
Adjusted endless scroll parameters for smoother
4:50 PM Changeset [124] by j@…
Updated TODO
4:49 PM Changeset [123] by j@…
Comment to not forget some tests
4:49 PM Changeset [122] by j@…
Batch loader now loads next 100 proteins
4:49 PM Changeset [121] by j@…
Batch view loads the next 100 proteins, hardcoded
4:48 PM Changeset [120] by j@…
tal expression for batch_view lodader
4:48 PM Changeset [119] by j@…
Test Ajax call upon reaching the bottom of the page
4:48 PM Changeset [118] by j@…
Updated TODO
4:47 PM Changeset [117] by j@…
Updated experiment template and css to show protein description
4:47 PM Changeset [116] by j@…
Parsing description of proteins
4:47 PM Changeset [115] by j@…
Added extra attributes to protein model
4:47 PM Changeset [114] by j@…
Updated TODO
4:46 PM Changeset [113] by j@…
Printing modification symbols before Aa in peptides
4:46 PM Changeset [112] by j@…
Using the mascot_ptm to user ptm map while parsing
4:46 PM Changeset [111] by j@…
Added map for mascot ptms to user desired terms
4:45 PM Changeset [110] by j@…
Added sequence formatting method to peptide model. It's the human …
4:45 PM Changeset [109] by j@…
Deactivated template debugger (start up too slow)
4:45 PM Changeset [108] by j@…
Updated TODO.

Aug 18, 2010:

5:29 PM Changeset [107] by j@…
Added real links to proteins in experiment view
5:29 PM Changeset [106] by j@…
Added test view for protein
5:28 PM Changeset [105] by j@…
Updated Experiment view with dummy links
5:28 PM Changeset [104] by j@…
Updated TODO
5:28 PM Changeset [103] by j@…
Experiment view showing protein ids only. Deleted old apply_mods function
5:27 PM Changeset [102] by j@…
Added function to apply modifications to a peptide sequence from …
5:27 PM Changeset [101] by j@…
Added parsing for Mascot masses
5:27 PM Changeset [100] by j@…
Updated TODO

Aug 17, 2010:

5:11 PM Changeset [99] by j@…
Parsing SER paramaters and adding them to each PSM
5:11 PM Changeset [98] by j@…
Updated TODO
5:11 PM Changeset [97] by j@…
Fixed stripping bug, added parsing of fragmentation type
5:11 PM Changeset [96] by j@…
Parsing quantitation mode
5:10 PM Changeset [95] by j@…
Deleted charges parameter
5:10 PM Changeset [94] by j@…
Parsing peak list file name from dat file
5:10 PM Changeset [93] by j@…
Parses enzyme type
5:09 PM Changeset [92] by j@…
Parsed Fasta database name
5:09 PM Changeset [91] by j@…
Merged parsing parameters method in 1 method
5:09 PM Changeset [90] by j@…
Added reference to SER parameter for every PSM
5:08 PM Changeset [89] by j@…
Rearranged priorities

Aug 16, 2010:

5:28 PM Changeset [88] by j@…
Better formatting for experiment template
5:27 PM Changeset [87] by j@…
Added parse method for fragment tolerance
5:27 PM Changeset [86] by j@…
Deleted unnecessary TODO
5:27 PM Changeset [85] by j@…
Cosmetic changes to parsers module
5:27 PM Changeset [84] by j@…
Added TODO for parsers module
5:26 PM Changeset [83] by j@…
Added parser for precursor tolerance
5:26 PM Changeset [82] by j@…
Docstring for Experiment model
5:26 PM Changeset [81] by j@…
Added SerParameters? model
5:25 PM Changeset [80] by j@…
Fixed attribute assignment in Ptms
5:25 PM Changeset [79] by j@…
Added Ptm model
5:25 PM Changeset [78] by j@…
Updated TODO
12:58 PM Changeset [77] by j@…
Added test function for jQuery endless scrolling. Didn't work with …
12:56 PM Changeset [76] by j@…
Tried to implement endless scrolling, not working

Aug 13, 2010:

1:45 PM Changeset [75] by j@…
Dummy view for proteins
1:45 PM Changeset [74] by j@…
Activated template debugger
1:45 PM Changeset [73] by j@…
Updated setup.py for new document file extension
1:45 PM Changeset [72] by j@…
Added table to master template
9:57 AM Changeset [71] by j@…
Updated TODO with hints about parsing dat files directly to the database

Aug 12, 2010:

5:21 PM Changeset [70] by j@…
Updated TODO
4:47 PM Changeset [69] by j@…
Merged from traunk because repository couldn't be pushed
2:28 PM Changeset [68] by j@…
This is a test commit without authentication
12:08 PM Changeset [67] by j@…
Replaced messy fasta parser with a much better implementation
11:36 AM Changeset [66] by j@…
Renamed the .txt files to .rst
11:36 AM Changeset [65] by j@…
Converted TODO to proper reST fromat
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