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Activity (RSS)

Monday, May 25 2009
additional updates for version 0.3.0 ... was committed by Simon Chiang at 8:43 PM
updates for Tap-0.17.0 http://github.... was committed by Simon Chiang at 8:43 PM
Thursday, May 14 2009
15 Average masses not matching up to online source was updated
  • jtprince
    jtprince commented at 3:23 PM

    That sounds good. I was mostly worried I was doing the calculations wrong :)

    Thanks!
  • bahuvrihi
    bahuvrihi commented at 2:07 PM

    My guess is that this is an issue of uncertainty and probably not a numerical issue. I'm fairly sure the numbers produced by the Molecules library are numerical...
  • jtprince
    jtprince created the ticket at 11:48 AM

    When I generate average masses for peptides using this:


    require 'molecules'

    Molecules::Libraries::Residue['C'].mass {|e| e.std_atomic_weight.value }

    => 103.142...
Wednesday, April 01 2009
added class for accessing xml results... was committed by Simon Chiang at 8:08 PM
added filtering to load/mgf http://gi... was committed by Simon Chiang at 4:14 PM
dump/mgf now allows and mgf entry htt... was committed by Simon Chiang at 3:47 PM
added a load/mgf task http://github.c... was committed by Simon Chiang at 3:12 PM
reworked format_mgf as a dump task ht... was committed by Simon Chiang at 3:12 PM
Tuesday, March 31 2009
cleanup for release http://github.com... was committed by Simon Chiang at 3:43 PM
Monday, March 30 2009
incremented version to 0.2.2 http://g... was committed by Simon Chiang at 5:00 PM
minor updates http://github.com/bahuv... was committed by Simon Chiang at 4:50 PM
Tuesday, March 24 2009
14 Add fasta defline parsing was created
Monday, March 23 2009
removed Interface module http://githu... was committed by Simon Chiang at 11:02 PM
fixed failing specs. Query now uses R... was committed by Simon Chiang at 11:01 PM
Merge commit 'jtprince/master' into i... was committed by Simon Chiang at 10:38 PM
unescape Dat::Query title on initiali... was committed by John Prince at 10:38 PM
quadrupled block size for some files ... was committed by John Prince at 10:38 PM
option to specify valid headers in Qu... was committed by John Prince at 10:38 PM
little bug on struct http://github.co... was committed by John Prince at 10:38 PM
ms/mascot pulls in mgf and dat http:/... was committed by John Prince at 10:38 PM
in Query#to_mgf: unescape title, ensu... was committed by John Prince at 10:38 PM
BROKEN specs right now http://github.... was committed by John Prince at 10:38 PM
added upper level spec and implementa... was committed by John Prince at 10:38 PM
increased default block size for dat ... was committed by John Prince at 10:38 PM
Merge git://github.com/bahuvrihi/ms-m... was committed by John Prince at 10:38 PM
some documentation to lighthouse http... was committed by John Prince at 10:38 PM
fixed failing dat_spec spec: query(nu... was committed by John Prince at 10:38 PM
updates to use tap-mechanize http://g... was committed by Simon Chiang at 10:31 PM
added tap-mechanize as a submodule ht... was committed by Simon Chiang at 10:31 PM
removed tap-http submodule http://git... was committed by Simon Chiang at 10:31 PM
Sunday, March 22 2009
13 to/from map lookup by regexp was created
  • bahuvrihi
    bahuvrihi created the ticket at 10:47 AM

    Currently it's too difficult to remember and type full mappings in either form:

    
        "UniProtKB AC" => "UNIPROTACCS",
        "UniProtKB ID" => "UNIPROTI...
Thursday, March 19 2009
refactored MASCOT_SWITCH into a separ... was committed by Simon Chiang at 7:26 PM
updated export to use latest tap-http... was committed by Simon Chiang at 7:20 PM
Wednesday, March 18 2009
updated Submit task for latest tap-ht... was committed by Simon Chiang at 12:20 PM
Wednesday, March 04 2009
12 Submit/Export overrides was created
  • bahuvrihi
    bahuvrihi created the ticket at 9:00 PM

    It sure would be nice if there were an established way to override just a few config parameters. Maybe generate a delegates hash and nest them?
11 Make mascot task to transform output to std format was created
  • bahuvrihi
    bahuvrihi created the ticket at 9:01 AM

    TOPP does something similar and it's a good idea. While they make it happen by default, mspire could implement a separate task as a potential path in the analys...
Friday, February 27 2009
10 Add success checks to Map tasks was created
  • bahuvrihi
    bahuvrihi created the ticket at 11:48 PM

    Uniprot::Map and Pir::Map both could start failing on a dime and there's little helpful feedback.
9 Allow options for Dat::Archive reindex was created
  • bahuvrihi
    bahuvrihi created the ticket at 6:07 PM

    For example, to set the default_blksize and carryover_limit.
Thursday, February 26 2009
8 Dat parser needs to handle \r\n was created
  • bahuvrihi
    bahuvrihi created the ticket at 1:34 PM

    Considering that is the more common line ending for HTTP exchanges.
incremented version to 0.2.1 http://g... was committed by Simon Chiang at 12:50 PM
implemented high level el spec for fi... was committed by Simon Chiang at 11:33 AM
cleanup of Peptides http://github.com... was committed by Simon Chiang at 9:12 AM
development of Summary http://github.... was committed by Simon Chiang at 9:12 AM
moved various functionality from clas... was committed by Simon Chiang at 9:12 AM
7 Dat checks was created
  • bahuvrihi
    bahuvrihi created the ticket at 12:32 AM
    • Check re multiple entries per value
    • Check how modification sequences work when multiple modifications are at a single site
sketched out (incomplete) Summary htt... was committed by Simon Chiang at 12:31 AM
minor bug fixes in documentation and ... was committed by Simon Chiang at 12:31 AM
fixed Proteins to_s formatting http:/... was committed by Simon Chiang at 12:31 AM