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toppic_1.3.0+dfsg1-1_amd64.changes (click to toggle)
Format:1.8
Date:Tue, 19 May 2020 22:46:41 +0200
Source:toppic
Binary:toppic toppic-common toppic-dbgsym
Architecture:source all amd64
Version:1.3.0+dfsg1-1
Distribution:unstable
Urgency:medium
Maintainer:The Debichem Group <debichem-devel@lists.alioth.debian.org>
Changed-By:Filippo Rusconi <lopippo@debian.org>
Description:
toppic     - Top-down proteoform identification and characterization (programs
toppic-common - Top-down proteoform identification and characterization (common d
Closes:961085
Changes:
toppic (1.3.0+dfsg1-1) unstable; urgency=medium

  * Initial release (Closes: #961085).
Files:
34ed3e44e2dd2bcb14ffb75104851684 2416 science optional toppic_1.3.0+dfsg1-1.dsc
def29fb4efefd5e4c835b15b21088d3b 15948091 science optional toppic_1.3.0+dfsg1.orig.tar.gz
10dd39ff52a05a464ea50327988cb040 138792 science optional toppic_1.3.0+dfsg1-1.debian.tar.xz
67f8bf7b5152462fddf314853b6211f3 5464108 science optional toppic-common_1.3.0+dfsg1-1_all.deb
0ca10924a3df2404cf853d3b47b54875 63668808 debug optional toppic-dbgsym_1.3.0+dfsg1-1_amd64.deb
e9ab1ce6f190108eb527eeb4c2f06810 12570 science optional toppic_1.3.0+dfsg1-1_amd64.buildinfo
0b8e448f27b1622a9323ead0e8d15b01 2358688 science optional toppic_1.3.0+dfsg1-1_amd64.deb
toppic_1.3.0+dfsg1-1.dsc (click to toggle)
Format:3.0 (quilt)
Source:toppic
Binary:toppic, toppic-common
Architecture:any all
Version:1.3.0+dfsg1-1
Maintainer:The Debichem Group <debichem-devel@lists.alioth.debian.org>
Uploaders:Filippo Rusconi <lopippo@debian.org>
Homepage:http://proteomics.informatics.iupui.edu/software/toppic/index.html
Standards-Version:4.5.0
Vcs-Browser:https://salsa.debian.org/debian/toppic
Vcs-Git:https://salsa.debian.org/debian/toppic.git
Build-Depends:debhelper-compat (=12), dpkg-dev (>=1.18.25), cmake (>=3.12), libhts-dev, libboost-dev, libboost-filesystem-dev, libboost-program-options-dev, libboost-thread-dev, libboost-system-dev, libboost-iostreams-dev, libboost-chrono-dev, libxerces-c-dev, qtbase5-dev, zlib1g-dev, python3-docutils, libjs-filesaver, fonts-font-awesome, fonts-freefont-ttf, libjs-bootstrap4, libjs-popper.js, libjs-jquery-ui, node-jquery
Package-List:toppic deb science optional arch=any toppic-common deb science optional arch=all
Files:
def29fb4efefd5e4c835b15b21088d3b 15948091 toppic_1.3.0+dfsg1.orig.tar.gz
10dd39ff52a05a464ea50327988cb040 138792 toppic_1.3.0+dfsg1-1.debian.tar.xz
lintian 2.76.0~bpo10+1 check for toppic_1.3.0+dfsg1-1.dsc (click to toggle)
README.source for toppic_1.3.0+dfsg1-1.dsc (click to toggle)
No README.source in this package
control file for toppic_1.3.0+dfsg1-1_amd64.deb (click to toggle)
Package:toppic
Version:1.3.0+dfsg1-1
Architecture:amd64
Maintainer:The Debichem Group <debichem-devel@lists.alioth.debian.org>
Installed-Size:14067
Depends:libboost-chrono1.67.0, libboost-filesystem1.67.0, libboost-iostreams1.67.0, libboost-program-options1.67.0, libboost-system1.67.0, libboost-thread1.67.0, libc6 (>=2.29), libgcc-s1 (>=3.4), libhts3 (>=1.10), libstdc++6 (>=9), libxerces-c3.2, zlib1g (>=1:1.2.0), toppic-common (=1.3.0+dfsg1-1)
Section:science
Priority:optional
Homepage:http://proteomics.informatics.iupui.edu/software/toppic/index.html
Description:
Top-down proteoform identification and characterization (programs)
 The TopPIC Suite consists of four software tools for the interpretation
 of top-down mass spectrometry data: TopFD, TopPIC, TopMG, and TopDiff.
 .
  -TopFD (Top-down mass spectral Feature Detection) is a software tool
    for top-down spectral deconvolution and a successor to MS-Deconv.  It
    groups top-down spectral peaks into isotopomer envelopes and converts
    isotopomer envelopes to monoisotopic neutral masses. In addition, it
    extracts proteoform features from LC-MS or CE-MS data.
 .
  -TopPIC (Top-down mass spectrometry based Proteoform Identification
    and Characterization) identifies and characterizes proteoforms at the
    proteome level by searching top-down tandem mass spectra against a
    protein sequence database. TopPIC is a successor to MS-Align+. It
    efficiently identifies proteoforms with unexpected alterations, such
    as mutations and post-translational modifications (PTMs), accurately
    estimates the statistical significance of identifications, and
    characterizes reported proteoforms with unknown mass shifts. It uses
    several techniques, such as indexes, spectral alignment, generation
    function methods, and the modification identification score (MIScore),
    to increase the speed, sensitivity, and accuracy.
 .
  -TopMG (Top-down mass spectrometry based proteoform identification
    using Mass Graphs) is a software tool for identifying ultra-modified
    proteoforms by searching top-down tandem mass spectra against a
    protein sequence database.  It is capable of identifying proteoforms
    with multiple variable PTMs and unexpected alterations, such as
    histone proteoforms and phosphorylated ones.  It uses mass graphs,
    which efficiently represent candidate proteoforms with multiple
    variable PTMs, to increase the speed and sensitivity in proteoform
    identification. In addition, approximate spectrum-based filtering
    methods are employed for protein sequence filtering, and a Markov
    chain Monte Carlo method (TopMCMC) is used for estimating the
    statistical significance of identifications.
 .
  -TopDiff (Top-down mass spectrometry-based identification of
    Differentially expressed proteoforms) compares the abundances of
    proteoforms and finds differentially expressed proteoforms by using
    identifications of top-down mass spectrometry data of several protein
    samples.
lintian 2.76.0~bpo10+1 check for toppic_1.3.0+dfsg1-1_amd64.deb (click to toggle)
contents of toppic_1.3.0+dfsg1-1_amd64.deb (click to toggle)
drwxr-xr-x root/root         0 2020-05-19 20:46 ./
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/bin/
-rwxr-xr-x root/root   2152928 2020-05-19 20:46 ./usr/bin/topdiff
-rwxr-xr-x root/root   5703376 2020-05-19 20:46 ./usr/bin/topfd
-rwxr-xr-x root/root   3287528 2020-05-19 20:46 ./usr/bin/topmg
-rwxr-xr-x root/root   3221992 2020-05-19 20:46 ./usr/bin/toppic
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/share/
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/share/doc/
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/share/doc/toppic/
-rw-r--r-- root/root       165 2020-05-19 20:46 ./usr/share/doc/toppic/changelog.Debian.gz
-rw-r--r-- root/root     13870 2020-05-19 20:46 ./usr/share/doc/toppic/copyright
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/share/man/
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/share/man/man1/
-rw-r--r-- root/root      1427 2020-05-19 20:46 ./usr/share/man/man1/topdiff.1.gz
-rw-r--r-- root/root      1782 2020-05-19 20:46 ./usr/share/man/man1/topfd.1.gz
-rw-r--r-- root/root      3535 2020-05-19 20:46 ./usr/share/man/man1/topmg.1.gz
-rw-r--r-- root/root      3706 2020-05-19 20:46 ./usr/share/man/man1/toppic.1.gz
control file for toppic-common_1.3.0+dfsg1-1_all.deb (click to toggle)
Package:toppic-common
Source:toppic
Version:1.3.0+dfsg1-1
Architecture:all
Maintainer:The Debichem Group <debichem-devel@lists.alioth.debian.org>
Installed-Size:24346
Depends:fonts-font-awesome, fonts-freefont-ttf, libjs-filesaver, libjs-bootstrap4, libjs-popper.js, libjs-jquery-ui, node-jquery
Section:science
Priority:optional
Homepage:http://proteomics.informatics.iupui.edu/software/toppic/index.html
Description:
Top-down proteoform identification and characterization (common data)
 The TopPIC Suite consists of four software tools for the interpretation
 of top-down mass spectrometry data: TopFD, TopPIC, TopMG, and TopDiff.
 .
  -TopFD (Top-down mass spectral Feature Detection) is a software tool
    for top-down spectral deconvolution and a successor to MS-Deconv.  It
    groups top-down spectral peaks into isotopomer envelopes and converts
    isotopomer envelopes to monoisotopic neutral masses. In addition, it
    extracts proteoform features from LC-MS or CE-MS data.
 .
  -TopPIC (Top-down mass spectrometry based Proteoform Identification
    and Characterization) identifies and characterizes proteoforms at the
    proteome level by searching top-down tandem mass spectra against a
    protein sequence database. TopPIC is a successor to MS-Align+. It
    efficiently identifies proteoforms with unexpected alterations, such
    as mutations and post-translational modifications (PTMs), accurately
    estimates the statistical significance of identifications, and
    characterizes reported proteoforms with unknown mass shifts. It uses
    several techniques, such as indexes, spectral alignment, generation
    function methods, and the modification identification score (MIScore),
    to increase the speed, sensitivity, and accuracy.
 .
  -TopMG (Top-down mass spectrometry based proteoform identification
    using Mass Graphs) is a software tool for identifying ultra-modified
    proteoforms by searching top-down tandem mass spectra against a
    protein sequence database.  It is capable of identifying proteoforms
    with multiple variable PTMs and unexpected alterations, such as
    histone proteoforms and phosphorylated ones.  It uses mass graphs,
    which efficiently represent candidate proteoforms with multiple
    variable PTMs, to increase the speed and sensitivity in proteoform
    identification. In addition, approximate spectrum-based filtering
    methods are employed for protein sequence filtering, and a Markov
    chain Monte Carlo method (TopMCMC) is used for estimating the
    statistical significance of identifications.
 .
  -TopDiff (Top-down mass spectrometry-based identification of
    Differentially expressed proteoforms) compares the abundances of
    proteoforms and finds differentially expressed proteoforms by using
    identifications of top-down mass spectrometry data of several protein
    samples.
 .
 This package ships common data used by the various program in the
 toppic package.
lintian 2.76.0~bpo10+1 check for toppic-common_1.3.0+dfsg1-1_all.deb (click to toggle)
contents of toppic-common_1.3.0+dfsg1-1_all.deb (click to toggle)
drwxr-xr-x root/root         0 2020-05-19 20:46 ./
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/share/
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/share/doc/
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/share/doc/toppic-common/
-rw-r--r-- root/root       165 2020-05-19 20:46 ./usr/share/doc/toppic-common/changelog.Debian.gz
-rw-r--r-- root/root     13870 2020-05-19 20:46 ./usr/share/doc/toppic-common/copyright
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/share/toppic/
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/share/toppic/base_data/
-rw-r--r-- root/root       266 2019-12-31 15:48 ./usr/share/toppic/base_data/env_rescore_para.txt
-rw-r--r-- root/root     35542 2019-12-31 15:48 ./usr/share/toppic/base_data/mass_table.txt
-rw-r--r-- root/root  18409124 2019-12-31 15:48 ./usr/share/toppic/base_data/theo_patt.txt
-rw-r--r-- root/root    236099 2019-12-31 15:48 ./usr/share/toppic/base_data/unimod_ptm.xml
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/share/toppic/local-source-copies/
-rw-r--r-- root/root     14297 2020-05-19 20:46 ./usr/share/toppic/local-source-copies/datatables.min.css
-rw-r--r-- root/root     84975 2020-05-19 20:46 ./usr/share/toppic/local-source-copies/datatables.min.js
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/share/toppic/p_value_table/
-rw-r--r-- root/root     19619 2019-12-31 15:48 ./usr/share/toppic/p_value_table/ppm10_ptm0.txt
-rw-r--r-- root/root     19477 2019-12-31 15:48 ./usr/share/toppic/p_value_table/ppm10_ptm1.txt
-rw-r--r-- root/root     18038 2019-12-31 15:48 ./usr/share/toppic/p_value_table/ppm10_ptm2.txt
-rw-r--r-- root/root     19492 2019-12-31 15:48 ./usr/share/toppic/p_value_table/ppm15_ptm0.txt
-rw-r--r-- root/root     19289 2019-12-31 15:48 ./usr/share/toppic/p_value_table/ppm15_ptm1.txt
-rw-r--r-- root/root     17508 2019-12-31 15:48 ./usr/share/toppic/p_value_table/ppm15_ptm2.txt
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-rw-r--r-- root/root     18611 2019-12-31 15:48 ./usr/share/toppic/p_value_table/ppm5_ptm2.txt
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/share/toppic/promex/
-rw-r--r-- root/root    413131 2019-12-31 15:48 ./usr/share/toppic/promex/AbuScore.tsv
-rw-r--r-- root/root    404786 2019-12-31 15:48 ./usr/share/toppic/promex/CorrScore.tsv
-rw-r--r-- root/root    416903 2019-12-31 15:48 ./usr/share/toppic/promex/DistScore.tsv
-rw-r--r-- root/root    412133 2019-12-31 15:48 ./usr/share/toppic/promex/IntScore.tsv
-rw-r--r-- root/root    411624 2019-12-31 15:48 ./usr/share/toppic/promex/SummedCorrScore.tsv
-rw-r--r-- root/root    410765 2019-12-31 15:48 ./usr/share/toppic/promex/SummedDistScore.tsv
-rw-r--r-- root/root    402703 2019-12-31 15:48 ./usr/share/toppic/promex/SummedIntScore.tsv
-rw-r--r-- root/root    393994 2019-12-31 15:48 ./usr/share/toppic/promex/XicCorrScore1.tsv
-rw-r--r-- root/root    394616 2019-12-31 15:48 ./usr/share/toppic/promex/XicCorrScore2.tsv
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/share/toppic/topview/
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/share/toppic/topview/css/
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/share/toppic/topview/css/images/
-rw-r--r-- root/root     27490 2019-12-31 15:48 ./usr/share/toppic/topview/css/images/Sorting icons.psd
-rw-r--r-- root/root      1361 2019-12-31 15:48 ./usr/share/toppic/topview/css/images/back_disabled.png
-rw-r--r-- root/root      1379 2019-12-31 15:48 ./usr/share/toppic/topview/css/images/back_enabled.png
-rw-r--r-- root/root      1375 2019-12-31 15:48 ./usr/share/toppic/topview/css/images/back_enabled_hover.png
-rw-r--r-- root/root       894 2019-12-31 15:48 ./usr/share/toppic/topview/css/images/favicon.ico
-rw-r--r-- root/root      1363 2019-12-31 15:48 ./usr/share/toppic/topview/css/images/forward_disabled.png
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-rw-r--r-- root/root      1379 2019-12-31 15:48 ./usr/share/toppic/topview/css/images/forward_enabled_hover.png
-rw-r--r-- root/root      1118 2019-12-31 15:48 ./usr/share/toppic/topview/css/images/sort_asc.png
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-rw-r--r-- root/root       683 2019-12-31 15:48 ./usr/share/toppic/topview/css/index.css
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/share/toppic/topview/css/lib/
-rw-r--r-- root/root    155758 2019-12-31 15:48 ./usr/share/toppic/topview/css/lib/bootstrap.min.css
-rw-r--r-- root/root     17202 2019-12-31 15:48 ./usr/share/toppic/topview/css/lib/jquery.dataTables.css
-rw-r--r-- root/root       746 2019-12-31 15:48 ./usr/share/toppic/topview/css/lib/nav_bar.css
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/share/toppic/topview/doc/
-rw-r--r-- root/root     17133 2019-12-31 15:48 ./usr/share/toppic/topview/doc/spectrum_graph.docx
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/share/toppic/topview/images/
-rw-r--r-- root/root      5430 2019-12-31 15:48 ./usr/share/toppic/topview/images/toppic.ico
-rw-r--r-- root/root      4215 2020-05-19 20:46 ./usr/share/toppic/topview/index.html
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/share/toppic/topview/inspect/
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/share/toppic/topview/inspect/css/
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-rw-r--r-- root/root      2503 2019-12-31 15:48 ./usr/share/toppic/topview/inspect/css/spectrum.css
-rw-r--r-- root/root       861 2019-12-31 15:48 ./usr/share/toppic/topview/inspect/css/svg.css
-rw-r--r-- root/root      2614 2020-05-19 20:46 ./usr/share/toppic/topview/inspect/help.html
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drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/share/toppic/topview/inspect/js/
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lrwxrwxrwx root/root         0 2020-05-19 20:46 ./usr/share/toppic/topview/inspect/js/download/FileSaver.js -> ../../../../../javascript/filesaver/FileSaver.js
lrwxrwxrwx root/root         0 2020-05-19 20:46 ./usr/share/toppic/topview/js/lib/bootstrap/bootstrap.min.js -> ../../../../../nodejs/bootstrap/dist/js/bootstrap.min.js
lrwxrwxrwx root/root         0 2020-05-19 20:46 ./usr/share/toppic/topview/js/lib/download/FileSaver.js -> ../../../../../javascript/filesaver/FileSaver.js
lrwxrwxrwx root/root         0 2020-05-19 20:46 ./usr/share/toppic/topview/js/lib/jQuery-ui_1_11_4.min.js -> ../../../../javascript/jquery-ui/jquery-ui.min.js
lrwxrwxrwx root/root         0 2020-05-19 20:46 ./usr/share/toppic/topview/js/lib/jQuery_3_4.js -> ../../../../nodejs/jquery/dist/jquery.js
lrwxrwxrwx root/root         0 2020-05-19 20:46 ./usr/share/toppic/topview/js/lib/popper.min.js -> ../../../../nodejs/popper.js/dist/popper.min.js
lrwxrwxrwx root/root         0 2020-05-19 20:46 ./usr/share/toppic/topview/visual/css/FreeMono.ttf -> ../../../../fonts/truetype/freefont/FreeMono.ttf
lrwxrwxrwx root/root         0 2020-05-19 20:46 ./usr/share/toppic/topview/visual/js/prsm/FileSaver.js -> ../../../../../javascript/filesaver/FileSaver.js
control file for toppic-dbgsym_1.3.0+dfsg1-1_amd64.deb (click to toggle)
Package:toppic-dbgsym
Source:toppic
Version:1.3.0+dfsg1-1
Auto-Built-Package:debug-symbols
Architecture:amd64
Maintainer:The Debichem Group <debichem-devel@lists.alioth.debian.org>
Installed-Size:65226
Depends:toppic (=1.3.0+dfsg1-1)
Section:debug
Priority:optional
Description:
debug symbols for toppic
Build-Ids:0efb802522ba77b0cdc0807671313cee3b24524e 3b02bd143ace84fdf1a0fe1040c8dcdbf90d4339 aab7f6ebf53a8ae9c175bc76265e13a686609941 c86e7ed715b221a270cf9c84d4168fc6b0c1c2d0
lintian 2.76.0~bpo10+1 check for toppic-dbgsym_1.3.0+dfsg1-1_amd64.deb (click to toggle)
contents of toppic-dbgsym_1.3.0+dfsg1-1_amd64.deb (click to toggle)
drwxr-xr-x root/root         0 2020-05-19 20:46 ./
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/lib/
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/lib/debug/
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/lib/debug/.build-id/0e/
-rw-r--r-- root/root  17207632 2020-05-19 20:46 ./usr/lib/debug/.build-id/0e/fb802522ba77b0cdc0807671313cee3b24524e.debug
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/lib/debug/.build-id/3b/
-rw-r--r-- root/root   9252544 2020-05-19 20:46 ./usr/lib/debug/.build-id/3b/02bd143ace84fdf1a0fe1040c8dcdbf90d4339.debug
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/lib/debug/.build-id/aa/
-rw-r--r-- root/root  18160912 2020-05-19 20:46 ./usr/lib/debug/.build-id/aa/b7f6ebf53a8ae9c175bc76265e13a686609941.debug
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/lib/debug/.build-id/c8/
-rw-r--r-- root/root  16482040 2020-05-19 20:46 ./usr/lib/debug/.build-id/c8/6e7ed715b221a270cf9c84d4168fc6b0c1c2d0.debug
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/lib/debug/.dwz/x86_64-linux-gnu/
-rw-r--r-- root/root   5670064 2020-05-19 20:46 ./usr/lib/debug/.dwz/x86_64-linux-gnu/toppic.debug
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/share/
drwxr-xr-x root/root         0 2020-05-19 20:46 ./usr/share/doc/
lrwxrwxrwx root/root         0 2020-05-19 20:46 ./usr/share/doc/toppic-dbgsym -> toppic

Timestamp: 28.05.2020 / 09:01:36 (UTC)