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Bug#961085: marked as done (ITP: toppic -- Top-down proteoform identification and characterization)

Your message dated Sat, 07 Nov 2020 14:53:24 +0000
with message-id <E1kbPam-000IAj-TT@fasolo.debian.org>
and subject line Bug#961085: fixed in toppic 1.3.0+dfsg1-3
has caused the Debian Bug report #961085,
regarding ITP: toppic -- Top-down proteoform identification and characterization
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
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-- 
961085: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=961085
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
Source: toppic
Section: science
Priority: optional
Maintainer: The Debichem Group <debichem-devel@lists.alioth.debian.org>
Uploaders: Filippo Rusconi <lopippo@debian.org>
Build-Depends: debhelper-compat (= 12),
               dpkg-dev (>= 1.18.25),
               cmake (>= 3.12)
Standards-Version: 4.5.0
Homepage: http://proteomics.informatics.iupui.edu/software/toppic/index.html
Vcs-Browser: https://salsa.debian.org/debian/toppic
Vcs-Git: https://salsa.debian.org/debian/toppic.git

Package: wnpp
Severity: wishlist
Owner: Filippo Rusconi <lopippo@debian.org>

~~~~
I intend to package the toppic software that is necessary to perform mass
spectrometry-based protein identifications. 

This software will become essential in my own laboratory research, along with
other software packages that I created and that I already maintain with the
debichem team.

I will maintain the package within the debichem team.

Package: toppic
Architecture: any
Depends: ${shlibs:Depends}, 
         ${misc:Depends}
Description: Top-down proteoform identification and characterization
 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.

Regards,

Filippo

-- 

⢀⣴⠾⠻⢶⣦⠀  Filippo Rusconi, PhD
⣾⠁⢠⠒⠀⣿⡁   Research scientist at CNRS
⢿⡄⠘⠷⠚⠋⠀   Debian Developer
⠈⠳⣄⠀⠀⠀⠀  http://msxpertsuite.org
          http://www.debian.org

--- End Message ---
--- Begin Message --- 
Source: toppic
Source-Version: 1.3.0+dfsg1-3
Done: Filippo Rusconi <lopippo@debian.org>

We believe that the bug you reported is fixed in the latest version of
toppic, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 961085@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Filippo Rusconi <lopippo@debian.org> (supplier of updated toppic package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 1.8
Date: Tue, 03 Nov 2020 09:28:06 +0100
Source: toppic
Binary: toppic toppic-common toppic-dbgsym
Architecture: source all amd64
Version: 1.3.0+dfsg1-3
Distribution: unstable
Urgency: low
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+dfsg1-3) unstable; urgency=low
 .
   * Reinstating the ITP bug closing statement (Closes: #961085).
 .
   * Patch the build system so that the external libpwiz subset code that is
     included is not used. Instead, link to the pwizlite library that I have
     created and packaged for Debian. Use CMake to find libpwizlite and libhts.
 .
   * Remove from the d/copyright all the stanzas related to the pwiz/boost code
     since it does not belong to the cleaned package anymore. Add the
     corresponding files to the Files-Excluded stanza.
 .
   * d/s/lintian-overrides: override E for missing sources files that are
     genuine package authors' code (lintian is triggered by long lines > 512
     chars).
Checksums-Sha1:
 57d0f62f98a4838db67fe18581e216d01a9ae894 2445 toppic_1.3.0+dfsg1-3.dsc
 fadfe4e10df4320f6a01f4c6767e97fa955c190f 11008208 toppic_1.3.0+dfsg1.orig.tar.xz
 7e405bc0b135698adf114f4bf728557046c92592 135836 toppic_1.3.0+dfsg1-3.debian.tar.xz
 e81d1797e1f40593279847685d5105010f962f83 5470596 toppic-common_1.3.0+dfsg1-3_all.deb
 42c7ba9b08c31cfeebb5146f37bd1db41e731698 90475444 toppic-dbgsym_1.3.0+dfsg1-3_amd64.deb
 78fcda12cb0a8f1cb89d91aa4c99c13c437fe175 12948 toppic_1.3.0+dfsg1-3_amd64.buildinfo
 ec7ec452391f2596a0979370b2e2179e1f4f2b20 2412384 toppic_1.3.0+dfsg1-3_amd64.deb
Checksums-Sha256:
 ba9e74a306bb1eec6189ce852a2b07081b4fbeccd0e51e65e7a1c271db4db7f2 2445 toppic_1.3.0+dfsg1-3.dsc
 070c8d3dd3475d2a54896cc1127929ca7659552b2b5af97766f869c5a473dab7 11008208 toppic_1.3.0+dfsg1.orig.tar.xz
 e4c9fda20e81b178ccb063f4e13432c45a5ac5eb6e70c3712d83e8e3c86c106c 135836 toppic_1.3.0+dfsg1-3.debian.tar.xz
 b7302a0a2490545e4218df493839fe3406c6cdded2eb3d56b32f98f4c1793b3f 5470596 toppic-common_1.3.0+dfsg1-3_all.deb
 4151bb3847d05443c999cbe4660bfd8ea4089d97457afbb97abccdcaf9797a67 90475444 toppic-dbgsym_1.3.0+dfsg1-3_amd64.deb
 15a32bf8df78272c877a480160683afa09e34c93a452502c3bfc318b7821ab3a 12948 toppic_1.3.0+dfsg1-3_amd64.buildinfo
 4232d74f213d90d9b6ec94cbb091f7014dcfb272c1fd2f04517a8a23770ccb44 2412384 toppic_1.3.0+dfsg1-3_amd64.deb
Files:
 161a4e37b71ea8afb163be9bb62576c7 2445 science optional toppic_1.3.0+dfsg1-3.dsc
 7184991da303c0bf38543dbc90b6cd38 11008208 science optional toppic_1.3.0+dfsg1.orig.tar.xz
 37363e87e0773f4855c10a4d5b5eb7a1 135836 science optional toppic_1.3.0+dfsg1-3.debian.tar.xz
 37fbd99974a774688fe71a7ea8aa173d 5470596 science optional toppic-common_1.3.0+dfsg1-3_all.deb
 48f703a153e24a6e9362f275458249b3 90475444 debug optional toppic-dbgsym_1.3.0+dfsg1-3_amd64.deb
 652de370a9d66e07544e398fa2fcac2f 12948 science optional toppic_1.3.0+dfsg1-3_amd64.buildinfo
 c25e3c8d504bba43aa69456491d53763 2412384 science optional toppic_1.3.0+dfsg1-3_amd64.deb

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--- End Message ---
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