Your message dated Sat, 07 Nov 2020 14:53:24 +0000
with message-id <e1kbpam-000iaj...@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
message is talking about, this may indicate a serious mail system
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--
961085: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=961085
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: toppic
Section: science
Priority: optional
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Uploaders: Filippo Rusconi <lopi...@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 <lopi...@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 <lopi...@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 961...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Filippo Rusconi <lopi...@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 ftpmas...@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-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@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).
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Files:
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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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