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December 26, 2012, at 02:17 PM by 82.225.200.216 -
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  • 2011 10 22 New release, version 3.2.0. Update: Debian GNU/Linux users: a debugging symbols package will be available soon, as package massxpert-dbg;
October 23, 2011, at 06:39 PM by 82.225.200.216 -
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June 29, 2011, at 09:24 PM by 82.225.200.216 -
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June 06, 2011, at 08:01 AM by 82.225.200.216 -
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  • 2011 06 05 Performed my first debian package upload as a Debian Developer !
June 06, 2011, at 07:53 AM by 82.225.200.216 -
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June 05, 2011, at 07:07 PM by 82.225.200.216 -
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French users : massXpert is documented in a book about mass spectrometry for biochemists that I published.
See here for details.

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'French users : massXpert is documented in a book about mass spectrometry for biochemists that I published.'
See http://www.lavoisier.fr for details.

June 05, 2011, at 07:06 PM by 82.225.200.216 -
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See [http://www.lavoisier.fr/livre/notice.asp?id=3LKW2OAR2KROWZ | here ] for details.

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See here for details.

June 05, 2011, at 07:06 PM by 82.225.200.216 -
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French users : massXpert is documented in a book about mass spectrometry for biochemists that I published. See [http://www.lavoisier.fr/livre/notice.asp?id=3LKW2OAR2KROWZ | here ] for details.

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French users : massXpert is documented in a book about mass spectrometry for biochemists that I published.
See [http://www.lavoisier.fr/livre/notice.asp?id=3LKW2OAR2KROWZ | here ] for details.

June 05, 2011, at 07:05 PM by 82.225.200.216 -
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French users : massXpert is documented in a book about mass spectrometry for biochemists that I published. See [http://www.lavoisier.fr/livre/notice.asp?id=3LKW2OAR2KROWZ | here ] for details.

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May 22, 2011, at 08:51 PM by 82.225.200.216 -
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February 20, 2011, at 11:15 AM by 82.225.200.216 -
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I cannot prepare MacOSX packages anymore as I have no more a MacOSX computer at my disposal. If anyone wants to donate a Mac computer, I'll resume package creation. Thank you.

February 20, 2011, at 11:13 AM by 82.225.200.216 -
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January 26, 2011, at 03:16 PM by 129.175.202.39 -
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October 05, 2010, at 02:19 PM by 82.225.200.216 -
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'For any comment, please use the maintainer address from here. Thank you.'

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For any comment, please use the maintainer address from here. Thank you.

October 05, 2010, at 02:19 PM by 82.225.200.216 -
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'However, I would greatly appreciate having comments from you. I see dozens of downloads and rather rare comments. It would be rewarding if you would comment (positively or negatively) on your user experience with massXpert. For this, please use the maintainer address from here. Thank you.'

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'For any comment, please use the maintainer address from here. Thank you.'

May 11, 2010, at 07:27 AM by 82.225.200.216 -
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  • 2010 05 10 New release, version 2.3.6;
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May 11, 2010, at 07:26 AM by 82.225.200.216 -
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  • 2010 05 10 New release, version 2.3.6;
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  • 2010 05 10 New release, version 2.3.6;
May 11, 2010, at 07:25 AM by 82.225.200.216 -
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  • 2010 05 03 New release, version 2.3.5;
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  • 2010 05 10 New release, version 2.3.6;
May 03, 2010, at 10:15 AM by 192.134.152.177 -
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  • 2010 04 22 New release, version 2.2.0;
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  • 2010 05 03 New release, version 2.3.5;
April 22, 2010, at 09:57 PM by 82.225.200.216 -
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  • 2010 01 25 New setup package for windows released (fixes lack of a required dll).
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  • 2010 04 22 New release, version 2.2.0;
January 25, 2010, at 09:34 PM by 82.225.200.216 -
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  • 2009 12 22 New version released (v 2.1.0).
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  • 2010 01 25 New setup package for windows released (fixes lack of a required dll).
December 22, 2009, at 04:35 PM by 193.54.201.151 -
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  • 2009 11 26 New version released.
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  • 2009 12 22 New version released (v 2.1.0).
November 26, 2009, at 09:52 PM by 82.225.200.216 -
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  • 2009 10 06 New version released.
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  • 2009 11 26 New version released.
  • The packages for MS-Windows and MacOSX no more ship the user manual. Please download it from the website.
October 06, 2009, at 11:22 AM by 193.54.201.151 -
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  • 2009 09 18 Detected and fixed a serious bug making massXpert crash upon re-cleaving a polymer sequence in the same cleavage dialog window.MacOSX packaging is still ongoing. Packages for MS-Windows and Mac-OS-X are now ready.
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  • 2009 10 06 New version released.
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  • Last released version: 2.0.4 (2009 09 09).
  • First official upload of the Debian package as a Debian Maintainer (thanks to Debian Developer Lionel Mamane for tutoring me).

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September 21, 2009, at 11:43 AM by 193.54.201.151 -
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  • 2009 09 18 Detected and fixed a serious bug making massXpert crash upon re-cleaving a polymer sequence in the same cleavage dialog window.MacOSX packaging is still ongoing.
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  • 2009 09 18 Detected and fixed a serious bug making massXpert crash upon re-cleaving a polymer sequence in the same cleavage dialog window.MacOSX packaging is still ongoing. Packages for MS-Windows and Mac-OS-X are now ready.
September 19, 2009, at 07:16 PM by 82.225.200.216 -
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  • 2009 09 18 Detected and fixed a serious bug making massXpert crash upon re-cleaving a polymer sequence in the same cleavage dialog window.Packages are being prepared: stay tuned! For users proficient with software building, they might use the git cloning utility to download the latest source state with the following command:

git clone git://git.tuxfamily.org/gitroot/massxpert/massxpert.git massxpert

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  • 2009 09 18 Detected and fixed a serious bug making massXpert crash upon re-cleaving a polymer sequence in the same cleavage dialog window.MacOSX packaging is still ongoing.
September 18, 2009, at 09:27 AM by 82.225.200.216 -
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  • Detected and fixed a serious bug making massXpert crash upon re-cleaving a polymer sequence in the same cleavage dialog window.Packages are being prepared: stay tuned! For users proficient with software building, they might use the git cloning utility to download the latest source state with the following command:
to:
  • 2009 09 18 Detected and fixed a serious bug making massXpert crash upon re-cleaving a polymer sequence in the same cleavage dialog window.Packages are being prepared: stay tuned! For users proficient with software building, they might use the git cloning utility to download the latest source state with the following command:
September 18, 2009, at 09:26 AM by 82.225.200.216 -
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  • Detected and fixed a serious bug making massXpert crash upon re-cleaving a polymer sequence in the same cleavage dialog window.Users proficient with software building might use the git cloning utility to download the latest source state with the following command:
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  • Detected and fixed a serious bug making massXpert crash upon re-cleaving a polymer sequence in the same cleavage dialog window.Packages are being prepared: stay tuned! For users proficient with software building, they might use the git cloning utility to download the latest source state with the following command:
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For other users, packages are being prepared. Stay tuned !

September 18, 2009, at 09:25 AM by 82.225.200.216 -
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For other users, packages are being prepared. Stay tuned !

September 18, 2009, at 09:11 AM by 82.225.200.216 -
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  1. Detected and fixed a serious bug making massXpert crash upon re-cleaving a polymer sequence in the same cleavage dialog window.Users proficient with software building might use the git cloning utility to download the latest source state with the following command:
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  • Detected and fixed a serious bug making massXpert crash upon re-cleaving a polymer sequence in the same cleavage dialog window.Users proficient with software building might use the git cloning utility to download the latest source state with the following command:
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  1. Publication of massXpert in the prestigious british journal Bioinformatics, UK. See News (Section July)!
  2. Last released version: 2.0.4 (2009 09 09).
  3. First official upload of the Debian package as a Debian Maintainer (thanks to Debian Developer Lionel Mamane for tutoring me).

to:
  • Publication of massXpert in the prestigious british journal Bioinformatics, UK. See News (Section July)!
  • Last released version: 2.0.4 (2009 09 09).
  • First official upload of the Debian package as a Debian Maintainer (thanks to Debian Developer Lionel Mamane for tutoring me).

September 18, 2009, at 09:11 AM by 82.225.200.216 -
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September 18, 2009, at 09:10 AM by 82.225.200.216 -
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git-clone git://git.tuxfamily.org/gitroot/massxpert/massxpert.git massxpert

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git clone git://git.tuxfamily.org/gitroot/massxpert/massxpert.git massxpert

September 18, 2009, at 09:09 AM by 82.225.200.216 -
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git-clone git://git.tuxfamily.org/gitroot/massxpert/massxpert.git massxpert

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git-clone git://git.tuxfamily.org/gitroot/massxpert/massxpert.git massxpert

September 18, 2009, at 09:08 AM by 82.225.200.216 -
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  1. Detected and fixed a serious bug making massXpert crash upon re-cleaving a polymer sequence in the same cleavage dialog window.Users proficient with software building might use the git cloning utility to download the latest source state with the following command:

git-clone git://git.tuxfamily.org/gitroot/massxpert/massxpert.git massxpert

September 15, 2009, at 04:09 PM by 193.54.201.151 -
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massXpert is Free Software.

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massXpert is Free Software licensed under the GNU General Public License version 3.

September 09, 2009, at 08:39 AM by 82.225.200.216 -
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  1. First official upload of the Debian package as a Debian Maintainer (thanks to Debian Developer Lionel Mamane for tutoring me).

September 09, 2009, at 08:38 AM by 82.225.200.216 -
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Flash news: Publication of massXpert in the prestigious british journal Bioinformatics, UK. See News!

to:

Flash news

  1. Publication of massXpert in the prestigious british journal Bioinformatics, UK. See News (Section July)!
  2. Last released version: 2.0.4 (2009 09 09).

August 28, 2009, at 01:48 PM by 82.225.200.216 -
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Flash news: Publication of massXpert in prestigious journal Bioinformatics, UK. See News!

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Flash news: Publication of massXpert in the prestigious british journal Bioinformatics, UK. See News!

August 28, 2009, at 01:35 PM by 82.225.200.216 -
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Flash news: Publication of massXpert in prestigious journal Bioinformatics, UK News.

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Flash news: Publication of massXpert in prestigious journal Bioinformatics, UK. See News!

August 28, 2009, at 01:34 PM by 82.225.200.216 -
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Flash news: Publication of massXpert in prestigious journal Bioinformatics, UK

News.

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Flash news: Publication of massXpert in prestigious journal Bioinformatics, UK News.

August 28, 2009, at 01:34 PM by 82.225.200.216 -
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Flash news: version 2.0.1 released, see the News.

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Flash news: Publication of massXpert in prestigious journal Bioinformatics, UK

News.

April 16, 2009, at 09:29 AM by 193.54.201.151 -
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Flash news: version 2.0.1 released, see the News.

March 10, 2009, at 04:55 PM by 82.225.200.216 -
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massXpert is about mass spectrometry. This is software that runs on MS-Windows, Apple-Mac-OS-X, GNU-Linux, and almost all variants of the UNIX system.

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massXpert is about mass spectrometry.

This is software that runs on MS-Windows, Apple-Mac-OS-X, GNU-Linux, and almost all variants of the UNIX system.

March 10, 2009, at 04:54 PM by 82.225.200.216 -
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massXpert is about mass spectrometry

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massXpert is about mass spectrometry. This is software that runs on MS-Windows, Apple-Mac-OS-X, GNU-Linux, and almost all variants of the UNIX system.

December 19, 2008, at 07:34 PM by 82.225.200.216 -
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  1. With the XperCalc module, you get a desktop calculator that understands your polymer chemistry definitions as defined in XpertDef. The calculator allows any kind of chemical reaction and is infinitely programmable. Any calculation is recorded in a logbook that is exportable to put in the lab-book;
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  1. With the XpertCalc module, you get a desktop calculator that understands your polymer chemistry definitions as defined in XpertDef. The calculator allows any kind of chemical reaction and is infinitely programmable. Any calculation is recorded in a logbook that is exportable to put in the lab-book;
May 28, 2008, at 08:08 PM by 82.225.200.216 -
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http://massxpert.org/wiki/Site/SideBar?action=edit

May 28, 2008, at 07:54 PM by 82.225.200.216 -
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<<<<<<< ======= A Git repository was setup. Use that repository either throught the web interface, or via a console using the following command: git-clone git://git.tuxfamily.org/gitroot/massxpert/massxpert.git massxpert

April 2008


25

Last version: 1.7.5

Please, test the software thoroughly, and specifically the Mac OS X package. Report any failure or any success to the maintainer address here.

  1. Finally one Mac OS X package (experimental, for Leopard 10.5);
  2. The whole software program is now relocatable;
  3. The french translation is now 100 % complete;
  4. Huge code cleanup work, along with implementation of namespaces in the whole project;
  5. Some classes added along with some existing classes redesigned;
  6. Bug fixes here and there;
  7. Updated the documentation.

3

Last version: 1.7.4

  1. Implemented a new fragmentation specification method for fragmentation patterns where the monomer undergoing fragmentation has its lateral chain decomposed. This is particularly useful in nucleic acids chemistry where the nucleic base might be eliminated at the monomer undergoing fragmentation according to the pattern `a';
  2. Updated the french translation;
  3. Fixed memory leak and bugs;
  4. Updated the user manual.

March 2008


30

Last version: 1.7.3

  1. Implemented dynamic mass data filtering on the oligomer data obtained after a polymer sequence fragmentation or after arbitrary mass searches;
  2. Fixed regression after the implementation of last release's features;
  3. Fixed minor bugs and cleaned up code;
  4. Improved the user experience in the graphical user interface;
  5. Updated the documentation.

26

Last version: 1.7.2

  1. Implemented dynamic mass data filtering on the oligomer data obtained after a polymer sequence cleavage. The filtered data show up in place without needing to open a new window each time. Pretty powerful stuff, here;
  2. Updated the user manual to show that new feature;
  3. Minor bug fixes.

19

Last version: 1.7.1

  1. Implemented intra-molecular cross-links. For protein chemists, this means that sulfide bonds are now handled in the sequence and that simulation of the fluorescent proteins also (their chromophore is created by internal cross-links involving three monomers). Because this new feature required extensive rewrite of the internals of massXpert, I suspect that bugs might have crept in. So, please, be sure to double-check your results prior to publication;
  2. Implemented find sequence motif in polymer sequence. This is a rather simple implementation but a very handy one when long polymer sequences are dealt with;
  3. Fixed a serious bug with how composite formulas are handled in certain cases. You should really be upgrading to version 1.7.1 for this reason;
  4. Various bug fixes and other small improvements.

17

  1. For the MS-Windows users, a new version of the package (not of the software) is available that includes all the libraries required for the program to run on machines in which the Qt library is not installed. Filename : massxpert-1.7.0-1-setup.exe or massxpert-1.7.0-1.zip;
  2. Done huge coding work with interesting features added with intra-molecular cross-links and find sequence motif, above all. I am still testing the soft, and when it seems ready for public consumption I'll release it for bug hunting.

February 2008


22

Last version: 1.7.0

  1. Bug-fix release;
  2. Fixed a serious crash when computing elemental composition of a polymer sequence that beared a formula-defined modification as opposed to selecting a modification from the list;
  3. The bugfix triggered a wave of code cleanup and the coding of a new more robust way of modifiying the polymer sequence;
  4. The polymer sequence file format changed but older formats are handled with a versioning scheme that was coded in this release;
  5. Updated the user manual.

15

Last version: 1.6.9

  1. Improved the flexibility of the monomer modification procedure: now it is possible to define a modification in the monomer modification dialog, without the modification having to be defined in the polymer chemistry definition. This makes it much more quick to test structural hypotheses;
  2. Also, the polymer modifications are now easily visualized in the polymer sequence editor, and there they can be easily modified. Updated the documentation;
  3. Versioning of the polymer sequence files is now in place (which was the case only for the polymer chemistry definition files, so far).

December 2007


18

Last version: 1.6.8

  1. The polymer chemistry definition code has been fully rewritten and the user interface redesigned;
  2. There are bugfixes here and there;
  3. Coding of the framework for intra-molecular cross-link has begun;
  4. There is a new package for Fedora core, and the usual packages for Debian GNU/Linux.

09

Last version: 1.6.7.

  1. Fixed a bug with the calculation of polymer net charges given a pH. That bug would not show up at each calculation. pI calculations were affected also.
  2. Converted the project from the qmake build system to the more powerful CMake build system, that is portable and can build the software for all the Qt-supported platforms.
  3. Note that the documentation still does not reflect the conversion.

September 2007


23

Last version: 1.6.6.

  1. New possibility, when cleaving or fragmenting a sequence, to ask for the generation of cleavage- or fragmentation-based oligomers of any given ionization state. For example, when cleaving a protein using an enzyme, it is possible to ask that the generated peptides be in an ionized state between z=1 and z=5.
  2. Fixed bug with the acido-basicity calculations, where the user could only enter integer pH values. Now double values (precision 2 decimals) might be used to allow better fine-grained calculations.
  3. Updated the french translation and the documentation to reflect the new developments.

Try it out, there might well be bugs that need reporting ! Ah by the way, tomorrow I'll turn 40 ! Thanks to free software I still feel like being 20 ! The free software universe seems to be eternally fresh, with enthusiastic people (especially in the KDE (kde.org) or Qt (trolltech.com) universes)...

21

Came back from Pau, south of France, where the annual French Mass Spec Society meeting was held. Well organized, interesting stuff in there. Found some free moments to code some stuff. I'll soon make a release with multi-charged oligomers obtained by either cleaving or fragmenting a sequence. This is a feature I wanted to code since some time, as I needed it from time to time. I had the pleasure to meet Maya Belghazi, a long-time friend and colleague who assured me the mass stuff she would be doing in the near future will involve heavy usage of massXpert. I suspect that I will be having bug reports flowing to my development station... wonderful!

August 2007


20

Last version: 1.6.5.

  1. Implemented a feature whereby the user might define monomers to which a given chemical modification is restricted. For example, the "Phosphorylation" modification might be restricted to Seryl, Threonyl and Tyrosinyl monomers. When trying to use such a modification on a Glycyl monomer, the program would complain that Glycyl monomer is not a target of "Phosphorylation". This will be most useful for later features that will involve automatically screening modifications for mass matches between measured m/z values and theoretical ones. False positives will be prevented by ensuring that a match is not found by modifying a Glycyl monomer with "Phosphorylation", for example. In other words, more chemical intelligence is enshrined in the chemical modification object. A mechanism allowing easy overriding of the chemical limitations above is available to allow maximum flexibility.
  2. Fixed a bunch of bugs, in particular related to the chemical modification of monomers. These bugs were gui-related bugs, not actually chemistry- or mass-related bugs, so no fear for mass calculations.
  3. Fixed a bug which would show up when using atom symbols of more than two characters.
  4. Updated the User Manual so as to reflect the changes in the features of the program.
  5. Updated the french translation.

July 2007


28

Managed to get all the new monomer modification stuff coded and at least partly tested. Not released stuff yet, but this is what you will be getting as release 1.6.5 hits the streets: the modifications get chemical intelligence (as usual, only if the user wants to put some in) as they will be knowing what monomers they might modify and what not. Thus, when modifying monomers, if one monomer is not a target of the monomer being used, the program will complain and not perform the modification. However, it is possible to override the modification targets limitation and thus modify any monomer with that modification (flexibility for the user who knows what she is doing). As soon as all this new stuff is tested, it will be released.

24

Last version: 1.6.4.

  1. Setup the translation framework and fully translated the program to french (one of my native tongues, with italian). If anybody would like to help, I'm receiving any proposal (I'd be happy with a german translation or spanish, for example, but any other is all the more welcome);
  2. Improved the handling of monomer modifications when no svg file has been defined for them (this was a bug report by a user who did not read the doc and defined a new modification in the polymer chemistry definition without assigning a modification svg graphics file. When using that modification massXpert would crash. This no longer is the case, as now a default modification svg file is provided in the polymer chemistry definition directory and if such file is not found, one svg file is hard-coded in massxpert so as to be perfectly crash-proof on that matter;
  3. Fixed a bunch of bugs around the modifications being declared in the polymer chemistry definitions but not available as svg files;
  4. Performed user-invisible improvements in the development toolchain so as to prepare more reliable packages (Debian/MS-Windows) binary packages.

21

Fixed the User Manual (missing chapters) in packages 1.6.3 (unless for the debian doc package that was updated). The fixed User Manual is available on-line in pdf or html format. I am working hard today to improve the toolchain so as to avoid this kind of mishandling of the packages.

20

Last version: 1.6.3.

  1. Added possibility to modify a polymer sequence using arbitrary formulas, not necessarily modifications from the polymer chemistry definition. The use of modifications with no graphical rendering svg vignettes is in the works. It will be based on the use of a default modification-rendering file which will be used whenever no svg file is associated to any given modification in the polymer chemistry definition.
  2. Fixed a bunch of bugs with the modifications in the modification_dictionary file and related graphical vignettes.
  3. Updated the code to comply with new Qt version 4.3.0 on GNU/Linux.
  4. Some glitches fixed in the sequence editor window.
  5. Improved recorder output in the calculator window.
  6. Greatly improved the documentation by making it more concise and specific.
  7. Hopefully fixed the problematic MS-Windows package creation procedure.
  8. Detected nasty behaviour of the Qt's GraphicsScene widget which is different (for the same code) from GNU/Linux to MS-Windows. Will have to file a bug report to the Trolls.

Note that it is possible to install this 1.6.3 version using either the "Next-next-next" setup package or simply by extracting the zip file in C:\Program Files\massxpert. In this latter case, then, no icons are installed. To uninstall, simply remove the C:\Program Files\massxpert directory, and that's done. The GNU/Linux folks have no problem with the source/binary tarball or the binary Debian GNU/Linux package.

19

Still having a problem with the windows installer (Innosetup). Instead, unzipping this zip file in the C:\Program Files directory, so that massXpert is in C:\Program Files\massxpert works flawlessly. You only need to run C:\Program Files\massxpert\basebin\massxpert.exe. The user manual is in C:\Program Files\massxpert\doc\userman.

17

Update: A fixed package is now available again in the downloads directory... Attention MS-Windows package is flawed. I am correcting it. I have removed it for now.

12

Last version: 1.6.2. Fixed a nasty bug that would show up only during mass calculation of oligomers obtained by cleaving a sequence with a cleaving agent that applies a cleavage rule to the oligomer (and only in case the charge of the oligomer is > 1).

10

Last version: 1.6.1. Implemented a proof-of-concept version of a facility to compare mass lists. If matches cannot be done between lists, try to force matches using a list of modifications. This should be useful when trying to find peaks in a mass spectrum that might be of interest because they do not match theoretically-obtained masses (like by cleavage in silico). Updated the documentation. Also added a plugin to help convert numerical values from one locale to another (for example from locale fr_FR to locale en_US) which is useful if the mass spectrometer acquisition software does not comply with the locale of the MS-Windows platform.

3

The big single Debian package is now divided into two distinct packages: one for the binary program and its chemical data (massxpert) and one for the User Manual (massxpert-doc). Go get them here. Installing is as easy as usual (as root): dpkg -i massxpert_1.6.0-rc2-1_i386.deb and dpkg -i massxpert-doc_1.6.0-rc2-1_i386.deb.

2

Made a new Debian package. Download it here and, as root, issue that command: dpkg -i massxpert_1.6.0-rc2-1_i386.deb. That's a single package including absolutely everything: the program, the chemical data and the documentation. I am working on separated binary packages starting from a single source. Happy massXpert'ing.

1

The first release of massXpert licensed under the GNU General Public License version 3 (published by the FSF the 29th of june 2007) is available as version 1.6.0-rc2.

June 2007


27

The first public release of massXpert is now available for download. The software is available as a source tarball for all platforms (GNU/Linux, MacOSX and MS-Windows). There are binary packages for GNU/linux and for MS-Windows (one Inno Setup executable installation program; thanks Jordan Russell). The User Manual is available in the packages and the potential users are invited to peruse the installation chapter in the User Manual available online.

16

Wrote all the code allowing the user to export any kind of data either to the clipboard or to a file on disk or both.

May 2007


25

Code cleanup, code documentation and bug fixing these days. In the next week I'll be busy attending a conference on DNA replication, recombination and repair in Hyères, South of France.

22

Finally finished coding the "Net Charge" and "pI" calculations. We are nearing the finishing of the GNU polyxmass port to Qt! I also managed to fix some bugs in the mean time.

14

Being forced to bed due to severe back-ache, I could put my laptop at work with computation-intensive activities: simulating isotopic patterns for small proteins. The feature is now implemented and is reacheable via the XpertCalc module. Still have some minor tweaks to do to that code but the feature is cool. This is a feature that GNU polyxmass did not have! Check the screenshot.

1

After a full (yester-)day of tweaking the qmake configuration, I finally got the project to build/install identically on GNU/Linux (Debian) and MS-Windows-XP. The version of the released Qt library on MS-Windows is 4.2.3. All in all, it really seems that the cross-platform promises of the Qt library are well met! This means I'll soon be able to provide source and binary packages.

April 2007


29

The site is now up and running, thanks to the wonderful crew at bioinformatics.org (with a special mention to Jeff Bizzaro). I'll start populating this page day after day.

I first would like to mention some history about the massXpert project and next I'll start the distribution of the software. I still have some code to write and compilable packages to prepare. When everything is ready, I'll be back with news from the front.

At the moment massXpert is able to do a number of interesting things and runs equally well on GNU/Linux and MS-Windows-XP. I still have to find a Mac-OS-X computer to build the package and to be able to distribute binary packages along with the source code.

In the last weeks I discovered how easy it was to code Qt plugins, and coded a plugin with some sequence manipulation tools of interest according to the suggestions of my PhD student, Naïma Ouarti. She wanted to be able to convert a 1-letter code protein sequence to a 3-letter code protein sequence. I wrote that plugin so that such kind of conversions could be performed on the base of a dictionary listing code equivalences, like "M>Met" or "Arg>R", for example. Another function is simply the change of case from uppercase to lowercase and vice versa.

13

I have bought massxpert.org for a duration of three years. As soon as the site is ready, I'll migrate all this stuff in it. The name of this new projet will therefore be 'massXpert'. It is in fact a revival of the massXpert project I published in Bioinformatics in 2002. Note however, that the present massXpert project is a full rewrite of the GNU polyXmass project and as such is so much more powerful than the initial massXpert project.

'For this reason, whenever you see mass[Xx]treme in the remaining of this page, you should read mass[Xx]pert.'

From a coding standpoint, the mass search feature that was still lacking in massXpert is now implemented in a way that is more powerful than in GNU polyXmass. Further, the copy/paste functionality is now implemented, which makes it possible to create new sequences by copying/pasting sequences off a browser. A powerful "purification" dialog displays all the material that does not corrspond to valid monomer codes. The user may purify the sequence before actually copying it in the sequence editor.

The port of the fundamental features from polyXmass is well on track. First of all the usual paradigm of real-time automatic mass calculation in the sequence editor is done. Second, the program now allows to make the biochemical (cleavage) and the gas-phase fragmentation simulations. I have compiled it successfully on MS-Windows XP and it runs exactly the same as on GNU/Linux. I still have to code the third fundamental feature, that is mass search in the polymer sequence. After that, I'll start coding of the copy/paste operations (with sequence verification) in the sequence editor and the exporting of the data to the clipboard. When all the coding is almost finished, I'll have to search for a new name. Am I going to use massXtreme, massXpress or massXpert (one name I used for a program that I published in 2002) ? Screenshots: screenshots.

March 2007


The sequence editor is now able to perform all the editing tasks that one would expect from a sequence editor (not yet copy/paste stuff, though). It is now possible to modify any monomer in the sequence and to modify any/both end(s) of the polymer sequence. In the former case, the chemically modified monomer gets a redraw in the sequence with the modification vignette being transparently composited onto the non-modified monomer vignette.

February 2007


Well, the program is coming along well. I even have a number of screenshots of Mac-OS-X and MS-Windows XP massXtreme sessions. The Mac-OS-X stuff was provided by my dear friend Olivier Kaloudoff of Linux-Azur fame.

As of today, the editor can load a polymer sequence and display it, with all the sequence scrolling and line numbering OK, but not much more than that, for the moment :-).

Note that the sequence rendering is now completely SVG-based, so that it is based on a widely popular scalar vector graphics format that is a web consortium standard (w3). Also, the rendering is always at the best resolution whatever the size of the monomer vignettes. My vignettes were prepared using the wonderful Inkscape program although I guess Karbon would do also.

Go see the screenshots to ascertain that work is indeed going on!

January 2007


Yeah, it is proceeding smoothly. I have finished porting the atom and polymer chemistry definition infrastructure. The chemical desktop calculator is almost finished also. A conspicuous part of the low-level chemical modelling library is ported and working. I'll have to start coding the polymer sequence editor, which is a prerequisite for doing the hard-core mass spec/(bio)chemical simulations (which take place in the sequence editor module). Those interested in the alpha code can send an email (see below for mail addresses).

I'll have to buy the www.massxtreme.org domain. Something like three or more years in a row. If anybody is willing to make a donation, I'll accept with immense pleasure :-)

'Happy new year for those who are starting a new year these days!'

November-December 2006


Following a number of requests about the portability of GNU polyxmass to either MacOSX and MS-Windows, I decided to develop its successor in C++ using a development toolkit renowned for its portability capabilities : the QT library from http://www.trolltech.com/products/qt/. This toolkit is published under the GNU General Public License and features all the technical requirements for writing a GUI mass spectrometric software that is maintainable and expandable (with the PyQT Python scripting module). This successor to GNU polyxmass will be called massXtreme. This program will not be endorsed by the GNU project, as it won't use the Gtk+ libraries anymore. >>>>>>>

to:
May 28, 2008, at 07:48 PM by 82.225.200.216 -
Changed lines 5-6 from:

This means that you can use it freely for whatever need you may have, you may study the code underlying the program, you may modify that code freely and redistribute it freely with the same license as the one you got with the package.

to:

This means that you can use it freely for whatever need you may have, you may study the code underlying the program, you may modify that code freely and redistribute it freely with the same license as the one you got with the package.

Added lines 21-22:

<<<<<<< =======

Changed lines 261-262 from:

Following a number of requests about the portability of GNU polyxmass to either MacOSX and MS-Windows, I decided to develop its successor in C++ using a development toolkit renowned for its portability capabilities : the QT library from http://www.trolltech.com/products/qt/. This toolkit is published under the GNU General Public License and features all the technical requirements for writing a GUI mass spectrometric software that is maintainable and expandable (with the PyQT Python scripting module). This successor to GNU polyxmass will be called massXtreme. This program will not be endorsed by the GNU project, as it won't use the Gtk+ libraries anymore.

to:

Following a number of requests about the portability of GNU polyxmass to either MacOSX and MS-Windows, I decided to develop its successor in C++ using a development toolkit renowned for its portability capabilities : the QT library from http://www.trolltech.com/products/qt/. This toolkit is published under the GNU General Public License and features all the technical requirements for writing a GUI mass spectrometric software that is maintainable and expandable (with the PyQT Python scripting module). This successor to GNU polyxmass will be called massXtreme. This program will not be endorsed by the GNU project, as it won't use the Gtk+ libraries anymore. >>>>>>>

May 28, 2008, at 06:37 PM by 82.225.200.216 -
Changed lines 21-23 from:

Latest News

Citation of this work:

to:

A Git repository was setup. Use that repository either throught the web interface, or via a console using the following command: git-clone git://git.tuxfamily.org/gitroot/massxpert/massxpert.git massxpert

April 2008

Deleted lines 24-33:
Filippo Rusconi and Maya Belghazi. Desktop prediction/analysis of 
mass spectrometric data in proteomic projects by using massXpert. 
Bioinformatics. 2002, 18, 644.

Note that because the program has been rewritten over the years and the website has changed since the publication of the paper, mentioning http://www.massxpert.org along with the reference is certainly a good idea. A future article describing in detail all the new features will update everything.

A Git repository was setup. Use that repository either throught the web interface, or via a console using the following command: git-clone git://git.tuxfamily.org/gitroot/massxpert/massxpert.git massxpert

April 2008


May 18, 2008, at 07:11 AM by 82.225.200.216 -
Changed line 40 from:
  1. Finally one Mac OS X package;
to:
  1. Finally one Mac OS X package (experimental, for Leopard 10.5);
May 16, 2008, at 06:52 PM by 82.225.200.216 -
Changed lines 7-8 from:

However, I would greatly appreciate having comments from you. I see dozens of downloads and rather rare comments. It would be rewarding if you would comment (positively or negatively) on your user experience with massXpert. For this please, use the maintainer address from here.

to:

'However, I would greatly appreciate having comments from you. I see dozens of downloads and rather rare comments. It would be rewarding if you would comment (positively or negatively) on your user experience with massXpert. For this, please use the maintainer address from here. Thank you.'

May 16, 2008, at 06:50 PM by 82.225.200.216 -
Added lines 7-8:

However, I would greatly appreciate having comments from you. I see dozens of downloads and rather rare comments. It would be rewarding if you would comment (positively or negatively) on your user experience with massXpert. For this please, use the maintainer address from here.

May 14, 2008, at 02:56 AM by 82.225.200.216 -
Added lines 1-18:

About massXpert

massXpert is Free Software.

This means that you can use it freely for whatever need you may have, you may study the code underlying the program, you may modify that code freely and redistribute it freely with the same license as the one you got with the package.

massXpert is about mass spectrometry

With massXpert you actually have four programs in one :

  1. With the XpertDef module you define brand new polymer chemistries (what are the atoms, what are the monomers that make the polymer, what are the chemical modifications that you might need to simulate biological or synthetic chemical reactions, what are the different ways you might need to cut a polymer sequence into pieces (chemical or enzymatic), what are the different ways that a small oligomer might fragment in the mass spectrometer's gas phase, and so on...

  2. With the XperCalc module, you get a desktop calculator that understands your polymer chemistry definitions as defined in XpertDef. The calculator allows any kind of chemical reaction and is infinitely programmable. Any calculation is recorded in a logbook that is exportable to put in the lab-book;

  3. With the XpertEdit module, you get a sophisticated polymer sequence editor and a chemical center where a huge amount of simulations might be performed. Anything mass-related is virtually feasible in XpertEdit.

  4. With the XpertMiner module, you will get (it is being implemented) a data mining center. You'll be able to drag and drop data from the mass spectra (in the form of m/z lists) and data from the simulations performed in the XpertEdit module. Once there, all the data will be available for comparison, arbitrary calculations like, say : "this list of m/z values should be applied the following mass increase" or "this list of m/z values should be appplied this reaction: -H+Na". The possibilities should be infinite.
April 26, 2008, at 06:28 AM by 82.225.200.216 -
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Plans

to:

April 2008

Deleted lines 14-17:

Implement a much more powerful m/z comparison paradigm (lists of m/z values, measured and theoretical, should be easily compared so as to find matches between the m/z in the lists using different z values (ion charge) or by performing combinatorial chemistry using the list of modifications available in the polymer chemistry definition. Get bug reports and patches from users. Test the software myself with real mass spectrometric experiments (lots of these await me).

April 2008


April 26, 2008, at 06:27 AM by 82.225.200.216 -
Changed lines 9-10 from:

Note that because the program has been rewritten over the years and the website has changed since the publication of the paper, mentioning http://www.massxpert.org in the reference might be a good idea. A future article describing in detail all the new features will update everything.

to:

Note that because the program has been rewritten over the years and the website has changed since the publication of the paper, mentioning http://www.massxpert.org along with the reference is certainly a good idea. A future article describing in detail all the new features will update everything.

April 26, 2008, at 06:26 AM by 82.225.200.216 -
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Please, test the software thoroughly, and specifically the Mac OS X package. Report any failure or any success to the maintainer address here.

Deleted lines 32-33:

Please, test the software thoroughly, and specifically the Mac OS X package. Report any failure or any success to the maintainer address at the Contact page.

April 25, 2008, at 08:22 PM by 82.225.200.216 -
Added lines 20-31:

25

Last version: 1.7.5

  1. Finally one Mac OS X package;
  2. The whole software program is now relocatable;
  3. The french translation is now 100 % complete;
  4. Huge code cleanup work, along with implementation of namespaces in the whole project;
  5. Some classes added along with some existing classes redesigned;
  6. Bug fixes here and there;
  7. Updated the documentation.

Please, test the software thoroughly, and specifically the Mac OS X package. Report any failure or any success to the maintainer address at the Contact page.

April 03, 2008, at 09:02 AM by 193.54.201.151 -
Changed lines 18-19 from:

March 2008

to:

April 2008

Added lines 20-28:

3

Last version: 1.7.4

  1. Implemented a new fragmentation specification method for fragmentation patterns where the monomer undergoing fragmentation has its lateral chain decomposed. This is particularly useful in nucleic acids chemistry where the nucleic base might be eliminated at the monomer undergoing fragmentation according to the pattern `a';
  2. Updated the french translation;
  3. Fixed memory leak and bugs;
  4. Updated the user manual.

March 2008


March 30, 2008, at 05:50 PM by 82.225.200.216 -
Changed line 25 from:
  1. Fixed minor bugs fixes and cleaned up code;
to:
  1. Fixed minor bugs and cleaned up code;
March 30, 2008, at 05:50 PM by 82.225.200.216 -
Added lines 21-28:

30

Last version: 1.7.3

  1. Implemented dynamic mass data filtering on the oligomer data obtained after a polymer sequence fragmentation or after arbitrary mass searches;
  2. Fixed regression after the implementation of last release's features;
  3. Fixed minor bugs fixes and cleaned up code;
  4. Improved the user experience in the graphical user interface;
  5. Updated the documentation.
March 26, 2008, at 11:45 AM by 193.54.201.151 -
Added lines 21-26:

26

Last version: 1.7.2

  1. Implemented dynamic mass data filtering on the oligomer data obtained after a polymer sequence cleavage. The filtered data show up in place without needing to open a new window each time. Pretty powerful stuff, here;
  2. Updated the user manual to show that new feature;
  3. Minor bug fixes.
March 23, 2008, at 06:39 PM by 82.225.200.216 -
Changed lines 105-106 from:

Fixed the User Manual (missing chapters) in packages 1.6.3 (unless for the debian doc package that was updated). The fixed User Manual is available on-line in pdf or html format. I am working hard today to improve the toolchain so as to avoid this kind of mishandling of the packages.

to:

Fixed the User Manual (missing chapters) in packages 1.6.3 (unless for the debian doc package that was updated). The fixed User Manual is available on-line in pdf or html format. I am working hard today to improve the toolchain so as to avoid this kind of mishandling of the packages.

March 23, 2008, at 06:29 PM by 82.225.200.216 -
Changed lines 11-13 from:

A Git repository was setup. Use that repository either throught the web interface, or via a console using the following command: git-clone git://git.tuxfamily.org/gitroot/massxpert/massxpert.git massxpert

to:

A Git repository was setup. Use that repository either throught the web interface, or via a console using the following command: git-clone git://git.tuxfamily.org/gitroot/massxpert/massxpert.git massxpert

March 23, 2008, at 06:28 PM by 82.225.200.216 -
Changed lines 11-13 from:

A Git repository was setup. Use that repository either throught the web interface, or via a console using the following command: git-clone git://git.tuxfamily.org/gitroot/massxpert/massxpert.git

to:

A Git repository was setup. Use that repository either throught the web interface, or via a console using the following command: git-clone git://git.tuxfamily.org/gitroot/massxpert/massxpert.git massxpert

March 23, 2008, at 06:07 PM by 82.225.200.216 -
Changed lines 11-13 from:

A Git repository was setup. Use that repository either throught the webinterface, or via a console using the following command: git-clone git://git.tuxfamily.org/gitroot/massxpert/massxpert.git

to:

A Git repository was setup. Use that repository either throught the web interface, or via a console using the following command: git-clone git://git.tuxfamily.org/gitroot/massxpert/massxpert.git

March 23, 2008, at 06:07 PM by 82.225.200.216 -
Changed lines 11-13 from:

A Git repository was setup. Use that repository either throught the webinterface, or via a console using the following command: http://git.tuxfamily.org/massxpert/massxpert.git.

to:

A Git repository was setup. Use that repository either throught the webinterface, or via a console using the following command: git-clone git://git.tuxfamily.org/gitroot/massxpert/massxpert.git

March 23, 2008, at 06:06 PM by 82.225.200.216 -
Changed lines 11-13 from:

Git repository

to:

A Git repository was setup. Use that repository either throught the webinterface, or via a console using the following command: http://git.tuxfamily.org/massxpert/massxpert.git.

March 23, 2008, at 05:58 PM by 82.225.200.216 -
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to:

Git repository

March 19, 2008, at 03:18 PM by 193.54.201.151 -
Changed lines 14-16 from:

Develop the find/replace feature. This might require some heavy rewriting of the sequence editor... Implement a much more powerful m/z comparison paradigm (lists of m/z values, measured and theoretical, should be easily compared so as to find matches between the m/z in the lists using different z values (ion charge) or by performing combinatorial chemistry using the list of modifications available in the polymer chemistry definition. Get bug reports and patches from users. Test the software myself with real mass spectrometric experiments (lots of these await me).

to:

Implement a much more powerful m/z comparison paradigm (lists of m/z values, measured and theoretical, should be easily compared so as to find matches between the m/z in the lists using different z values (ion charge) or by performing combinatorial chemistry using the list of modifications available in the polymer chemistry definition. Get bug reports and patches from users. Test the software myself with real mass spectrometric experiments (lots of these await me).

Changed lines 21-23 from:
  1. Implemented intra-molecular cross-links. For protein chemists, this means that sulfide bonds are now handled in the sequence and that simulation of the fluorescent proteins also (their chromophore is created by internal cross-links involving three monomers);
  2. Implemented find sequence motif in polymer sequence. This is a rather simple implementation but very handy for long polymer sequences;
  3. Fixed a serious bug with how composite formulas are handled in certain cases. You should really be upgrading to version 1.7.1 for this reason;
to:
  1. Implemented intra-molecular cross-links. For protein chemists, this means that sulfide bonds are now handled in the sequence and that simulation of the fluorescent proteins also (their chromophore is created by internal cross-links involving three monomers). Because this new feature required extensive rewrite of the internals of massXpert, I suspect that bugs might have crept in. So, please, be sure to double-check your results prior to publication;
  2. Implemented find sequence motif in polymer sequence. This is a rather simple implementation but a very handy one when long polymer sequences are dealt with;
  3. Fixed a serious bug with how composite formulas are handled in certain cases. You should really be upgrading to version 1.7.1 for this reason;
March 19, 2008, at 02:25 PM by 193.54.201.151 -
Added lines 19-25:

19

Last version: 1.7.1

  1. Implemented intra-molecular cross-links. For protein chemists, this means that sulfide bonds are now handled in the sequence and that simulation of the fluorescent proteins also (their chromophore is created by internal cross-links involving three monomers);
  2. Implemented find sequence motif in polymer sequence. This is a rather simple implementation but very handy for long polymer sequences;
  3. Fixed a serious bug with how composite formulas are handled in certain cases. You should really be upgrading to version 1.7.1 for this reason;
  4. Various bug fixes and other small improvements.
March 17, 2008, at 09:33 PM by 82.225.200.216 -
Changed lines 20-22 from:

Last version: 1.7.0. For the MS-Windows users, a new version of the package (not of the software) is available that includes all the libraries required for the program to run on machines in which the Qt library is not installed. Filename : massxpert-1.7.0-1-setup.exe or massxpert-1.7.0-1.zip.

to:
  1. For the MS-Windows users, a new version of the package (not of the software) is available that includes all the libraries required for the program to run on machines in which the Qt library is not installed. Filename : massxpert-1.7.0-1-setup.exe or massxpert-1.7.0-1.zip;
  2. Done huge coding work with interesting features added with intra-molecular cross-links and find sequence motif, above all. I am still testing the soft, and when it seems ready for public consumption I'll release it for bug hunting.

March 17, 2008, at 09:29 PM by 82.225.200.216 -
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February 2008

to:

March 2008

Added lines 19-24:

17

Last version: 1.7.0. For the MS-Windows users, a new version of the package (not of the software) is available that includes all the libraries required for the program to run on machines in which the Qt library is not installed. Filename : massxpert-1.7.0-1-setup.exe or massxpert-1.7.0-1.zip.

February 2008


February 23, 2008, at 01:33 PM by 82.225.200.216 -
Changed lines 22-24 from:
  1. The bugfix triggered a wave of code cleanup and the coding of a new more robust way of modifiying the polymer sequence.
  2. The polymer sequence file format changed but older formats are handled with a versioning scheme that was coded in this release.
to:
  1. The bugfix triggered a wave of code cleanup and the coding of a new more robust way of modifiying the polymer sequence;
  2. The polymer sequence file format changed but older formats are handled with a versioning scheme that was coded in this release;
  3. Updated the user manual.
February 23, 2008, at 01:31 PM by 82.225.200.216 -
Added lines 18-24:

22

Last version: 1.7.0

  1. Bug-fix release;
  2. Fixed a serious crash when computing elemental composition of a polymer sequence that beared a formula-defined modification as opposed to selecting a modification from the list;
  3. The bugfix triggered a wave of code cleanup and the coding of a new more robust way of modifiying the polymer sequence.
  4. The polymer sequence file format changed but older formats are handled with a versioning scheme that was coded in this release.
Changed line 26 from:

Last version: 16.9

to:

Last version: 1.6.9

February 15, 2008, at 03:41 PM by 193.54.201.151 -
Changed lines 20-23 from:
  1. Improved the flexibility of the monomer modification procedure: now it is possible to define a modification in the monomer modification dialog, without the modification having to be defined in the polymer chemistry definition. This makes it much more quick to test structural hypotheses.
  2. Also, the polymer modifications are now easily visualized in the polymer sequence editor, and there they can be easily modified. Updated the documentation.

to:
  1. Improved the flexibility of the monomer modification procedure: now it is possible to define a modification in the monomer modification dialog, without the modification having to be defined in the polymer chemistry definition. This makes it much more quick to test structural hypotheses;
  2. Also, the polymer modifications are now easily visualized in the polymer sequence editor, and there they can be easily modified. Updated the documentation;
  3. Versioning of the polymer sequence files is now in place (which was the case only for the polymer chemistry definition files, so far).

February 15, 2008, at 03:41 PM by 193.54.201.151 -
Changed lines 20-22 from:
  1. Improved the flexibility of the monomer modification procedure: now it is possible to define a modification in the monomer modification dialog, without the modification having to be defined in the polymer chemistry definition. This makes it much more quick to test structural hypotheses. #Also, the polymer modifications are now easily visualized in the polymer sequence editor, and there they can be easily modified. Updated the documentation.

to:
  1. Improved the flexibility of the monomer modification procedure: now it is possible to define a modification in the monomer modification dialog, without the modification having to be defined in the polymer chemistry definition. This makes it much more quick to test structural hypotheses.
  2. Also, the polymer modifications are now easily visualized in the polymer sequence editor, and there they can be easily modified. Updated the documentation.

February 15, 2008, at 03:40 PM by 193.54.201.151 -
Changed line 16 from:

December 2007

to:

February 2008

Added lines 18-24:

15

Last version: 16.9

  1. Improved the flexibility of the monomer modification procedure: now it is possible to define a modification in the monomer modification dialog, without the modification having to be defined in the polymer chemistry definition. This makes it much more quick to test structural hypotheses. #Also, the polymer modifications are now easily visualized in the polymer sequence editor, and there they can be easily modified. Updated the documentation.

December 2007


December 19, 2007, at 08:47 AM by 193.54.201.151 -
Added lines 18-24:

18

Last version: 1.6.8

  1. The polymer chemistry definition code has been fully rewritten and the user interface redesigned;
  2. There are bugfixes here and there;
  3. Coding of the framework for intra-molecular cross-link has begun;
  4. There is a new package for Fedora core, and the usual packages for Debian GNU/Linux.
December 09, 2007, at 06:48 PM by 82.225.200.216 -
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September 2007

to:

December 2007

Added lines 18-25:

09

Last version: 1.6.7.

  1. Fixed a bug with the calculation of polymer net charges given a pH. That bug would not show up at each calculation. pI calculations were affected also.
  2. Converted the project from the qmake build system to the more powerful CMake build system, that is portable and can build the software for all the Qt-supported platforms.
  3. Note that the documentation still does not reflect the conversion.

September 2007


September 26, 2007, at 08:21 AM by 82.225.200.216 -
Changed line 14 from:

Get bug reports and patches from users ! Test the software myself with real mass spectrometric experiments (lots of these await me). Implement a much more powerful m/z comparison paradigm (lists of m/z values, measured and theoretical, should be easily compared so as to find matches between the m/z in the lists using different z values (ion charge) or by performing combinatorial chemistry using the list of modifications available in the polymer chemistry definition.

to:

Develop the find/replace feature. This might require some heavy rewriting of the sequence editor... Implement a much more powerful m/z comparison paradigm (lists of m/z values, measured and theoretical, should be easily compared so as to find matches between the m/z in the lists using different z values (ion charge) or by performing combinatorial chemistry using the list of modifications available in the polymer chemistry definition. Get bug reports and patches from users. Test the software myself with real mass spectrometric experiments (lots of these await me).

September 23, 2007, at 03:16 PM by 82.225.200.216 -
Changed lines 25-26 from:

Try it out, there might well be bugs to need reporting ! Ah by the way, tomorrow I'll turn 40 ! Thanks to free software I still feel like being 20 ! The free software universe seems to be eternally fresh, with enthusiastic people (especially in the KDE (kde.org) or Qt (trolltech.com) universes)...

to:

Try it out, there might well be bugs that need reporting ! Ah by the way, tomorrow I'll turn 40 ! Thanks to free software I still feel like being 20 ! The free software universe seems to be eternally fresh, with enthusiastic people (especially in the KDE (kde.org) or Qt (trolltech.com) universes)...

September 23, 2007, at 03:16 PM by 82.225.200.216 -
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23

Last version: 1.6.6.

  1. New possibility, when cleaving or fragmenting a sequence, to ask for the generation of cleavage- or fragmentation-based oligomers of any given ionization state. For example, when cleaving a protein using an enzyme, it is possible to ask that the generated peptides be in an ionized state between z=1 and z=5.
  2. Fixed bug with the acido-basicity calculations, where the user could only enter integer pH values. Now double values (precision 2 decimals) might be used to allow better fine-grained calculations.
  3. Updated the french translation and the documentation to reflect the new developments.

Try it out, there might well be bugs to need reporting ! Ah by the way, tomorrow I'll turn 40 ! Thanks to free software I still feel like being 20 ! The free software universe seems to be eternally fresh, with enthusiastic people (especially in the KDE (kde.org) or Qt (trolltech.com) universes)...

September 21, 2007, at 10:14 PM by 82.225.200.216 -
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[-[@Filippo Rusconi and Maya Belghazi. Desktop prediction/analysis of

to:

[@Filippo Rusconi and Maya Belghazi. Desktop prediction/analysis of

Changed lines 7-8 from:

Bioinformatics. 2002, 18, 644.@]-]

to:

Bioinformatics. 2002, 18, 644.@]

September 21, 2007, at 10:13 PM by 82.225.200.216 -
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[-@@Filippo Rusconi and Maya Belghazi. Desktop prediction/analysis of

to:

[-[@Filippo Rusconi and Maya Belghazi. Desktop prediction/analysis of

Changed lines 7-8 from:

Bioinformatics. 2002, 18, 644.@@-]

to:

Bioinformatics. 2002, 18, 644.@]-]

September 21, 2007, at 10:13 PM by 82.225.200.216 -
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[@Filippo Rusconi and Maya Belghazi. Desktop prediction/analysis of

to:

[-@@Filippo Rusconi and Maya Belghazi. Desktop prediction/analysis of

Changed lines 7-8 from:

Bioinformatics. 2002, 18, 644.@]

to:

Bioinformatics. 2002, 18, 644.@@-]

September 21, 2007, at 10:12 PM by 82.225.200.216 -
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[@ Filippo Rusconi and Maya Belghazi. Desktop prediction/analysis of

to:

[@Filippo Rusconi and Maya Belghazi. Desktop prediction/analysis of

Changed lines 7-8 from:

Bioinformatics. 2002, 18, 644. @]

to:

Bioinformatics. 2002, 18, 644.@]

September 21, 2007, at 10:12 PM by 82.225.200.216 -
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September 21, 2007, at 10:11 PM by 82.225.200.216 -
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[- [@ Filippo Rusconi and Maya Belghazi. Desktop prediction/analysis of

to:

[@ Filippo Rusconi and Maya Belghazi. Desktop prediction/analysis of

Changed lines 10-20 from:

Bioinformatics. 2002, 18, 644. @] Because the program has been rewritten

 over the years and the website has changed since the publication of the

 paper, mentioning http://www.massxpert.org in the reference might 

be a good idea. A future article describing in detail all the new

features will update everything. -]

to:

Bioinformatics. 2002, 18, 644. @]

Note that because the program has been rewritten over the years and the website has changed since the publication of the paper, mentioning http://www.massxpert.org in the reference might be a good idea. A future article describing in detail all the new features will update everything.

September 21, 2007, at 10:10 PM by 82.225.200.216 -
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[-[@ Filippo Rusconi and Maya Belghazi. Desktop prediction/analysis of

to:

[- [@ Filippo Rusconi and Maya Belghazi. Desktop prediction/analysis of

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features will update everything.-]

to:

features will update everything. -]

September 21, 2007, at 10:09 PM by 82.225.200.216 -
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[-[@Filippo Rusconi and Maya Belghazi. Desktop prediction/analysis of

to:

[-[@ Filippo Rusconi and Maya Belghazi. Desktop prediction/analysis of

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Bioinformatics. 2002, 18, 644.@] Because the program has been rewritten

to:

Bioinformatics. 2002, 18, 644. @] Because the program has been rewritten

September 21, 2007, at 10:09 PM by 82.225.200.216 -
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September 21, 2007, at 10:09 PM by 82.225.200.216 -
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September 21, 2007, at 10:08 PM by 82.225.200.216 -
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[-[@Filippo Rusconi and Maya Belghazi. Desktop prediction/analysis of mass spectrometric data in proteomic projects by using massXpert.

to:

[-[@Filippo Rusconi and Maya Belghazi. Desktop prediction/analysis of mass spectrometric data in proteomic projects by using massXpert.

September 21, 2007, at 10:08 PM by 82.225.200.216 -
Changed lines 5-8 from:
Rusconi, F. and Belghazi, M. Desktop prediction/analysis of mass 
spectrometric data in proteomic projects by using massXpert. Bioinformatics. 2002, 18, 644.
Because the program has been rewritten over the years and the website has changed since the publication of the paper, mentioning http://www.massxpert.org in the reference might be a good idea. A future article describing in detail all the new features will update everything.

to:
[-
Filippo Rusconi and Maya Belghazi. Desktop prediction/analysis of mass spectrometric data in proteomic projects by using massXpert. 
Bioinformatics. 2002, 18, 644.
Because the program has been rewritten
 over the years and the website has changed since the publication of the
 paper, mentioning http://www.massxpert.org in the reference might 

be a good idea. A future article describing in detail all the new features will update everything.-]

September 21, 2007, at 10:06 PM by 82.225.200.216 -
Changed lines 6-8 from:

spectrometric data in proteomic projects by using massXpert. Bioinformatics. 2002, 18, 644.@] Because the program has been considerably modified over the years, mentioning the http://www.massxpert.org website in the reference might be a good idea, just waiting for a new article describing in detail all the new features.-]

to:

spectrometric data in proteomic projects by using massXpert. Bioinformatics. 2002, 18, 644.@] Because the program has been rewritten over the years and the website has changed since the publication of the paper, mentioning http://www.massxpert.org in the reference might be a good idea. A future article describing in detail all the new features will update everything.-]

September 21, 2007, at 10:04 PM by 82.225.200.216 -
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Citation of this work:

to:

Citation of this work:


September 21, 2007, at 10:03 PM by 82.225.200.216 -
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spectrometric data in proteomic projects by using massXpert. Bioinformatics. 2002, 18, 644.@] Because the program has been considerably modified over the years, mentioning (http://www.massxpert.org) might be a good idea, just waiting for a new article describing in detail all the new features.-]

to:

spectrometric data in proteomic projects by using massXpert. Bioinformatics. 2002, 18, 644.@] Because the program has been considerably modified over the years, mentioning the http://www.massxpert.org website in the reference might be a good idea, just waiting for a new article describing in detail all the new features.-]

September 21, 2007, at 10:01 PM by 82.225.200.216 -
Changed lines 7-10 from:

spectrometric data in proteomic projects by using massXpert (http://www.massxpert.org). Bioinformatics. 2002, 18, 644.@]-]

to:

spectrometric data in proteomic projects by using massXpert. Bioinformatics. 2002, 18, 644.@] Because the program has been considerably modified over the years, mentioning (http://www.massxpert.org) might be a good idea, just waiting for a new article describing in detail all the new features.-]

September 21, 2007, at 02:57 PM by 82.225.200.216 -
Changed line 13 from:

Get tons of bug reports and patches from users ! Test the software myself with real mass spectrometric experiments (lots of these await me). Implement a much more powerful m/z comparison paradigm (lists of m/z values, measured and theoretical, should be easily compared so as to find matches between the m/z in the lists using different z values (ion charge) or by performing combinatorial chemistry using the list of modifications available in the polymer chemistry definition.

to:

Get bug reports and patches from users ! Test the software myself with real mass spectrometric experiments (lots of these await me). Implement a much more powerful m/z comparison paradigm (lists of m/z values, measured and theoretical, should be easily compared so as to find matches between the m/z in the lists using different z values (ion charge) or by performing combinatorial chemistry using the list of modifications available in the polymer chemistry definition.

Added line 15:
Changed lines 19-21 from:

Came back from Pau, south of France, where the annual French Mass Spec meeting was held. Well organized, interesting stuff in there. Found some free moments to code some stuff. I'll soon make a release with multi-charged oligomers obtained by either cleaving or fragmenting a sequence. This is a feature I wanted to code in since some time, as I need it from time to time.

to:

Came back from Pau, south of France, where the annual French Mass Spec Society meeting was held. Well organized, interesting stuff in there. Found some free moments to code some stuff. I'll soon make a release with multi-charged oligomers obtained by either cleaving or fragmenting a sequence. This is a feature I wanted to code since some time, as I needed it from time to time. I had the pleasure to meet Maya Belghazi, a long-time friend and colleague who assured me the mass stuff she would be doing in the near future will involve heavy usage of massXpert. I suspect that I will be having bug reports flowing to my development station... wonderful!

September 21, 2007, at 02:54 PM by 82.225.200.216 -
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August 2007

to:

September 2007

Added lines 17-22:

21

Came back from Pau, south of France, where the annual French Mass Spec meeting was held. Well organized, interesting stuff in there. Found some free moments to code some stuff. I'll soon make a release with multi-charged oligomers obtained by either cleaving or fragmenting a sequence. This is a feature I wanted to code in since some time, as I need it from time to time.

August 2007


September 21, 2007, at 02:50 PM by 82.225.200.216 -
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[@Rusconi, F. and Belghazi, M. Desktop prediction/analysis of mass

to:

[-[@Rusconi, F. and Belghazi, M. Desktop prediction/analysis of mass

Changed lines 8-10 from:

(http://www.massxpert.org). Bioinformatics. 2002, 18, 644.@]

to:

(http://www.massxpert.org). Bioinformatics. 2002, 18, 644.@]-]

September 21, 2007, at 02:50 PM by 82.225.200.216 -
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September 21, 2007, at 02:49 PM by 82.225.200.216 -
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(http://www.massxpert.org). Bioinformatics. 2002, 18, 644.@]

to:

(http://www.massxpert.org). Bioinformatics. 2002, 18, 644.@]

September 21, 2007, at 02:49 PM by 82.225.200.216 -
Changed lines 5-7 from:

Rusconi, F. and Belghazi, M. Desktop prediction/analysis of mass spectrometric data in proteomic projects by using massXpert (http://www.massxpert.org). ''Bioinformatics''. 2002, 18, 644.

to:
Rusconi, F. and Belghazi, M. Desktop prediction/analysis of mass 
spectrometric data in proteomic projects by using massXpert 
(http://www.massxpert.org). ''Bioinformatics''. 2002, 18, 644.

September 21, 2007, at 02:48 PM by 82.225.200.216 -
Changed lines 5-7 from:

[Rusconi, F. and Belghazi, M. Desktop prediction/analysis of mass spectrometric data in proteomic projects by using massXpert (http://www.massxpert.org). Bioinformatics. 2002, 18, 644.]

to:

Rusconi, F. and Belghazi, M. Desktop prediction/analysis of mass spectrometric data in proteomic projects by using massXpert (http://www.massxpert.org). ''Bioinformatics''. 2002, 18, 644.

September 21, 2007, at 02:48 PM by 82.225.200.216 -
Changed lines 5-8 from:
massXpert: a cross-platfom Free Software mass spectrometric package,
by Filippo Rusconi (http://www.massxpert.org).

to:

[Rusconi, F. and Belghazi, M. Desktop prediction/analysis of mass spectrometric data in proteomic projects by using massXpert (http://www.massxpert.org). Bioinformatics. 2002, 18, 644.]

August 27, 2007, at 12:12 PM by Filippo Rusconi -
Changed lines 5-8 from:
@massXpert: a cross-platfom Free Software mass spectrometric package,
by Filippo Rusconi (http://www.massxpert.org).@

to:
massXpert: a cross-platfom Free Software mass spectrometric package,
by Filippo Rusconi (http://www.massxpert.org).

August 27, 2007, at 12:11 PM by Filippo Rusconi -
Changed lines 5-8 from:

@@massXpert: a cross-platfom Free Software mass spectrometric package,

 by Filippo Rusconi (http://www.massxpert.org).@@

to:
@massXpert: a cross-platfom Free Software mass spectrometric package,
by Filippo Rusconi (http://www.massxpert.org).@

August 27, 2007, at 12:10 PM by Filippo Rusconi -
Changed lines 5-7 from:

massXpert: a cross-platfom Free Software mass spectrometric package, by Filippo Rusconi (http://www.massxpert.org).

to:

@@massXpert: a cross-platfom Free Software mass spectrometric package,

 by Filippo Rusconi (http://www.massxpert.org).@@

August 20, 2007, at 12:18 PM by Filippo Rusconi -
Changed line 17 from:
  1. Implemented a feature whereby the user might define monomers to which a given chemical modification is restricted. For example, the "Phosphorylation" modification might be restricted to Seryl, Threonyl and Tyrosinyl monomers. When trying to use such a modification on a Glycyl monomer, the program would complain that Glycyl monomer is not a target of "Phosphorylation". This will be most useful for later features that will involve automatically screening modifications for mass matches between measured m/z values and theoretical ones. False positives will be prevented by ensuring that a match is not found by modifying a Glycyl monomer with "Phosphorylation", for example. In other words, more chemical intelligence is enshrined in the chemical modification object. A mechanism allowing easy overridding of the chemical limitations above is available to allow maximum flexibility.
to:
  1. Implemented a feature whereby the user might define monomers to which a given chemical modification is restricted. For example, the "Phosphorylation" modification might be restricted to Seryl, Threonyl and Tyrosinyl monomers. When trying to use such a modification on a Glycyl monomer, the program would complain that Glycyl monomer is not a target of "Phosphorylation". This will be most useful for later features that will involve automatically screening modifications for mass matches between measured m/z values and theoretical ones. False positives will be prevented by ensuring that a match is not found by modifying a Glycyl monomer with "Phosphorylation", for example. In other words, more chemical intelligence is enshrined in the chemical modification object. A mechanism allowing easy overriding of the chemical limitations above is available to allow maximum flexibility.
August 20, 2007, at 12:16 PM by Filippo Rusconi -
Changed line 17 from:
  1. Implemented a feature whereby the user might define monomers to which a given chemical modification is restricted. For example, the "Phosphorylation" modification might be restricted to Seryl, Threonyl and Tyrosinyl monomers. When trying to use such a modification on a Glycyl monomer, the program would complain that Glycyl monomer is not a target of "Phosphorylation". This will be most useful for later features that will involve automatically screening modifications for mass matches between measured m/z values and theoretical ones. False positives will be prevented by ensuring that a match is not found by modifying a Glycyl monomer with "Phosphorylation", for example. In other words, more chemical intelligence is enshrined in the chemical modification object.
to:
  1. Implemented a feature whereby the user might define monomers to which a given chemical modification is restricted. For example, the "Phosphorylation" modification might be restricted to Seryl, Threonyl and Tyrosinyl monomers. When trying to use such a modification on a Glycyl monomer, the program would complain that Glycyl monomer is not a target of "Phosphorylation". This will be most useful for later features that will involve automatically screening modifications for mass matches between measured m/z values and theoretical ones. False positives will be prevented by ensuring that a match is not found by modifying a Glycyl monomer with "Phosphorylation", for example. In other words, more chemical intelligence is enshrined in the chemical modification object. A mechanism allowing easy overridding of the chemical limitations above is available to allow maximum flexibility.
Changed lines 21-23 from:

to:
  1. Updated the french translation.

Changed lines 28-29 from:

Managed to get all the new monomer modification stuff coded and at least partly tested. Not released stuff yet, but this is what you will be getting as release 1.6.5 hits the streets: the modifications get chemical intelligence (as usual, only if the user wants to put some in) as they will be knowing what monomers they might modify and what not. Thus, when modifying monomers, if one monomer is not a target of the monomer being used, the program will complain and not perform the modification. However, it is possible to override the modification targets limitation and thus modify any monomer with that modification (flexibility for the user who knows what she is doing). As soon as all this new stuff is tested, it will be release.

to:

Managed to get all the new monomer modification stuff coded and at least partly tested. Not released stuff yet, but this is what you will be getting as release 1.6.5 hits the streets: the modifications get chemical intelligence (as usual, only if the user wants to put some in) as they will be knowing what monomers they might modify and what not. Thus, when modifying monomers, if one monomer is not a target of the monomer being used, the program will complain and not perform the modification. However, it is possible to override the modification targets limitation and thus modify any monomer with that modification (flexibility for the user who knows what she is doing). As soon as all this new stuff is tested, it will be released.

August 20, 2007, at 12:14 PM by Filippo Rusconi - Main massxpert page
Changed lines 5-7 from:

massXpert: a Free Software mass spectrometric package, by Filippo Rusconi (http://www.massxpert.org).

to:

massXpert: a cross-platfom Free Software mass spectrometric package, by Filippo Rusconi (http://www.massxpert.org).

Changed line 10 from:

Get tons of bug reports and patches from users ! Test the software myself with real mass spectrometric experiments (lots of these await me).

to:

Get tons of bug reports and patches from users ! Test the software myself with real mass spectrometric experiments (lots of these await me). Implement a much more powerful m/z comparison paradigm (lists of m/z values, measured and theoretical, should be easily compared so as to find matches between the m/z in the lists using different z values (ion charge) or by performing combinatorial chemistry using the list of modifications available in the polymer chemistry definition.

Added line 12:
Changed lines 17-18 from:
  1. Implemented a feature whereby the user might define monomers to which a given chemical modification is restricted. For example, the "Phosphorylation" modification might be restricted to Seryl, Threonyl and Tyrosinyl monomers. When trying to use such a modification on a Glycyl monomer, the program would complain that Glycyl monomer is not a target of "Phosphorylation". This will be most useful for later features that will involve automatically screening modifications for mass matches between measured m/z values and theoretical ones. False positives will be prevented by ensuring that a match is not found by modifying a Glycyl monomer with "Phosphorylation", for example. In other words, more chemical intelligence is enshrined in the chemical modification object.
to:
  1. Implemented a feature whereby the user might define monomers to which a given chemical modification is restricted. For example, the "Phosphorylation" modification might be restricted to Seryl, Threonyl and Tyrosinyl monomers. When trying to use such a modification on a Glycyl monomer, the program would complain that Glycyl monomer is not a target of "Phosphorylation". This will be most useful for later features that will involve automatically screening modifications for mass matches between measured m/z values and theoretical ones. False positives will be prevented by ensuring that a match is not found by modifying a Glycyl monomer with "Phosphorylation", for example. In other words, more chemical intelligence is enshrined in the chemical modification object.
  2. Fixed a bunch of bugs, in particular related to the chemical modification of monomers. These bugs were gui-related bugs, not actually chemistry- or mass-related bugs, so no fear for mass calculations.
  3. Fixed a bug which would show up when using atom symbols of more than two characters.
  4. Updated the User Manual so as to reflect the changes in the features of the program.

August 20, 2007, at 12:08 PM by Filippo Rusconi - Main massxpert page
Changed lines 12-13 from:

July 2007

to:

August 2007

Added lines 14-19:

20

Last version: 1.6.5.

  1. Implemented a feature whereby the user might define monomers to which a given chemical modification is restricted. For example, the "Phosphorylation" modification might be restricted to Seryl, Threonyl and Tyrosinyl monomers. When trying to use such a modification on a Glycyl monomer, the program would complain that Glycyl monomer is not a target of "Phosphorylation". This will be most useful for later features that will involve automatically screening modifications for mass matches between measured m/z values and theoretical ones. False positives will be prevented by ensuring that a match is not found by modifying a Glycyl monomer with "Phosphorylation", for example. In other words, more chemical intelligence is enshrined in the chemical modification object.

July 2007


July 28, 2007, at 07:18 PM by 82.225.200.216 -
Changed lines 16-17 from:

Managed to get all the new monomer modification stuff coded and at least partly tested. Not released stuff yet, but this is what you will be getting as release 1.6.5 hits the streets: the modifications get chemical intelligence (as usual, only if the user wants to put some in) as they will be knowing what mononmers they might modify and what not. Thus, when modifying monomers, if one monomer is not a target of the monomer being used, the program will complain and not perform the modification. However, it is possible to override the modification targets limitation and thus modify any monomer with that modification (flexibility for the user who knows what she is doing). As soon as all this new stuff is tested, it will be release.

to:

Managed to get all the new monomer modification stuff coded and at least partly tested. Not released stuff yet, but this is what you will be getting as release 1.6.5 hits the streets: the modifications get chemical intelligence (as usual, only if the user wants to put some in) as they will be knowing what monomers they might modify and what not. Thus, when modifying monomers, if one monomer is not a target of the monomer being used, the program will complain and not perform the modification. However, it is possible to override the modification targets limitation and thus modify any monomer with that modification (flexibility for the user who knows what she is doing). As soon as all this new stuff is tested, it will be release.

July 28, 2007, at 07:12 PM by 82.225.200.216 -
Added lines 15-17:

28

Managed to get all the new monomer modification stuff coded and at least partly tested. Not released stuff yet, but this is what you will be getting as release 1.6.5 hits the streets: the modifications get chemical intelligence (as usual, only if the user wants to put some in) as they will be knowing what mononmers they might modify and what not. Thus, when modifying monomers, if one monomer is not a target of the monomer being used, the program will complain and not perform the modification. However, it is possible to override the modification targets limitation and thus modify any monomer with that modification (flexibility for the user who knows what she is doing). As soon as all this new stuff is tested, it will be release.

July 24, 2007, at 09:24 PM by 82.225.200.216 -
Changed line 18 from:
  1. Improved the handling of monomer modifications when no svg file has been defined for them (this was a bug report by a user who did not read the doc and defined a new modification in the polymer chemistry definition without assigning a modification svg graphics file. When using that modification massXpert would crash. This no longer is the case, as now a default modification svg file is provided in the polymer chemistry definition directory and if such file is not found one svg file is hard-coded in massxpert so as to be perfectly crash-proof on that matter;
to:
  1. Improved the handling of monomer modifications when no svg file has been defined for them (this was a bug report by a user who did not read the doc and defined a new modification in the polymer chemistry definition without assigning a modification svg graphics file. When using that modification massXpert would crash. This no longer is the case, as now a default modification svg file is provided in the polymer chemistry definition directory and if such file is not found, one svg file is hard-coded in massxpert so as to be perfectly crash-proof on that matter;
Changed lines 20-21 from:
to:
  1. Performed user-invisible improvements in the development toolchain so as to prepare more reliable packages (Debian/MS-Windows) binary packages.

July 24, 2007, at 09:20 PM by 82.225.200.216 -
Added lines 15-21:

24

Last version: 1.6.4.

  1. Setup the translation framework and fully translated the program to french (one of my native tongues, with italian). If anybody would like to help, I'm receiving any proposal (I'd be happy with a german translation or spanish, for example, but any other is all the more welcome);
  2. Improved the handling of monomer modifications when no svg file has been defined for them (this was a bug report by a user who did not read the doc and defined a new modification in the polymer chemistry definition without assigning a modification svg graphics file. When using that modification massXpert would crash. This no longer is the case, as now a default modification svg file is provided in the polymer chemistry definition directory and if such file is not found one svg file is hard-coded in massxpert so as to be perfectly crash-proof on that matter;
  3. Fixed a bunch of bugs around the modifications being declared in the polymer chemistry definitions but not available as svg files;

July 21, 2007, at 08:37 PM by 82.225.200.216 -
Changed lines 16-17 from:

Fixed the User Manual (missing chapters) in packages 1.6.3 (unless for the debian doc package that was updated). The fixed User Manual is available on-line in pdf or html format.

to:

Fixed the User Manual (missing chapters) in packages 1.6.3 (unless for the debian doc package that was updated). The fixed User Manual is available on-line in pdf or html format. I am working hard today to improve the toolchain so as to avoid this kind of mishandling of the packages.

July 21, 2007, at 09:01 AM by 82.225.200.216 -
Changed lines 16-17 from:

Fixed the User Manual (missing chapters), that is now available in pdf or html format.

to:

Fixed the User Manual (missing chapters) in packages 1.6.3 (unless for the debian doc package that was updated). The fixed User Manual is available on-line in pdf or html format.

July 21, 2007, at 08:43 AM by 82.225.200.216 -
Added lines 15-17:

21

Fixed the User Manual (missing chapters), that is now available in pdf or html format.

July 20, 2007, at 08:24 PM by 82.225.200.216 -
Changed lines 22-24 from:
  1. Greatly improved the documentation by making it more concise and specific.
  2. Hopefully fixed the problematic MS-Windows package creation procedure.
to:
  1. Greatly improved the documentation by making it more concise and specific.
  2. Hopefully fixed the problematic MS-Windows package creation procedure.
  3. Detected nasty behaviour of the Qt's GraphicsScene widget which is different (for the same code) from GNU/Linux to MS-Windows. Will have to file a bug report to the Trolls.
July 20, 2007, at 08:22 PM by 82.225.200.216 -
Changed line 17 from:
  1. Added possibility to modify a polymer sequence using arbitrary formulas, not necessarily modifications from the polymer chemistry definition.
to:
  1. Added possibility to modify a polymer sequence using arbitrary formulas, not necessarily modifications from the polymer chemistry definition. The use of modifications with no graphical rendering svg vignettes is in the works. It will be based on the use of a default modification-rendering file which will be used whenever no svg file is associated to any given modification in the polymer chemistry definition.
July 20, 2007, at 06:38 PM by 82.225.200.216 -
Changed lines 25-26 from:

Note that it is possible to install this 1.6.3 version using either the "Next-next-next" setup package or simply by extracting the zip file in C:\Program Files\massxpert. In this latter case, then, no icons are installed. To uninstall, simply remove the C:\Program Files\massxpert directory, and that's done.

to:

Note that it is possible to install this 1.6.3 version using either the "Next-next-next" setup package or simply by extracting the zip file in C:\Program Files\massxpert. In this latter case, then, no icons are installed. To uninstall, simply remove the C:\Program Files\massxpert directory, and that's done. The GNU/Linux folks have no problem with the source/binary tarball or the binary Debian GNU/Linux package.

July 20, 2007, at 06:37 PM by 82.225.200.216 -
Added lines 25-26:

Note that it is possible to install this 1.6.3 version using either the "Next-next-next" setup package or simply by extracting the zip file in C:\Program Files\massxpert. In this latter case, then, no icons are installed. To uninstall, simply remove the C:\Program Files\massxpert directory, and that's done.

July 20, 2007, at 06:34 PM by 82.225.200.216 -
Added lines 15-24:

20

Last version: 1.6.3.

  1. Added possibility to modify a polymer sequence using arbitrary formulas, not necessarily modifications from the polymer chemistry definition.
  2. Fixed a bunch of bugs with the modifications in the modification_dictionary file and related graphical vignettes.
  3. Updated the code to comply with new Qt version 4.3.0 on GNU/Linux.
  4. Some glitches fixed in the sequence editor window.
  5. Improved recorder output in the calculator window.
  6. Greatly improved the documentation by making it more concise and specific.
  7. Hopefully fixed the problematic MS-Windows package creation procedure.
July 19, 2007, at 06:33 PM by 82.225.200.216 -
Changed lines 16-17 from:

Still having a problem with the windows installer (Innosetup). Instead, unzipping this zip file in the C:\Program Files directory, so that massXpert is in C:\Program Files\massxpert works flawlessly. You only need to run C:\Program Files\massxpert\basebin\massxpert.exe.

to:

Still having a problem with the windows installer (Innosetup). Instead, unzipping this zip file in the C:\Program Files directory, so that massXpert is in C:\Program Files\massxpert works flawlessly. You only need to run C:\Program Files\massxpert\basebin\massxpert.exe. The user manual is in C:\Program Files\massxpert\doc\userman.

July 19, 2007, at 06:31 PM by 82.225.200.216 -
Changed lines 16-17 from:

Still having a problem with the windows installer (Innosetup). Instead, unzipping this [[http://www.massxpert.org/downloads/mswindows/ |zip file] in the C:\Program Files directory, so that massXpert is in C:\Program Files\massxpert works flawlessly. You only need to run C:\Program Files\massxpert\basebin\massxpert.exe.

to:

Still having a problem with the windows installer (Innosetup). Instead, unzipping this zip file in the C:\Program Files directory, so that massXpert is in C:\Program Files\massxpert works flawlessly. You only need to run C:\Program Files\massxpert\basebin\massxpert.exe.

July 19, 2007, at 06:30 PM by 82.225.200.216 -
Added lines 15-17:

19

Still having a problem with the windows installer (Innosetup). Instead, unzipping this [[http://www.massxpert.org/downloads/mswindows/ |zip file] in the C:\Program Files directory, so that massXpert is in C:\Program Files\massxpert works flawlessly. You only need to run C:\Program Files\massxpert\basebin\massxpert.exe.

July 17, 2007, at 07:23 PM by 82.225.200.216 -
Changed lines 16-17 from:

Update: The new package is now available in the downloads directory... Attention MS-Windows package is flawed. I am correcting it. I have removed it for now.

to:

Update: A fixed package is now available again in the downloads directory... Attention MS-Windows package is flawed. I am correcting it. I have removed it for now.

July 17, 2007, at 07:22 PM by 82.225.200.216 -
Changed lines 16-18 from:

Update: The new package is now available in the downloads directory... Attention MS-Windows package is flawed. I am correcting it. I have removed it for now.

to:

Update: The new package is now available in the downloads directory... Attention MS-Windows package is flawed. I am correcting it. I have removed it for now.

July 17, 2007, at 07:19 PM by 82.225.200.216 -
Added line 16:

Update: The new package is now available in the downloads directory...

July 17, 2007, at 05:28 PM by 82.225.200.216 -
Added lines 15-17:

17

Attention MS-Windows package is flawed. I am correcting it. I have removed it for now.

July 12, 2007, at 12:19 PM by 193.54.201.151 -
Added lines 15-17:

12

Last version: 1.6.2. Fixed a nasty bug that would show up only during mass calculation of oligomers obtained by cleaving a sequence with a cleaving agent that applies a cleavage rule to the oligomer (and only in case the charge of the oligomer is > 1).

July 10, 2007, at 09:46 PM by 82.225.200.216 -
Added lines 15-17:

10

Last version: 1.6.1. Implemented a proof-of-concept version of a facility to compare mass lists. If matches cannot be done between lists, try to force matches using a list of modifications. This should be useful when trying to find peaks in a mass spectrum that might be of interest because they do not match theoretically-obtained masses (like by cleavage in silico). Updated the documentation. Also added a plugin to help convert numerical values from one locale to another (for example from locale fr_FR to locale en_US) which is useful if the mass spectrometer acquisition software does not comply with the locale of the MS-Windows platform.

July 03, 2007, at 05:03 PM by 82.225.200.216 -
Changed lines 16-17 from:

The big single Debian package is now divided into two distinct packages: one for the binary program and its chemical data (massxpert) and one for the User Manual (massxpert-doc). Go get them here.

to:

The big single Debian package is now divided into two distinct packages: one for the binary program and its chemical data (massxpert) and one for the User Manual (massxpert-doc). Go get them here. Installing is as easy as usual (as root): dpkg -i massxpert_1.6.0-rc2-1_i386.deb and dpkg -i massxpert-doc_1.6.0-rc2-1_i386.deb.

July 03, 2007, at 01:25 PM by 193.54.201.151 -
Added lines 15-17:

3

The big single Debian package is now divided into two distinct packages: one for the binary program and its chemical data (massxpert) and one for the User Manual (massxpert-doc). Go get them here.

July 03, 2007, at 12:40 PM by 193.54.201.151 -
Changed lines 16-17 from:

Made a new Debian package. Download it here and, as root, issue that command: dpkg -i massxpert_1.6.0-rc2-1_i386.deb. Happy massXpert'ing.

to:

Made a new Debian package. Download it here and, as root, issue that command: dpkg -i massxpert_1.6.0-rc2-1_i386.deb. That's a single package including absolutely everything: the program, the chemical data and the documentation. I am working on separated binary packages starting from a single source. Happy massXpert'ing.

July 02, 2007, at 09:48 PM by 82.225.200.216 -
Added lines 15-17:

2

Made a new Debian package. Download it here and, as root, issue that command: dpkg -i massxpert_1.6.0-rc2-1_i386.deb. Happy massXpert'ing.

July 01, 2007, at 10:01 AM by 82.225.200.216 -
Changed lines 16-19 from:

The first release of massXpert licensed under the GNU General Public License version 3 (published by the FSF is available as version 1.6.0-rc2.

to:

The first release of massXpert licensed under the GNU General Public License version 3 (published by the FSF the 29th of june 2007) is available as version 1.6.0-rc2.

July 01, 2007, at 10:00 AM by 82.225.200.216 -
Changed lines 16-19 from:

The first release of massXpert licensed under the GNU General Public License 'version 3' (published by the FSF is available as version 1.6.0-rc2.

to:

The first release of massXpert licensed under the GNU General Public License version 3 (published by the FSF is available as version 1.6.0-rc2.

July 01, 2007, at 09:59 AM by 82.225.200.216 -
Changed lines 16-18 from:

The first release of massXpert licensed using the GNU General Public License 'version 3' (published by the FSF is available as version 1.6.0-rc2.

to:

The first release of massXpert licensed under the GNU General Public License 'version 3' (published by the FSF is available as version 1.6.0-rc2.

July 01, 2007, at 09:37 AM by 82.225.200.216 -
Changed line 13 from:

June 2007

to:

July 2007

Added lines 15-20:

1

The first release of massXpert licensed using the GNU General Public License 'version 3' (published by the FSF is available as version 1.6.0-rc2.

June 2007


June 27, 2007, at 07:34 PM by 82.225.200.216 -
Added lines 3-7:

Citation of this work:

massXpert: a Free Software mass spectrometric package, by Filippo Rusconi (http://www.massxpert.org).

June 27, 2007, at 06:35 PM by 82.225.200.216 -
Changed line 5 from:

Still have to write the user manual, which shoud be available in the form of an HTML tree and in the form of a PDF file. The original source code for the user manual are LaTeX files.

to:

Get tons of bug reports and patches from users ! Test the software myself with real mass spectrometric experiments (lots of these await me).

Changed lines 10-12 from:
to:

27

The first public release of massXpert is now available for download. The software is available as a source tarball for all platforms (GNU/Linux, MacOSX and MS-Windows). There are binary packages for GNU/linux and for MS-Windows (one Inno Setup executable installation program; thanks Jordan Russell). The User Manual is available in the packages and the potential users are invited to peruse the installation chapter in the User Manual available online.

June 16, 2007, at 01:54 PM by 82.225.200.216 -
Changed line 5 from:

Write the user manual, which shoud be available in the form of an HTML tree and in the form of a PDF file. The original source code for the user manual are LaTeX files.

to:

Still have to write the user manual, which shoud be available in the form of an HTML tree and in the form of a PDF file. The original source code for the user manual are LaTeX files.

June 16, 2007, at 01:47 PM by 82.225.200.216 -
Changed lines 5-7 from:
to:

Write the user manual, which shoud be available in the form of an HTML tree and in the form of a PDF file. The original source code for the user manual are LaTeX files.

June 16, 2007, at 01:45 PM by 82.225.200.216 -
Deleted lines 2-3:

May 2007


Changed lines 4-5 from:

I still have to write all the code to make any kind of result available either as text files or as clipboard text. That's a lot of work.

to:

June 2007


16

Wrote all the code allowing the user to export any kind of data either to the clipboard or to a file on disk or both.

May 2007


June 16, 2007, at 11:33 AM by 82.225.200.216 -
Changed line 18 from:

After a full (yester-)day of tweaking the qmake configuration, I finally got the project to build/install identically on GNU/Linux (Debian) and MS-Windows-XP. The version of the release Qt library on MS-Windows is 4.2.3. All in all, it really seems that the cross-platform promises of the Qt library are well met! This means I'll soon be able to provide source and binary packages.

to:

After a full (yester-)day of tweaking the qmake configuration, I finally got the project to build/install identically on GNU/Linux (Debian) and MS-Windows-XP. The version of the released Qt library on MS-Windows is 4.2.3. All in all, it really seems that the cross-platform promises of the Qt library are well met! This means I'll soon be able to provide source and binary packages.

May 26, 2007, at 09:25 PM by 82.225.200.216 -
Changed lines 9-10 from:

Code cleanup, code documentation and bug fixing these days.

to:

Code cleanup, code documentation and bug fixing these days. In the next week I'll be busy attending a conference on DNA replication, recombination and repair in Hyères, South of France.

May 26, 2007, at 09:13 PM by 82.225.200.216 -
Changed lines 9-10 from:

Code cleanup these days and bug fixing activity.

to:

Code cleanup, code documentation and bug fixing these days.

May 26, 2007, at 12:50 PM by 82.225.200.216 -
Added lines 8-10:

25

Code cleanup these days and bug fixing activity.

May 22, 2007, at 05:50 PM by 82.225.200.216 -
Changed lines 6-7 from:

I still have to write all the results exporting code. That's a lot of work.

to:

I still have to write all the code to make any kind of result available either as text files or as clipboard text. That's a lot of work.

May 22, 2007, at 05:34 PM by 82.225.200.216 -
Changed lines 6-7 from:

I still have to port the code for the pI calculations. That's a lot of work. Also, I still have to write all the results exporting code. Yet some more work.

to:

I still have to write all the results exporting code. That's a lot of work.

22

Finally finished coding the "Net Charge" and "pI" calculations. We are nearing the finishing of the GNU polyxmass port to Qt! I also managed to fix some bugs in the mean time.

May 15, 2007, at 04:45 PM by 82.225.200.216 -
Changed lines 9-10 from:

Being forced to bed due to severe back-ache, I could put my laptop at work with computation-intensive activities: simulating isotopic patterns for small proteins. The feature is now implemented and is reacheable via the XpertCalc module. Still have some minor tweaks to do to that code but the feature is cool. This is a feature that GNU polyxmass did not have!

to:

Being forced to bed due to severe back-ache, I could put my laptop at work with computation-intensive activities: simulating isotopic patterns for small proteins. The feature is now implemented and is reacheable via the XpertCalc module. Still have some minor tweaks to do to that code but the feature is cool. This is a feature that GNU polyxmass did not have! Check the screenshot.

May 14, 2007, at 08:42 PM by 82.225.200.216 -
Changed lines 5-10 from:
to:

Plans

I still have to port the code for the pI calculations. That's a lot of work. Also, I still have to write all the results exporting code. Yet some more work.

14

Being forced to bed due to severe back-ache, I could put my laptop at work with computation-intensive activities: simulating isotopic patterns for small proteins. The feature is now implemented and is reacheable via the XpertCalc module. Still have some minor tweaks to do to that code but the feature is cool. This is a feature that GNU polyxmass did not have!

May 02, 2007, at 06:03 PM by 82.225.200.216 -
Changed line 7 from:

After a full (yester-)day of tweaking the qmake configuration, I finally got the project to build/install identically on GNU/Linux (Debian) and MS-Windows-XP. I am now trying to setup a development environment on MS-Windows-XP using MinGW/MSys according to a procedure that I found on http://www.storybridge.org. If that works, I'll publish an equivalent story so that readers of this site will be able to build massXpert from sources. All in all, it really seems that the cross-platform promises of the Qt library are well met! This means I'll soon be able to provide source and binary packages.

to:

After a full (yester-)day of tweaking the qmake configuration, I finally got the project to build/install identically on GNU/Linux (Debian) and MS-Windows-XP. The version of the release Qt library on MS-Windows is 4.2.3. All in all, it really seems that the cross-platform promises of the Qt library are well met! This means I'll soon be able to provide source and binary packages.

May 01, 2007, at 10:29 AM by 82.225.200.216 -
Changed line 7 from:

After a full day of tweaking the qmake configuration (yesterday), I finally got the project to build/install identically on GNU/Linux (Debian) and MS-Windows-XP. I am now trying to setup a development environment on MS-Windows-XP using MinGW/MSys according to a procedure that I found on http://www.storybridge.org. If that works, I'll publish an equivalent story so that readers of this site will be able to build massXpert from sources. All in all, it really seems that the cross-platform promises of the Qt library are well met! This means I'll soon be able to provide source and binary packages.

to:

After a full (yester-)day of tweaking the qmake configuration, I finally got the project to build/install identically on GNU/Linux (Debian) and MS-Windows-XP. I am now trying to setup a development environment on MS-Windows-XP using MinGW/MSys according to a procedure that I found on http://www.storybridge.org. If that works, I'll publish an equivalent story so that readers of this site will be able to build massXpert from sources. All in all, it really seems that the cross-platform promises of the Qt library are well met! This means I'll soon be able to provide source and binary packages.

May 01, 2007, at 10:28 AM by 82.225.200.216 -
Changed line 7 from:

After a full day of tweaking the qmake configuration (yesterday), I finally got the project to build/install identically on GNU/Linux (Debian) and MS-Windows-XP. I am now trying to setup a development environment on MS-Windows-XP using MinGW/MSys according to a procedure that I found on storybridge.org?. The cross-platform promises of the Qt library are well met! This means I'll soon be able to provide source and binary packages.

to:

After a full day of tweaking the qmake configuration (yesterday), I finally got the project to build/install identically on GNU/Linux (Debian) and MS-Windows-XP. I am now trying to setup a development environment on MS-Windows-XP using MinGW/MSys according to a procedure that I found on http://www.storybridge.org. If that works, I'll publish an equivalent story so that readers of this site will be able to build massXpert from sources. All in all, it really seems that the cross-platform promises of the Qt library are well met! This means I'll soon be able to provide source and binary packages.

May 01, 2007, at 10:26 AM by 82.225.200.216 -
Changed line 7 from:

After a full day of tweaking the qmake configuration, I finally got the project to build/install identically on GNU/Linux (Debian) and MS-Windows-XP. The cross-platform promises of the Qt library are well met! This means I'll soon be able to provide source and binary packages.

to:

After a full day of tweaking the qmake configuration (yesterday), I finally got the project to build/install identically on GNU/Linux (Debian) and MS-Windows-XP. I am now trying to setup a development environment on MS-Windows-XP using MinGW/MSys according to a procedure that I found on storybridge.org?. The cross-platform promises of the Qt library are well met! This means I'll soon be able to provide source and binary packages.

April 30, 2007, at 10:07 PM by 82.225.200.216 -
Changed line 3 from:

April 2007

to:

May 2007

Added lines 6-12:

1

After a full day of tweaking the qmake configuration, I finally got the project to build/install identically on GNU/Linux (Debian) and MS-Windows-XP. The cross-platform promises of the Qt library are well met! This means I'll soon be able to provide source and binary packages.

April 2007


April 29, 2007, at 04:55 PM by 82.225.200.216 -
Changed lines 38-40 from:

Go see the screenshots to ascertain that work is indeed going on!

to:

Go see the screenshots to ascertain that work is indeed going on!

April 29, 2007, at 04:54 PM by 82.225.200.216 -
Changed lines 11-12 from:

At the moment massXpert is able to do a number of interesting things and runs equally well on GNU/Linux and MS-Windows-XP. I still have to find a Mac-OS-X computer to build the package and to be able to distribute binary packages along with the source code.

to:

At the moment massXpert is able to do a number of interesting things and runs equally well on GNU/Linux and MS-Windows-XP. I still have to find a Mac-OS-X computer to build the package and to be able to distribute binary packages along with the source code.

Changed lines 16-19 from:

I have bought massxpert.org for a duration of three years. As soon as the site is ready, I'll migrate all this stuff in it. The name of this new projet will therefore be 'massXpert'. It is in fact a revival of the massXpert project I published in Bioinformatics in 2002. Note however, that the present massXpert project is a full rewrite of the GNU polyXmass project and as such is so much more powerful than the initial massXpert project.

'For this reason, whenever you see massxtreme in the remaining of this page, you should read massxpert.'

to:

I have bought massxpert.org for a duration of three years. As soon as the site is ready, I'll migrate all this stuff in it. The name of this new projet will therefore be 'massXpert'. It is in fact a revival of the massXpert project I published in Bioinformatics in 2002. Note however, that the present massXpert project is a full rewrite of the GNU polyXmass project and as such is so much more powerful than the initial massXpert project.

'For this reason, whenever you see mass[Xx]treme in the remaining of this page, you should read mass[Xx]pert.'

Changed lines 22-24 from:

The port of the fundamental features from polyXmass is well on track. First of all the usual paradigm of real-time automatic mass calculation in the sequence editor is done. Second, the program now allows to make the biochemical (cleavage) and the gas-phase fragmentation simulations. I have compiled it successfully on MS-Windows XP and it runs exactly the same as on GNU/Linux. I still have to code the third fundamental feature, that is mass search in the polymer sequence. After that, I'll start coding of the copy/paste operations (with sequence verification) in the sequence editor and the exporting of the data to the clipboard. When all the coding is almost finished, I'll have to search for a new name. Am I going to use massXtreme, massXpress or massXpert (one name I used for a program that I published in 2002) ? Screenshots: screenshots.

to:

The port of the fundamental features from polyXmass is well on track. First of all the usual paradigm of real-time automatic mass calculation in the sequence editor is done. Second, the program now allows to make the biochemical (cleavage) and the gas-phase fragmentation simulations. I have compiled it successfully on MS-Windows XP and it runs exactly the same as on GNU/Linux. I still have to code the third fundamental feature, that is mass search in the polymer sequence. After that, I'll start coding of the copy/paste operations (with sequence verification) in the sequence editor and the exporting of the data to the clipboard. When all the coding is almost finished, I'll have to search for a new name. Am I going to use massXtreme, massXpress or massXpert (one name I used for a program that I published in 2002) ? Screenshots: screenshots.

April 29, 2007, at 04:52 PM by 82.225.200.216 -
Changed lines 16-17 from:

I have bought massxpert.org for a duration of three years. As soon as the site is ready, I'll migrate all this stuff in it. The name of this new projet will therefore be 'massXpert'. It is in fact a revival of the massXpert project I published in Bioinformatics in 2002. Note however, that the present massXpert project is a full rewrite of the GNU polyXmass project and as such is so much more powerful than the initial massXpert project.

to:

I have bought massxpert.org for a duration of three years. As soon as the site is ready, I'll migrate all this stuff in it. The name of this new projet will therefore be 'massXpert'. It is in fact a revival of the massXpert project I published in Bioinformatics in 2002. Note however, that the present massXpert project is a full rewrite of the GNU polyXmass project and as such is so much more powerful than the initial massXpert project.

'For this reason, whenever you see massxtreme in the remaining of this page, you should read massxpert.'

Changed line 30 from:

Feb. 2007

to:

February 2007

Changed line 41 from:

Jan. 2007

to:

January 2007

April 29, 2007, at 04:50 PM by 82.225.200.216 -
Added line 5:
April 29, 2007, at 04:49 PM by 82.225.200.216 -
Added line 5:

29

April 29, 2007, at 04:49 PM by 82.225.200.216 -
Added lines 13-21:

13

I have bought massxpert.org for a duration of three years. As soon as the site is ready, I'll migrate all this stuff in it. The name of this new projet will therefore be 'massXpert'. It is in fact a revival of the massXpert project I published in Bioinformatics in 2002. Note however, that the present massXpert project is a full rewrite of the GNU polyXmass project and as such is so much more powerful than the initial massXpert project.

From a coding standpoint, the mass search feature that was still lacking in massXpert is now implemented in a way that is more powerful than in GNU polyXmass. Further, the copy/paste functionality is now implemented, which makes it possible to create new sequences by copying/pasting sequences off a browser. A powerful "purification" dialog displays all the material that does not corrspond to valid monomer codes. The user may purify the sequence before actually copying it in the sequence editor.

The port of the fundamental features from polyXmass is well on track. First of all the usual paradigm of real-time automatic mass calculation in the sequence editor is done. Second, the program now allows to make the biochemical (cleavage) and the gas-phase fragmentation simulations. I have compiled it successfully on MS-Windows XP and it runs exactly the same as on GNU/Linux. I still have to code the third fundamental feature, that is mass search in the polymer sequence. After that, I'll start coding of the copy/paste operations (with sequence verification) in the sequence editor and the exporting of the data to the clipboard. When all the coding is almost finished, I'll have to search for a new name. Am I going to use massXtreme, massXpress or massXpert (one name I used for a program that I published in 2002) ? Screenshots: screenshots.

March 2007

Changed lines 23-53 from:

April 2007

Big news: I have bought massxpert.org for a duration of three years. As soon as the site is ready, I'll migrate all this stuff in it. The name of this new projet will therefore be 'massXpert'. It is in fact a revival of the massXpert project I published in Bioinformatics in 2002. Note however, that the present massXpert project is a full rewrite of the GNU polyXmass project and as such is so much more powerful than the initial massXpert project.

From a coding standpoint, the mass search feature that was still lacking in massXpert is now implemented in a way that is more powerful than in GNU polyXmass. Further, the copy/paste functionality is now implemented, which makes it possible to create new sequences by copying/pasting sequences off a browser. A powerful "purification" dialog displays all the material that does not corrspond to valid monomer codes. The user may purify the sequence before actually copying it in the sequence editor.

  • April 2007 massXtreme coding The port of the fundamental features from polyXmass is well on track. First of all the usual paradigm of real-time automatic mass calculation in the sequence editor is done. Second, the program now allows to make the biochemical (cleavage) and the gas-phase fragmentation simulations. I have compiled it successfully on MS-Windows XP and it runs exactly the same as on GNU/Linux. I still have to code the third fundamental feature, that is mass search in the polymer sequence. After that, I'll start coding of the copy/paste operations (with sequence verification) in the sequence editor and the exporting of the data to the clipboard. When all the coding is almost finished, I'll have to search for a new name. Am I going to use massXtreme, massXpress or massXpert (one name I used for a program that I published in 2002) ? Screenshots: screenshots.

  • March 2007 massXtreme coding The sequence editor is now able to perform all the editing tasks that one would expect from a sequence editor (not yet copy/paste stuff, though). It is now possible to modify any monomer in the sequence and to modify any/both end(s) of the polymer sequence. In the former case, the chemically modified monomer gets a redraw in the sequence with the modification vignette being transparently composited onto the non-modified monomer vignette.

  • Feb. 2007 massXtreme coding Well, the program is coming along well. I even have a number of screenshots of Mac-OS-X and MS-Windows XP massXtreme sessions. The Mac-OS-X stuff was provided by my dear friend Olivier Kaloudoff of Linux-Azur fame.

As of today, the editor can load a polymer sequence and display it, with all the sequence scrolling and line numbering OK, but not much more than that, for the moment :-).

Note that the sequence rendering is now completely SVG-based, so that it is based on a widely popular scalar vector graphics format that is a web consortium standard (w3). Also, the rendering is always at the best resolution whatever the size of the monomer vignettes. My vignettes were prepared using the wonderful Inkscape program although I guess Karbon would do also.

Go see the screenshots to ascertain that work is indeed going on!

  • Jan. 2007 massXtreme coding Yeah, it is proceeding smoothly. I have finished porting the atom and polymer chemistry definition infrastructure. The chemical desktop calculator is almost finished also. A conspicuous part of the low-level chemical modelling library is ported and working. I'll have to start coding the polymer sequence editor, which is a prerequisite for doing the hard-core mass spec/(bio)chemical simulations (which take place in the sequence editor module). Those interested in the alpha code can send an email (see below for mail addresses).

  • Jan. 2007 www.massxtreme.org I'll have to buy the www.massxtreme.org domain. Something like three or more years in a row. If anybody is willing to make a donation, I'll accept with immense pleasure :-)

  • Jan. 2007 Happy new year for those who are starting a new year these days !

  • November-December 2006 Following a number of requests about the portability of GNU polyxmass to either MacOSX and MS-Windows, I decided to develop its successor in C++ using a development toolkit renowned for its portability capabilities : the QT library from http://www.trolltech.com/products/qt/. This toolkit is published under the GNU General Public License and features all the technical requirements for writing a GUI mass spectrometric software that is maintainable and expandable (with the PyQT Python scripting module). This successor to GNU polyxmass will be called massXtreme. This program will not be endorsed by the GNU project, as it won't use the Gtk+ libraries anymore.
to:

The sequence editor is now able to perform all the editing tasks that one would expect from a sequence editor (not yet copy/paste stuff, though). It is now possible to modify any monomer in the sequence and to modify any/both end(s) of the polymer sequence. In the former case, the chemically modified monomer gets a redraw in the sequence with the modification vignette being transparently composited onto the non-modified monomer vignette.

Feb. 2007


Well, the program is coming along well. I even have a number of screenshots of Mac-OS-X and MS-Windows XP massXtreme sessions. The Mac-OS-X stuff was provided by my dear friend Olivier Kaloudoff of Linux-Azur fame.

As of today, the editor can load a polymer sequence and display it, with all the sequence scrolling and line numbering OK, but not much more than that, for the moment :-).

Note that the sequence rendering is now completely SVG-based, so that it is based on a widely popular scalar vector graphics format that is a web consortium standard (w3). Also, the rendering is always at the best resolution whatever the size of the monomer vignettes. My vignettes were prepared using the wonderful Inkscape program although I guess Karbon would do also.

Go see the screenshots to ascertain that work is indeed going on!

Jan. 2007


Yeah, it is proceeding smoothly. I have finished porting the atom and polymer chemistry definition infrastructure. The chemical desktop calculator is almost finished also. A conspicuous part of the low-level chemical modelling library is ported and working. I'll have to start coding the polymer sequence editor, which is a prerequisite for doing the hard-core mass spec/(bio)chemical simulations (which take place in the sequence editor module). Those interested in the alpha code can send an email (see below for mail addresses).

I'll have to buy the www.massxtreme.org domain. Something like three or more years in a row. If anybody is willing to make a donation, I'll accept with immense pleasure :-)

'Happy new year for those who are starting a new year these days!'

November-December 2006


Following a number of requests about the portability of GNU polyxmass to either MacOSX and MS-Windows, I decided to develop its successor in C++ using a development toolkit renowned for its portability capabilities : the QT library from http://www.trolltech.com/products/qt/. This toolkit is published under the GNU General Public License and features all the technical requirements for writing a GUI mass spectrometric software that is maintainable and expandable (with the PyQT Python scripting module). This successor to GNU polyxmass will be called massXtreme. This program will not be endorsed by the GNU project, as it won't use the Gtk+ libraries anymore.

April 29, 2007, at 04:45 PM by 82.225.200.216 -
Changed line 3 from:
  • April 2007
to:

April 2007

Changed lines 7-8 from:
I first would like to mention some history about the massXpert project and next I'll start the distribution of the software. I still have some code to write and compilable packages to prepare. When everything is ready, I'll be back with news from the front.
to:

I first would like to mention some history about the massXpert project and next I'll start the distribution of the software. I still have some code to write and compilable packages to prepare. When everything is ready, I'll be back with news from the front.

At the moment massXpert is able to do a number of interesting things and runs equally well on GNU/Linux and MS-Windows-XP. I still have to find a Mac-OS-X computer to build the package and to be able to distribute binary packages along with the source code.

In the last weeks I discovered how easy it was to code Qt plugins, and coded a plugin with some sequence manipulation tools of interest according to the suggestions of my PhD student, Naïma Ouarti. She wanted to be able to convert a 1-letter code protein sequence to a 3-letter code protein sequence. I wrote that plugin so that such kind of conversions could be performed on the base of a dictionary listing code equivalences, like "M>Met" or "Arg>R", for example. Another function is simply the change of case from uppercase to lowercase and vice versa.

Changed lines 14-20 from:
At the moment massXpert is able to do a number of interesting things and runs equally well on GNU/Linux and MS-Windows-XP. I still have to find a Mac-OS-X computer to build the package and to be able to distribute binary packages along with the source code.

In the last weeks I discovered how easy it was to code Qt plugins, and coded a plugin with some sequence manipulation tools of interest according to the suggestions of my PhD student, Naïma Ouarti. She wanted to be able to convert a 1-letter code protein sequence to a 3-letter code protein sequence. I wrote that plugin so that such kind of conversions could be performed on the base of a dictionary listing code equivalences, like "M>Met" or "Arg>R", for example. Another function is simply the change of case from uppercase to lowercase and vice versa.

  • April 2007 Big news: I have bought massxpert.org for a duration of three years. As soon as the site is ready, I'll migrate all this stuff in it. The name of this new projet will therefore be 'massXpert'. It is in fact a revival of the massXpert project I published in Bioinformatics in 2002. Note however, that the present massXpert project is a full rewrite of the GNU polyXmass project and as such is so much more powerful than the initial massXpert project.
to:

April 2007

Big news: I have bought massxpert.org for a duration of three years. As soon as the site is ready, I'll migrate all this stuff in it. The name of this new projet will therefore be 'massXpert'. It is in fact a revival of the massXpert project I published in Bioinformatics in 2002. Note however, that the present massXpert project is a full rewrite of the GNU polyXmass project and as such is so much more powerful than the initial massXpert project.

April 29, 2007, at 04:44 PM by 82.225.200.216 -
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  • April 2007\\
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  • April 2007

April 29, 2007, at 04:44 PM by 82.225.200.216 -
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  • April 2007 The site is now up and running, thanks to the wonderful crew at bioinformatics.org (with a special mention to Jeff Bizzaro). I'll start populating this page day after day.
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  • April 2007
    The site is now up and running, thanks to the wonderful crew at bioinformatics.org (with a special mention to Jeff Bizzaro). I'll start populating this page day after day.
April 29, 2007, at 04:42 PM by 82.225.200.216 -
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At the moment massXpert is able to do a number of interesting things and runs equally well on GNU/Linux and MS-Windows-XP. I still have to find a Mac-OS-X computer to build the package and to be able to distribute binary packages along with the source code.

  • April 2007 Big news: I have bought massxpert.org for a duration of three years. As soon as the site is ready, I'll migrate all this stuff in it. The name of this new projet will therefore be 'massXpert'. It is in fact a revival of the massXpert project I published in Bioinformatics in 2002. Note however, that the present massXpert project is a full rewrite of the polyXmass project and as such is so much more powerful than the initial massXpert project. From a coding standpoint, the mass search feature that was still lacking in massXpert is now implemented in a way that is more powerful than in polyXmass. Further, the copy/paste functionality is now implemented, which makes it possible to create new sequences by copying/pasting sequences off a browser. A powerful "purification" dialog displays all the material that does not corrspond to valid monomer codes. The user may purify the sequence before actually copying it in the sequence editor.
to:
At the moment massXpert is able to do a number of interesting things and runs equally well on GNU/Linux and MS-Windows-XP. I still have to find a Mac-OS-X computer to build the package and to be able to distribute binary packages along with the source code.

In the last weeks I discovered how easy it was to code Qt plugins, and coded a plugin with some sequence manipulation tools of interest according to the suggestions of my PhD student, Naïma Ouarti. She wanted to be able to convert a 1-letter code protein sequence to a 3-letter code protein sequence. I wrote that plugin so that such kind of conversions could be performed on the base of a dictionary listing code equivalences, like "M>Met" or "Arg>R", for example. Another function is simply the change of case from uppercase to lowercase and vice versa.

  • April 2007 Big news: I have bought massxpert.org for a duration of three years. As soon as the site is ready, I'll migrate all this stuff in it. The name of this new projet will therefore be 'massXpert'. It is in fact a revival of the massXpert project I published in Bioinformatics in 2002. Note however, that the present massXpert project is a full rewrite of the GNU polyXmass project and as such is so much more powerful than the initial massXpert project.

From a coding standpoint, the mass search feature that was still lacking in massXpert is now implemented in a way that is more powerful than in GNU polyXmass. Further, the copy/paste functionality is now implemented, which makes it possible to create new sequences by copying/pasting sequences off a browser. A powerful "purification" dialog displays all the material that does not corrspond to valid monomer codes. The user may purify the sequence before actually copying it in the sequence editor.

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As of today, the editor can load a polymer sequence and display it, with all the sequence scrolling and line numbering OK, but not much more than that, for the moment :-).

Note that the sequence rendering is now completely SVG-based, so that it is based on a widely popular scalar vector graphics format that is a web consortium standard (w3). Also, the rendering is always at the best resolution whatever the size of the monomer vignettes. My vignettes were prepared using the wonderful Inkscape program although I guess Karbon would do also.

Go see the dated screenshots to ascertain that work is indeed going on!

to:
As of today, the editor can load a polymer sequence and display it, with all the sequence scrolling and line numbering OK, but not much more than that, for the moment :-).

Note that the sequence rendering is now completely SVG-based, so that it is based on a widely popular scalar vector graphics format that is a web consortium standard (w3). Also, the rendering is always at the best resolution whatever the size of the monomer vignettes. My vignettes were prepared using the wonderful Inkscape program although I guess Karbon would do also.

Go see the screenshots to ascertain that work is indeed going on!

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April 29, 2007, at 04:37 PM by 82.225.200.216 -
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I first would like to mention some history about the massXpert project and next I'll start the distribution of the software. I still have some code to write and compilable packages to prepare. When everything is ready, I'll be back with news from the front.

to:
I first would like to mention some history about the massXpert project and next I'll start the distribution of the software. I still have some code to write and compilable packages to prepare. When everything is ready, I'll be back with news from the front.
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At the moment massXpert is able to do a number of interesting things and runs equally well on GNU/Linux and MS-Windows-XP. I still have to find a Mac-OS-X computer to build the package and to be able to distribute binary packages along with the source code.

to:
At the moment massXpert is able to do a number of interesting things and runs equally well on GNU/Linux and MS-Windows-XP. I still have to find a Mac-OS-X computer to build the package and to be able to distribute binary packages along with the source code.
April 29, 2007, at 04:35 PM by 82.225.200.216 -
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I would like to mention some history about the massXpert project and next to start the distribution of the software.

to:

I first would like to mention some history about the massXpert project and next I'll start the distribution of the software. I still have some code to write and compilable packages to prepare. When everything is ready, I'll be back with news from the front.


April 29, 2007, at 04:10 PM by 82.225.200.216 -
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I would like to mention some history about the massXpert project and next to start the distribution of the software.

to:

I would like to mention some history about the massXpert project and next to start the distribution of the software.

April 29, 2007, at 03:20 PM by 82.225.200.216 -
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  • April 2007 The site is now up and running, thanks to crew at bioinformatics.org (with a special mention to Jeff Bizzaro). I'll start populating this page day after day.

I would like to mention some history about the massXpert project and next to start the distribution of the software.

to:
  • April 2007 The site is now up and running, thanks to the wonderful crew at bioinformatics.org (with a special mention to Jeff Bizzaro). I'll start populating this page day after day.

I would like to mention some history about the massXpert project and next to start the distribution of the software.

April 29, 2007, at 03:15 PM by 82.225.200.216 -
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  • April 2007 massXtreme coding The port of the fundamental features from polyXmass is well on track. First of all the usual paradigm of real-time automatic mass calculation in the sequence editor is done. Second, the program now allows to make the biochemical (cleavage) and the gas-phase fragmentation simulations. I have compiled it successfully on MS-Windows XP and it runs exactly the same as on GNU/Linux. I still have to code the third fundamental feature, that is mass search in the polymer sequence. After that, I'll start coding of the copy/paste operations (with sequence verification) in the sequence editor and the exporting of the data to the clipboard. When all the coding is almost finished, I'll have to search for a new name. Am I going to use massXtreme, massXpress or massXpert (one name I used for a program that I published in 2002) ? Screenshots: screenshots.
to:
  • April 2007 massXtreme coding The port of the fundamental features from polyXmass is well on track. First of all the usual paradigm of real-time automatic mass calculation in the sequence editor is done. Second, the program now allows to make the biochemical (cleavage) and the gas-phase fragmentation simulations. I have compiled it successfully on MS-Windows XP and it runs exactly the same as on GNU/Linux. I still have to code the third fundamental feature, that is mass search in the polymer sequence. After that, I'll start coding of the copy/paste operations (with sequence verification) in the sequence editor and the exporting of the data to the clipboard. When all the coding is almost finished, I'll have to search for a new name. Am I going to use massXtreme, massXpress or massXpert (one name I used for a program that I published in 2002) ? Screenshots: screenshots.
April 29, 2007, at 03:14 PM by 82.225.200.216 -
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  • April 2007 massXtreme coding The port of the fundamental features from polyXmass is well on track. First of all the usual paradigm of real-time automatic mass calculation in the sequence editor is done. Second, the program now allows to make the biochemical (cleavage) and the gas-phase fragmentation simulations. I have compiled it successfully on MS-Windows XP and it runs exactly the same as on GNU/Linux. I still have to code the third fundamental feature, that is mass search in the polymer sequence. After that, I'll start coding of the copy/paste operations (with sequence verification) in the sequence editor and the exporting of the data to the clipboard. When all the coding is almost finished, I'll have to search for a new name. Am I going to use massXtreme, massXpress or massXpert (one name I used for a program that I published in 2002) ? Screenshots: screenshots.
to:
  • April 2007 massXtreme coding The port of the fundamental features from polyXmass is well on track. First of all the usual paradigm of real-time automatic mass calculation in the sequence editor is done. Second, the program now allows to make the biochemical (cleavage) and the gas-phase fragmentation simulations. I have compiled it successfully on MS-Windows XP and it runs exactly the same as on GNU/Linux. I still have to code the third fundamental feature, that is mass search in the polymer sequence. After that, I'll start coding of the copy/paste operations (with sequence verification) in the sequence editor and the exporting of the data to the clipboard. When all the coding is almost finished, I'll have to search for a new name. Am I going to use massXtreme, massXpress or massXpert (one name I used for a program that I published in 2002) ? Screenshots: screenshots.
April 29, 2007, at 03:01 PM by 82.225.200.216 -
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  • April 2007 Big news: I have bought massxpert.org for a duration of three years. As soon as the site is ready, I'll migrate all this stuff in it. The name of this new projet will therefore be 'massXpert'. It is in fact a revival of the massXpert project I published in Bioinformatics in 2002. Note however, that the present massXpert project is a full rewrite of the polyXmass project and as such is so much more powerful than the initial massXpert project. From a coding standpoint, the mass search feature that was still lacking in massXpert is now implemented in a way that is more powerful than in polyXmass. Further, the copy/paste functionality is now implemented, which makes it possible to create new sequences by copying/pasting sequences off a browser. A powerful "purification" dialog displays all the material that does not corrspond to valid monomer codes. The user may purify the sequence before actually copying it in the sequence editor.

  • April 2007 massXtreme coding The port of the fundamental features from polyXmass is well on track. First of all the usual paradigm of real-time automatic mass calculation in the sequence editor is done. Second, the program now allows to make the biochemical (cleavage) and the gas-phase fragmentation simulations. I have compiled it successfully on MS-Windows XP and it runs exactly the same as on GNU/Linux. I still have to code the third fundamental feature, that is mass search in the polymer sequence. After that, I'll start coding of the copy/paste operations (with sequence verification) in the sequence editor and the exporting of the data to the clipboard. When all the coding is almost finished, I'll have to search for a new name. Am I going to use massXtreme, massXpress or massXpert (one name I used for a program that I published in 2002) ? Screenshots: screenshots.

  • March 2007 massXtreme coding The sequence editor is now able to perform all the editing tasks that one would expect from a sequence editor (not yet copy/paste stuff, though). It is now possible to modify any monomer in the sequence and to modify any/both end(s) of the polymer sequence. In the former case, the chemically modified monomer gets a redraw in the sequence with the modification vignette being transparently composited onto the non-modified monomer vignette.

  • Feb. 2007 massXtreme coding Well, the program is coming along well. I even have a number of screenshots of Mac-OS-X and MS-Windows XP massXtreme sessions. The Mac-OS-X stuff was provided by my dear friend Olivier Kaloudoff of Linux-Azur fame.

As of today, the editor can load a polymer sequence and display it, with all the sequence scrolling and line numbering OK, but not much more than that, for the moment :-).

Note that the sequence rendering is now completely SVG-based, so that it is based on a widely popular scalar vector graphics format that is a web consortium standard (w3). Also, the rendering is always at the best resolution whatever the size of the monomer vignettes. My vignettes were prepared using the wonderful Inkscape program although I guess Karbon would do also.

Go see the dated screenshots to ascertain that work is indeed going on!

  • Jan. 2007 massXtreme coding Yeah, it is proceeding smoothly. I have finished porting the atom and polymer chemistry definition infrastructure. The chemical desktop calculator is almost finished also. A conspicuous part of the low-level chemical modelling library is ported and working. I'll have to start coding the polymer sequence editor, which is a prerequisite for doing the hard-core mass spec/(bio)chemical simulations (which take place in the sequence editor module). Those interested in the alpha code can send an email (see below for mail addresses).

  • Jan. 2007 www.massxtreme.org I'll have to buy the www.massxtreme.org domain. Something like three or more years in a row. If anybody is willing to make a donation, I'll accept with immense pleasure :-)

  • Jan. 2007 Happy new year for those who are starting a new year these days !

  • November-December 2006 Following a number of requests about the portability of GNU polyxmass to either MacOSX and MS-Windows, I decided to develop its successor in C++ using a development toolkit renowned for its portability capabilities : the QT library from http://www.trolltech.com/products/qt/. This toolkit is published under the GNU General Public License and features all the technical requirements for writing a GUI mass spectrometric software that is maintainable and expandable (with the PyQT Python scripting module). This successor to GNU polyxmass will be called massXtreme. This program will not be endorsed by the GNU project, as it won't use the Gtk+ libraries anymore.
April 29, 2007, at 02:49 PM by 82.225.200.216 -
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Latest News

  • April 2007 The site is now up and running, thanks to crew at bioinformatics.org (with a special mention to Jeff Bizzaro). I'll start populating this page day after day.

I would like to mention some history about the massXpert project and next to start the distribution of the software.

At the moment massXpert is able to do a number of interesting things and runs equally well on GNU/Linux and MS-Windows-XP. I still have to find a Mac-OS-X computer to build the package and to be able to distribute binary packages along with the source code.