Latest News

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

July 2008

8

Last version: 1.7.8

  1. Implemented the possibility to add oligomers obtained via cleavage with different cleaving agents in the same window;
  2. Updated the User Manual;
  3. Usual bug fixes.

4

Last version: 1.7.7

  1. Implemented a new powerful feature: multi-region selection and multi-selection regions. Multi-region selections make it possible to select any number of polymer sequence regions which are all distinct. Multi-selection regions make it possible to select overlapping sequences in the polymer sequence. These selections make it possible to simulate cross-linked oligomers (typically disulfide bond-linked pepties, for example) directly from the sequence editor.
  2. Updated the User Manual;
  3. Usual bug fixes.

May 2008

28

Last version: 1.7.6

  1. Switch to the GNU General Public License version 3;
  2. Following reports that the previous Mac OS X package did not install on certain platforms, the build system was reworked and universal binaries have been produced. The massXpert program should run on Mac OS X platform starting at version 10.3.9. Tested OK on Mac OS X 10.3.9 (PPC), on MAC OS X version 10.4.11 (PPC) and on MAC OS X version 10.5.2 (Intel). Note that the package is self-contained and does not require installation of the Qt libraries anymore. Simply drop the massXpert.app bundle somewhere and start using the software;
  3. Started implementation of a new data mining feature: mzLab. This is still experimental software;
  4. Big code cleanup, classes were redesigned and numerous bug fixes (GUI and non-GUI) were made.

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.