OMICtools can help a) experimental researchers/clinicians find appropriate tools for their needs b) developers to stay up to date and to avoid redundancy c) funding agencies to ensure that the submitted projects are high value-added. Do you want help us to improve OMICtools? Call for curators

(Henry et al., 2014) OMICtools: an informative directory for multi-omic data analysis. Database.

TOPPAS
  (4/5)
TOPPAS is a workflow editor based OpenMS library and thus enjoys all the algorithms developed within it. It is easy to learn, the interface is attractive. In short, we spend time tweaking its pipeline by changing a particular algorithm for peak picking or alignment of LC-MS maps for example.
Posted by Marc Dubois on Oct 22, 2014
OpenMS
  (3/5)
OpenMS is a C++ library for developers. Their programming interface is well done and very clear. A Python binding exposing most classes C ++ was created, an initiative that should be welcomed. It includes many algorithms for metabolomics and proteomics, all of which can be finely set. It brings new concepts of data reduction rather interesting (concept RawMap, PeakMap, FeatureMap) to theoretically manage large amounts of data. In theory only, since the development team announced reviewing the kernel openMS to greatly improve performance.
Posted by Marc Dubois on Oct 22, 2014
Mascot
  (3/5)
One of the most used search engines with an algorithm that has been proven. However, the GUI to launch tasks is unresponsive (crash). The price of the software is significant since Matrix Sciences bill the number of processors of the machine on which you install Mascot!
Posted by Marc Dubois on Oct 22, 2014
Skyline
  (4/5)
Simply one of the most accomplished tools for dealing with MRM data. I strongly recommend!
Posted by Marc Dubois on Oct 22, 2014
MFPaQ
  (3/5)
A useful tool for proteomic analyzes with and without isotopic labeling. However, it supports only the mascot search engine and unfortunately remains slow for the quantization step (Perl). The results are still good.
Posted by Marc Dubois on Oct 22, 2014
MaxQuant
  (4/5)
Probably one of the best tools currently analyzing proteomic data: Andromeda, their search engine is very powerful, the algorithm for label-free quantification fast and reliable. The end of the pipeline is provided by Perseus, a statistical analysis tool.
Posted by Marc Dubois on Oct 22, 2014
ProteoWizard
  (4/5)
Proteowizard written in C ++, provides a clear and readable interface programming. It is based on modern design and application of new standards c ++ 11 (including smart pointers). It also provides many algorithms for processing data spectrometry (peak picking ...) and allows the reading of many raw files owners. This is an indispensable tool for application developers proteomics / metabolomics. The only downside is that it still uses a build system based on bjam that requires a long learning curve.
Posted by Marc Dubois on Oct 21, 2014
Platanus
The source code is still not availabe, although they said they will make it public "ASAP" couple months ago
Posted by Kevin on Oct 24, 2014
BreakDancer
Hi there,
when I run "make" during the installation process I receive the following output:

[ 14%] Built target boost-libs
[ 15%] Performing build step for 'samtools-lib'
make[2]: *** [vendor/src/samtools-lib-stamp/samtools-lib-build] Errore 2
make[1]: *** [CMakeFiles/samtools-lib.dir/all] Errore 2
make: *** [all] Errore 2
salvo@linux-t9bq:~/breakdancer/build> su -x "make clean"
su: opzione non valida -- "x"
Try 'su --help' for more information.
salvo@linux-t9bq:~/breakdancer/build> su -c "make clean"
Password:
salvo@linux-t9bq:~/breakdancer/build> su -c "make"
Password:
[ 1%] Creating directories for 'boost-libs'
[ 3%] Performing download step (verify and extract) for 'boost-libs'
-- verifying file...
file='/home/salvo/breakdancer/vendor/boost-1.54-breakdancer.tar.gz'
-- verifying file... warning: did not verify file - no URL_MD5 checksum argument? corrupt file?
-- extracting...
src='/home/salvo/breakdancer/vendor/boost-1.54-breakdancer.tar.gz'
dst='/home/salvo/breakdancer/build/vendor/boost/boost-src'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 5%] No patch step for 'boost-libs'
[ 7%] No update step for 'boost-libs'
[ 8%] Performing configure step for 'boost-libs'
Building Boost.Build engine with toolset gcc... tools/build/v2/engine/bin.linuxx86_64/b2
Detecting Python version... 2.7
Detecting Python root... /usr
Unicode/ICU support for Boost.Regex?... not found.
Generating Boost.Build configuration in project-config.jam...

Bootstrapping is done. To build, run:

./b2

To adjust configuration, edit 'project-config.jam'.
Further information:

- Command line help:
./b2 --help

- Getting started guide:
http://www.boost.org/more/getting_started/unix-variants.html

- Boost.Build documentation:
http://www.boost.org/boost-build2/doc/html/index.html

[ 10%] Performing build step for 'boost-libs'
[ 12%] No install step for 'boost-libs'
[ 14%] Completed 'boost-libs'
[ 14%] Built target boost-libs
[ 15%] Creating directories for 'samtools-lib'
[ 17%] Performing download step (verify and extract) for 'samtools-lib'
-- verifying file...
file='/home/salvo/breakdancer/vendor/samtools-0.1.19.tar.gz'
-- verifying file... warning: did not verify file - no URL_MD5 checksum argument? corrupt file?
-- extracting...
src='/home/salvo/breakdancer/vendor/samtools-0.1.19.tar.gz'
dst='/home/salvo/breakdancer/build/vendor/samtools'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 19%] No patch step for 'samtools-lib'
[ 21%] No update step for 'samtools-lib'
[ 22%] Performing configure step for 'samtools-lib'
Building samtools, build log at /home/salvo/breakdancer/build/vendor/samtools/build.log
[ 24%] Performing build step for 'samtools-lib'
make[2]: *** [vendor/src/samtools-lib-stamp/samtools-lib-build] Errore 2
make[1]: *** [CMakeFiles/samtools-lib.dir/all] Errore 2
make: *** [all] Errore 2

Salvo
email: salvatore_camiolo@yahoo.it
Posted by Salvo on Oct 21, 2014
F-Seq
F-Seq tool has been moved into "Peak detection". Thank you.
Posted by Arnaud Desfeux on Oct 17, 2014
F-Seq
This is a peak caller, not for motif discovery ! Should be moved !
Posted by fabien pichon on Oct 17, 2014
COV2HTML
Dear Marc,

I have moved COV2HTML into "Data visualization".

Best regards,
Arnaud
Posted by Arnaud Desfeux on Oct 17, 2014
COV2HTML
Could you move COV2HTML into "Data visualization",
Best Regards,
Marc
--
Dr Marc Monot - PhD - Institut Pasteur
Laboratoire Pathogenese des Bacteries Anaerobies
25 rue du docteur roux 75015 Paris
Phone / Fax. +33145688390 ; +33140613123
Webpage. http://www.mmonot.eu
Posted by Monot on Oct 16, 2014
RCGDB
The Roche Cancer Genome Database cannot be accessed.
Posted by Euphemia on Oct 15, 2014