INSTALLATION INSTRUCTIONS


System requirements:

- 64-bit Windows or Linux system (tested on Windows 7, Windows Server 2008, Ubuntu Linux 12.04 and 13.04)
- at least 4 to 8 GB RAM
- a few GB of free disk space for temporary index files


Installation (Windows):

1. Download and install OpenMS-1.11_Win_64bit_setup.exe.
2. Download and unpack the lastest release of SimTandem for Windows (see section download).
3. (SimTandem >= v. 1.1.96 only) Put the file "SimTandem.ttd" into the subdirectory "OpenMS-1.11\share\OpenMS\TOOLS\INTERNAL". Put the files "SimTandem.exe" and "tbb.dll" into the "OpenMS-1.11\bin" where the binaries of other TOPP tools are located.
4. (SimTandem <= v. 1.1.74 only) Put the file "SimTandem.ttd" into the subdirectory "OpenMS-1.11\share\OpenMS\TOOLS\EXTERNAL".
5. Restart your computer (if you proceeded the step 1).


Installation (example for Ubuntu Linux):

1. Download and install OpenMS-1.11.0.tar.gz.
2. Download and unpack (e.g., "tar -xvzf simtandem_x.x.xx.tgz") the lastest release of SimTandem for Linux (see section download).
3. Install Threading Building Blocks (TBB), e.g., by "sudo apt-get install libtbb2".
4. Install SimTandem using the provided .deb file, e.g., "sudo dpkg -i simtandem_x.x.xx-1_amd64.deb".
5. (SimTandem >= v. 1.1.96 only) Put the file "SimTandem.ttd" into the subdirectory "OpenMS-1.11.0/share/OpenMS/TOOLS/INTERNAL". You can locate SimTandem's binary file by "whereis SimTandem" (it will be likely located in "/usr/bin/"). Now make a symbolic link in the directory where the binaries of other TOPP tools are located (e.g., "ln -s /usr/bin/SimTandem OpenMS-1.11.0/bin/SimTandem")
6. (SimTandem <= v. 1.1.74 only) Put the file "SimTandem.ttd" into the subdirectory "OpenMS-1.11.0/share/OpenMS/TOOLS/EXTERNAL".

Notes:
- make sure that the path to "OpenMS-1.11.0/lib" is in your LD_LIBRARY_PATH (e.g., put "export LD_LIBRARY_PATH=/home/myusername/OpenMS-1.11.0/lib:$LD_LIBRARY_PATH" into your .bashrc file)
- make sure that .mgf and .fasta files proceeded by SimTandem have Linux line endings (you can use "dos2unix filename.fasta" or "dos2unix filename.mgf" to convert the files having Windows line endings)
- if you need .rpm file instead of .deb file, you can use alien, e.g., "sudo alien -r simtandem_x.x.xx-1_amd64.deb" to make the .rpm file


Usage:

1. Run TOPPAS.
2. SimTandem is available in the left menu "TOPP tools" in "Identification/SimTandem" (SimTandem >= v. 1.1.96) or "EXTERNAL/GenericWrapper/SimTandem" (SimTandem <= v. 1.1.74).
3. Drag & Drop SimTandem into the workspace.
4. Click with the right mouse button on the box and select "edit parameters".
5. Set the correct location of "simtandem_openms.exe" in the option "executable" (SimTandem <= v. 1.1.74 only).
6. Optionally, you can change the path in "indexDir" where indexed files are stored (make sure that the path is writable).
7. Connect input files *.mgf and *.fasta with SimTandem and connect also the output *.IdXML file with an output box or another tool.
8. If you have another input file than *.mgf, the tool "File Handling/FileConverter" can be used as SimTandem's predecessor.
9. Syntax of variable modifications: common modifications, e.g., "M(Oxidation)+15.994915;" or "N(Deamidated)+0.984016;", N-term or C-term modifications "Q(Gln->pyro-Glu)N-term-17.026549;", non-specific N-term or C-term "X(Acetyl)N-term+42.010565;".
10. If you want to use ConsensusID, replace the file "OpenMS-1.11\bin\IDPosteriorErrorProbability.exe" with a modified version to enable the support of SimTandem by the IDPosteriorErrorProbability tool. Optionally, you can compile OpenMS library from the source code. In this case, just replace the file "OpenMS-1.11\source\APPLICATIONS\TOPP\IDPosteriorErrorProbability.C" with the modified source file before the compilation.


Examples of Workflows:


All workflows (*.toppas) are available here.



A simple identification workflow.



A simple label-free quantification workflow.



An identification workflow with ConsensusID.



A label-free quantification workflow with ConsensusID.


Configuration of SimTandem.
Configuration of SimTandem.

 

Contact information

Jiri Novak
SIRET Research Group
Department of Software Engineering
Faculty of Mathematics and Physics
Charles University in Prague
Malostranske nam. 25
118 00 Prague
Czech Republic

E-mail:
novak [at] ksi.mff.cuni.cz

Web:
http://siret.cz/novak
http://cuni.academia.edu/JiriNovak