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SLM FAQ

(Frequently Asked Questions)

• What is SLM?:
• SLM Versions:
• Main Features of SLM:
• Installing SLM:
• What documentation exists for SLM?:
• Citing SLM:
• Reporting bugs

What is SLM?

SLM Versions

Main Features of SLM

• Background correction
• Normalization
• Enrichment
• Peaks detection

Installing SLM?

• For Unix/Linux:
• For Mac OS
• For Windows:
• Other Notes:

For Unix/Linux
Installing SLM

   1. Download the most recent version of the source code of SLM from the website
   2. Unzip the package

          %> unzip SLMplus_v?.zip

   3. compile with the provided makefile by typing on the terminal

          %> make SLM


For MAC OS
Installing SLM

   1. Download the most recent version of the source code of SLM from the website
   2. Unzip the package preserving the directory structure, e.g. in the folder /usr/local/bin/SLM/
   3. Run a terminal
   4. Access the directory where the SLM package has been unzipped. E.g.

         %> cd /usr/local/bin/SLM

   5. Compile with the provided makefile

         %> make SLM

        If DarwinPorts has been used to port the GSL library, specify the library path with the LIBPATH option

         %> make SLM LIBPATH=/opt/local

        If Fink has been used to port the GSL library, specify the library path with the LIBPATH option

         %> make SLM LIBPATH=/sw


For Windows
SLM has not yet been tested on Windows systems.


Other Notes
SLM requires GSL libraries to compile successfully.
Without proper installation of the required libraries, SLM will fail to install on your system.

What documentation exists for SLM?

• Online help: Online documentation for most of the functions and methods in SLM exists, and can be visualized from this website
• Publications: The reference article describing the main methods and algorithms for SLM is “Identifying synergistic regulation involving c-Myc and sp1 in human tissues.” (Parisi, Wirapati and Naef – NAR 2007). A link is available in the "Publications" section of this website.

Citing SLM

• “Identifying synergistic regulation involving c-Myc and sp1 in human tissues.” (Parisi, Wirapati and Naef – NAR 2007).

SLM Bugs