REST 2009 for 64bit Windows

REST 2009 is a popular bioinformatics tool to analyze relevant gene expression changes from crossing points (CP) of amplification curves gathered by a Real-Time PCR (qPCR) experiment. REST was developed by M. Pfaffl (Technical University Munich) and QIAGEN.

However, I found REST 2009 (v2.0.13) to cease working when moving from a 32bit Windows operating system (Windows XP) to a 64bit Windows operating system (Windows 7). The accepted solution until now was, to install a VirtualPC software including a Windows XP image optimized to run under Windows 7 (dubbed Windows XP Mode). Resourcewise it was a disaster, not to mention the hassle of backing up an entire second system. Also, the need for additional security software in your virtual image made the system even slower, remember Microsoft ceased to provide security updates for Windows XP from the 8th of April 2014. Occasionally your would need need to install other 3rd party software to complete your analyses, in my case, I needed to install a PDF printer to be able to save my REST 2009 reports in a standardazied way. On top of all that, you always need to cope with net drive assignments, virtual net drives that will provide access to the underlying OS from inside your virtual XP and that behave a lot different in XP than Windows 7, as well as some restrictions regarding the virtual desktop or virtual windows the VirtualPC software provides. For example, you won't be able to move the emulated REST 2009 windows to a second monitor.

After all this complaining about how bad this free functionality in Windows 7 is, I want to present my workaround that has since then worked very well for me.

Downloads needed

Patching REST 2009

The problem with REST 2009, which was most probably written in .NET is, that the author missed to flag the code as 32bit code. What happens, when executing undefined code under a 64bit system is, that the code is executed as 64bit and thus fails. Under a 32bit system, the 32bit code works fine.

Using CorFlags.exe, it is possible to subsequently edit those header flags, making a 64bit Windows able to correctly identify and interpret the code.

After the above mentioned software components are installed, CorFlags.exe should reside in
%PROGRAMFILES%\Microsoft SDKs\Windows\v6.1\bin

whereas Rest.exe is located at

Using an elevated command prompt (hit the WINDOWS key, search for cmd.exe, right-click cmd.exe and select "Run as administrator..."), simply enter the following command (or paste the code using the right mouse button):

cmd.exe /c ""%PROGRAMFILES%\Microsoft SDKs\Windows\v6.1\bin\CorFlags.exe" "%PROGRAMFILES(X86)%\REST 2009\Rest.exe" "/32bit+"" & pause

If there is no error message appearing in your command prompt, everything worked as expected and you might try running the Rest.exe directly under your 64bit Windows installation.


This instruction is copyright by Christian Wolf (2015) and may not be reproduced without written permission, instead you may freely link to this page to help others coping with the same problem.
Last updated: 27.05.2015