Recent Posts

Pages: 1 ... 7 8 [9]
Documentation / Set up the REDUCE Suite
« Last post by xiangjun on April 21, 2016, 11:13:30 am »
Starting from REDUCE Suite v2.2, we've streamlined the downloading process. Users just need to register on this Forum, and log in to see the member-only download section (at the upper-left corner). The Suite is distributed with the source code (in ANSI C) available. Moreover, for user convenience, we have compiled the Suite on common operating systems, including Mac OS X, Linux (64-bit), and Windows (via Cygwin).

Assume you have at least basic knowledge of Linux (Unix/Mac OS X) and know how to use the shell, getting the REDUCE Suite up and running is a really simple process. It involves to set up an environment variable REDUCE_SUITE so the system knows where the Suite has been installed, and an update of your command PATH so that you can run the associated programs conveniently. The whole process is further facilitated by the REDUCE_Suite_setup script, as shown below:

Code: [Select]
To install the REDUCE Suite, do as follows:
  (0) Download the Suite from
      You also need to have Perl installed for the setup step.
      Note that you *must* register and log in to see the download page.
      Assuming your downloaded tarball is for the macOS:

  (1) tar zxvf REDUCE-Suite-v2.2-macosx-intel.tar.gz
        This will create a directory named REDUCE-Suite-v2.2/

  (2) cd REDUCE-Suite-v2.2/
        You are now in the REDUCE-Suite-v2.2/ directory

  (3) >>> [optional] ONLY IF you compile REDUCE Suite from source <<<
        (3a) cd src/
        (3b) make
        (3c) cd ../   # back to REDUCE-Suite-v2.2/, as with step (2)

  (4) ./bin/REDUCE_Suite_setup    # assuming you are at directory: REDUCE-Suite-v2.2/
        To run the REDUCE Suite, you need to set up the followings:
          o the environment variable REDUCE_SUITE
          o add $REDUCE_SUITE/bin to your command line search path

        for your 'bash' shell, please add the following into ~/.bashrc:
            export REDUCE_SUITE='/Users/xiangjun/Luxes/REDUCE_Suite'
            export PATH='/Users/xiangjun/Luxes/REDUCE_Suite/bin':$PATH

         and then logout and login again, or run the following command:
              source ~/.bashrc

  (5) type MatrixREDUCE -h
           LogoGenerator -h
           HTMLSummary -h
      etc for command-line help and worked examples

  (6) Note: to use HTMLSummary for the summary page, you need to install
            GhostScript. See $REDUCE_SUITE/config/pkg_settings.cfg for
            setting path to the command 'gs'. LogoGenerator generates
            the logo image in EPS format, and uses 'gs' to convert EPS
            into PDF, PNG, or JPG. Additionally, with ImageMagick, you
            can also get the logo image in GIF.

The above instruction should help get you started with the Suite. If you have any questions, please do not hesitate to ask. The Forum has been created for any related questions, comments, or suggestions.

Announcements / REDUCE Suite v2.2 is available
« Last post by xiangjun on February 15, 2016, 12:47:46 pm »
We are pleased to announce the release of the REDUCE Suite v2.2, a set of software tools to model the regulation of gene expression by transcription factors (TF). By directly correlating genome-wide mRNA expression or TF binding data (e.g. ChIP-chip) with associated nucleotide sequences, the REDUCE Suite can discover the sequence-specific binding affinity of a TF from a single experiment, using all measurements simultaneously, and without using any "background" sequence model.

The REDUCE Suite of software programs has been developed and actively maintained by the Laboratory of Dr. Harmen Bussemaker at the Department of Biological Sciences, Columbia University in the City of New York. The suite has its origin in the REDUCE algorithm of Bussemaker et al. in Nature Genetics (2001), which pioneered the use of motif-based linear regression model to discover cis-regulatory elements (motifs) and infer condition-specific transcription factor activities from a single genome-wide mRNA expression profile. Dr. Barrett Foat, a former graduate student in the Bussemaker Lab, extended REDUCE by adding an optimization procedure to obtain a so-called Position Specific Affinity Matrix (PSAM). He implemented his algorithm in a new program, MatrixREDUCE, using Perl and GNU Scientific Library (GSL). Dr. Xiang-Jun Lu has completely rewritten and significantly enhanced the code using pure ANSI C to make each component program efficient and the whole package self-contained.

Following the release of MatrixREDUCE v1.0 in late 2006, we have made many significant additions and improvements to the software based on extensive feedback from within and outside the lab. Specially, we have greatly improved the calculation of P-values based on a heuristic null model described in Foat et al (2008), and developed a versatile topology-based approach to specify motif patterns. Moreover, we have implemented MotifREDUCE as a standalone, yet more robust and efficient, replacement of the original REDUCE program, and created a command-line driven, general-purpose DNA/RNA-related LogoGenerator. Overall, the suite now consists of more than ten standalone, yet interconnected programs. To better reflect both its root and new versatile functionality, the package has been renamed the "REDUCE Suite", currently at version 2.2.

We understand that getting a scientific software tool published is just the beginning; in the long run, it is the continuous refinements and adaptation to the changing world that make a software suite alive. As a matter of fact, the REDUCE Suite contain many unpublished features. Moreover, while standard "no warranty" applies, we stand firmly behind the software. We strive to get back to your questions, suggestions and bug reports quickly and concretely on the Forum. Browsing the Forum should convince you of our dedication to the REDUCE Suite!

The C source code is in the src/ directory with each tarball. Please refer to the post titled "Set up the REDUCE Suite" on how to compile the code yourself. All REDUCE Suite related questions are welcome on the Forum (only). Do not be shy in sharing openly, but CONCRETELY, any difficult/negative experiences you may have in installing or using the software. By asking your questions on the public Forum, you're benefiting not only yourself but also the user community.

Welcome to the REDUCE Suite, and we look forward to communicating with you on the Forum.

Xiang-Jun Lu & Harmen Bussemaker
Pages: 1 ... 7 8 [9]
Created and maintained by Dr. Xiang-Jun Lu [律祥俊]. See also and