Author Topic: REDUCE Suite v2.2 is available  (Read 1139 times)

xiangjun

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REDUCE Suite v2.2 is available
« 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


PS: The REDUCE Suite v2.2 is in a stable status: its key code components and functionality features, without material changes, have been extensively tested and utilized in real-world applications of nearly a decade. Due to my commitment to the NIH funded 3DNA/DSSR project, I am supporting the REDUCE Suite in maintenance mode. No new features are planned, but I will promptly address any REDUCE Suite related questions/bugs, exclusively, via this open Forum.


Note added on July 17, 2018: FeatureREDUCE is not included in the suite and it is not supported on the Forum.
« Last Edit: July 17, 2018, 07:07:05 pm by xiangjun »

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊]. See also http://forum.x3dna.org and http://x3dna.org