The Center for Quantitative Biology provides several tools and libraries for computational analysis of biological systems. The CQB Integrated Tools provides a framework for these tools and supports pipelining and batch processing on a compute cluster.
http://quantbio-tools.princeton.edu/
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CQB Integrated Tools | quantbio-tools.princeton.edu Reviews
https://quantbio-tools.princeton.edu
The Center for Quantitative Biology provides several tools and libraries for computational analysis of biological systems. The CQB Integrated Tools provides a framework for these tools and supports pipelining and batch processing on a compute cluster.
quantbio-tools.princeton.edu
CQB Tools : PruneTree
http://quantbio-tools.princeton.edu/ple/help/prunetree.html
Run time and complexity issues. This little script takes clustered files (a CDT file and an associated GTR file) and clips the tree at the given correlation. Each node beyond the cut (each node with a higher correlation) is then output. There are two input modes. In individual file mode. You may provide or select both the CDT file and the GTR file independently. In batch mode. You select the GTR file only (or the set of GTR files). The CDT file name is derived from the GTR file name. The perl script is f...
CQB Tools : PLE
http://quantbio-tools.princeton.edu/cgi-bin/ple
CQB Tools : DME
http://quantbio-tools.princeton.edu/ple/help/dme.html
Data matrix extractor (DME). The input file should be a delimited text file. Usually the delimiters are tabs or spaces, but others may be specified within the form. Within the file, there should be a body of numerical data occupying some number of consecutive rows and columns, with no other text in between. (Blank fields and the string 'NaN' are ok.) This data may be surrounded by rows and columns containing other information. The extractor locates and outputs this body of data. If there are empty fields...
Quantitative Biology Tools : Cluster your data with Iclust
http://quantbio-tools.princeton.edu/cgi-bin/Iclust
Cluster your data with Iclust. Iclust is an information-theoretic, model-independent clustering application. It can be applied to many different kinds of data. It typically starts by producing a mutual information pairwise relations matrix based on the input data. Iclust then uses this matrix to group the input data into separate clusters. The theory along with several examples are described in Slonim et al., PNAS, 2005. Please provide a file to process:.
CQB Tools : Iclust
http://quantbio-tools.princeton.edu/ple/help/Iclust.html
Run time and complexity issues. Iclust is an information-theoretic cluster analysis framework, originally published in Slonim et al., PNAS, 2005. In this manner most common data formats (raw, pcl, cdt, etc.) are supported. Some known input formats, identified by the input file extension, will trigger additional filtering (such as excluding the GWEIGHT column and the EWEIGHT row). The simplest option is to run Iclust. However, you can specify other similarity options using the advanced menu. If your i...
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CQB Integrated Tools
This collection of tools is a subset of the tools, applications, and libraries developed within the Center for Quantitative Biology. At Princeton University's Lewis-Sigler Institute. They are provided here within a common framework, called the CQB Integrated Tools. Which allows for data to be processed and passed between them easily. The Integrated Tools framework also supports batch processing for multiple data sets natively within each tool and utilizes the local computing grid for high throughput.
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