:: DESCRIPTION
Payao Uploader is to allow the user to upload CellDesigner pathway models to Payao system – a web-based community curation platform
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Compatibility: Built for CellDesigner 4.1.
:: DESCRIPTION
Merge Models is a CellDesigner plugin. The purpose of Merge Models is to allow the user to merge different biological pathway models and build new pathway maps. It also provides the ability to analysis two or more models for merging, to identify the duplicate species and highlight them on the merged model map.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Compatibility: Built for CellDesigner 4.1.
:: DESCRIPTION
CellDesigner allow developers to supply Plugins to extend the function of CellDesigner.
Import Notes is used to import notes data from CSV file.
::DEVELOPER
N/A
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Work in CellDesigner 4.0 and above.
:: DESCRIPTION
LCMT is a small program performing “combining” association test over multiple genetic markers.LCMT implements the “combining” method for the association test over multiple genetic markers. It optimally utilizes the information from those markers. It is preferred over several competing tests, such as the Bonferroni procedure, the permutation procedure, the traditional χ2 procedure, the regression procedure (Hotelling T2 test) and the haplotype-based test.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
References
H zhou, L wei, X Xu, X Xu (2006) Combining association tests across multiple genetic markers in case-control studies
:: DESCRIPTION
XWXW implements the Unified Haseman-Elston method for non-parametric linkage test with quantitative traits. It optimally utilizes the information from a sib-pair. It is uniformly more powerful than both the classical H-E method and the revistited H-E method. Program GENIBD from SAGE or GeneHunter2 is required for sib-pair ibd estimation.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
References
Xu X, Palmer LJ, Horvath S, and Wei LJ. Combining Multiple Phenotypic Traits Optimally for Detecting Linkage with Sib-pair Observations. (2001) Genet. Epidemiol.
Xu X., Weiss S. Xu X., Wei LJ. A unified Haseman-Elston regression method for testing linkage with quantitative trait (2000) Am. J. Hum. Genet. 67: 1025-8
:: DESCRIPTION
ProbeWithO incorporates all-atom contacts into the popular model building program O. An O macro and an unix shell script conduit the dot information between Probe and O to give “almost” interactive updates of clashes.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
ProbeWithO is free software available under the terms of its own BSD-style license.
:: DESCRIPTION
PDBCNS is a perl script to convert atom names for common amino acids and nucleic acid bases from PDB format to CNS (or XPLOR) style atom names.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
PDBCNS is free software available under the terms of its own BSD-style license.
:: DESCRIPTION
Mapvol is an awk script which reads a PDB file and tries to assign a volume to each atom based on residue and atom names. The output is a table, listing the volume and the atomic coordinates, which can be contoured with Kin3Dcont to show the distribution of atomic volume in a protein.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
MapVol is free software available under the terms of its own BSD-style license.
:: DESCRIPTION
CoCAS is a standalone Chromatin immunoprecipitation microarray (ChIP-on-chip) analysis application. It has been designed to be used primarily on Agilent microarrays scanned with an Agilent scanner.
CoCAS can readily be used on the latest generation of Agilent high-density arrays. Unlike other tools available, Cocas allows dye-swap, replicate correlation and connects easily with other software (genome browsers and peak detection). The peak detection methods implemented in CoCAS can be used for any set of data including ChIP-Seq data.
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:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
COCAS for Win ; for Mac ; for Linux
:: MORE INFORMATION
Citation:
Benoukraf T, Cauchy P, Fenouil R, Jeanniard A, Koch F, Jaeger S, Thieffry D, Imbert J, Andrau JC, Spicuglia S, Ferrier P (2009). CoCAS: A ChIP-on-chip Analysis Suite. Bioinformatics 25: 954-5.
:: DESCRIPTION
VIZARD is a Java program for analysis and visualization of Affymetrix GeneChip® data.VIZARD includes several integrated tools for filtering, sorting, clustering and visualization of gene expression data as well as tools for discovery of regulatory motifs in upstream sequences. It also includes annotation and upstream sequence databases for the majority of genes represented on the Affymetrix Arabidopsis 8K GeneChip® array.
When VIZARD was created its name originated from VIsualiZe microARray Data. Now it does much more than visualization of gene expression data, however, we have decided to keep the name.
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:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
It is available free of charge for educational, research, and not-for-profit purposes. To read full text of the terms under which the program is distributed, click here.