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Please cite: An, J., Lai, J., Lehman, M.L. and Nelson, C.C. (2013) miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res, 41, 727-737.
We will create index for you if you tell us your interested species (j.an@qut.edu.au).
download command line version "MDS_command_line_Vxx.zip" clicking "Browse All Files"
please find miRPlant in sourceforge for plant miRNA prediction.
Graphics generator for pie diagram matrix from spreadsheets
For comparative plus/minus spreadsheet data, Coulson Plot Generator application creates a multiple pie diagram, for a rapid visual comparison of subunit occupancy across a range of entities. Numbers of pies, segments, labels and colours are customisable. Creates an editable PDF from a comma separated text file. Now with zoom capability and more memory, for larger datasets. Save images in several formats including SVG.
GNAT is an open source, platform-independent MATLAB based toolbox. It is written in MATLAB and Java. It has been tested in Windows (Windows 7), Linux (Ubuntu), and Mac OS (X Lion) platforms.
The original GNAT package (file GNAT.zip) provides functions for reading, writing, manipulation, visualization and simulation of glycan structures and glycosylation reaction networks (citation [1]).
The second version of this software (GNATv2beta.zip) upgrades the original GNAT program with additional features that are geared towards incorporating glycan-structure experimental data into the simulation environment.
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Gemini Enterprise Agent Platform lets you rapidly build, scale, govern and optimize production-ready agents grounded in your organization's data. The platform enables developers to build custom or pre-built agents for virtually any use case. New customers get $300 in free credits.
Open2Dprot is an open-source proteomics project for the development of bioinformatic tools for n-dimensional protein expression data analysis of quantified protein expression across multiple samples from research experiments.
Manuelito is a Java tool for decrypting posttranslational modification (PTM) patterns of proteins based on MALDI mass spectrometry spectra. It was built for analysing the 'histone code' but it can be applied to any other highly modified protein.
Set of Java packages to apply Genetic Algorithms to any kind of problem. Various genetic operators are implemented and an example shows of how the system could be applied to digital circuit evolution.
EcoloSim is a Simulation Framework for simple spatial models in biology and ecology, in Java.
Typical problems are behavior of a herd of cattle, growth of microbe cells and other populations.
** IMPORTANT NOTICE ** 10 Feb 2006 Code is being moved to the SMI subversion repository (http://smi-protege.stanford.edu/svn/owl/trunk/) Project will continue to be open source. ProtegeOWL info at: http://protege.stanford.edu/overview/protege-owl.html