“…We use DiNAMIC to analyze two publicly available tumor datasets, and our results show that DiNAMIC detects multiple loci that have biological relevance. Availability: Source code implemented in R, as well as text files containing examples and sample datasets are available at http://www.bios.unc.edu/research/genomic_software/DiNAMIC. …”
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“…In addition, NPMVS exploits a non-parametric regression between mean and variance, instead of assuming a specific parametric relationship between mean and variance. The source code written in R is available from the authors on request.…”
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“…Availability and Implementation: The Objective Caml source code and executables for GNU/Linux and Mac OS X are freely available at http://compbio.mit.edu/PhyloCSF Contact: mlin@mit.edu; manoli@mit.edu…”
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“…Availability and implementation: Domain examples, source code and ontology are freely available on the web at http://www.cin.ufpe.br/~ntdo. …”
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“…JSBML also supports modules that can facilitate the development of plugins for end user applications, as well as ease migration from a libSBML-based backend. Availability: Source code, binaries and documentation for JSBML can be freely obtained under the terms of the LGPL 2.1 from the website http://sbml.org/Software/JSBML. …”
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“…MACSE is distributed as an open-source java file executable with freely available source code and can be used via a web interface at: http://mbb.univ-montp2.fr/macse.…”
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“…Availability: The CodonLogo source code and its implementation (in a local version of the Galaxy Browser) are available at http://recode.ucc.ie/CodonLogo and through the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/. …”
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“…Availability and implementation: The methods presented here are implemented in THESEUS 2.0, a program for superpositioning macromolecular structures. ANSI C source code and selected compiled binaries for various computing platforms are freely available under the GNU open source license from http://www.theseus3d.org. …”
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“…A well distributed sample, that is representative of the complete set of EMs, should be suitable to most EM-based methods for analysis and optimization of metabolic networks. Availability: Source code for a cross-platform implementation in Python is freely available at http://code.google.com/p/emsampler. …”
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“…Availability: MetiTree is accessible at http://www.MetiTree.nl. The source code is available at https://github.com/NetherlandsMetabolomicsCentre/metitree/wiki. …”
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“…Availability and implementation: crAss is available as a web server at http://edwards.sdsu.edu/crass/, and the Perl source code can be downloaded to run as a stand-alone command line tool. …”
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“…It is publicly available in source code and as a user-friendly web service framework.…”
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“…Therefore the proposed spectral clustering framework over combined local alignment kernels with modified symmetry based correction achieves superior performance for unsupervised remote homolog detection even in multi-domain and promiscuous domain proteins from Genolevures database families with better biological relevance. Source code available upon request. Contact: sarkar@labri.fr.…”
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“…Our study also supports the advantages of using cancer specific characteristics in feature design and pooling multiple rounds of classification results to improve accuracy. We provide R source code and processed datasets at www.ChengLiLab.org/software.…”
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“…In addition, our approach reports likelihood scores of putative reactions, which can be used to identify important reactions and metabolic pathways that reflect the environmental adaptation of the microbial communities. Source code for sampling metabolic networks is available online at http://omics.informatics.indiana.edu/mg/MetaNetSam/.…”
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“…The ImageMagick Perl API has been used for pre-processing the images. The source code is made available at www.sanchak.com/imaculat.html.…”
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“…The R package along with it source code is available at http://CRAN.R-project.org/package=mobForest.…”
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