“…We also reveal various topologies of association networks among COGs (modules) from extracted multiple-to-one correlation rules relevant with the six phenotypes; including a well-connected network for motility, a star-shaped network for aerobic and intermediate topologies for the other phenotypes. netCAR outperforms a standard CAR mining algorithm, CARapriori, while requiring several orders of magnitude less computational time for extracting 3-COG sets. Availability: Source code of the Java implementation is available as Supplementary Material at the Bioinformatics online website, or upon request to the author. …”
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“…Availability: The program, in the form of source code and binary code along with tutorials and reference manuals, is available at http://pine.nmrfam.wisc.edu/PINE-SPARKY. …”
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“…CONCLUSION: It is hoped that through the data mined reconstructed signal transduction networks, well developed models of the published data can be built which in the end would guide the prediction of new targets based on the pathway's environment for further analysis. Source code is available upon request.…”
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“…Moreover, we were able to correlate clinically relevant features like necrosis or metastasis with the detected paths. Availability: C++ source code is freely available, BiNA can be downloaded from http://www.bnplusplus.org/. …”
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“…MP-PBmice can be easily adapted for other large-scale insertional mutation mapping projects and the source code of this software is freely available at http://www.idmshanghai.cn/PBmice. …”
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“…Bioclipse 2 is implemented in Java and supported on all major platforms; Source code and binaries are freely available at http://www.bioclipse.net.…”
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“…Our main motivation is to use this tool to survey the genetic diversity of endangered species as the identified sequence differences can be used to design genotyping arrays to assist in the species' management. The DIAL source code is freely available at http://www.bx.psu.edu/miller_lab/.…”
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“…Availability: Mitochondrial cell images, their corresponding feature sets (SSLF and WSLF) and the source code of our proposed method are available at http://aiia.iis.sinica.edu.tw/. …”
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“…MetaBar requests and stores contextual data in compliance to the Genomic Standards Consortium specifications. The MetaBar open source code base for local installation is available under the GNU General Public License version 3 (GNU GPL3). …”
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“…The database is available at http://kid.tu-bs.de. The source code of the algorithm is provided under the GNU General Public Licence and available on request from the author.…”
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“…The program and its source code were made available as open-source software on the internet.…”
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“…Availability: The data and software source code for model training and validation are freely available online at http://magnet.systemsbiology.net/hac. …”
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“…We hope that the provided algorithms and source code will be a starting point for modelers to develop their own GPU implementations, and encourage others to implement their modeling methods on the GPU and to make that code available to the wider community.…”
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“…All the related materials including source code and genome-wide prediction of human targets are available at http://compgenomics.utsa.edu/svmicro.html. …”
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“…Availability: Our implementation, which uses Bonferroni correction to account for multiple hypotheses testing, is available at http://www.ncbi.nlm.nih.gov/CBBresearch/qmbp/mn/enrich/. Source code for the standalone version can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/pub/qmbpmn/SaddleSum/. …”
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“…CONCLUSIONS: We show that domain-domain interaction prediction can be significantly enhanced by exploiting information inherent in the domain profiles via feature selection based on Fisher scores, singular value decomposition and supervised learning based on support vector machines. Datasets and source code are freely available on the web at http://liao.cis.udel.edu/pub/svdsvm. …”
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“…Use of locally optimal structure leads to state-of-the-art secondary structure prediction, as benchmarked against methods involving the computation of minimum free energy and of maximum expected accuracy. Web server and source code available at http://bioinformatics.bc.edu/clotelab/RNAlocopt/.…”
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“…CONCLUSIONS: To retain flexibility and compatibility with existing bioinformatics tools, MTML-msBayes is a pipeline software package consisting of Perl, C and R programs that are executed via the command line. Source code and binaries are available for download at http://msbayes.sourceforge.net/ under an open source license (GNU Public License).…”
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