“…All algorithms and the analysis pipeline are packaged into a plugin for Fiji (ImageJ), with the source code freely available online at https://github.com/VTcbil/FASP.…”
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“…Multiple GATK 3.x versions were benchmarked and the execution time of HaplotypeCaller was optimized by various system level parameters which included: (i) tuning the parallel garbage collection and kernel shared memory to simulate in-memory computing, (ii) architecture-specific tuning in the PairHMM library for vectorization, (iii) including Java 1.8 features through GATK source code compilation and building a runtime environment for parallel sorting and bulk data transfer (iv) the default ’on-demand’ mode of CPU frequency is over-clocked by using ’performance-mode’ to accelerate the Java multi-threads. …”
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“…CONCLUSIONS: Our study presents a comprehensive repertoire of potential neoepitopes in childhood cancers, and will facilitate the development of immunotherapeutic approaches designed to exploit them. The source code of the workflow is available at GitHub (https://github.com/zhanglabstjude/neoepitope). …”
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“…CONCLUSION: The simulation results show better material model accuracy, calculation robustness and improved muscle routing capability compared to *MAT_156. The FORTRAN source code for the user material subroutine dyn21.f and the muscle parameters for all simulations, conducted in the study, are given at https://zenodo.org/record/826209 under an open source license. …”
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“…It provides a complementary paired-end read homology search tool to HMMER. The source code is freely available at https://sourceforge.net/projects/short-pair/.…”
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“…Considering the JNLPBA corpus, our model achieves the best results, outperforming the previously top performing systems. The source code of our method is freely available under GPL at https://github.com/lvchen1989/BNER.…”
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“…CONCLUSIONS: As ClusterTAD is based on a proven clustering approach, it opens a new avenue to apply a large array of clustering methods developed in the machine learning field to the TAD identification problem. The source code, the results, and the TADs generated for the simulated and real Hi-C datasets are available here: https://github.com/BDM-Lab/ClusterTAD.…”
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“…GeMSE is available at http://www.bioinformatics.deib.polimi.it/GeMSE/, and its source code is available at https://github.com/Genometric/GeMSE under GPLv3 open-source license.…”
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“…Experiment results demonstrate that Tiresias outperforms existing solutions and can achieve a high F1 score. Source code of Tiresias is available at https://bitbucket.org/cellsandmachines/.…”
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“…The software its available in the Apple Store and Android Market and the source code is publicly available in Github. CONCLUSIONS: Mobile devices are becoming increasingly important in the scientific world due to their strong potential impact on scientific applications. …”
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“…Installation instructions, documentation and source code can be found at http://bowhead.lindinglab.science licensed under GPLv3.…”
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“…It also represents a significant independent code base for replicating results from other simulation platforms. The PhysiCell source code, examples, documentation, and support are available under the BSD license at http://PhysiCell.MathCancer.org and http://PhysiCell.sf.net.…”
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“…AVAILABILITY AND IMPLEMENTATION: Source code and comprehensive documentation are freely available at https://github.com/yiming-kang/NetProphet_2.0. …”
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“…CONCLUSIONS: Sparse principal covariates regression is a promising and competitive tool for obtaining insights from high-dimensional data. AVAILABILITY: The source code implementing our proposed method is available from GitHub, together with all scripts used to extract, pre-process, analyze, and post-process the data: https://github.com/katrijnvandeun/SPCovR.…”
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“…AVAILABILITY AND IMPLEMENTATION: The full source code of MALAX is available at https://github.com/omerwe/MALAX. …”
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“…AVAILABILITY AND IMPLEMENTATION: A web-based system for biomedical semantic sentence similarity computation, the source code, and the annotated benchmark data set are available at: http://tabilab.cmpe.boun.edu.tr/BIOSSES/.…”
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“…AVAILABILITY AND IMPLEMENTATION: Source code and datasets are available at http://snap.stanford.edu/ohmnet.…”
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“…We expect Bamgineer to be of use for development and systematic benchmarking of CNV calling algorithms by users using locally-generated data for a variety of applications. The source code is freely available at http://github.com/pughlab/bamgineer.…”
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“…AVAILABILITY AND IMPLEMENTATION: RG was implemented in Java, source code and binaries are freely available for non-commercial use at https://github.com/popitsch/wtchg-rg/. …”
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“…The ability to easily and effectively characterize the accessory genome of a sequence collection may provide a better understanding of the accessory genome’s contribution to a species’ adaptation and pathogenesis. The ClustAGE source code can be downloaded from https://clustage.sourceforge.io and a limited web-based implementation is available at http://vfsmspineagent.fsm.northwestern.edu/cgi-bin/clustage.cgi. …”
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