“…By doing so, service providers may increase the visibility of their services while enriching the software discovery function that bio.tools provides for its users. The source code of ReGaTE is freely available on Github at https://github.com/C3BI-pasteur-fr/ReGaTE.…”
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“…CONCLUSION: The proposed method outperforms other similar classification methods based on secondary structure features and machine learning algorithms, including the RNAcon tool that, to date, is the reference classifier. nRC tool is freely available as a docker image at https://hub.docker.com/r/tblab/nrc/. The source code of nRC tool is also available at https://github.com/IcarPA-TBlab/nrc.…”
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“…Specifically, we discuss the adoption of scientific software engineering principles and best-practices such as test-driven development, source code revision control systems, literate programming and the standardization and re-use of common data management and analytical approaches. …”
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“…Our goal is to transform the very challenging problem of predicting the entire human interactome into a routine task. AVAILABILITY: The source code of SPRINT is freely available from https://github.com/lucian-ilie/SPRINT/ and the datasets and predicted PPIs from www.csd.uwo.ca/faculty/ilie/SPRINT/. …”
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“…We expect that DeBooster will be widely applied to analyze large-scale CLIP-seq experimental data and can provide a practically useful tool for novel biological discoveries in understanding the regulatory mechanisms of RBPs. The source code of DeBooster can be downloaded from http://github.com/dongfanghong/deepboost.…”
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“…The algorithm proposed is benchmarked against alternative methods by using synthetic data sets and applied to real RNA sequencing data. Source code is available on line from https://github.com/mqbssppe/cjBitSeq.…”
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“…Spherical is implemented in Python 2.7 and freely available for use under the MIT license. Source code and documentation is hosted publically at: https://github.com/thh32/Spherical. …”
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“…CONCLUSION: CONFOLD2 allows to quickly generate top five structural models for a protein sequence when its secondary structures and contacts predictions at hand. The source code of CONFOLD2 is publicly available at https://github.com/multicom-toolbox/CONFOLD2/. …”
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“…ProteoSign is available at http://bioinformatics.med.uoc.gr/ProteoSign and the source code at https://github.com/yorgodillo/ProteoSign.…”
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“…We fixed the errors identified in this evaluation that were amenable to correction to further improve the accuracy of the system. The source code of the updated CDSS is available at https://github.com/ohnlp/MayoNlpPapCdss . …”
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“…To facilitate identification of novel genes regulating important biological processes and phenotypes in other plants or animals, we have published the source code of NetMiner, making it freely available at https://github.com/czllab/NetMiner.…”
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“…We benchmark and validate the results of our analysis pipeline using the consensus of several manually curated segmentations using commonly used computer tools. The source code of our implementation is released under version 3 of the GNU General Public License (https://www.mathworks.com/matlabcentral/fileexchange/65699-javimazzaf-qurva).…”
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“…When used as a detector, the system reaches high sensitivity with very few false positive marks per image on the INbreast dataset. Source code, the trained model and an OsiriX plugin are published online at https://github.com/riblidezso/frcnn_cad.…”
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“…Both the knowledge-integrated organismal databases and the code package (containing source code, the graphical user interface, and a user manual) are available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads/raid.html. …”
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“…AVAILABILITY AND IMPLEMENTATION: Source code is freely available on https://bitbucket.org/genomicepidemiology/rucs. …”
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“…AVAILABILITY AND IMPLEMENTATION: The R source code of SCODE is available at https://github.com/hmatsu1226/SCODE SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.…”
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“…AVAILABILITY AND IMPLEMENTATION: The PySB/cupSODA interface has been integrated into the PySB modeling framework (version 1.4.0), which can be installed from the Python Package Index (PyPI) using a Python package manager such as pip. cupSODA source code and precompiled binaries (Linux, Mac OS/X, Windows) are available at github.com/aresio/cupSODA (requires an Nvidia GPU; developer.nvidia.com/cuda-gpus). …”
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“…AVAILABILITY AND IMPLEMENTATION: The source code of the method is available at https://github.com/suleimank/mvlr. …”
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“…AVAILABILITY AND IMPLEMENTATION: The source code and data are available as a Reproducible Research Archive at http://murphylab.cbd.cmu.edu/software/2017_TcellCausalModels/…”
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“…AVAILABILITY AND IMPLEMENTATION: The source code of PEP is available at: https://github.com/ma-compbio/PEP. …”
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