“…The predicted modules are functionally coherent and are more in line with current biological knowledge compared to modules obtained using previous disease-centric methods. The source code for GLADIATOR can be downloaded from http://www.cs.tau.ac.il/~roded/GLADIATOR.zip. …”
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“…Besides, adopting the co-run computation model can maximize the entire system utilization significantly. The source code is available at https://github.com/wangvsa/CMSA.…”
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“…Both the TaxMapper tool and the workflow are available as open-source code at Bitbucket under the MIT license: https://bitbucket.org/dbeisser/taxmapperand as a Bioconda package: https://bioconda.github.io/recipes/taxmapper/README.html. …”
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“…Each tumor was delineated using PET Edge (MIM Software Inc., Cleveland, OH), and texture parameters were calculated using open-source code CGITA. From (18)F-FDG PET/CT images, three conventional parameters, including maximum standardized uptake value (SUV), metabolic tumor volume (MTV) and total lesion glycolysis (TLG), and four texture parameters, including entropy and dissimilarity (derived from a co-occurrence matrix) and high-intensity large-area emphasis (HILAE) and zone percentage (derived from a size-zone matrix) were analyzed. …”
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“…CONCLUSION: Briefly, PGAP-X directly presents the characteristics of bacterial genomic diversity with different visualization methods, which could help us to intuitively understand dynamics and evolution in bacterial genomes. The source code and the pre-complied executable programs are freely available from http://pgapx.ybzhao.com. …”
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“…The results, and the models generated for the simulated and real Hi-C datasets are available here: http://sysbio.rnet.missouri.edu/bdm_download/3DMax/. The source code is available here: https://github.com/BDM-Lab/3DMax. …”
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“…AVAILABILITY AND IMPLEMENTATION: Source code is at https://github.com/datduong/RECOV. …”
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“…AVAILABILITY AND IMPLEMENTATION: The source code can be downloaded from https://github.com/minxueric/ismb2017_lstm. …”
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“…AVAILABILITY AND IMPLEMENTATION: The R source code described in this article is publicly available at https://bitbucket.org/kleinstein/logminer. …”
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“…The software including source code is released freely for research.…”
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“…AVAILABILITY AND IMPLEMENTATION: The web server of DNCON2 is at http://sysbio.rnet.missouri.edu/dncon2/ where training and testing datasets as well as the predictions for CASP10, 11 and 12 free-modeling datasets can also be downloaded. Its source code is available at https://github.com/multicom-toolbox/DNCON2/. …”
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“…AVAILABILITY AND IMPLEMENTATION: Source code and binaries of the QuantumClone R package are freely available for download at https://CRAN.R-project.org/package=QuantumClone. …”
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“…AVAILABILITY AND IMPLEMENTATION: Source code and preprocessed datasets are at: http://snap.stanford.edu/decagon.…”
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“…The PathCORE-T framework includes a demonstration web interface, with source code, that users can launch to (1) visualize the network and (2) review the expression levels of associated genes in the original data. …”
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“…Our bound analysis therefore does not rely on external techniques for invariant generation. (3) We demonstrate that difference constraints are a suitable abstract program model for automatic complexity and resource bound analysis: we provide efficient abstraction techniques for obtaining difference constraint programs from imperative code. (4) We report on a thorough experimental comparison of state-of-the-art bound analysis tools: we set up a tool comparison on (a) a large benchmark of real-world C code, (b) a benchmark built of examples taken from the bound analysis literature and (c) a benchmark of challenging iteration patterns which we found in real source code. (5) Our analysis is more scalable than existing approaches: we discuss how we achieve scalability. …”
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“…LogLoss-BERAF is implemented as a standalone python code and open-source code is freely available from https://github.com/bioinformatics-IBCH/logloss-beraf along with the models described in this article.…”
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“…The functional characterisation is achieved using structured knowledge from data sources such as Gene Ontology, KEGG and Reactome pathways, Human Protein Atlas, and Human Phenotype Ontology. funcExplorer includes various measures for finding biologically meaningful clusters, provides a modern graphical user interface, and has wide-ranging data export and sharing options as well as software transparency by open-source code. The results are presented in a visually compact and interactive format, enabling users to explore the biological essence of the data. …”
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“…Machine learning is an effective and reliable technique to decipher ASD mechanism by identifying novel disease genes, but this study further demonstrated that their performance can be improved by incorporating a quantitative measure of gene functional similarities. Source code and the workflow of the proposed methodology are available at https://github.com/Muh-Asif/ASD-genes-prediction.…”
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“…Additionally, PASNet would be promising due to its flexible model representation and interpretability, embodying the strengths of deep learning. The open-source code of PASNet is available at https://github.com/DataX-JieHao/PASNet.…”
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“…CONCULSION: We developed a deep-learning-based framework to predict and characterize m6A-containing sequences and hope to help investigators to gain more insights for m6A research. The source code is available at https://github.com/rreybeyb/DeepM6ASeq. …”
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