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  1. 2041
    “…CircularLogo is implemented in JavaScript and Python based on the Django web framework. The program’s source code and user’s manual are freely available at http://circularlogo.sourceforge.net. …”
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    CircularLogo: A lightweight web application to visualize intra-motif dependencies
  2. 2042
    “…We welcome reuse and contributions: our databases and APIs are publicly available, all of our source code is released with a permissive Apache v2.0 licence at http://github.com/Ensembl and we have an active developer mailing list (http://www.ensembl.org/info/about/contact/index.html). …”
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    Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation
  3. 2043
    por Bhattacharya, Anindya, Cui, Yan
    Publicado 2017
    “…We implemented the CCS algorithm using C and implemented the parallelized CCS algorithm using CUDA C for GPU computing. The source code of CCS is available from https://github.com/abhatta3/Condition-dependent-Correlation-Subgroups-CCS.…”
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    A GPU-accelerated algorithm for biclustering analysis and detection of condition-dependent coexpression network modules
  4. 2044
    por Jiménez, Rafael C., Kuzak, Mateusz, Alhamdoosh, Monther, Barker, Michelle, Batut, Bérénice, Borg, Mikael, Capella-Gutierrez, Salvador, Chue Hong, Neil, Cook, Martin, Corpas, Manuel, Flannery, Madison, Garcia, Leyla, Gelpí, Josep Ll., Gladman, Simon, Goble, Carole, González Ferreiro, Montserrat, Gonzalez-Beltran, Alejandra, Griffin, Philippa C., Grüning, Björn, Hagberg, Jonas, Holub, Petr, Hooft, Rob, Ison, Jon, Katz, Daniel S., Leskošek, Brane, López Gómez, Federico, Oliveira, Luis J., Mellor, David, Mosbergen, Rowland, Mulder, Nicola, Perez-Riverol, Yasset, Pergl, Robert, Pichler, Horst, Pope, Bernard, Sanz, Ferran, Schneider, Maria V., Stodden, Victoria, Suchecki, Radosław, Svobodová Vařeková, Radka, Talvik, Harry-Anton, Todorov, Ilian, Treloar, Andrew, Tyagi, Sonika, van Gompel, Maarten, Vaughan, Daniel, Via, Allegra, Wang, Xiaochuan, Watson-Haigh, Nathan S., Crouch, Steve
    Publicado 2017
    “…These recommendations are designed around Open Source values, and provide practical suggestions that contribute to making research software and its source code more discoverable, reusable and transparent. …”
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    Four simple recommendations to encourage best practices in research software
  5. 2045
    “…CRISPRpred is enough flexible to extract relevant features and use them in a learning algorithm. The source code of our entire software with relevant dataset can be found in the following link: https://github.com/khaled-buet/CRISPRpred.…”
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    CRISPRpred: A flexible and efficient tool for sgRNAs on-target activity prediction in CRISPR/Cas9 systems
  6. 2046
    “…One can incorporate the Scoria source code directly into their own programs. But Scoria is not designed to compete with other similar packages. …”
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    Scoria: a Python module for manipulating 3D molecular data
  7. 2047
    “…PBrowse is available at http://pbrowse.victorchang.edu.au, and its source code is available via an open source BSD 3 license at http://github.com/VCCRI/PBrowse.…”
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    PBrowse: a web-based platform for real-time collaborative exploration of genomic data
  8. 2048
    “…The performance of independent test also shows that our method has a certain ability to be effectively used for DNA-binding protein prediction. The data and source code are at https://doi.org/10.6084/m9.figshare.5104084.…”
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    Improved detection of DNA-binding proteins via compression technology on PSSM information
  9. 2049
    por Hayes, Matthew, Pearson, Jeremy S.
    Publicado 2017
    “…However, the method must be extended to allow for germline variant filtering and heterozygous deletion detection. The source code that implements Pegasus can be downloaded from the following URL: http://github.com/mhayes20/Pegasus.…”
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    Detecting large deletions at base pair level by combining split read and paired read data
  10. 2050
    “…The platform was developed openly, and all source code hosted on the GitHub platform with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. …”
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    Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application
  11. 2051
    “…We further demonstrate their effectiveness in identifying mixture substructure in true breast cancer CNV data from the Cancer Genome Atlas (TCGA). Source code is available at https://github.com/tedroman/WSCUnmix…”
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    Automated deconvolution of structured mixtures from heterogeneous tumor genomic data
  12. 2052
    “…The system presented here is the first of this kind made publicly available, including source code and hardware specifications. We hope this will foster quantitative analyses of the honey bee waggle dance.…”
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    Automatic detection and decoding of honey bee waggle dances
  13. 2053
    “…The analysis time of whole LINCS phase I dataset (GSE92742) was reduced to nearly half hour on a 1000 node cluster on Tianhe-2, or within 120 hours on a 96-core workstation. The source code of paraGSEA is licensed under the GPLv3 and available at http://github.com/ysycloud/paraGSEA.…”
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    paraGSEA: a scalable approach for large-scale gene expression profiling
  14. 2054
    “…Moreover, our study of the quality of the new domains in terms of alignment and physicochemical properties show that they are close to that of standard Pfam domains. Source code of the proposed approach and supplementary data are available at: https://gite.lirmm.fr/menichelli/pairwise-comparison-with-cooccurrence…”
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    Improving pairwise comparison of protein sequences with domain co-occurrence
  15. 2055
    “…The software for the DP algorithm is freely available as open source code at https://github.com/smirarab/DynaDup.…”
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    Gene tree parsimony for incomplete gene trees: addressing true biological loss
  16. 2056
    “…We test it on real and simulated data to show that MentaLiST is faster than any other available MLST caller while providing the same or better accuracy, and is capable of dealing with MLST schemes with up to thousands of genes while requiring limited computational resources. MentaLiST source code and easy installation instructions using a Conda package are available at https://github.com/WGS-TB/MentaLiST.…”
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    MentaLiST – A fast MLST caller for large MLST schemes
  17. 2057
    “…AVAILABILITY AND IMPLEMENTATION: Web server: http://deepgo.bio2vec.net, Source code: https://github.com/bio-ontology-research-group/deepgo SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.…”
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    DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier
  18. 2058
    “…AVAILABILITY AND IMPLEMENTATION: The SinCHet software is freely available for non-profit academic use. The source code, example datasets, and the compiled package are available at http://labpages2.moffitt.org/chen/software/. …”
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    SinCHet: a MATLAB toolbox for single cell heterogeneity analysis in cancer
  19. 2059
    “…AVAILABILITY AND IMPLEMENTATION: The pgRNAFinder is freely available at http://songyanglab.sysu.edu.cn/wangwebs/pgRNAFinder/, and the source code and user manual can be obtained from https://github.com/xiexiaowei/pgRNAFinder. …”
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    pgRNAFinder: a web-based tool to design distance independent paired-gRNA
  20. 2060
    “…AVAILABILITY AND IMPLEMENTATION: The source code is licensed under the Apache 2.0 License and is freely available on GitHub: https://github.com/transmart/SmartR. …”
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    SmartR: an open-source platform for interactive visual analytics for translational research data
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