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  1. 3141
    “…The platform is publicly accessible at http://nasqar.abudhabi.nyu.edu/. Open-source code is on GitHub at https://github.com/nasqar/NASQAR, and the system is also available as a Docker image at https://hub.docker.com/r/aymanm/nasqarall. …”
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    Online Artículo Texto
    NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization
  2. 3142
    “…Accessible via standard or cloud-based implementation, CICERO enhances driver fusion detection for research and precision oncology. The CICERO source code is available at https://github.com/stjude/Cicero.…”
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    CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data
  3. 3143
    por Popp, Denny, Centler, Florian
    Publicado 2020
    “…Simulated trajectories can be used to contextualize experimental meta-OMICS data and to derive hypotheses on cause-effect relationships driving community dynamics based on scenario simulations. μbialSim is implemented in Matlab and relies on the COBRA Toolbox or CellNetAnalyzer for FBA calculations. The source code is available under the GNU General Public License v3.0 at https://git.ufz.de/UMBSysBio/microbialsim.…”
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    μBialSim: Constraint-Based Dynamic Simulation of Complex Microbiomes
  4. 3144
    “…The COVID-ABS model was implemented in Python programming language, with source code publicly available. The model can be easily extended to other societies by changing the input parameters, as well as allowing the creation of a multitude of other scenarios. …”
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    COVID-ABS: An agent-based model of COVID-19 epidemic to simulate health and economic effects of social distancing interventions
  5. 3145
    “…It is difficult, nay impossible, for researchers to check the accuracy of software by reading the source code; ground truth test datasets are needed. …”
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    A validation framework for neuroimaging software: The case of population receptive fields
  6. 3146
    “…Detailed documentation for the software is available at: https://bioinformatics-recipes.readthedocs.io. The source code for the software is distributed through GitHub at https://github.com/ialbert/biostar-central. …”
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    Bioinformatics recipes: creating, executing and distributing reproducible data analysis workflows
  7. 3147
    “…CONCLUSION: By investigating three different factors and improving registration results, we defined a generalizable evaluation pipeline and automatic post-processing strategies that were deemed helpful. All source code, reference data, models, and evaluation results are openly available for download: https://github.com/ghattab/EvalPBSM/.…”
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    Online Artículo Texto
    A case study: impact of target surface mesh size and mesh quality on volume-to-surface registration performance in hepatic soft tissue navigation
  8. 3148
    “…AVAILABILITY AND IMPLEMENTATION: The source code is freely available at: https://github.com/anuradhawick/MetaBCC-LR. …”
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    Online Artículo Texto
    MetaBCC-LR: metagenomics binning by coverage and composition for long reads
  9. 3149
    “…We provide a detailed description of how SPUDNIG detects hand movement initiation and termination, as well as open-source code and a short tutorial on an easy-to-use graphical user interface (GUI) of our tool. …”
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    Speeding up the detection of non-iconic and iconic gestures (SPUDNIG): A toolkit for the automatic detection of hand movements and gestures in video data
  10. 3150
    “…Incorporation into the MNI ecosystem now provides CBRAIN registered users access to its full functionality and is accompanied by a public release of the source code on GitHub and Zenodo repositories. Among other features are the calculation of EEG scalp spectra, and the estimation of their source spectra using the Variable Resolution Electrical Tomography (VARETA) source imaging. …”
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    A Quantitative EEG Toolbox for the MNI Neuroinformatics Ecosystem: Normative SPM of EEG Source Spectra
  11. 3151
    “…The relevant benchmark dataset and source code are freely available at: https://github.com/Fatima-Khan12/iRspot_DNN/tree/master/iRspot_DNN.…”
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    Prediction of Recombination Spots Using Novel Hybrid Feature Extraction Method via Deep Learning Approach
  12. 3152
    “…We released and support the complete technique as a free and open-source code package.…”
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    Epifluorescence-based three-dimensional traction force microscopy
  13. 3153
    por Deschamps, Joran, Ries, Jonas
    Publicado 2020
    “…Since even similar devices can have different Micro-Manager device properties, such as power percentage versus absolute power, directly transferring a GUI to another instrument usually requires changing the source-code. RESULTS: We developed Easier Micro-Manager User interface (EMU), a Micro-Manager plugin, to simplify building flexible and reconfigurable GUIs. …”
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    EMU: reconfigurable graphical user interfaces for Micro-Manager
  14. 3154
    “…In conclusion, this study was able to create an accurate CADx system for the 3-category classification. Source code of our CADx system is available as open source for COVID-19 research.…”
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    Automatic classification between COVID-19 pneumonia, non-COVID-19 pneumonia, and the healthy on chest X-ray image: combination of data augmentation methods
  15. 3155
    “…p=RCG_lungNENomics/LNEN). The data, source code, and compute environments used to generate and evaluate the map as well as the raw data are available, respectively, in a Nextjournal interactive notebook (https://nextjournal.com/rarecancersgenomics/a-molecular-map-of-lung-neuroendocrine-neoplasms/) and at the EMBL-EBI European Genome-phenome Archive and Gene Expression Omnibus data repositories. …”
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    A molecular map of lung neuroendocrine neoplasms
  16. 3156
    “…Our experiments show that the automated segmentation provides safe and coherent surface models that can be used in collision detection during motion planning. The source code of the algorithms will be made publicly available. …”
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    Retrospective in silico evaluation of optimized preoperative planning for temporal bone surgery
  17. 3157
    “…Complementing the NCATS COVID19 portal, REDIAL-2020 can serve as a rapid online tool for identifying active molecules for COVID-19 treatment. The source code and specific models are available through Github (https://github.com/sirimullalab/redial-2020), or via Docker Hub (https://hub.docker.com/r/sirimullalab/redial-2020) for users preferring a containerized version.…”
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    REDIAL-2020: A suite of machine learning models to estimate Anti-SARS-CoV-2 activities
  18. 3158
    “…AVAILABILITY AND IMPLEMENTATION: The DiscoRhythm R package is available on Bioconductor (https://bioconductor.org/packages/DiscoRhythm), with source code available on GitHub (https://github.com/matthewcarlucci/DiscoRhythm) under a GPL-3 license. …”
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    DiscoRhythm: an easy-to-use web application and R package for discovering rhythmicity
  19. 3159
    “…AVAILABILITY AND IMPLEMENTATION: We make the pre-trained weights of BioBERT freely available at https://github.com/naver/biobert-pretrained, and the source code for fine-tuning BioBERT available at https://github.com/dmis-lab/biobert.…”
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    BioBERT: a pre-trained biomedical language representation model for biomedical text mining
  20. 3160
    “…This might be clinically irrelevant, depending on the context of use and should, therefore, be evaluated by the potential user regarding the specific application. The entire source code of the A&A method and the data used in the study is open source and can be accessed via https://github.com/RWTHmediTEC/FemoralCoordinateSystem.…”
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    Online Artículo Texto
    A robust method for automatic identification of femoral landmarks, axes, planes and bone coordinate systems using surface models
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