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  1. 2641
    “…For a coupled use of the described workflow, we provide documentation and disclose the full source code of the developed tools.…”
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    A flexible workflow for simulating transcranial electric stimulation in healthy and lesioned brains
  2. 2642
    “…AVAILABILITY AND IMPLEMENTATION: The V-SVA Shiny application is publicly hosted at https://vsva.jax.org/ and the source code is freely available at https://github.com/nlawlor/V-SVA. …”
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    V-SVA: an R Shiny application for detecting and annotating hidden sources of variation in single-cell RNA-seq data
  3. 2643
    “…AVAILABILITY AND IMPLEMENTATION: The source code of MetaRib is freely available at https://github.com/yxxue/MetaRib. …”
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    Reconstructing ribosomal genes from large scale total RNA meta-transcriptomic data
  4. 2644
    “…Our approach provides a cost effective, broad and reliable examination of DNA methylation profile on MspI/HpaII restriction sites, is fully reproducible and the source code is available on GitHub (https://github.com/wendelljpereira/ms-dart-seq).…”
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    A cost-effective approach to DNA methylation detection by Methyl Sensitive DArT sequencing
  5. 2645
    “…To facilitate widely studies and encourage future proteomics research, a freely available web server called RNN-SIFT-SIPs was developed at http://219.219.62.123:8888/RNNSIFT/ including the source code and the SIP datasets.…”
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    Predicting Self-Interacting Proteins Using a Recurrent Neural Network and Protein Evolutionary Information
  6. 2646
    “…AVAILABILITY AND IMPLEMENTATION: ICGS2 is implemented in Python. The source code and documentation are available at http://altanalyze.org. …”
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    Resolving single-cell heterogeneity from hundreds of thousands of cells through sequential hybrid clustering and NMF
  7. 2647
    “…As an example, the ODE models that capture the effect of cis-regulatory elements involving protein complex binding, based on the model in the GeneNetWeaver source code, are described in detail and shown to satisfy the global constant sign property with a unique consistent gene regulatory graph. …”
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    From graph topology to ODE models for gene regulatory networks
  8. 2648
    por Liu, Tong, Wang, Zheng
    Publicado 2020
    “…CONCLUSIONS: MASS and the source code for all MASS potentials are publicly available at http://dna.cs.miami.edu/MASS/.…”
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    MASS: predict the global qualities of individual protein models using random forests and novel statistical potentials
  9. 2649
    “…This paper presents a methodology utilizing existing components of SWMM to represent unsaturated zone hydrology in an accessible format that does not require adjustments to the SWMM source code. The methodology simulated the unsaturated soil water movement by considering flow caused by differences of soil matric head and flow caused by gravity between soil layers with finite depth/length. …”
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    Methodology to simulate unsaturated zone hydrology in Storm Water Management Model (SWMM) for green infrastructure design and evaluation
  10. 2650
    por Wang, Zichen, Zhou, Mu, Arnold, Corey
    Publicado 2020
    “…AVAILABILITY AND IMPLEMENTATION: Source code and preprocessed datasets are at: https://github.com/zcwang0702/BiFusion.…”
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    Toward heterogeneous information fusion: bipartite graph convolutional networks for in silico drug repurposing
  11. 2651
    “…AVAILABILITY AND IMPLEMENTATION: The data and source code are available at https://github.com/gopuvenkat/MHCAttnNet.…”
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    MHCAttnNet: predicting MHC-peptide bindings for MHC alleles classes I and II using an attention-based deep neural model
  12. 2652
    “…AVAILABILITY AND IMPLEMENTATION: The source code of the RAD package, models, experiments and technical details such as parameters, is available at https://github.com/CMUSchwartzLab/RAD. …”
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    Robust and accurate deconvolution of tumor populations uncovers evolutionary mechanisms of breast cancer metastasis
  13. 2653
    “…AVAILABILITY AND IMPLEMENTATION: Source code of MutSpace can be accessed at: https://github.com/ma-compbio/MutSpace. …”
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    Cancer mutational signatures representation by large-scale context embedding
  14. 2654
    “…Presented results were generalized evaluation of both balanced and imbalanced models, which implies their ability of classifying, to classify novel riboswitches. The Python source code is available at https://github.com/Seasonsling/riboswitch.…”
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    A novel riboswitch classification based on imbalanced sequences achieved by machine learning
  15. 2655
    por Zhang, Lei, Xiao, Xuan, Xu, Zhao-Chun
    Publicado 2020
    “…A user-friendly web-server called iPromoter-5mC could be freely accessible at http://www.jci-bioinfo.cn/iPromoter-5mC, which will provide simple and effective means for users to study promoter 5mC modification. The source code of the proposed methods is freely available for academic research at https://github.com/zlwuxi/iPromoter-5mC.…”
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    iPromoter-5mC: A Novel Fusion Decision Predictor for the Identification of 5-Methylcytosine Sites in Genome-Wide DNA Promoters
  16. 2656
    “…RNAmigos shows that RNA binding data contains structural patterns with potential for drug discovery, and provides methodological insights for possible applications to other structure-function learning tasks. The source code, data and a Web server are freely available at http://rnamigos.cs.mcgill.ca.…”
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    Augmented base pairing networks encode RNA-small molecule binding preferences
  17. 2657
    “…The new estimates are useful for investigating changes in water availability, or benchmarking new hydrological models and data products developed for the Laurentian Great Lakes Region. The source code and inputs of the L2SWBM model are also made available, and can be adapted to include new data sources for the Great Lakes, or to address water balance problems on other large lake systems.…”
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    Seventy-year long record of monthly water balance estimates for Earth’s largest lake system
  18. 2658
    “…The sampled CT processes are commonly encoded using a source code to facilitate storage or transmission over wireless networks, e.g., using compress-and-forward relaying. …”
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    On the Rate-Distortion Function of Sampled Cyclostationary Gaussian Processes
  19. 2659
    “…To teach interested students and scientists how to analyze RNA-Seq and ChIP-Seq data, we present a start-to-finish tutorial for analyzing RNA-Seq and ChIP-Seq data: SeqAcademy ( source code:  https://github.com/NCBI-Hackathons/seqacademy, webpage: http://www.seqacademy.org/). …”
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    SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis
  20. 2660
    “…The resulting model, data, and analysis are available as open-source code on GitHub and an open-access data set is available for download.…”
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    Synthea™ Novel coronavirus (COVID-19) model and synthetic data set
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