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  1. 2541
    “…AVAILABILITY AND IMPLEMENTATION: The source code for LSTM-CRF is available at https://github.com/glample/tagger and the links to the corpora are available at https://corposaurus.github.io/corpora/.…”
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    Deep learning with word embeddings improves biomedical named entity recognition
  2. 2542
    “…Finally, we compare our whole genome tiling array designs with commercially available designs. AVAILABILITY: Source code is available under an open source license from http://www.ebi.ac.uk/~graef/arraydesign/…”
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    Optimized design and assessment of whole genome tiling arrays
  3. 2543
    “…AVAILABILITY AND IMPLEMENTATION: The GRAM-CNN source code, datasets and pre-trained model are available online at: https://github.com/valdersoul/GRAM-CNN. …”
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    GRAM-CNN: a deep learning approach with local context for named entity recognition in biomedical text
  4. 2544
    “…Here, we introduce the R packages adnuts and tmbstan, which provide NUTS sampling in parallel and interactive diagnostics with ShinyStan. The ADMB source code was modified to provide NUTS, while TMB models are linked directly into Stan. …”
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    No-U-turn sampling for fast Bayesian inference in ADMB and TMB: Introducing the adnuts and tmbstan R packages
  5. 2545
    “…The dataset, along with python source code for file input and signal processing, is made freely available at the Open Science Framework through the link https://osf.io/chav7/.…”
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    A high-density scalp EEG dataset acquired during brief naps after a visual working memory task
  6. 2546
    “…It is accessible online at http://bioinfo.ciberehd.org/GPtoCRC/en/tools.html and source code is freely available at https://github.com/marcos-diazg/musica. …”
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    Mutational Signatures in Cancer (MuSiCa): a web application to implement mutational signatures analysis in cancer samples
  7. 2547
    “…CONCLUSION: The experimental results indicate that our method can significantly improve the prediction accuracy of subcellular localization of apoptosis proteins, which is quite high to be able to become a promising tool for further proteomics studies. The source code and all datasets are available at https://github.com/QUST-BSBRC/PsePSSM-DCCA-LFDA/.…”
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    Prediction of subcellular location of apoptosis proteins by incorporating PsePSSM and DCCA coefficient based on LFDA dimensionality reduction
  8. 2548
    “…We have made the Epilepsy Knowledge Assembly available at https://www.scai.fraunhofer.de/content/dam/scai/de/downloads/bioinformatik/epilepsy.bel and queryable through NeuroMMSig at http://neurommsig.scai.fraunhofer.de. The source code used for analysis and tutorials for reproduction are available on GitHub at https://github.com/cthoyt/epicom.…”
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    A systematic approach for identifying shared mechanisms in epilepsy and its comorbidities
  9. 2549
    “…These results suggest that our method was very promising for predicting succinylation sites. The source code and data of this paper are freely available athttps://github.com/ningq669/PSuccE. …”
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    Detecting Succinylation sites from protein sequences using ensemble support vector machine
  10. 2550
    “…AVAILABILITY AND IMPLEMENTATION: HyPPO is a modular framework with a core developed in Python and is provided with a variety of C++ modules. The source code is available at https://github.com/manuellafond/HyPPO. …”
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    Accurate prediction of orthologs in the presence of divergence after duplication
  11. 2551
    “…AVAILABILITY AND IMPLEMENTATION: The source code and documentation are freely available on https://github.com/BlueBrain/NeuroMorphoVis under the GNU public license. …”
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    NeuroMorphoVis: a collaborative framework for analysis and visualization of neuronal morphology skeletons reconstructed from microscopy stacks
  12. 2552
    “…AVAILABILITY AND IMPLEMENTATION: aliFreeFold was implemented in C++. Source code and Linux binary are freely available at https://github.com/UdeS-CoBIUS/aliFreeFold. …”
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    aliFreeFold: an alignment-free approach to predict secondary structure from homologous RNA sequences
  13. 2553
    “…AVAILABILITY AND IMPLEMENTATION: Source code is available at https://github.com/yjzhang/uncurl_python. …”
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    Scalable preprocessing for sparse scRNA-seq data exploiting prior knowledge
  14. 2554
    “…The diagram viewer is part of the Reactome pathway browser (https://reactome.org/PathwayBrowser/) and also available as a stand-alone widget at: https://reactome.org/dev/diagram/. The source code is freely available at: https://github.com/reactome-pwp/diagram. …”
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    Reactome diagram viewer: data structures and strategies to boost performance
  15. 2555
    por Han, Renmin, Zhang, Fa, Gao, Xin
    Publicado 2018
    “…AVAILABILITY AND IMPLEMENTATION: The C/C ++ source code that implements the fast fiducial marker tracking is available at https://github.com/icthrm/gmm-marker-tracking. …”
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    A fast fiducial marker tracking model for fully automatic alignment in electron tomography
  16. 2556
    por Proost, Sebastian, Mutwil, Marek
    Publicado 2018
    “…CoNekT-Plants is freely available from http://conekt.plant.tools, while the CoNekT source code and documentation can be found at https://github.molgen.mpg.de/proost/CoNekT/.…”
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    CoNekT: an open-source framework for comparative genomic and transcriptomic network analyses
  17. 2557
    “…The underlying algorithm and source code makes use of several methods to increase computational speed. …”
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    joineRML: a joint model and software package for time-to-event and multivariate longitudinal outcomes
  18. 2558
    “…We provide both the source code of the pipeline as well as an online web-service based on this pipeline http://combio.abo.fi/nc/net_control/remote_call.php. …”
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    NetControl4BioMed: a pipeline for biomedical data acquisition and analysis of network controllability
  19. 2559
    “…To demonstrate these issues, we provide a worked example of reproducing a seminal study for which, unusually, source code was provided at time of publication. Despite this seemingly optimal starting position, reproducing the results was time consuming and frustrating. …”
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    Reproducing Polychronization: A Guide to Maximizing the Reproducibility of Spiking Network Models
  20. 2560
    “…AVAILABILITY AND IMPLEMENTATION: All analyses were implemented in R. Source code and the experimental data are available at https://github.com/SimoneTiberi/Bayesian-inference-on-stochastic-gene-transcription-from-flow-cytometry-data. …”
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    Bayesian inference on stochastic gene transcription from flow cytometry data
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