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  1. 3661
    “…We demonstrated that evolution in the ledger platform (MultiChain 1 to 2) yielded a 30%-40% increase in insertion efficiency. All source code for this challenge has been made available under a BSD-3 license from https://github.com/sandialabs/idash2018task1/.…”
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    Online Artículo Texto
    Decentralized genomics audit logging via permissioned blockchain ledgering
  2. 3662
    “…GenomeChronicler can be run for one sample at a time, or in parallel making use of the Nextflow workflow manager. The source code is available from GitHub (https://github.com/PGP-UK/GenomeChronicler), container recipes are available for Docker and Singularity, as well as a pre-built container from SingularityHub (https://singularity-hub.org/collections/3664) enabling easy deployment in a variety of settings. …”
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    Online Artículo Texto
    GenomeChronicler: The Personal Genome Project UK Genomic Report Generator Pipeline
  3. 3663
    “…CONCLUSION: The proposed non-linear optimisation method is an improvement on the existing method when only a KM plot and P value are included and as such will enhance the accuracy of meta-analyses performed for studies analysing time-to-event outcomes. The nlopt source code is available, as is a simple-to-use web implementation of the method.…”
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    Online Artículo Texto
    A non-linear optimisation method to extract summary statistics from Kaplan-Meier survival plots using the published P value
  4. 3664
    “…Based on the predicted results of DLDTI model, we found TMPZ could attenuate atherosclerosis by inhibiting signal transductions in platelets. The source code and datasets explored in this work are available at https://github.com/CUMTzackGit/DLDTI.…”
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    Online Artículo Texto
    DLDTI: a learning-based framework for drug-target interaction identification using neural networks and network representation
  5. 3665
    “…CONCLUSIONS: A strategy based on “self-consistency”, captured through our method, I-Impute, gave imputation results better than the state-of-the-art tools. Source code of I-Impute can be accessed at https://github.com/xikanfeng2/I-Impute.…”
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    Online Artículo Texto
    I-Impute: a self-consistent method to impute single cell RNA sequencing data
  6. 3666
    “…The distributed representations of RNA sequences and secondary structures can effectively detect the latent relationship and similarity between k-mers, and thus improve the predictive performance. The source code of DeepRKE is available at https://github.com/youzhiliu/DeepRKE/. …”
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    Online Artículo Texto
    Deep neural networks for inferring binding sites of RNA-binding proteins by using distributed representations of RNA primary sequence and secondary structure
  7. 3667
    “…Next, we present a large-scale comparative study among the proposed network-based methods, canonical prediction algorithms (i.e., Elastic Net, Random Forest, Partial Least Squares Regression, and Support Vector Regression), and deep neural network models for drug sensitivity prediction. All the source code and processed datasets in this study are available at https://github.com/compbiolabucf/drug-sensitivity-prediction. …”
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    Online Artículo Texto
    Network-based drug sensitivity prediction
  8. 3668
    por Emdadi, Akram, Eslahchi, Changiz
    Publicado 2021
    “…CONCLUSIONS: We depicted an application of Auto-HMM-LMF in exploring the new candidate drugs for head and neck cancer that showed the proposed method is useful in drug repositioning and personalized medicine. The source code of Auto-HMM-LMF method is available in https://github.com/emdadi/Auto-HMM-LMF.…”
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    Online Artículo Texto
    Auto-HMM-LMF: feature selection based method for prediction of drug response via autoencoder and hidden Markov model
  9. 3669
    “…CONCLUSION: With multi-classifier and modular design, VirSorter2 demonstrates higher overall accuracy across major viral groups and will advance our knowledge of virus evolution, diversity, and virus-microbe interaction in various ecosystems. Source code of VirSorter2 is freely available (https://bitbucket.org/MAVERICLab/virsorter2), and VirSorter2 is also available both on bioconda and as an iVirus app on CyVerse (https://de.cyverse.org/de). …”
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    Online Artículo Texto
    VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses
  10. 3670
    “…MAD-HiDTree was developed in C/C(++) in Linux. Both the source code and test data are publicly available at https://bioinfo.noble.org/MAD-HiDTree/.…”
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    Online Artículo Texto
    Distinguishing HapMap Accessions Through Recursive Set Partitioning in Hierarchical Decision Trees
  11. 3671
    “…PubChemLite is a living collection, updating as annotation content in PubChem is updated, and exported to allow direct integration into existing workflows such as MetFrag. The source code and files necessary to recreate or adjust this are jointly hosted between the research parties (see data availability statement). …”
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    Online Artículo Texto
    Empowering large chemical knowledge bases for exposomics: PubChemLite meets MetFrag
  12. 3672
    “…CONCLUSIONS: In general, our proposed method EDLMFC improved the accuracy of ncRNA–protein interaction predictions and anticipated providing some helpful guidance on ncRNA functions research. The source code of EDLMFC and the datasets used in this work are available at https://github.com/JingjingWang-87/EDLMFC. …”
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    Online Artículo Texto
    EDLMFC: an ensemble deep learning framework with multi-scale features combination for ncRNA–protein interaction prediction
  13. 3673
    “…RESULTS: Our OSINT approach and subsequent analysis of the collected documents resulted in the definition of the following five main categories and associated subcategories: (1) background information (open-source code, public information, and collaborators); (2) purpose and workflow (secondary data use and warning process design); (3) technical information (protocol, tracing technology, exposure notification system, and interoperability); (4) privacy protection (the entity of trust and anonymity); and (5) availability and use (release date and the number of downloads). …”
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    Online Artículo Texto
    Analyzing the Essential Attributes of Nationally Issued COVID-19 Contact Tracing Apps: Open-Source Intelligence Approach and Content Analysis
  14. 3674
    “…During testing, the high task completion rate (78%) and low overall number of non-critical errors indicated good usability, while the quantitative data (system usability scoring) also indicates high ease of use. The source code for the tool is open-source and can be adapted by other medical faculties. …”
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    Online Artículo Texto
    Design and usability testing of an in-house developed performance feedback tool for medical students
  15. 3675
    “…HAVoC user manual and source code are available at https://www.helsinki.fi/en/projects/havoc and https://bitbucket.org/auto_cov_pipeline/havoc, respectively.…”
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    Online Artículo Texto
    HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences
  16. 3676
    por Sun, Hua, Cao, Song, Mashl, R. Jay, Mo, Chia-Kuei, Zaccaria, Simone, Wendl, Michael C., Davies, Sherri R., Bailey, Matthew H., Primeau, Tina M., Hoog, Jeremy, Mudd, Jacqueline L., Dean, Dennis A., Patidar, Rajesh, Chen, Li, Wyczalkowski, Matthew A., Jayasinghe, Reyka G., Rodrigues, Fernanda Martins, Terekhanova, Nadezhda V., Li, Yize, Lim, Kian-Huat, Wang-Gillam, Andrea, Van Tine, Brian A., Ma, Cynthia X., Aft, Rebecca, Fuh, Katherine C., Schwarz, Julie K., Zevallos, Jose P., Puram, Sidharth V., Dipersio, John F., Davis-Dusenbery, Brandi, Ellis, Matthew J., Lewis, Michael T., Davies, Michael A., Herlyn, Meenhard, Fang, Bingliang, Roth, Jack A., Welm, Alana L., Welm, Bryan E., Meric-Bernstam, Funda, Chen, Feng, Fields, Ryan C., Li, Shunqiang, Govindan, Ramaswamy, Doroshow, James H., Moscow, Jeffrey A., Evrard, Yvonne A., Chuang, Jeffrey H., Raphael, Benjamin J., Ding, Li
    Publicado 2021
    “…Lastly, we provide a web portal having comprehensive pan-cancer PDX genomic profiles and source code to facilitate identification of more druggable events and further insights into PDXs’ recapitulation of human tumors.…”
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    Online Artículo Texto
    Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment
  17. 3677
    “…DECONbench performs a systematic performance evaluation of each new methodological contribution and provides the possibility to publicly share source code and scoring. CONCLUSION: DECONbench allows continuous submission of new methods in a user-friendly fashion, each novel contribution being automatically compared to the reference baseline methods, which enables crowdsourced benchmarking. …”
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    Online Artículo Texto
    DECONbench: a benchmarking platform dedicated to deconvolution methods for tumor heterogeneity quantification
  18. 3678
    “…Furthermore, our calculation results also highlight the importance of the incorporation of the cross-docked poses into the training of the SFs with wide application domain and high robustness for binding pose prediction. The source code and the newly-developed cross-docking datasets can be freely available at https://github.com/sc8668/ml_pose_prediction and https://zenodo.org/record/5525936, respectively, under an open-source license. …”
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    Online Artículo Texto
    The impact of cross-docked poses on performance of machine learning classifier for protein–ligand binding pose prediction
  19. 3679
    “…Our method generalizes well to data from different institutions, pathologies and modalities. Source code, segmentation models and the EPISURG dataset are available at https://github.com/fepegar/resseg-ijcars.…”
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    A self-supervised learning strategy for postoperative brain cavity segmentation simulating resections
  20. 3680
    “…CONCLUSIONS: a novel low-rank tensor completion-based method scLRTC gave imputation results better than the state-of-the-art tools. Source code of scLRTC can be accessed at https://github.com/jianghuaijie/scLRTC.…”
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    ScLRTC: imputation for single-cell RNA-seq data via low-rank tensor completion
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