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  1. 11381
    por Herrick, Noah, Walsh, Susan
    Publicado 2023
    “…Iliad was developed to be portable, compatible, scalable, robust, and repeatable with a simplistic setup, so biologists that are less familiar with programming can manage their own big data with this open-source suite of workflows. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-023-05548-x.…”
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    ILIAD: a suite of automated Snakemake workflows for processing genomic data for downstream applications
  2. 11382
    “…In comparison with the feature alignment methods in OpenMS, MZmine2 and XCMS on three public metabolomics benchmark datasets, G-Aligner achieved the best feature alignment performance on all the three datasets with up to 9.8% and 26.6% increase in accurately aligned features and analytes, and helped all comparison software obtain more accurate results on their self-extracted features by integrating G-Aligner to their analysis workflow. G-Aligner is open-source and freely available at https://github.com/CSi-Studio/G-Aligner under a permissive license. …”
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    Online Artículo Texto
    G-Aligner: a graph-based feature alignment method for untargeted LC–MS-based metabolomics
  3. 11383
    “…The application is open source, and all contents are offered in English and German. …”
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    Online Artículo Texto
    A Web-Based COVID-19 Tool for Testing Residents in Retirement Homes: Development Study
  4. 11384
    “…CONCLUSION: We expanded a low-cost, open-source saliva-based PCR test for detection of other common respiratory pathogens. …”
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    Online Artículo Texto
    881. Saliva-Based, Extraction-Free PCR Testing For The Detection Of Key Respiratory Pathogens
  5. 11385
    “…OBJECTIVE: This study aimed to develop a predictive model of postoperative adverse outcomes in older patients following general surgery with an open-source, patient-level prediction from the Observational Health Data Sciences and Informatics for internal and external validation. …”
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    Online Artículo Texto
    Development and Validation of a Prognostic Classification Model Predicting Postoperative Adverse Outcomes in Older Surgical Patients Using a Machine Learning Algorithm: Retrospective Observational Network Study
  6. 11386
    “…Unlike previous remote power side-channel attacks, which either require a considerable number of victim traces or attack large victim circuits such as machine learning accelerators, we take an evaluator’s point of view and provide an analysis of the instruction-level power side-channel leakage of a small open-source RISC-V soft processor core. To investigate whether the power side-channel traces leak secrets, we profile the victim device and implement various instruction opcode classifiers based on both classical machine learning algorithms used in disassembly attacks, and novel, deep learning approaches. …”
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    Online Artículo Texto
    Instruction-Level Power Side-Channel Leakage Evaluation of Soft-Core CPUs on Shared FPGAs
  7. 11387
    “…Although the accuracy of the algorithm is high, it is probably insufficient to be used to publicly disseminate medical data. The open-source de-identification software and the gold standard re-identified corpus of medical records have therefore been made available to researchers via the PhysioNet website to encourage improvements in the algorithm.…”
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    Automated de-identification of free-text medical records
  8. 11388
    “…As a publicly available tool, Pep-3D-Search can be utilized and conveniently evaluated, and it can also be used to complement other existing tools. The data sets and open source code used to obtain the results in this paper are available on-line and as supplementary material. …”
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    Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis
  9. 11389
    “…The WildSpan executable and open source codes are available on the web (http://biominer.csie.cyu.edu.tw/wildspan).…”
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    WildSpan: mining structured motifs from protein sequences
  10. 11390
    por Goff, Stephen A., Vaughn, Matthew, McKay, Sheldon, Lyons, Eric, Stapleton, Ann E., Gessler, Damian, Matasci, Naim, Wang, Liya, Hanlon, Matthew, Lenards, Andrew, Muir, Andy, Merchant, Nirav, Lowry, Sonya, Mock, Stephen, Helmke, Matthew, Kubach, Adam, Narro, Martha, Hopkins, Nicole, Micklos, David, Hilgert, Uwe, Gonzales, Michael, Jordan, Chris, Skidmore, Edwin, Dooley, Rion, Cazes, John, McLay, Robert, Lu, Zhenyuan, Pasternak, Shiran, Koesterke, Lars, Piel, William H., Grene, Ruth, Noutsos, Christos, Gendler, Karla, Feng, Xin, Tang, Chunlao, Lent, Monica, Kim, Seung-Jin, Kvilekval, Kristian, Manjunath, B. S., Tannen, Val, Stamatakis, Alexandros, Sanderson, Michael, Welch, Stephen M., Cranston, Karen A., Soltis, Pamela, Soltis, Doug, O'Meara, Brian, Ane, Cecile, Brutnell, Tom, Kleibenstein, Daniel J., White, Jeffery W., Leebens-Mack, James, Donoghue, Michael J., Spalding, Edgar P., Vision, Todd J., Myers, Christopher R., Lowenthal, David, Enquist, Brian J., Boyle, Brad, Akoglu, Ali, Andrews, Greg, Ram, Sudha, Ware, Doreen, Stein, Lincoln, Stanzione, Dan
    Publicado 2011
    “…The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. …”
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    The iPlant Collaborative: Cyberinfrastructure for Plant Biology
  11. 11391
    “…Capacity building and applying creative commons and open source solutions are showing promise, as is international collaboration. …”
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    Online Artículo Texto
    Tool, weapon, or white elephant? A realist analysis of the five phases of a twenty-year programme of occupational health information system implementation in the health sector
  12. 11392
    “…The point-of-care platform is open source and customizable, allowing doctors to encode new assessments onto smart-phones for a specific application, or to use existing ones. …”
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    Sana: democratizing access to quality healthcare using an open mhealth architecture
  13. 11393
    “…Our system uses an open source enterprise bus ‘Mirth Connect’ to receive and store data in HL7 format. …”
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    Online Artículo Texto
    A System for Surveillance Directly from the EMR
  14. 11394
    por Donner, Claudio F, Visconti, Alberto
    Publicado 2014
    “…The data thus collected were memorized directly within a relational database, based on consolidated open-source MySQL technology, and thus were immediately available for examination also during the course of the survey. …”
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    AIMAR survey on complex forms of bronchial asthma and COPD, their management and perception of critical issues
  15. 11395
    “…To do so, we searched protein sequences predicted from 29 fully-sequenced genomes and built trees using tools for phylogenetic analysis in the Osiris package of Galaxy (an open-source workflow management system). Next, to rapidly annotate transcriptomes from organisms that lack sequenced genomes, we repurposed a maximum likelihood-based Evolutionary Placement Algorithm (implemented in RAxML) to place sequences of potential LIT genes on to our pre-calculated gene trees. …”
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    Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms
  16. 11396
    “…METHODS: The PPAP app was constructed using an open-source software platform and a custom, multi-sensor AM capable of accurately measuring heart rate and physical activity. …”
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    Feasibility of a Dynamic Web Guidance Approach for Personalized Physical Activity Prescription Based on Daily Information From Wearable Technology
  17. 11397
    “…CONCLUSIONS: KneeTex is an open–source, stand–alone application for information extraction from narrative reports that describe an MRI scan of the knee. …”
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    KneeTex: an ontology–driven system for information extraction from MRI reports
  18. 11398
    “…DESCRIPTION: Here, we present an open-source phenomics platform “DIRT”, as a means to integrate scalable supercomputing architectures into field experiments and analysis pipelines. …”
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    Digital imaging of root traits (DIRT): a high-throughput computing and collaboration platform for field-based root phenomics
  19. 11399
    “…Such programs would find value in an open-source bioinformatics pipeline that can maximize GBS data usage and perform high-density SNP genotyping in the absence of a reference. …”
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    GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data
  20. 11400
    “…METHODS: We developed the pilot program based on existing face-to-face relapse prevention approaches using an open source Web application to build an e-learning website, including relapse prevention sessions with videos, exercises, a diary function, and self-monitoring. …”
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    Web-Based Cognitive Behavioral Relapse Prevention Program With Tailored Feedback for People With Methamphetamine and Other Drug Use Problems: Development and Usability Study
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