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  1. 11601
    “…Medical data of 246 558 805 patients from multiple countries from the Observational Health Data Sciences and Informatics (OHDSI) initiative were included and medical data sets were transformed into a unified common data model, with analysis done using open-source analytical tools. Participants included patients with T2D receiving metformin with at least 1 prior HbA(1c) laboratory test who were then prescribed either sulfonylureas, DPP-4 inhibitors, or thiazolidinediones. …”
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    Association of Hemoglobin A(1c) Levels With Use of Sulfonylureas, Dipeptidyl Peptidase 4 Inhibitors, and Thiazolidinediones in Patients With Type 2 Diabetes Treated With Metformin: Analysis From the Observational Health Data Sciences and Informatics Initiative
  2. 11602
    “…However, while the data analysis can be readily undertaken using open source or other software tools, large SMLM data volumes and the complexity of the algorithms used often lead to long image data processing times that can hinder the iterative optimization of experiments. …”
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    Accelerating single molecule localization microscopy through parallel processing on a high‐performance computing cluster
  3. 11603
    “…To implement the crawler, we extended the open-source framework StormCrawler. The actual crawl was conducted for 227 days. …”
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    Crawling the German Health Web: Exploratory Study and Graph Analysis
  4. 11604
    “…The prototype was built on Hyperledger Fabric, an open-source, permissioned blockchain framework. Data sharing transactions were implemented using chaincode and exposed as representational state transfer application programming interfaces used for the web portal for patients and users. …”
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    ACTION-EHR: Patient-Centric Blockchain-Based Electronic Health Record Data Management for Cancer Care
  5. 11605
    “…Kinematics were studied for scapulothoracic and glenohumeral movements using the Upper Limb Evaluation in Movement Analysis (ULEMA) open-source model. The main motion studied was active arm elevation in the scapular plane. …”
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    How Do Scapulothoracic Kinematics During Shoulder Elevation Differ Between Adults With and Without Rotator Cuff Arthropathy?
  6. 11606
    “…All analyses were conducted using the open-source R/Bioconductor software framework. RESULTS: A linear regression step was found to perform well in removing RNA degradation-related bias among the main principal components of the gene expression data, increasing the number of genes detectable as differentially expressed in asthma and COPD sputa (compared to controls). …”
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    Exploration of the sputum methylome and omics deconvolution by quadratic programming in molecular profiling of asthma and COPD: the road to sputum omics 2.0
  7. 11607
    “…A separate AI-mode function that could quickly recognize pulmonary infiltrates on chest x-rays was merged into the smart clinical assisting system (SCAS), and this model was subsequently trained with COVID-19 pneumonia cases from the GitHub open source data set. The detection rates for posteroanterior and anteroposterior chest x-rays were 55/59 (93%) and 5/11 (45%), respectively. …”
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    Application of an Artificial Intelligence Trilogy to Accelerate Processing of Suspected Patients With SARS-CoV-2 at a Smart Quarantine Station: Observational Study
  8. 11608
    “…CONCLUSIONS: HiCNAtra is a Hi-C-based computational tool that provides an analytical and visualization framework for DNA copy number profiling and chromatin contact map correction of karyotypically abnormal cell lines. HiCNAtra is an open-source software implemented in MATLAB and is available at https://github.com/AISKhalil/HiCNAtra.…”
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    Identification and utilization of copy number information for correcting Hi-C contact map of cancer cell lines
  9. 11609
    “…METHODS: The DMT app was developed using Apple’s ResearchKit (iOS) and Android’s ResearchStack open source frameworks for developing health research study apps. …”
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    The Digital Marshmallow Test (DMT) Diagnostic and Monitoring Mobile Health App for Impulsive Behavior: Development and Validation Study
  10. 11610
    “…These datasets were rigorously analyzed using automated, Galaxy-based workflows containing tools such as PepQuery, BLAST-P, and the Multi-omic Visualization Platform as well as the open-source tools MetaTryp and Proteomics Data Viewer (PDV). …”
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    A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19)
  11. 11611
    “…OBJECTIVE: This study aimed to develop practical deep learning models with electronic medical records from 284 health care institutions and open-source corpus data sets for automatically classifying 3 thyroid conditions: healthy, caution required, and critical. …”
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    Automatic Classification of Thyroid Findings Using Static and Contextualized Ensemble Natural Language Processing Systems: Development Study
  12. 11612
    “…METHODS AND RESULTS: In our design we modify the current open-source state-of-the-art model (POCOVID-NET). A convolutional neural network (CNN) extracts spatially encoded features from POCUS-L images, which are fed to a novel attention-based transformer encoder to capture temporal information across frames, which then narrows focus to key frames. …”
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    COVID-19 DIAGNOSIS BY POINT OF CARE LUNG ULTRASOUND: A NOVEL DEEP LEARNING ARTIFICIAL INTELLIGENCE METHOD
  13. 11613
    “…Methods With the use of vast open-source libraries and collaboration with engineers and doctors fighting the COVID-19 pandemic, respirator prototypes were produced with special consideration to the sizing to fit median facial sizes. …”
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    The Designing, Testing, and Utility of a 3D-Printed Respirator: A Hospital's Journey Into Self-Sustainability During COVID-19
  14. 11614
    por Ollier, Joseph, Neff, Simon, Dworschak, Christine, Sejdiji, Arber, Santhanam, Prabhakaran, Keller, Roman, Xiao, Grace, Asisof, Alina, Rüegger, Dominik, Bérubé, Caterina, Hilfiker Tomas, Lena, Neff, Joël, Yao, Jiali, Alattas, Aishah, Varela-Mato, Veronica, Pitkethly, Amanda, Vara, Mª Dolores, Herrero, Rocío, Baños, Rosa Mª, Parada, Carolina, Agatheswaran, Rajashree Sundaram, Villalobos, Victor, Keller, Olivia Clare, Chan, Wai Sze, Mishra, Varun, Jacobson, Nicholas, Stanger, Catherine, He, Xinming, von Wyl, Viktor, Weidt, Steffi, Haug, Severin, Schaub, Michael, Kleim, Birgit, Barth, Jürgen, Witt, Claudia, Scholz, Urte, Fleisch, Elgar, von Wangenheim, Florian, Car, Lorainne Tudor, Müller-Riemenschneider, Falk, Hauser-Ulrich, Sandra, Asomoza, Alejandra Núñez, Salamanca-Sanabria, Alicia, Mair, Jacqueline Louise, Kowatsch, Tobias
    Publicado 2021
    “…The Elena+ intervention is open-source under the Apache 2 license (MobileCoach software) and the Creative Commons 4.0 license CC BY-NC-SA (intervention logic and content), allowing future collaborations; such as cultural adaptions, integration of new sensor-related features or the development of new topics. …”
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    Elena+ Care for COVID-19, a Pandemic Lifestyle Care Intervention: Intervention Design and Study Protocol
  15. 11615
    “…It was developed using SAS Institute software analytics tool and SAS® Vyia® environment and Open-Source environment R ® and Python ® for fast prototyping and modeling. …”
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    A real-time integrated framework to support clinical decision making for covid-19 patients
  16. 11616
    por Baxi, Emily G., Thompson, Terri, Li, Jonathan, Kaye, Julia A., Lim, Ryan G., Wu, Jie, Ramamoorthy, Divya, Lima, Leandro, Vaibhav, Vineet, Matlock, Andrea, Frank, Aaron, Coyne, Alyssa N., Landin, Barry, Ornelas, Loren, Mosmiller, Elizabeth, Thrower, Sara, Farr, S. Michelle, Panther, Lindsey, Gomez, Emilda, Galvez, Erick, Perez, Daniel, Meepe, Imara, Lei, Susan, Mandefro, Berhan, Trost, Hannah, Pinedo, Louis, Banuelos, Maria G., Liu, Chunyan, Moran, Ruby, Garcia, Veronica, Workman, Michael, Ho, Richie, Wyman, Stacia, Roggenbuck, Jennifer, Harms, Matthew B., Stocksdale, Jennifer, Miramontes, Ricardo, Wang, Keona, Venkatraman, Vidya, Holewenski, Ronald, Sundararaman, Niveda, Pandey, Rakhi, Manalo, Danica-Mae, Donde, Aneesh, Huynh, Nhan, Adam, Miriam, Wassie, Brook T., Vertudes, Edward, Amirani, Naufa, Raja, Krishna, Thomas, Reuben, Hayes, Lindsey, Lenail, Alex, Cerezo, Aianna, Luppino, Sarah, Farrar, Alanna, Pothier, Lindsay, Prina, Carolyn, Morgan, Todd, Jamil, Arish, Heintzman, Sarah, Jockel-Balsarotti, Jennifer, Karanja, Elizabeth, Markway, Jesse, McCallum, Molly, Joslin, Ben, Alibazoglu, Deniz, Kolb, Stephen, Ajroud-Driss, Senda, Baloh, Robert, Heitzman, Daragh, Miller, Tim, Glass, Jonathan D., Patel-Murray, Natasha Leanna, Yu, Hong, Sinani, Ervin, Vigneswaran, Prasha, Sherman, Alexander V., Ahmad, Omar, Roy, Promit, Beavers, Jay C., Zeiler, Steven, Krakauer, John W., Agurto, Carla, Cecchi, Guillermo, Bellard, Mary, Raghav, Yogindra, Sachs, Karen, Ehrenberger, Tobias, Bruce, Elizabeth, Cudkowicz, Merit E., Maragakis, Nicholas, Norel, Raquel, Van Eyk, Jennifer E., Finkbeiner, Steven, Berry, James, Sareen, Dhruv, Thompson, Leslie M., Fraenkel, Ernest, Svendsen, Clive N., Rothstein, Jeffrey D.
    Publicado 2022
    “…The intent of these data is for the generation of integrated clinical and biological signatures using bioinformatics, statistics and computational biology to establish patterns that may lead to a better understanding of the underlying mechanisms of disease, including subgroup identification. A web portal for open-source sharing of all data was developed for widespread community-based data analytics.…”
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    Answer ALS, a large-scale resource for sporadic and familial ALS combining clinical and multi-omics data from induced pluripotent cell lines
  17. 11617
    “…METHODS: A gene presence/absence-based classification algorithm was developed, which employs the open-source gene-detection tool SRST2 and a new classification database comprising 36 genes, including capsule loci for serotyping. …”
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    Whole genome sequencing-based classification of human-related Haemophilus species and detection of antimicrobial resistance genes
  18. 11618
    “…This PCR typing strategy allowed the detection of five major variants of concern and also provided an open-source PCR assay which could rapidly be deployed in laboratories around the world to enhance surveillance for the local emergence and spread of B.1.1.7, B.1.351, P.1, and B.1.617.2 variants and of four Omicron mutations on the spike protein (ΔHV 69/70, K417N, N501Y, P681H). …”
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    Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance
  19. 11619
    “…Based on the high-positive drug-likeness score, the reported derivatives of quercetin obtained from an open-source database were further filtered. Compounds with positive and high drug-likeness scores were further predicted for their potential targets using DIGEP-Pred software, and STRING was used to evaluate the interaction between modulated proteins. …”
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    In silico discovery of 3 novel quercetin derivatives against papain-like protease, spike protein, and 3C-like protease of SARS-CoV-2
  20. 11620
    “…Methods: We used snRNASeq datasets from the scREAD database originally derived from astrocytes isolated from the entorhinal cortex of AD and healthy brains from the Gene Expression Omnibus (GEO) (GSE138852 and GSE147528) and analyzed them using next-generation knowledge discovery (NGKD) platforms. scREAD is a user-friendly open-source interface available at https://bmbls.bmi.osumc.edu/scread/that enables more discovery-oriented strategies. snRNASeq data and metadata can also be visualized and downloaded via an interactive web application at adsn.ddnetbio.com. …”
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    Decoding the Role of Astrocytes in the Entorhinal Cortex in Alzheimer’s Disease Using High-Dimensional Single-Nucleus RNA Sequencing Data and Next-Generation Knowledge Discovery Methodologies: Focus on Drugs and Natural Product Remedies for Dementia
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