Contigs directed gene annotation (ConDiGA) for accurate protein sequence database construction in metaproteomics by Enhui Wu, Vijini Mallawaarachchi, Jinzhi Zhao, Yi Yang, Hebin Liu, Xiaoqing Wang, Chengpin Shen, Yu Lin, Liang Qiao

“…The code of ConDiGA is open access at GitHub for the analysis of microbiota samples. Video Abstract…”
Get full text

Sync for Genes Phase 5: Computable artifacts for sharing dynamically annotated FHIR‐formatted genomic variants by Robert Dolin, Bret S. E. Heale, Rohan Gupta, Carla Alvarez, Justin Aronson, Aziz Boxwala, Shaileshbhai R. Gothi, Ammar Husami, James Shalaby, Lawrence Babb, Alex Wagner, Srikar Chamala

“…Results Primary public artifacts from this project include a GitHub repository with all source code, a Swagger interface that allows anyone to visualize and interact with the code using only a web browser, and a backend database where all (synthetic and anonymized) patient data and knowledge are housed. …”
Get full text

DEVEA: an interactive shiny application for Differential Expression analysis, data Visualization and Enrichment Analysis of transcriptomics data [version 2; peer review: 2 approved... by Solène Brohard, Carole Escartin, Eric Bonnet, Fernando Perez-Sanz, Jean-François Deleuze, Miriam Riquelme-Perez

“…DEVEA is freely accessible at https://shiny.imib.es/devea/ and the source code is available on our GitHub repository https://github.com/MiriamRiquelmeP/DEVEA.…”
Get full text

An Android-Based Mobile App (ARVPredictor) for the Detection of HIV Drug-Resistance Mutations and Treatment at the Point of Care: Development Study by Beatrice Ongadi, Raphael Lihana, John Kiiru, Musa Ngayo, George Obiero

“…This mobile app is enlisted in the Google Play Store as an “ARVPredictor” and the source code is available under MIT permissive license at a GitHub repository. To test for agreement between the ARVPredictor and Stanford HIV Database in detecting HIV subtype and NNRT and NRTI mutations, a total of 100 known HIV sequences were evaluated. …”
Get full text

CANOPS-GRB v1.0: a new Earth system model for simulating the evolution of ocean–atmosphere chemistry over geologic timescales by K. Ozaki, K. Ozaki, K. Ozaki, D. B. Cole, C. T. Reinhard, C. T. Reinhard, C. T. Reinhard, E. Tajika

“…The model source code is available on GitHub and represents a unique community tool for investigating the dynamics and stability of atmospheric and oceanic chemistry on long timescales.…”
Get full text

Solar-MACH: An open-source tool to analyze solar magnetic connection configurations by Jan Gieseler, Nina Dresing, Christian Palmroos, Johan L. Freiherr von Forstner, Johan L. Freiherr von Forstner, Daniel J. Price, Rami Vainio, Athanasios Kouloumvakos, Laura Rodríguez-García, Domenico Trotta, Vincent Génot, Arnaud Masson, Markus Roth, Astrid Veronig

“…The development of Solar-MACH is open to everyone and takes place on GitHub, where the source code is publicly available under the BSD 3-Clause License. …”
Get full text

A New Algorithm Inspired on Reversible Elementary Cellular Automata for Global Optimization by Juan Carlos Seck-Tuoh-Mora, Omar Lopez-Arias, Norberto Hernandez-Romero, Genaro J. Martinez, Valeria Volpi-Leon

“…RECAA was implemented in MATLAB, and its source code can be consulted in GitHub. <monospace><uri>https://github.com/juanseck/RECAA</uri></monospace>…”
Get full text

Immunolyser: A web-based computational pipeline for analysing and mining immunopeptidomic data by Prithvi Raj Munday, Joshua Fehring, Jerico Revote, Kirti Pandey, Mohammad Shahbazy, Katherine E. Scull, Sri H. Ramarathinam, Pouya Faridi, Nathan P. Croft, Asolina Braun, Chen Li, Anthony W. Purcell

“…The open-access source code can be downloaded at our GitHub repository: https://github.com/prmunday/Immunolyser. …”
Get full text

A comprehensive and version-controlled database of glacial lake outburst floods in High Mountain Asia by F. Shrestha, J. F. Steiner, J. F. Steiner, R. Shrestha, R. Shrestha, Y. Dhungel, Y. Dhungel, S. P. Joshi, S. Inglis, A. Ashraf, S. Wali, K. M. Walizada, T. Zhang, T. Zhang

“…The database is available at <a href="https://doi.org/10.5281/zenodo.7271187">https://doi.org/10.5281/zenodo.7271187</a> (Steiner and Shrestha, 2023), while the code including a development version is available on GitHub.</p>…”
Get full text

RP-REP Ribosomal Profiling Reports: an open-source cloud-enabled framework for reproducible ribosomal profiling data processing, analysis, and result reporting [version 1; peer rev... by Johannes B. Goll, Sami R. Cherikh, Travis L. Jensen, William F. Hooper

“…Case study results, Ubuntu installation scripts, and the most recent RP-REP source code are accessible at GitHub. The cloud-ready AMI is available at AWS (AMI ID: RPREP RSEQREP (Ribosome Profiling and RNA-Seq Reports) v2.1 (ami-00b92f52d763145d3)).…”
Get full text

Analysis of Swin-UNet vision transformer for Inferior Vena Cava filter segmentation from CT scans by Rahul Gomes, Tyler Pham, Nichol He, Connor Kamrowski, Joseph Wildenberg

“…The Swin UNETR will reduce the time spent manually tracking IVC filters by centralizing within the electronic health record. Link to GitHub repository.…”
Get full text

Out-of-the-box calving-front detection method using deep learning by O. Herrmann, N. Gourmelon, T. Seehaus, A. Maier, J. J. Fürst, M. H. Braun, V. Christlein

“…The scripts for our experiments are published on GitHub (<span class="uri">https://github.com/ho11laqe/nnUNet_calvingfront_detection</span>, last access: 20 November 2023). …”
Get full text

DILIC: An AI-Based Classifier to Search for Drug-Induced Liver Injury Literature by Sanjay Rathee, Meabh MacMahon, Meabh MacMahon, Anika Liu, Anika Liu, Nicholas M. Katritsis, Nicholas M. Katritsis, Gehad Youssef, Woochang Hwang, Lilly Wollman, Namshik Han, Namshik Han

“…To make DILIC as accessible as possible, including to researchers without coding experience, an R Shiny app capable of classifying single or multiple entries for DILI is developed to enhance ease of user experience and made available at https://researchmind.co.uk/diliclassifier/. Additionally, a GitHub link (https://github.com/sanjaysinghrathi/DILI-Classifier) for app source code and ISMB extended video talk (https://www.youtube.com/watch?…”
Get full text

Attention Connect Network for Liver Tumor Segmentation from CT and MRI Images by Jiakang Shao MS, Shunyao Luan PhD, Yi Ding PhD, Xudong Xue PhD, Benpeng Zhu PhD, Wei Wei

“…For those interested, the code for this research article can be accessed at the following GitHub repository: https://github.com/killian-zero/py_tumor-segmentation.git .…”
Get full text

Cloud-based interactive susceptibility modeling of gully erosion in Google Earth Engine by Giacomo Titti, Gabriele Nicola Napoli, Christian Conoscenti, Luigi Lombardo

“…To promote the use of our tool, we are sharing it in a GitHub repository accessible at this link: https://github.com/giactitti/STGEE.…”
Get full text

The hypoglycaemia error grid: A UK-wide consensus on CGM accuracy assessment in hyperinsulinism by Chris Worth, Chris Worth, Mark J. Dunne, Maria Salomon-Estebanez, Simon Harper, Paul W. Nutter, Antonia Dastamani, Senthil Senniappan, Indraneel Banerjee, Indraneel Banerjee

“…The HEG is freely available on GitHub for use by other researchers to assess accuracy in their patient populations and validate these findings.…”
Get full text

Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package by Tuncbag, Nurcan, Gosline, Sara Calafell, Kedaigle, Amanda Joy, Soltis, Anthony Robert, Gitter, Anthony, Fraenkel, Ernest

“…It is available at http://fraenkel.mit.edu/omicsintegrator and on GitHub at https://github.com/fraenkel-lab/OmicsIntegrator.…”
Get full text
Get full text
Get full text
Get full text
Get full text

New optimization approaches to matrix factorization problems with connections to natural language processing by Berk, Lauren Elizabeth.

Get full text

Unraveling COVID-19: a large-scale characterization of 4.5 million COVID-19 cases using CHARYBDIS by Kostka, K, Duarte-Salles, T, Prats-Uribe, A, Sena, AG, Pistillo, A, Khalid, S, Lai, LYH, Golozar, A, Alshammari, TM, Dawoud, DM, Nyberg, F, Wilcox, AB, Andryc, A, Williams, A, Ostropolets, A, Areia, C, Jung, CY, Harle, CA, Reich, CG, Blacketer, C, Morales, DR, Dorr, DA, Burn, E, Roel, E, Tan, EH, Minty, E, DeFalco, F, de Maeztu, G, Lipori, G, Alghoul, H, Zhu, H, Thomas, JA, Bian, J, Park, J, Martínez Roldán, J, Posada, JD, Banda, JM, Horcajada, JP, Kohler, J, Shah, K, Natarajan, K, Lynch, KE, Liu, L, Schilling, LM, Recalde, M, Spotnitz, M, Gong, M, Matheny, ME, Valveny, N, Weiskopf, NG, Shah, N, Alser, O, Casajust, P, Park, RW, Schuff, R, Seager, S, DuVall, SL, You, SC, Song, S, Fernández-Bertolín, S, Fortin, S, Magoc, T, Falconer, T, Subbian, V, Huser, V, Ahmed, W-U-R, Carter, W, Guan, Y, Galvan, Y, He, X, Rijnbeek, PR, Hripcsak, G, Ryan, PB, Suchard, MA, Prieto-Alhambra, D

“…The study protocol and analytical package were released on 11th June 2020 and are iteratively updated via GitHub. We identified three non-mutually exclusive cohorts of 4,537,153 individuals with a clinical COVID-19 diagnosis or positive test, 886,193 hospitalized with COVID-19, and 113,627 hospitalized with COVID-19 requiring intensive services.…”

BpWrapper: BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines by Yözen Hernández, Rocky Bernstein, Pedro Pagan, Levy Vargas, William McCaig, Girish Ramrattan, Saymon Akther, Amanda Larracuente, Lia Di, Filipe G. Vieira, Wei-Gang Qiu

“…Source code is available on GitHub at https://github.com/bioperl/p5-bpwrapper. …”
Get full text