pyCAST, a Python package for the detection of cavities on surface proteins by Giorgio Luciano, Ulderico Fugacci, Silvia Biasotti

“…Furthermore, it discusses the limitations of the technique and potential future improvements. pyCAST is user-friendly, modular, adaptable to diverse applications, and openly available under the MIT license.…”
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Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space by Jeet Sukumaran, Marina Meila

“…Conclusions Piikun is available under the MIT license from its public repository ( https://github.com/jeetsukumaran/piikun ), and can be installed locally using the Python package manager ‘pip‘.…”
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Pathway metrics accurately stratify T cells to their cells states by Dani Livne, Sol Efroni

“…Designed to be open-source, extensible, and computationally efficient, PathSingle is available at https://github.com/zurkin1/PathSingle under the MIT license. This tool provides researchers with a versatile framework for uncovering biologically meaningful insights from high-dimensional single-cell transcriptomics data, facilitating a deeper understanding of cellular regulation and function.…”
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ARACHNE: A neural-neuroglial network builder with remotely controlled parallel computing. by Sergey G Aleksin, Kaiyu Zheng, Dmitri A Rusakov, Leonid P Savtchenko

“…The program and documentation (current version) are available at GitHub repository https://github.com/LeonidSavtchenko/Arachne under the MIT License (MIT).…”
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CytoPy: An autonomous cytometry analysis framework. by Ross J Burton, Raya Ahmed, Simone M Cuff, Sarah Baker, Andreas Artemiou, Matthias Eberl

“…CytoPy is open-source and licensed under the MIT license. CytoPy is available at https://github.com/burtonrj/CytoPy, with notebooks accompanying this manuscript (https://github.com/burtonrj/CytoPyManuscript) and software documentation at https://cytopy.readthedocs.io/.…”
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Local Universal Rule-based eXplainer (LUX) by Szymon Bobek, Grzegorz J. Nalepa

“…The software implementation was released as an open-source Python package under the MIT License. It is compliant with the scikit-learn API interface, allowing for seamless integration with machine learning pipelines.…”
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DIAMOND2GO: rapid Gene Ontology assignment and enrichment detection for functional genomics by Christopher Golden, David J. Studholme, Rhys A. Farrer

“…D2GO is open-source and freely available under the MIT license at https://github.com/rhysf/DIAMOND2GO.…”
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A Particle-Based COVID-19 Simulator With Contact Tracing and Testing by Askat Kuzdeuov, Aknur Karabay, Daulet Baimukashev, Bauyrzhan Ibragimov, Huseyin Atakan Varol

“…The simulator is available on GitHub under the MIT license. <italic>Results:</italic> The results show that the synergistic use of contact tracing and massive testing is effective in suppressing the epidemic (the number of deaths was reduced by 72%). …”
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Assessing long-term hydrological dynamics and water quality using Google Earth Engine: A case study of Ilgın Lake (1985–2024) by O. F. Atiz, S. Durduran

“…All code and workflow are publicly available as Jupyter Notebook on GitHub under the open-source MIT license (<code>https://github.com/earth-obs/lake-gee-hydrology-water-quality</code>).…”
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Heat4Future: A strategic planning tool for decarbonizing district heating systems by Nina Kicherer, Pablo Benalcazar, Peter Lorenzen, Olessya Kozlenko, Sadi Tomtulu, Jan Trosdorff

“…. • The tool is licensed under the MIT License and is available as an open-source repository on GitLab.…”
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Creating a Scholarly API Cookbook: Supporting Library Users with Programmatic Access to Information by Vincent F. Scalfani, Kevin W. Walker, Lance Simpson, Avery M. Fernandez, Vishank D. Patel, Anastasia Ramig, Cyrus Gomes, Michael T. Moen, Adam M. Nguyen

“…All code within the API Cookbook is licensed with the permissive MIT license, and as a result, users are free to reuse and adapt the code in their teaching and research. …”
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The OpenMindat v1.0.0 R package: a machine interface to Mindat open data to facilitate data-intensive geoscience discoveries by X. Que, J. Zhang, W. Chen, J. Ralph, X. Ma

“…The OpenMindat v1.0.0 package, which includes detailed tutorials and examples, is available on GitHub under the MIT license. The field of mineralogy and many other geoscience disciplines are facing opportunities enabled by open data. …”
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DISPEL: A Python Framework for Developing Measures From Digital Health Technologies by A. Scotland, G. Cosne, A. Juraver, A. Karatsidis, J. Penalver-Andres, E. Bartholome, C. M. Kanzler, C. Mazza, D. Roggen, C. Hinchliffe, S. Del Din, S. Belachew

“…<italic>Results</italic>: DISPEL is available under MIT license. It already supports formats from different data providers and allows traceable end-to-end processing from raw data collected with wearables and smartphones to structured SDM datasets. …”
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HIVGenoPipe: a nextflow pipeline for the detection of HIV-1 drug resistance using a real-time sample-specific reference sequence by Thoai Dotrang, Brad T. Sherman, Lisheng Dai, Muhammad Ayub Khan, Helene C. Highbarger, Whitney Bruchey, Sylvain Laverdure, Michael W. Baseler, Tomozumi Imamichi, Robin L. Dewar, Weizhong Chang

“…HIVGenoPipe is open source and freely available under the MIT license at https://github.com/LHRI-Bioinformatics/HIVGenoPipe . …”
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Epitopedia: identifying molecular mimicry between pathogens and known immune epitopes by Christian A Balbin, Janelle Nunez-Castilla, Vitalii Stebliankin, Prabin Baral, Masrur Sobhan, Trevor Cickovski, Ananda Mohan Mondal, Giri Narasimhan, Prem Chapagain, Kalai Mathee, Jessica Siltberg-Liberles

“…Epitopedia is open-source software released under the MIT license and is freely available on GitHub, including a Docker container with all other software dependencies preinstalled. …”
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The Paleochrono-1.1 probabilistic model to derive a common age model for several paleoclimatic sites using absolute and relative dating constraints by F. Parrenin, M. Bouchet, C. Buizert, E. Capron, E. Corrick, R. Drysdale, K. Kawamura, A. Landais, R. Mulvaney, I. Oyabu, S. O. Rasmussen

“…Paleochrono-1.1 is freely available under the open-source MIT License.</p>…”
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