Open Source Research Software

 

BIDS contributes to a number of open source, open science, and open data resource communities in support of academic research.   Browse a list of software projects currently active at BIDS, below, or see the project archive for a list of retired/archived projects.

Cesium ML

Cesium-ML is an end-to-end machine learning platform for time-series, that computes machine learning features, builds models, and does prediction. Cesium has two main components—a Python library, and a web application platform that allows interactive exploration of machine learning pipelines. The... more
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CRIC Cervix Collection

The CRIC Cervix Collection is a searchable image database — currently with 400 images (1,376 × 1,020 pixels) curated from conventional Pap smears, with manual classification of 11,534 cells —  that makes digital cell image collections available for reproducible research and... more
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iSamples: Internet of Samples

BIDS Research Affiliate Neil Davies (NSF 2004642) and colleagues at Columbia University (NSF 2004839), the University of Arizona (NSF 2004562), and the University of Kansas (NSF 2004815) have just published a new paper introducing the Internet of Samples (iSamples), a... more

Jupyter

Project Jupyter is a community of open-source developers, scientists, educators, and data scientists. Its goal is to build open-source tools and create a community that facilitates scientific research, reproducible and open workflows, education, computational narratives, and data analytics. Jupyter... more
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Mothra

Mothra analyzes images of butterflies and measures their wing lengths. Using binarization techniques and calculating the resolution of ruler ticks, we read in images of butterflies and output the millimeter lengths of their wings. The pipeline script combines four modules to analyze an image:... more
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NetworkX

BIDS hosts two core developers working with NetworkX, a Python package to create, manipulate, and study the structure, dynamics, and functions of graphs and networks. NetworkX is the reference library for network science algorithms in Python. Its creation and development was driven by... more
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NumPy

NumPy is the fundamental array package underpinning the Scientific Python ecosystem. BIDS hosts a team of four core developers that work with the NumPy community to develop the library in preparation for the next decade of data science. NumPy contains, among other things, the following: A... more
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rOpenSci

rOpenSci is a scientific open source project whose primary mission is to promote development and use of high-quality research software in the research community. The rOpenSci team and community enable this transformation by training domain experts in good software development practices and... more
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scikit-image

Scikit-image is a community-driven Python project, consisting of a vast collection of high-quality, peer-reviewed image processing algorithms that are made available to a global community of researchers free of charge and free of restriction. The library is widely used in many different fields,... more
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SciPy

SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000... more
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SkyPortal

SkyPortal is a fully open-source data portal for the collaborative study and management of time-domain sources and events. It interactively displays astronomical datasets for annotation, analysis, and discovery, and is designed to be modular and extensible, so it can be customized for various... more
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US Research Software Sustainability Institute

This project is conceptualizing a US Research Software Sustainability Institute that will focus on the entire research software ecosystem — including the people who create, maintain, and use research software — to validate and address various classes of concerns impacting all... more