Apache DataFusion
Foundational library for DBs and compute engines
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Foundational library for DBs and compute engines
The Foundation provides an established framework for intellectual property and financial contributions that simultaneously limits contributors potential legal exposure. Through a collaborative and meritocratic development process, Apache projects deliver enterprise-grade, freely available software products that attract large communities of users. The pragmatic Apache License makes it easy for all users, commercial and individual, to deploy Apache products.
Analytical solutions for Next-Generation Sequencing data
The cBioPortal for Cancer Genomics is a resource designed to provide broad community access to cancer genomic data. It provides a unique user-friendly and "biology-centric computational user interface", with the goal of making genomic data more easily accessible to translational scientists, biologists, and clinicians. The interface was explicitly built and continues to evolve with careful usability studies involving multiple biological and clinical users, and an active and engaged user base.
Amplifying Research Imapct through Open Source
Develop translational data science.
CERN-HSF (High-Energy Physics Software Foundation) is the umbrella organization for high-energy physics-related projects in GSoC. The HEP Software Foundation (http://hepsoftwarefoundation.org/) facilitates the coordination of common international efforts in high-energy physics software and computing.
Tool development in bioinformatics, computational biology, data visualization
DBpedia is a crowd-sourced community effort to extract structured information from Wikipedia and make this information available on the Web. It allows for a global and unified access to Knowledge Graphs.
EMBL-EBI is a global centre for biological data, developing and maintaining open data resources and open-source software that support life science research worldwide. Our services are used daily by researchers across academia, healthcare, and industry, and span genomics, transcriptomics, metagenomics, molecular interactions, chemistry, and functional annotation.
GeomScale is a research and development project that delivers open source code for state-of-the-art algorithms for problems at the intersection of data science, optimization, geometric, and statistical computing. The current focus of GeomScale is on scalable algorithms for sampling from high-dimensional distributions, integration, convex optimization, and their applications. One of our ambitions is to fill the gap between theory and practice by turning state-of-the-art theoretical tools in geometry and optimization to state-of-the-art implementations. Towards this goal, we will deliver various innovative solutions in a variety of application fields, like finance, computational biology, and statistics that will extend the limits of contemporary computational tools. GeomScale aims in serving as a building block for an international, interdisciplinary, and open community in high dimensional geometrical and statistical computing. The main development is currently performed in volesti, a generic open source C++ library, with R and python interfaces (the latter is hosted in package dingo), for high-dimensional sampling, volume approximation, and copula estimation for financial modelling. In particular, the current implementation scales up to hundred or thousand dimensions, depending on the problem. To our knowledge it is the most efficient software package for sampling and volume computation to date. It is, in several cases, orders of magnitude faster compared to packages that solve the same problems. It can be used to compute challenging multivariate integrals and to approximate optimal solutions in optimization problems. It has already found important applications in systems biology by analyzing large metabolic networks (e.g., the latest human network) and in FinTech by detecting shock events and by evaluating portfolios performance in stock markets with thousands of assets. Other application areas include AI and in particular approximate weighted model integration. Recent studies has shown a potential application of volesti methods in trustworthy AI, static analysis of programs and differential privacy.
The Global Alliance for Genomics and Health (GA4GH) was formed to help accelerate the potential of genomic medicine to advance human health. It brings together over 400 leading genome institutes and centers with IT industry leaders to create global standards and tools for the secure, privacy respecting and interoperable sharing of Genomic data.
The International Neuroinformatics Coordinating Facility (INCF; www.incf.org) is an international organization launched in 2005, following a proposal from the Global Science Forum of the OECD.
Integrating biological data sources, making it easy to query and analyse data
U.S. IOOS is a national and regional partnership working to provide ocean, coastal and Great Lakes observations, data, tools, and forecasts to improve safety, enhance the economy, and protect our environment. Our primary purpose is to provide free and open data about the state of our oceans and Great Lakes to our users. These data are fundamental to understanding the health of our marine ecosystems, to monitor the climate signal as captured in oceanographic conditions, and to provide predictions about the future state of our oceans and coasts.
Open for Innovation
MalariaGEN is a global network of global partners who share and integrate data relevant to inform malaria surveillance, our mission is to generate insights and tools that bridge the gaps for analysts in malaria endemic settings to use their data meaningfully to inform public health efforts. We build and optimise data resources and analytical tools to run directly in the cloud. Our flagship project is the Vector Observatory, which includes whole-genome sequence data for over 30,000 mosquitoes, integrating data from 70 partners across the globe from over 17 different mosquito species -- this is the largest resource on genetic variation data for any multicellular organism (other than humans!). Our goal is to enable analysts, scientists, students and public health practitioners to access these data without the need for any dedicated compute infrastructure, by optimising our resources to run within free compute environments (a big shout to Google Colab!) and by developing training resources that support partners to get confident with using cloud-native data and resources for their analysis.
The MetaBrainz Foundation is a non-profit that believes in free, open access to data. It has been set up to build community maintained databases and make them available in the public domain or under Creative Commons licenses.
Metaflow is a human-friendly Python library that makes it straightforward to develop, deploy, and operate various kinds of data-intensive applications, in particular those involving data science, ML, and AI. Metaflow was originally developed at Netflix to boost the productivity of data scientists who work on a wide variety of projects, from classical statistics to state-of-the-art deep learning.
a fast, flexible machine learning library
Open-source software for mass spectrometry
The National Resource for Network Biology (NRNB, https://nrnb.org) organizes the development of free, open-source software technologies to enable network-based visualization, analysis, and biomedical discovery. Biomedical research is increasingly dependent on knowledge expressed in terms of networks, including gene, protein and drug interactions, cell-cell and viral-host communication, and vast social networks. Our technologies enable researchers to assemble and analyze these networks and to use them to better understand biological systems and, in particular, how they fail in disease. The NRNB mentoring organization includes projects such as Cytoscape (https://cytoscape.org/), WikiPathways (https://wikipathways.org/), SBML (https://sbml.org/), SBGN (https://sbgn.github.io/) and others. This is a great opportunity to work at the intersection of biology and computing! For example, Cytoscape is downloaded over 24,000 times per month by researchers. We take mentoring seriously and are proud of our 96% success rate (https://nrnb.org/alumni.html#gsoc-tab) with former students and projects. But don’t take our word for it, read testimonials from prior NRNB students (https://nrnb.org/testimonials.html#student-tab) and mentors (https://nrnb.org/testimonials.html#mentor-tab). Find out more about the software projects being developed in coordination with NRNB at our website (https://nrnb.org). Also refer to our GSoC page (https://nrnb.org/gsoc.html) for additional resources and application tips.
NumFOCUS supports and promotes world-class, innovative, open source scientific software. Most individual projects, even the wildly successful ones, find the overhead of a non-profit to be too large for their community to bear. NumFOCUS provides a critical service as an umbrella organization for this projects.
Advancing Open Source & Open Science for Chemistry
Contributor counts are accepted projects per cycle.
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