Here's a work in progress (WIP) list of the people and projects involved in Science and Research OSS projects (SROSS), institutions and initiatives that we identified pre-outreach efforts as potential participants in interviews, surveys and work around the USER project.
Like much of the USER project work this is an iterative, evolving list of people and projects within the Science and Research ecosystem that are valuable as connectors and could provide critical insights into how design and usability is thought of and done in science and research OSS.
If you'd like to contribute a person or project to this list then please make a pull request on this markdown file adding the projects. The projects added must have a name, link to a visible place on the internet to see their work described and they must be open source.
| Name of organisation or project | Contact info (public) | Purpose of SROSS | Publications | Area of Science/Research | Notes | Users |
|---|---|---|---|---|---|---|
| vocalpy | https://github.com/vocalpy | For researchers that study animal acoustic communication or vocal behavior | https://conference.scipy.org/proceedings/scipy2023/pdfs/david_nicholson.pdf https://joss.theoj.org/papers/10.21105/joss.05338.pdf | Bio science | Software community | lab researchers, grad students |
| erddapy | https://pypi.org/project/erddapy/ | Client to access oceanographic data data + earth sciences | https://ieeexplore.ieee.org/abstract/document/9323962/ https://ieeexplore.ieee.org/abstract/document/9706028/ | Earth & Ocean Science | National Oceanic Atmospheric center US Govt | Earth and ocean scientists and then any researcher looking to plot map data |
| Scipy | https://scipy.org/ | Fundamental algorithms for scientific computing in Python | https://www.nature.com/articles/s41592%E2%80%90019%E2%80%900686%E2%80%902 https://books.google.com/books?hl=en&lr=&id=c-xzkDMDev0C&oi=fnd&pg=PR2&dq=scipy&ots=Z7XPD0ndub&sig=ASGg0J7ofrsL1pLoFkGPnQEpZSI https://www.uplooder.net/ofiles/8070e4043bdbe147393a443832d4b520/Learning-SciPy-for-Numerical-and-Scientific-Computing.pdf | Scientific computing | Unknown | Unknown |
| Python Ecosystem | https://pypi.org/ | The Python Package Index (PyPI) is a repository of software for the Python programming language. | https://arxiv.org/abs/1907.11073 https://dl.acm.org/doi/abs/10.1145/3236024.3236062 | All sciences | Unknown | People using python packages |
| Google Summer of Code | https://summerofcode.withgoogle.com/ | Not SROSS - Contribution initiative | https://www.sciencedirect.com/science/article/pii/S0164121219302614 https://dl.acm.org/doi/abs/10.1145/3131151.3131156 https://ieeexplore.ieee.org/abstract/document/8094410/ | N/A | Connect up contributors with OSS that needs contributions | Contributors |
| Xray/xarray | https://pypi.org/project/xray/ | open source project and Python package that aims to bring the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the core pandas data structures. | https://openresearchsoftware.metajnl.com/articles/10.5334/jors.148/galley/233/download/ | Physical Sciences | Unknown | Pandas users |
| NumPy | https://numpy.org/ | The fundamental package for scientific computing with Python | https://books.google.com/books?hl=en&lr=&id=c-xzkDMDev0C&oi=fnd&pg=PR2&dq=scipy&ots=Z7XPD0ndub&sig=ASGg0J7ofrsL1pLoFkGPnQEpZSI https://ecs.wgtn.ac.nz/foswiki/pub/Support/ManualPagesAndDocumentation/numpybook.pdf | Scientific computing with Python | Office of public outreach, Designers on team, NSF | Every scientist working in Python draws on the power of NumPy. |
| Folium | https://pypi.org/project/folium/ | Data wrangling strengths of the Python ecosystem and the mapping strengths of the Leaflet.js library. Manipulate your data in Python, then visualize it in a Leaflet map via folium. | https://joss.theoj.org/papers/10.21105/joss.03414.pdfhttps://waojournal.biomedcentral.com/articles/10.1186/s40413-018-0194-3 https://waojournal.biomedcentral.com/articles/10.1186/s40413-018-0194-3 | Mapping, Geo-sciences | Unknown | Mappers, Those looking to use leaflet.js |
| PyOpenSci | https://www.pyopensci.org/ | Community that supports free and open Python tools for processing scientific data. We also build technical skills needed to contribute to open source and that support open science. | https://go.gale.com/ps/i.do?id=GALE%7CA676853135&sid=googleScholar&v=2.1&it=r&linkaccess=abs&issn=25350897&p=AONE&sw=w https://ui.adsabs.harvard.edu/abs/2019AGUFMNS21A..13W/abstract | All sciences | Unknown | All sciences |
| Jupyter Labs | https://jupyter.org/ | Free software, open standards, and web services for interactive computing across all programming languages. web-based interactive development environment for notebooks, code, and data. | http://archive.ipython.org/media/SciPy2016JupyterLab.pdf https://link.springer.com/chapter/10.1007/978-1-4842-4470-8_6 | All sciences that use data | Unknown | Multi purpose for different sciences but giving a space for the data to be managed All kinds of science and research - anyone with big amounts of data to wrangle |
| Anon1 | N/A | Government/Sensitive, Math, physics, comp sci and mathematical epidemiology | Unknown | Math, physics, comp sci and mathematical epidemiology, Move towards Social Science users | Unknown | Math, physics, comp sci and mathematical epidemiology, Move towards Social Science users |
| Quansight labs | https://quansight.com/ | Connect organizations and individuals who participate in the development and use of open source tools that turn data into valuable insights. | https://scientific-python.org/doc/scientific-python-planning-grant-2020.pdf | organizations and individuals who participate in the development and use of open source tools | Unknown | organizations and individuals |
| Anon2 | N/A | Data collection system, Make conducting wearable sensor studies more accessibile to more researchers without technical expertise | N/A | Psychology researchers and professionals | small team, University funding, Data collection system | Psychology researchers and professionals |
| Anon3 | N/A | Data archive | N/A | Astronomers, astrophycists | National Funding | Astronomers, astrophycists |
| NASA | https://www.nasa.gov/ | The National Aeronautics and Space Administration is America’s civil space program and the global leader in space exploration. | https://www.press.jhu.edu/books/title/1795/inside-nasa https://books.google.com/books?hl=en&lr=&id=-UebVg1YqsoC&oi=fnd&pg=PP11&dq=NASA&ots=EykNgp-MDU&sig=3lYLD-du1BCWaMF6OZKkk7BZGJQ | Astronomers, astrophycists | Funds Jet Propulsion Lab | Astronomers, astrophycists |
| Transform to Open Science | https://science.nasa.gov/open-science/transform-to-open-science | The Transform to Open Science (TOPS) mission is a NASA initiative designed to rapidly transform agencies, organizations, and communities to an inclusive culture of open science. TOPS is part of NASA’s Open-Source Science Initiative. | N/A | individuals, organizations in the hard sciences, particularly chemistry, biology, and physics that tend to tend to use our resources, but they don't really have a lot of technical expertise. | N/A | individuals, organizations in the hard sciences, particularly chemistry, biology, and physics that tend to tend to use our resources, but they don't really have a lot of technical expertise. |
| Personal Project | N/A | to make financial mathematics much more accessible to programmers in general, because currently, there isn't really a dedicated library to finish mathematics, at least in PHP. | N/A | programmers in general, who might just come into a need for doing something financial mathematics related | Voluntary funding, PHP | programmers in general, who might just come into a need for doing something financial mathematics related |
| Open Sciencey | N/A | Community that helps inform scientists about the importance of open source software | N/A | Scientists | N/A | Scientists |
| Planet Profile | Unknown | connects magnetic measurements to physical properties in planets, geophysics of planetary bodies, especially icy moons in the outer solar system | N/A | geophysics | N/A | geophysics |
| MoonMag | https://pypi.org/project/MoonMag/ | "An analytic solution for evaluating the magnetic field induced from an arbitrary, asymmetric ocean world" | N/A | magnetic field, ocean science | N/A | magnetic field, ocean science |
| C-freeze | Unknown | Unknown | N/A | Unknown | Unknown | Unknown |
| Pyoma | https://github.com/dagghe/PyOMA | OMA allows the experimental estimation of the modal parameters (natural frequencies, mode shapes, damping ratios) of a structure from measurements of the vibration response in operational condition. | https://www.sciencedirect.com/science/article/pii/S2352711022001340 | measurement data | N/A | measurement data |
| NumFocus | https://numfocus.org/ | The mission of NumFOCUS is to promote open practices in research, data, and scientific computing by serving as a fiscal sponsor for open source projects and organizing community-driven educational programs. | https://scientific-python.org/doc/scientific-python-planning-grant-2020.pdf https://assets.pubpub.org/9sivo25o/11598545738913.pdf | research, data, and scientific computing | N/A | research, data, and scientific computing |
| Matplotlib | https://matplotlib.org/ | help people make plots using Python, visualization software | https://www.computer.org/csdl/magazine/cs/2007/03/c3090/13rRUwbJD0A https://adsabs.harvard.edu/full/2005ASPC..347...91B https://books.google.com/books?hl=en&lr=&id=8Fs3AgAAQBAJ&oi=fnd&pg=PT10&dq=Matplotlib&ots=i0tOk95R2t&sig=ZqVLkGck1VGNXxTPaj57odkQ6Lg | academic researchers and data scientists | CZI, NASA | academic researchers and data scientists |
| MATLAB | https://www.mathworks.com/products/matlab.html | Comprehensive library for creating static, animated, and interactive visualizations in Python. desktop environment tuned for iterative analysis and design processes with a programming language that expresses matrix and array mathematics directly. | https://epubs.siam.org/doi/pdf/10.1137/1.9781611974669.bm https://itb.biologie.hu-berlin.de/~kempter/Teaching/2003_SS/gettingstarted.pdf | engineering and science | N/A | engineering and science |
| CZI | https://chanzuckerberg.com/ | Fund very large projects, as well as some smaller, more niche projects more strictly associated with biomedicine. Tend to fund primarily software projects. Sometimes they include some infrastructure components, very rarely, they include things like database aggregations, and things like that. | N/A | Funder of science | Support all of the grantees included in our essential open source software for science program: Supports grantees to help get their work done and make connections. | Funder of science |
| CSCCE: Center for Scientific Collaboration adn Community Engagement | https://www.cscce.org/ | research and training center to support and study the emerging field of scientific community engagement. | N/A | scientific community engagement | N/A | scientific community engagement |
| Parsl | https://parsl-project.org/ | parallel programs composed of Python functions and external components. Python components and functions | https://dl.acm.org/doi/abs/10.1145/3307681.3325400 | Component builders, Platform builders | N/A | Component builders, Platform builders |
| Globus | Unknown | A commercial org that supports Uni's with design and marketing capacity when paid/asked | Unknown | Unknown | N/A | Unknown |
| OpenRefine | https://openrefine.org/ | data management/cleaning, a point and click tool for data preparation. been presented as Excel on steroids | https://books.google.com/books?hl=en&lr=&id=_WG1AAAAQBAJ&oi=fnd&pg=PT5&dq=openrefine&ots=LSVGhyWkcM&sig=LDdmJUfR0QP3QyjpVQ48Efp09QE https://ieeexplore.ieee.org/abstract/document/7858197/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3738091/ | info professionals: librarians, archivists, etc | N/A | info professionals: librarians, archivists, etc |
| Wikimedia | https://www.wikimedia.org/ | Open Science for art design and music (switzerland), Supports adoption of open science and open access practices across Switzerland | https://journals.aom.org/doi/abs/10.5465/ambpp.2012.43 | Archivists | N/A | Archivists |
| Qiime | http://qiime.org/ | Analysis of microbiome data, and on developing open source tools, open source tools for supporting analysis of microbiome data. | https://www.nature.com/articles/nmeth.f.303. https://peerj.com/preprints/27295.pdf | graduate students, postdocs, assistant professors, or data scientists microbial ecology early to mid career. | working in industry Northern Arizona University Rob Knight's lab at the University of Colorado National cancer institutre | graduate students, postdocs, assistant professors, or data scientists microbial ecology early to mid career. |
| scikit-learn | https://scikit-learn.org/ | reference implementation for machine learning algorithms so that they could be used in applications and research. people use the library to take decisions and to analyse their data | https://link.springer.com/chapter/10.1007/978-3-319-33383-0_5 https://books.google.com/books?hl=en&lr=&id=9-ZDDwAAQBAJ&oi=fnd&pg=PP1&dq=scikit+learn&ots=FNiDLr9SRf&sig=_WcfBaqO2_JpxY2CmD6JS3_-4PI | Industry, research, education, biologists, finance/ business / banks | INRIA - National Institutes in research in computer science and applied math (France). Public nonprofit organization, National Research Institute. Codified contribution pipelines/ processes | Industry, research, education, biologists, finance/ business / banks |
| ParaView | https://www.paraview.org/ | The world’s leading open source post-processing visualization engine Large Data Visualization Made Easier | https://www.researchgate.net/profile/Charles-Law/publication/51992227_The_Paraview_Guide/links/551c042e0cf2fe6cbf7621de/The-Paraview-Guide.pdf https://dl.acm.org/doi/abs/10.5555/2789330 | mostly nat'l labs, Partly driven by paying customers | Kitware (consultancy), National Labs | mostly nat'l labs, Partly driven by paying customers |
| Kitware | https://www.kitware.com/ | Software consulting | https://www.osti.gov/biblio/1784597 | Clients | N/A | Clients |
| Autspaces | https://github.com/alan-turing-institute/AutSPACEs | digital platform where autistic people can report their experiences on sensory processing differences in everyday life, and report what they think would have made it a better experience than the one they had on a given a given day. | https://osf.io/preprints/socarxiv/c2xe7/ https://kar.kent.ac.uk/62696/ | Autistic people (patients),citizen science | No particular domain expertise, but require reading/writing in English to participate The Autistic Foundation (UK) Turing Institute | Autistic people (patients),citizen science |
| Turing Institute | https://www.turing.ac.uk/ | Works with a lot of types of groups, British Library, Historians, Linguists (digital humanities), PhD Students & Post-docs, Profs getting involved in Open Science | https://drive.google.com/file/d/1H1kvHtkos7eFDngvc9SDZnpGSjBSXAOz/view | British Library, Historians, Linguists (digital humanities), PhD Students & Post-docs, Profs getting involved in Open Science | N/A | British Library, Historians, Linguists (digital humanities), PhD Students & Post-docs, Profs getting involved in Open Science |
| PECE | https://worldpece.org/about | Mix between a wiki, google drive, and a research tool for social science researchers | Unknown | Have an experimental design team of power users (mostly university professors and researchers) Researchers and professors | Through the design team | Have an experimental design team of power users (mostly university professors and researchers) Researchers and professors |
| Vuejs | https://vuejs.org/ | JavaScript framework for building user interfaces. It builds on top of standard HTML, CSS, and JavaScript | http://samples.leanpub.com/rapid-prototyping-with-js-sample.pdf | Coders, developers | Helped PECE with accessibility | Coders, developers |
| Drupal | https://www.drupal.org/ | Drupal is a free and open-source web content management system written in PHP | https://books.google.com/books?hl=en&lr=&id=LVz8q2qYQNUC&oi=fnd&pg=PR3&dq=drupal&ots=Wbhwt04pBd&sig=-6hiIDeX-v6ydX5uULLBBnvptWE https://link.springer.com/content/pdf/10.1007/978-1-4302-0190-8.pdf | Coders, developers, any website builder | Unknown | Coders, developers, any website builder |
| UVM OSPO | https://vermontcomplexsystems.org/education/verso/ | OSPO of the university of Vermont | Unknown | Supports OSS scienctists | Supported by Sloan Foundation | Supports OSS scienctists |
| King's Digital Lab | https://kdl.kcl.ac.uk/ | Supporting other lab software and other software related to research | http://eprints.bournemouth.ac.uk/32941 | different partners, academic partners, cultural heritage, government partners. | Public or private funding | different partners, academic partners, cultural heritage, government partners. |
| Open Source Centre in SLU | https://oss-slu.github.io/ | St. Louis University An OSS support centre - the infrastructure around students contributing via courses | Unknown | Students + OSS internally at SLU and external Clients with OSS projects | Mentor students and enable them to contribute to OSS that exists in the university | Students + OSS internally at SLU and external Clients with OSS projects |
| MLM network emulator OSS | Unknown | Unknown | Used by industry | Unknown | Used by industry | |
| Seeing is believing (spanish lang OSS app) | Unknown | Unknown | Used by prof's in student classes | Unknown | Used by prof's in student classes | |
| Mozer (sp?) | Unknown | platform for data collection for hamster-based research | Unknown | mostly one researcher @ St. Louis University | Unknown | mostly one researcher @ St. Louis University |