awesome-open-science

Science resources

A curated list of resources and tools for promoting data sharing, collaboration, and transparency in scientific research

books microscope unlock mag A curated list of resources, data, tools, scholarship related to Open Access, Data and Open Science books microscope unlock mag

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Note: this list is still under development / Research Data
E-learning platform
Finnish Social Science Data Archive
BASE Biefeld academic search engine
Academia Academia.edu is a platform for academics to share research papers
Research Gate ResearchGate is the professional network for scientists and researchers

Note: this list is still under development / Research Articles and Reports
Research Objects: Towards Exchange and Reuse of Digital Knowledge Bechhofer et al., 2010
The Enduring Value of Social Science Research: The Use and Reuse of Primary Research Data Pienta et al., 2010
The data paper: a mechanism to incentivize data publishing in biodiversity science Chavan and Penev, 2011
The Dataverse Network: An Open-Source Application for Sharing, Discovering and Preserving Data Crosas, 2011
Data sharing in neuroimaging research Poline et al., 2012
Toward interoperable bioscience data Sansone et al., 2012
Making data sharing count: a publication-based solution , Gorgolewski et al., 2013
EUDAT: A New Cross-Disciplinary Data Infrastructure for Science Lecarpentier et al., 2013
Data reuse and the open data citation advantage Piwowar and Vision, 2013
Nine simple ways to make it easier to (re)use your data White et al., 2013
The data sharing advantage in astrophysics Dorch et al., 2015
What Drives Academic Data Sharing? Fecher et al., 2015
From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics Gonzalez-Beltran et al., 2015
Making data count Kratz and Strasser, 2015
The center for expanded data annotation and retrieval Musen et al., 2015
Public Data Archiving in Ecology and Evolution: How Well Are We Doing? Roche et al., 2015
Achieving human and machine accessibility of cited data in scholarly publications Starr et al., 2015
The State of Open Data Report Treadway et al., 2016
The FAIR Guiding Principles for scientific data management and stewardship Wilkinson et al., 2016
Towards coordinated international support of core data resources for the life sciences Anderson et al., 2017
A reputation economy: how individual reward considerations trump systemic arguments for open access to data Fecher et al., 2017
Cloudy, increasingly FAIR; revisiting the FAIR Data guiding principles for the European Open Science Cloud Mons et al., 2017
Code of practice for research data usage metrics release 1 Fenner et al., 2018
Open Data as Open Educational Resources: Towards Transversal Skills and Global Citizenship Atenas, Havemann, Priego, 2015
Reproducibility, Virtual Appliances, and Cloud Computing , Howe,2012
The Ironic Effect of Significant Results on the Credibility of Multiple-Study Articles , Schimmack, 2012
Power failure: why small sample size undermines the reliability of neuroscience , Button et al., 2013
Git can facilitate greater reproducibility and increased transparency in science . Ram, 2013
Ten simple rules for reproducible computational research , Sandve et al., 2013
Investigating Variation in Replicability: A "Many Labs" Replication Project , Klein et al., 2014
An introduction to Docker for reproducible research , Boettiger, 2015
Opinion: Reproducible research can still be wrong: Adopting a prevention approach , Leek and Peng, 2015
Replicability vs. reproducibility -- or is it the other way around? , Liberman, 2015
The GRIM test: A simple technique detects numerous anomalies in the reporting of results in psychology , Brown and Heathers, 2016
What does research reproducibility mean? , Goodman et al., 2016
Tools and techniques for computational reproducibility , Piccolo and Frampton, 2016
Transparency, Reproducibility, and the Credibility of Economics Research , Christensen and Miguel, 2017
A trust approach for sharing research reagents , Edwards et al., 2017
Estimating the Reproducibility of Psychological Science , Nosek et al., 2017
Digital Open Science -- Teaching digital tools for reproducible and transparent research , Toelch and Ostwald, 2017
Terminologies for reproducible research , Barba, 2018
An introduction to statistical and data sciences via R , Ismay and Kim, 2018
The practice of reproducible research: case studies and lessons from the data-intensive sciences , Kitzes et al., 2018
bookdown: Authoring Books and Technical Documents with R Markdown , Xie, 2018
Our path to better science in less time using open data science tools , Lowndes et al. 2017
Haves and Have nots must find a better way: The case for Open Scientific Hardware , Chagas, 2018
Computational Reproducibility via Containers in Social Psychology , Green and Clyburne-Sherin, 2018
Developer Survey Results 2019 , stackoverflow, 2019

Note: this list is still under development / Tools
Sci-Hub Research Paper File Sharing Platform
EOSC
Journal of Open Research Software and the
InsideDNA
Galaxy Reproducible Research environments
Google Compute Engine (GCE)
Amazon Web Services (AWS), Cloud-based software environments
Software Citation Tools 23 over 5 years ago Mozilla Science Lab
Open Science, Open Data, Open Source Fernandes and Vos, 2017
Choose an open source license

Note: this list is still under development / Tools / Open Science Framework (COS)
Reproducibility Project: Cancer Biology
Reproducibility Project: Psychological Science
Registered Reports
Reproducible Research, Workshop CC-BY, April Clyburne-Sherin & Courtney Soderberg

Note: this list is still under development / Tools
Initial steps towards reproducible research Karl Broman
The Open Science and Reproducible Research course 57 over 5 years ago CC-BY, Christie Bahlai
Reproducibility Workshop Best practices and easy steps to save time for yourself and other researchers,
Reproducibility in Science: A guide to enhancing reproducibility in scientific results and writing ,ROpenSci
Reproducible Research using Jupyter Notebooks workshop , The Carpentries
R markdown workshop 27 about 6 years ago , (Liberate Science)
rrtools: Tools for Writing Reproducible Research in R 680 2 months ago Ben Marwick
ReproZip , an Open source tool for full computational reproducibility
Software Carpentry and lessons
Jupyter notebooks and , ,

Note: this list is still under development / Tools / Virtual Machines:
Docker
Vagrant
BinderHub 2,579 2 days ago
nteract.io
Binder Documentation for creating custom computing environments that can be shared and used by multiple remote users
Statcheck , GRIM
Scienceroot the first blockchain-based scientific ecosystem
Lando A local development and DevOps tool for all your projects
Podman Podman is a daemonless container engine for developing, managing, and running OCI Containers on your Linux System

Note: this list is still under development / Tools / Online repositories for open hardware:
PLOS open source toolkit channel
Open Neuroscience
Open Plant Science
Appropedia
DocuBricks
Hackaday.io
Bio-protocol a peer reviewed protocol journal
BMJ Open Science a new journal that aims to improve the transparency, integrity and reproducibility of biomedical research
Evernote
Labguru
sciNote
AsPredicted
The Sci-Gaia Open Science Platform
Improving your statistical inferences Daniel Lakens
Open Stats Lab Kevin McIntyre
R for Data Science
R tutorial: Introduction to cleaning data with R DataCamp
Nextflow open source tool than enables reproducible and portable computational workflows across cloud and clusters

Note: this list is still under development / Organizations
OpenScienceMOOC Community organisation for the development of an Massive Open Online Community for Open Science
Eclipse Science Open source and collaboration for computational science
Mozilla Science A community of researchers, developers, and librarians making research open and accessible
Research Data Alliance (RDA) is a community-driven organization supported by the European Commission, the United States Government's National Science Foundation and National Institute of Standards and Technology, and the Australian Government’s Department of Innovation with the goal of building the social and technical infrastructure to enable open sharing of data
The Software Sustainability Institute Cultivate better, more sustainable, research software to enable world-class research
Openscience.org Supports the development of open scientific software, in particular for cheminformatics
NumFOCUS Open-code, better science. Non-profit organization that promotes sustainable high-level programming languages, open code development, and reproducible scientific research
Center for Open Science Community for open science that also provides research and data software tools

Note: this list is still under development / Courses
Module 1: Open Principles
Module 5: Open Research Software and Open Source

Note: this list is still under development / Books
Opening Science The Evolving Guide on How the Web is Changing Research, Collaboration and Scholarly
Top 10 Must-Read Books for Computer Science Majors

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