arXiv Open access to one million e-prints in the fields of physics, mathematics, computer science, quantitative biology, quantitative finance and statistics; read about the growth of the arXiv database in this recent article: One Million Preprints and Counting, The Scientist, Dec. 29. 2014. See also Paperscape, a visual map of arxiv and another interface for arxiv at UC Davis called Front.
bioRxiv a preprint server for biology; maintained by Cold Spring Harbor Laboratory
CaltechAUTHORS search a collection of over 35,000 research papers authored by Caltech faculty
CiteSeerX scientific literature digital library and search engine that focuses primarily on the literature in computer and information science
CogPrints Cognitive Science E-Print Archive
Dept. of Energy Pages new beta site providing access to journal article and accepted manuscripts resulting from DOE research funding
EDP Open French publisher in the sciences; 78,000 open access articles and numerous books in both English and French
F1000 research search for articles, posters, and slideshows in the bio-medical sciences
Harvard Dataverse Network open to all scientific data from all disciplines
NARCIS National Academic Research and Collaborations Information System; "gateway to scholarly information in the Netherlands and contains publications from all Dutch universities, scientific institutes, KNAW and NWO, including Open Access e-theses from all Dutch universities."
The On-Line Encyclopedia of Integer Sequences use for identifying a sequence or to obtain more terms, formulas, references, links, programs, etc. for a sequence
Open Energy Information "Linked energy information on hundreds of topics crowdsourced from industry and government agencies."
Organic Eprints "an international open access archive for papers and projects related to research in organic food and farming."
PeerJ PrePrints fully open access preprints in the field of biology
Preprints The multidisciplinary preprint platform; the sciences are well represented
Pubget search engine for life science PDF's including everything from Medline
SciELO Scientific Electronic Library Online; database of South American scientific journals; for an in-depth discussion about SciELO download the free e-book SciELO - 15 Years of Open Access: an analytic study of Open Access and scholarly communication. UNESCO, 2014.
Science Accelerator "a gateway to science, including R&D results, project descriptions, accomplishments, and more, via resources from the Office of Scientific and Technical Information (OSTI), U.S. Department of Energy."
ScienceOpen search for open access science articles; can narrow search by discipline
Science Research search multiple sites in one search
Scirus for scientific research; Notice: this site is set to retire in 2014
SciTech Connect a search portal that consolidates the contents of OSTI's Information Bridge and Energy Citations Database (U.S. Dept. of Energy Office of Scientific and Technical Information)
SCOAP3 Repository open access literature in particle physics created by the Sponsoring Consortium for Open Access Publishing in Particle Physics
World Wide Science "a global science gateway comprised of national and international scientific databases and portals."
Find journal articles and other texts
Academic Journals publisher of over 100 peer-reviewed open access journals mainly in the sciences
ACS Publications American Chemical Society
AIP Publications search physical science publications from AIP Publishers; over 1 million articles; results will include free, open access and subscription based references
AMS American Mathematical Society and their open access journals
Bentham Open publisher of open access journals in the sciences
bioRxiv a preprint server for biology; maintained by Cold Spring Harbor Laboratory
BioHouse Journals open access journals in the sciences
Chemical Science Article Repository Royal Chemistry Society; "a non-commercial subject specific open access repository for chemistry papers"
Chemistry Central open access publisher in the field of chemistry
Copernicus Publications open access publisher
dblp computer science bibliography
De Gruyter Open open access science content
Elsevier Open access journals in the sciences
Friends Science Publishers agricultural publications
Frontiers open access publisher in the sciences
Inderscience Publishers publisher of many science journals; subscription required to view full text; abstracts available and rss alert service
IOS Press a direct link to the IOS Press open access book collection, including the publication of numerous conference proceedings
Liebert Open Access Journals a collection of open access journals in the sciences
Living Reviews a collection open access, peer-reviewed journals
MDPI publisher of open access journals in the sciences
NIST Publications Portal National Institute of Standards and Technology (U.S.)
Open Science blog hosted by De Gruyter with open access news for the sciences
Science Publishing Group list of open access science journals
Scientific Research Publishing an academic publisher of open access journals
SpringerOpen publisher providing open access journals in the sciences
SpringerOpen Books a direct link to open access books published on Springer Open; many books in the sciences
Ubiquity Press open access journals published by Ubiquity Press
Earth Science World Image Bank photographs of all aspects of Earth Science
NeuroMorpho.Org " ... a centrally curated inventory of digitally reconstructed neurons associated with peer-reviewed publications."
Annotate tool for uploading, annotating, reviewing documents in an online workspace; free and premium accounts available; for more about online annotation tools see "Annotating the scholarly web" by J. Perkel on Nature.com, Dec. 1, 2015.
arXiv to BibTeX a tool that generates a BibTeX record for any article in the arXiv database.
BibBase create a bibliography of your publications
Bibsonomy social bookmarking and sharing site; searchable
BibTeX learn about the BibTeX tool and file format for organizing lists of references
Deeplinks Electronic Frontier Foundation's blog covering digital rights and technology issues
Embargo Watch a blog that monitors scientific information embargoes and how they affect news coverage
Experiment crowdfunding for science projects, experiments, scientific research
Figshare store and share your data
Hypothesis Annotate documents; collaborate and share
Journal Metrics CiteScore is a free service from Scopus for journals in Scopus
LabWorm a collection of science tools selected and updated weekly by the science community
MathBook XML "A lightweight XML application for authors of scientific articles, textbooks and monographs." See the gallery of those who have put it to use
Mendeley free citation management tool and .pdf organizer
oaDOI find articles using the DOI (Digital Object Identifier)
Open Notebook Science Network publish your research project in an online notebook
Open Science Framework a scholarly research repository, "free and open source."
ORCID Open Research and Contributor ID is a non-profit that provides a registry of unique personal identifiers for researchers; sign up to create an ORCID ID.
paper-now an experimental location on GitHub where authors can "create, edit and display a journal article, entirely in GitHub"
PLOS Tech blog discussing tools and techniques in science communication
PubPeer "an online community that uses the publication of scientific results as an opening for fruitful discussion among scientists."
ResearchGate join free to search and share scientific output
Retraction Watch a blog that publicizes the retraction of scientific papers
Scimago Journal and Country Rank this tool will show the rank and impact of science journals contained in the Scopus database
Science of Science (Sci2) Tool Manual download the manual and toolset specifically designed for the study of science
Tabula open source download for massaging data extracted from .pdf files
Tools for Open Science from the Open Science Working Group of the Open Knowledge Foundation
What are Altmetrics a new web page that clearly explains altmetrics for researchers
Zenodo Upload, share, browse research
Open access journals in the sciences
Database: the journal of biological databases and curation; an open access journal from Oxford Journals
Earth and Space Science open access journal from the American Geophysical Union
Earth's Future an open access journal from the American Geophysical Union
Elementa new open access (Jan. 2017) journal published by the University of California Press covering the topic of climate change and the environment
GigaScience open access journal for life and biomedical sciences
IBIMA Publishing browse and search a collection of open access journals
Issues in Science and Technology Librarianship and open access journal published by the Association of College and Research Libraries, Science and Technology Section
Journal of Earth Modeling Systems open access journal from the American Geophysical Union
Journal of Visualized Experiments first PubMed-indexed scientific video journal, open access and peer-reviewed
Open Biology published by Royal Society Publishing
Plant Knowledge Journal an open access journal
Research Ideas and Outcomes the open science journal that "publishes all outputs of the research cycle"
Scientific Data "an open-access, peer-reviewed publication for descriptions of scientifically valuable data sets."
Scientific World Journal open access journal published by Hindawi; covers "a wide range of subjects in science, technology, and medicine."
Sensors a peer-reviewed, open access journal on the science and technology of sensors and biosensors published by MDPI
Veterinary Record Open open access journal from the British Veterinary Association
ZooKeys an open access peer-reviewed journal covering the topics of systematic zoology, phylogeny and biogeography.
Integrating Virtual Worlds with Tangible User Interfaces for Teaching Mathematics: A Pilot Study by Graciela Guerrero et al. Sensors (Basel). 2016 Nov; 16(11): 1775. Available at DOI
Other Databases and Repositories
Addgene a non-profit plasmid repository dedicated to helping scientists around the world share high-quality plasmids
BioSharing A catalogue of databases, listing nearly 800, including bioscience databases
Collected Papers of Einstein launched Dec. 2014 by Princeton University; a collection of over 5000 documents from the first 44 years of Einstein's life
Einstein Papers Project at Caltech a database of 80,000 records of Einstein papers and correspondence
Fossil Calibration Database an open access resource. "The database will help scientists estimate the timing of the origins of key plants and animals by combining vetted data from the fossil record with DNA sequences." 
F1000 Research "a unique open access repository for posters and slide presentations across biology and medicine"
The Genome Analysis Centre all TGAC publications are open access; covering the field of genomics and computational bioscience
Informal Science search a database of learning projects and other science resources
International Plant Names Index "a database of the names and associated basic bibliographical details of seed plants, ferns and lycophytes"
Optipedia "encyclopedic articles on key topics in optics and photonics"
The Plant List a working list of all plant species; a collaboration between the Royal Botanic Gardens, Kew and Missouri Botanical Garden
re3data.org registry of research data repositories
Wellcome Open Research Wellcome-funded research papers, open access
Zoo Bank The Official Registry of Zoological Nomenclature
Open: The Philosophy and Practices that are Revolutionizing Education and Science, edited by Rajiv Jhangiani and Robert Biswas-Diener. London: Ubiquity Press, 2017. This is an open access book. Download or read a free copy online; DOI: https://doi.org/10.5334/bbc
Open Science in a Digital Republic, a white paper by Scientific and Technical Information Department - CNRS. Open Edition Press, 2016. Read this open access white paper from the French National Centre for Scientific Research (CNRS) on Open Edition.
Opening Science: The Evolving Guide on How the Web is Changing Research, Collaboration and Scholarly Publishing, edited by Sönke Bartling & Sascha Friesike. SpringerOpen, 2014. The book is published in multiple formats: dynamic book format; open access book format; and printed book version.
Publishing Addiction Science: a guide for the perplexed, edited by T. Babor et al. London: Ubiquity Press, 2017. This is an open access book. Download or read a free copy online; DOI: https://doi.org/10.5334/bbd
The Scientific Revolution Revisited, by Mikuláš Teich. Open Edition Press, 2015. Read this open access book on Open Edition.
Turn on the light on science: A research-based guide to break down popular stereotypes about science and scientists by Antonio Tintori and Rossella Palomba. London: Ubiquity Press, 2017. This is an open access book. Download or read a free copy online; DOI: https://doi.org/10.5334/bba
What is Digital Identity? issues, tools, methodology, by Olivier Ertzscheid. Open Edition Press, 2016. Read this open access book on Open Edition.
What is Qualitative Interviewing? by Rosalind Edwards and Janet Holland. Bloomsbury Academic, 2013. Available online as a creative commons publication on Bloomsbury Open Access.