Digital tools for researchers

Find out how digital tools can help you:

explore Data and code Connect At the bench Write Publish Evaluate Research

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Explore the literature
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icon_6918Here is a collection of digital tools that are designed to help researchers explore the millions of research articles available to this date. Search engines and curators help you to quickly find the articles you are interested in and stay up to date with the literature. Article visualization tools enhance your reading experience, for instance, by helping you navigate from a paper to another.

Search engines and curators

  • BibSonomy – Share bookmarks and lists of literature.
  • CaptoMe – Metadata platform with rich biomedical content and information management tools for well-organized research.
  • CiteUlike – Search, organize, and share scholarly papers.
  • Colwiz – Create citations and bibliography and set up your research groups on the cloud to share files and references.
  • ContentMine – Uses machines to liberate 100,000,000 facts from the scientific literature.
  • Data Elixir – A weekly collection of the best data science news, resources, and inspirations from around the web.
  • DeepDyve – Instant access to the journals you need.
  • EvidenceFinder – Enriches your literature exploration by suggesting questions alongside your search results. (blog post)
  • F1000Prime – Leading biomedical experts helping scientists to discover, discuss and publish research.
  • Google Scholar – Provides a way to broadly search for scholarly literature across disciplines and sources.
  • Labii – A suite of web apps for researchers, including an online app for finding, commenting, rating and managing research papers. (blog post)
  • LazyScholar – Chrome extension to help your literature search.
  • Mendeley – A unique platform comprising a social network, reference manager, article visualization tools.
  • Microsoft Academic Search – Find information about academic papers, authors, conferences, journals, and organizations from multiple sources.
  • MyScienceWork – Diffuse scientific information and knowledge in a free and accessible way.
  • Nowomics – Follow genes, proteins and processes to keep up with the latest papers and data relevant to your research.
  • Paperity – Aggregator of open access papers and journals
  • Paperscape – Visualise the arXiv, an open, online repository for scientific research papers.
  • PubChase – Life sciences and medical literature recommendations engine. (blog post)
  • Pubget – Search engine for life-science PDFs.
  • PubNiche – A scientific research news curator.
  • PubPeer – Search for publications and provide feedback and/or start a conversation anonymously.
  • ReadCube – Read, manage & discover new literature.
  • Research Professional – Source of intelligence on funding opportunities and research policy.
  • Scicurve – Transforms systematic literature review into interactive and comprehensible environment.
  • Sciencescape – Innovation in the exploration of papers and authors.
  • Scientific Journal Finder (SJFinder) – A collection of tools including a journal search engine and rating which recommends a list of journals based on title and abstract of scientific manuscript, website builder, .(blog post)
  • SciFeed – Uses various data sources and natural language processing to identify important new scientific advances.
  • SciVal Funding  – Comprehensive source of funding information.
  • Scizzle – Curator that automagically finds new and relevant research papers. (blog post)
  • Sparrho – Personalized recommendation engine for science – allowing you to keep a bird’s eye view on all things scientific.
  • SSRN – Multi-disciplinary online repository of scholarly research and related materials in social sciences.
  • Symplur – Connecting the dots in healthcare social media.
  • Wiki Journal Club – Open, user-reviewed summaries of the top studies in medical research.
  • Zotero – Helps you collect, organize, cite, and share your research sources.

Article visualization

  • ACS ChemWorx – Collaborative reference manager coupled with tools and services for authors.
  • Colwiz – Create citations and bibliography and set up your research groups on the cloud to share files and references.
  • eLife Lens – Provides for researchers, reviewers, authors and readers a novel way of looking at online content.
  • Elsevier “Article of the Future” – Aims to revolutionize the format of the academic paper in regard to presentation, content and context.
  • Interactive Science Publishing – Allows authors to publish large datasets with original source data that can be viewed interactively by readers.
  • Mendeley – A platform comprising a social network, reference manager, article visualization tools.
  • Pubget – Search engine for life-science PDFs.
  • PubReader – Alternative web presentation that offers another, more reader-friendly way to read literature in PMC and Bookshelf.
  • ReadCube – Read, manage & discover new literature.
  • Utopia Docs – Pdf reader that connects the static content of scientific articles to the dynamic world of online content.
  • Wiley Anywhere Article – Enhanced HTML article from Whiley publisher.
  • Wiley Smart Article – Enhanced article tools for chemistry content in Whiley journals.

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Find and share data and code
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icon_21297Managing large sets of data and programing code is already unavoidable for most researchers. Tools have been developed to efficiently store and share data and code. These tools are become increasingly important as data and code sharing becomes the norm and a requirement of most funding agencies.

  • BioLINCC – Clinical specimen database.
  • ContentMine – Uses machines to liberate 100,000,000 facts from the scientific literature.
  • DataBank – Analysis and visualisation tool that contains collections of time series data on a variety of topics.
  • DataCite – Establish easier access to research data by providing persistent identifiers for data.
  • DataHub – Publish or register datasets, create and manage groups and communities
  • Dataverse Network – Harvard-based tool to share, cite, reuse and archive research data.
  • Dryad– Data repository for any files associated with any published article in the sciences or medicine.
  • Figshare – Manage your research in the cloud and control who you share it with or make it publicly available and citable
  • GenBank – Gene sequence database provided by the National Center for Biotechnology Information.
  • GitHub – Online software project hosting using the Git revision control system.
  • Nowomics – Follow genes, proteins and processes to keep up with the latest papers and data relevant to your research.
  • Open Science Framework – Gathers a network of research documents, a version control system, and a collaboration software.
  • Peer Evaluation – Open repository for data, papers, media coupled with an open review and discussion platform.
  • Quip – Combines chat, documents, spreadsheets, checklist, and more to collaborate on any device.
  • re3data – Global registry of research data repositories.
  • Research Compendia – Tools for researchers to connect their data, code and computational methods to their published research
  • SlideShare – Community for sharing presentations and other professional content
  • Socialsci – Help researchers collect data for their surveys and experiments (blog post).
  • Zenodo – A home for the long-tail of science, enabling researchers to share and preserve any research outputs.

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Connect with others
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icon_3683Research cannot stay buried in the lab anymore! Under Connect with experts and researchers, you will find a set of tools that help researchers reach out to other researcher and find expertise for new collaborations. Under Outreach, find tools that help you communicate your research to the general public. Citizen science, gathers tools to help you involve the general public in your research efforts, by sharing CPU time, or counting birds for example. And under Crowdfunding, you will find tools that help you collect funds for research from others.

Connect with experts and researchers

  • Academia – A place to share and follow research and researchers.
  • AcademicJoy – Share research ideas and story in research and innovation.
  • Addgene – Connect with other researchers through this plasmid sharing platform.
  • AssayDepot – Pharmaceutical marketplace for life science research services.
  • Benchling – Life science data management and collaboration platform.
  • BiomedExperts – Scientific social network to research, collaborate, and connect with researchers and medical experts worldwide.
  • BiomedUSA – Global open access hub for sharing and licensing of Biological Research Materials and related technologies.
  • Biowebspin – Platform in life science worldwide to networks, work, look up information.
  • Cureus – A free and open access the medical journal and a place for physicians to build a digital CV.
  • Direct2experts – A federated network of biomedical research expertise.
  • Expertnet – Helps you locate experts in Florida universities.
  • GlobalEventList – A comprehensive directory of scientific events worldwide.
  • Innocentive – Helps clients to engage a world of creative and diverse on-demand talent to rapidly generate novel ideas and solve important problems.
  • Journal of Brief Ideas – Provides a place for short ideas to be described – in 200 words or less -, archived, searchable and citable.
  • Kaggle – Connect with organisation in need of data prediction algorithms through open competitions for the best code. (blog post)
  • LabRoots – Social network for researchers.
  • LabsExplorer – Search for R&D partners, increase your visibility and gain financing.
  • LabWorm – Featuring the best scientific tools, updated weekly and upvoted by the community. (blog post)
  • LifeScience.net – Online platform for professional networking and sharing of knowledge in life sciences.
  • Linkedin – Professional networking site for all.
  • Loop – Open, cross-platform network for researchers and academics from the Frontiers journals.
  • MalariaWorld – The world’s scientific and social network for malaria professionals.
  • Mendeley – A unique platform comprising a social network, reference manager, article visualization tools
  • MyScienceWork – Diffuse scientific information and knowledge in a free and accessible way.
  • nanoHUB – Centralized platform for computational nanotechnology research, education, and collaboration.
  • Open Science Framework – Gathers a network of research documents, a version control system, and a collaboration software.
  • Piirus – Helps researchers meet potential collaborators, build networks and develop their core research.
  • Profeza – Showcasing the unvalued work behind each article to provide new, more accurate way of evaluating researchers.
  • Profology – A professional community created exclusively for higher education faculty, staff and administrators.
  • Research Connection – A searchable platform for research jobs and information.
  • ResearchGate – Social network for researchers.
  • ScienceExchange – Marketplace for shared lab instrumentations. (blog post)
  • SocialScienceSpace – Social network to bring for social scientists.
  • Speakezee – Bringing speakers and audiences together.
  • Trellis– A digital platform that connects you to the rest of the scientific community, ran by AAAS.

Outreach

  • AcademicJoy – Sharing research ideas and story in research and innovation.
  • AcaWiki – Summarizing academia and quasi-academia, one document at a time.
  • PubDraw – Take science articles, make pictures.
  • I Am Scientist – A science outreach education and engagement activity.
  • Kudos – Helps researchers explain, enrich and share their publications for greater research impact.
  • nanoHUB – Centralized platform for computational nanotechnology research, education, and collaboration.
  • Publiscize – Empowering scientists to free science and make their research available to everyone.
  • Science Simplified –  A science communication portal aiming to aggregate all academic public releases and serve as a direct communication channel with the general public.
  • SciVee – Science video sharing platform.
  • SciWorthy – A science news site for the everyday person to better understand science.
  • Speakezee – Bringing speakers and audiences together.
  • Useful Science – Summaries of the latest science useful in life.

Citizen science

  • Folding@home – Distributed computing project which studies protein folding, misfolding, aggregation, and related diseases.
  • Innocentive – Helps clients to engage a world of creative and diverse on-demand talent to rapidly generate novel ideas and solve important problems.
  • Kaggle – Platform for data prediction competitions.
  • Patient Innovation – Nonprofit, international, multilingual, free venue for patients and caregivers of any disease to share their innovations.
  • Project Noah – Explore and document wildlife on this citizen scientists platform.
  • SciStarter – Find, join, and contribute to science through recreational activities and citizen science research projects.
  • SETI@home – Put your CPU to work to help detect intelligent life outside Earth.
  • Zooniverse – Citizen science projects using the efforts and ability of volunteers to help scientists and researchers.

Crowdfunding

  • Benefunder – Facilitates connections with top researchers who are working on breakthrough discoveries that are impacting our world.
  • Experiment – Crowdfunding Platform for Scientific Research.
  • My Projects – Donate to the research work that means the most to you.
  • Petridish – Fund science & explore the world with renowned researchers.
  • SciFlies – Allows anyone, anywhere to directly support research they care about.
  • Consano – Research crowdfunding site to directly support innovative medical research that matters to you

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At the bench and in the office
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icon_26055Here is a collection of tools that help researchers in their everyday tasks. Go to Lab and project management, for tools that help manage stocks and equipments in the lab as well as project management tools for research. You’ll also find a selection of Electronic lab notebooks developed with academic researchers in mind first. Many others are available elsewhere. Outsourcing experiments is increasingly common in academic research, in part thanks to several sites that are making it easier and cheaper. Also on the hardware side, the internet of things is coming to laboratories and connecting instrumentation to the internet. Platforms to Find and share samples help you disseminate and find materials and biological samples. Under Protocol repository, you will find a collection of publicly accessible resource for experimental protocols. Work with code gathers tools designed to make the coder’s life easier and Work with data tools to generate and analyze data sets, including many R-based tools.

Lab and project management

  • 1degreebio – Reagent marketplace.
  • Antibody Registry – Gives researchers a way to universally identify antibodies used in in the course of their research.
  • Asana – Keeps your team organized, connected, and focused on results.
  • Biocompare – Find products, read reviews and hear about the latest technological developments.
  • ELabInventory – Web-based laboratory inventory management system designed for life science research laboratories.
  • ELabJournal – GLP-compliant Electronic Lab Notebook and lab management tool.
  • LabCritics – Provides researchers with a trust-able source of lab equipment reviews and comparisons.
  • LabGuru – Supports day to day activities of a research group, from vision to execution, from knowledge to logistics.
  • Lab Suit – Inventory Management, orders Management, materials Trade-In, price Comparison.
  • Life technologies Lab Management Tool – Management tool for lab equipment and services.
  • Open Science Framework – Gathers a network of research documents, a version control system, and a collaboration software.
  • Ovation – Simplifies your scientific life from sample tracking for startup labs to data management.
  • Quartzy – A free and easy way to manage your lab.
  • Quip – Combines chat, documents, spreadsheets, checklist, and more to collaborate on any device.
  • Riffyn – Cloud software for visual, collaborative, reproducible innovation.
  • StrainControl – Lab management tools that allows you to organize strains, plasmids, oligos, antibodies, chemicals and inventorie.
  • Synapse – Platform to support open, collaborative data analysis for clear, reproducible science

Electronic lab notebook

  • Docollab – Helps you manage your scientific research, collaborate with your colleagues and publish your findings.
  • elabftw – Electromic lab notebook made by researchers, for researchers, with usability in mind.
  • ELabJournal – GLP-compliant Electronic Lab Notebook and lab management tool.
  • Evernote – A place to collect inspirational ideas, write meaningful words, and move your important projects forward.
  • Findings App – Lab notebook app that allows to organize your experiments, keep track of results, and manage your protocols.
  • Hivebench – Hosted numeric laboratory notebook tool to manage protocols, experiments and share them with your team.
  • Journal Lab – A community of scientists who share open summaries and peer review of published articles. (blog post)
  • LabArchives – Web-based product to enable researchers to store, organize, and publish their research data.
  • Labfolder – Simple way to document your research and to organize your protocols and data. (blog post)
  • LabGuru – Supports day to day activities of a research group, from vision to execution, from knowledge to logistics.
  • Laboratory Logbook – Document projects running in a lab and manage experimentally obtained data and its metadata.
  • sciNote – Open source lab notebook with workflows and modular functionalities. (blog post)
  • Sumatra – Automated electronic lab notebook for computational projects.

Outsourcing experiments

  • Emerald Cloud Lab – A web-based life sciences lab, developed by scientists for scientists.
  • ScienceExchange – Marketplace for shared lab instrumentations. (blog post)
  • TetraScience – Allows you to monitor & manage your experiments from anywhere.
  • Transcriptic – A remote, on-demand robotic life science research lab with no hardware to buy or software to install.

Connected instrumentation

  • BioBright – Provide a better understanding of experimental conditions by connecting sensors to instruments. (blog post)

Find and share samples

  • Addgene – Plasmid sharing platform
  • Antibody Registery – Gives researchers a way to universally identify antibodies used in in the course of their research.
  • Biospecimens – Platform for biospecimen-based research.
  • Duke human heart – Repository for cardiovascular research scientists, including tissues samples and information.
  • ELabInventory – Web-based laboratory inventory management system designed for life science research laboratories.
  • Nanosupply – Platform facilitating sourcing and sharing of advanced materials for research and education.
  • Sample of Science – Peer-Sharing Platform for Scientific Samples. (blog post)

Protocol repository

  • SciVee – Science video sharing platform that includes protocols.
  • Benchfly – Video protocols and video platform for scientists.
  • Benchling – Life science data management and collaboration platform, where you can create, find, and discuss protocols.
  • IPOL journal – Research journal of image processing and image analysis with algorithm descriptions and its source code.
  • MyExperiment – Share workflows and in silico experiments.
  • OpenWetWare – Share information, know-how, wisdom, and protocols among researchers working in biological fields.
  • Pegasus – Platform that help workflow-based applications execute.
  • Protocols – Crowdsourced universal protocol repository. (blog post)
  • Protocol online – A curator of protocols contributed by researchers arounds the world.
  • Scientific Protocols – Share scientific protocols using the GitHub platform.

Work with code

  • CDE Tool – Deploy and run your Linux programs on other machines without any installation or configuration.
  • Dexy – Helps your code to speak for itself with beautiful syntax highlighting.
  • GitLab – A git repository management, code reviews, issue tracking and wiki’s all in one platform.
  • iPython notebook – Interactive computational environment that allows code execution, text, mathematics, plots, and rich media.
  • Kepler – Helps create, execute, and share models and analyses across scientific and engineering disciplines.
  • Mercurial – Control management tool with distributed source, giving each developer a local copy of the development history.
  • nanoHUB – Centralized platform for computational nanotechnology research, education, and collaboration.
  • ROpenSci – Packages that allow access to data repositories through the R statistical programming environment.
  • Sweave – Allows to embed the R code for complete data analyses in latex documents
  • System in Cloud – Platform, enabling clients to rapidly draw and execute data-flow diagram that run in cloud.

Work with data

  • Benchling – Life science data management and collaboration platform.
  • Castor EDC – User friendly and affordable online data collection for medical research.
  • Dat data – Open source, decentralized data tool for distributing datasets small and large.
  • Galaxy Project – Web-based platform for data intensive biomedical research.
  • GenePattern – Genomic analysis platform that provides access to hundreds of genomics tools.
  • TwistBioscience -Silicon-based DNA writing platform that provides access to high quality oligonucleotides, genes and libraries.
  • InSIlico DB – Genomics made possible for biologists without programming.
  • Kaggle – Patform for data prediction competitions.
  • Kitware – Advanced software solutions and services for data intensive R&D
  • mloss – Machine learning open source software.
  • MyExperiment – Share workflows and in silico experiments
  • nanoHUB – Centralized platform for computational nanotechnology research, education, and collaboration.
  • Ovation – Simplifies your scientific life from sample tracking for startup labs to data management.
  • PCR Drive – Free platform that supports researchers in all their PCR-related processes.
  • Pegasus – Platform that help workflow-based applications execute.
  • Plotly – Online tool to graph and share data.
  • Riffyn – Cloud software for visual, collaborative, reproducible innovation.
  • ROpenSci – Packages that allow access to data repositories through the R statistical programming environment.
  • Statcrunch  – Provides data analysis via the Web.
  • Sumatra – Automated electronic lab notebook for computational projects
  • SURF In context – Navigate through RDF relations in a smooth and understandable way.
  • Sweave – Allows to embed the R code for complete data analyses in latex documents.
  • Synapse – Platform to support open, collaborative data analysis for clear, reproducible science.
  • System in Cloud – Platform, enabling clients to rapidly draw and execute data-flow diagram that run in cloud.
  • Tableau – Easily and quickly analyze and present data and share insights.
  • Taverna – A suite of tools used to design and execute scientific workflows.
  • VisTrails – Scientific workflow and provenance management system that supports data exploration and visualization.
  • Wakari – Web-based python data analysis.
  • WebPlotDigitizer – Web based tool to extract data from plots, images, and maps. (blog post)
  • Wings – Semantic workflow system that assists scientists with the design of computational experiments.
  • Wolfram Alpha – Web-based tools for scientific calculations.
  • World Map – Allows users to explore, visualize, edit, collaborate with, and publish geospatial information.

Fundraising/Grantwriting

  • Grant Forward – Search engine for research grants.
  • Instrumentl – Grant database and search tool that learns about specific research projects and then matches them with the best grants available.
  • Pivot COS – A database which includes funding opportunities from all disciplines.

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Write
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icon_43189Writing tools are adapting to the needs of researchers. Tools to store and manage references are grouped under Reference managers. And with research being more and more dependent on collaborations across labs and continents, collaborative writing tools, help researchers write their manuscript while keeping close track of the modifications done by others to the text.

Reference managers

  • ACS ChemWorx – Collaborative reference manager coupled with tools and services for authors.
  • CitationStyles – Find and edit CSL citation styles.
  • Citavi – Reference management, knowledge organization, and task planning solution.
  • CiteUlike – Search, organize, and share scholarly papers.
  • Colwiz – Create citations and bibliography and set up your research groups on the cloud to share files and references.
  • EndNote – Software tool for publishing and managing bibliographies, citations and references
  • F1000 workspace – A workspace for scientists to collect, write and discuss scientific literature.
  • Mendeley – A unique platform comprising a social network, reference manager, article visualization tools.
  • Paperpile – No-fuss reference management for the web (Google docs plugin). (blog post)
  • Papers – Helps you collect and curate the research material that you’re passionate about.
  • Zotero – Helps you collect, organize, cite, and share your research sources

Collaborative writing tools

  • ASCII doctor – Text processor & publishing toolchain for converting AsciiDoc to HTML5, DocBook & more.
  • Atlas – Write, collaborate, design and publish on a single platform.
  • Authorea – Platform to write scientific, academic, and technical documents in collaboration. (blog post)
  • Draft – Version control and collaboration to improve your writing.
  • F1000 workspace – A workspace for scientists to collect, write and discuss scientific literature.
  • Fidus Writer – Online collaborative editor especially made for academics who need to use citations and/or formulas.
  • Overleaf – Online collaborative LaTeX editor, with direct submission to several publishers (ex WriteLaTex)
  • Penflip – Collaborative writing and version control. (blog post)
  • Pensoft Writing Tool – Collaborative authoring, reviewing and publishing in one place.
  • Poetica – Get clear feedback, wherever you’re writing.
  • ShareLaTex – Collaborative on-line editor for for Maths or Sciences.
  • Stackedit – Markdown editor based on PageDown, the Markdown library used by Stack Overflow.
  • Typewrite – A simple, real-time collaborative writing environment.
  • Quip – Combines chat, documents, spreadsheets, checklist, and more to collaborate on any device.

Manuscript Services and writing assistant tools (to come)

  • Ludwig – Helps you improve your English writing by comparing your words with those found on trusted sources such as the New York Time or the BBC.
  • Writefull – Provides feedback on your writing using data from the Google Books database. (blog post)

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Publish
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icon_41537Open Access platforms offer an alternative publishing model, allowing anyone to visualize published work for free. Researchers can also maximize the exposure of their work by placing their manuscripts in Paper repositories. In addition to becoming more open, articles are bound to become more interactive. A set of tools allowing you to bring additional functionalities such as executable code to your articles are grouped under Support to publication. You can also find tools to help your choose from the thousands of journals in activity under Journal reviews and advisors.

Open access platforms

  • eLife – Open access to the most promising advances in science.
  • F1000Research – Open science publishing, using immediate publication followed by transparent peer review.
  • GigaScience – Online open-access open-data journal that publishes ‘big-data’ studies from the life and biomedical sciences.
  • Limn – Free journal that outlines contemporary problems.
  • PeerJ – Open access pre-print and publishing of life science research with annotation.
  • Cureus – A free and open access the medical journal and a place for physicians to build a digital CV.
  • ScienceOpen – Freely accessible research network to share and evaluate scientific information.
  • The Winnower – Open access online science publishing platform that employs open post-publication peer review.

Paper repositories

  • ArXiv – E-prints in Physics, Mathematics, Computer Science, Quantitative Biology, Quantitative Finance and Statistics.
  • biorXiv – The preprint server for Biology.
  • F1000 – Leading biomedical experts helping scientists to discover, discuss and publish research.
  • Figshare – Manage your research in the cloud and control who you share it with or make it publicly available and citable.
  • Peer Evaluation – Open repository for data, papers, media coupled with an open review and discussion platform.
  • Peerage of Science – Pre-publication peer review and publishing for scientific articles.
  • PeerJ PrePrints – Pre-print repository for the biological and medical Sciences.
  • SlideShare – Community for sharing presentations and other professional content.
  • Zenodo – A home for the long-tail of science, enabling researchers to share and preserve any research outputs.

Support to publication

  • Collage Authoring Environment – Framework for collaborative preparation and publication of so-called executable paper.
  • Exec&Share – Openly share the code and data that underlie your research publications.
  • Google Charts – Create live and interactive charts in your browser.
  • RunMyCode – Openly share the code and data that underlie your research publications. (blog post)
  • ORCID – Provides a persistent digital identifier that distinguishes you from every other researcher.

Journal reviews and advisors

  • Cofactor Science Journal Selector – A journal selector from the editing service Cofactor.
  • Edanz’s journal advisor – Personal guide that recommends the tools and services you need to get published.
  • Journal Finder – Elsevier’s service that help you find journals that could be best suited for publishing your scientific article.
  • Journal Guide – Find the best journal for your research. (blog post)
  • Journal Reviewer – Aggregates information users provide about their experience with academic journals’ review processes.
  • Journalysis – A service for academic authors run by academic authors for reviewing experiences with academic journals.
  • RoMEO – Find out publisher copyright and self-archiving policies.
  • SciRev – Share your experience with the scientific review process and learn from others to decide where to submit your manuscripts. (blog post)

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Evaluate research
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icon_16325New tools are changing the way research in evaluated, both in terms of the scientific value of articles and the overall achievements of researchers. Find under Peer-review, a collection of tools that are changing the peer-review system into a more open and productive process by bypassing journals and editors. Altmetrics are a set of new tools that analyze the impact of you work by other means than impact factor and citations counts.

Peer-review

  • Academic Karma – Peer review and get peer reviewed faster.
  • F1000 – Leading biomedical experts helping scientists to discover, discuss and publish research.
  • Hypothes.is – Sentence-level peer-review to provide commentary, references, and insight on top of online content.
  • Journal Review – Rate, and review published medical journal articles.
  • Labii – A suite of web apps for researchers, including an online app for finding, commenting, rating  research papers. (blog post)
  • Libre – Participative reviewing platform (beta testing).
  • Paper Critic – Review platform for research publications (Mendeley plugin).
  • Peerage of Science – Pre-publication peer review and publishing for scientific articles.
  • PeerJ – Open access pre-print and publishing of life science research with annotation.
  • PubPeer – Search for publications and provide feedback and/or start a conversation anonymously.
  • Publons – Record, showcase, and verify all your peer review activity.
  • Pubmed Commons – Share opinions and information about scientific publications in PubMed. (blog post)
  • Rubriq – Provides an independent peer review prior to submission. (blog post)
  • ScienceOpen – Freely accessible research network to share and evaluate scientific information.
  • Wiki Journal Club – Open, user-reviewed summaries of the top studies in medical research.
  • The Winnower – Open access online science publishing platform that employs open post-publication peer review.

Altmetrics

  • Altmetric – Tracks what people are saying about papers online on behalf of publishers, authors, libraries and institutions.
  • ImpactStory – Share the full story of your research impact. (blog post)
  • PLOS Article-Level Metrics – A suite of established metrics that measure the overall performance and reach of research articles.
  • PlumAnalytics – Research altmetric service tracking more than 20 different types of artifacts.
  • Profeza – Showcasing the unvalued work behind each article to provide new, more accurate way of evaluating researchers.
  • Publons – Record, showcase, and verify all your peer review activity.

101 thoughts on “Digital tools for researchers

  1. Let me share Ravi’s sentiment: this is a wonderful collection of online resources for researchers! I would like to point out that American Journal Experts operates a free online resource site, Expert Edge (http://expertedge.journalexperts.com) in addition to fee-based manuscript services. Expert Edge contains articles focusing on English grammar, academic writing, and the publication process in general. It also features an English language glossary and several downloadable writing resources.

    Thank you again for curating this list of helpful resources!
    Ben Mudrak
    Education Program Manager, American Journal Experts

    • Ravi, Ben, thanks for the comments! I’ll add a link to authoraid.info and Expert Edge in a “related site” section very soon.

  2. Hello Jibril,

    I’m sorry if there was some confusion. AJE’s editing services do cost money. The Expert Edge site includes lots of resources about writing in English, though, and these articles and downloadable documents are free. In addition, if you have specific questions about your text as you write your manuscript (how to phrase a certain sentence, help finding the right term, etc.), you can send them to AskAnExpert@journalexperts.com. One of our experienced editors will be happy to assist you.

    Thanks,
    Ben Mudrak

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  5. Under the category “Specialised social science”, I wonder if there are any networks oriented towards History of India.

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  10. Thanks for sharing the tools. You may find interesting my “Research Tools” Mind Map.
    I have collected over 700 tools that can help researchers to do their work efficiently. It is assembled as an interactive Web-based mind map, titled Research Tools, which is available online at http://www.mindmeister.com/39583892/research-tools-by-nader-ale-ebrahim. This Mind map, consists of a hierarchical set of nodes. It has four main nodes: (1) Searching the literature, (2) Writing a paper, (3) Targeting suitable journals, and (4) Enhancing visibility and impact. (See more detail on http://ssrn.com/abstract=2280007)

  11. I would add Scoop.it which is a curation tool and can be used as for knowledge watching in published and grey literature, for research, teaching and learning
    the topics we are curating, focusing mainly on immunology

  12. This is just fantastic. Thank you so much for putting all of this together. I just stumbled upon the website, and I am so glad I did; what a useful list of resources. I am in the beginning stages of my dissertation and many of these resources will be invaluable!

  13. Pingback: Digital tool for researchers update | Connected Researchers

  14. Please consider adding to your list http://fetching.io. It’s a tool that can keep track of all the webpages you visit, then let’s you search them later. For doing research it’s a dramatically better way to capture the full text of *every* webpage you see, so you can be sure you can always re-find pages you’ve seen later. You don’t have to remember to bookmark a site to find it later.

  15. Pingback: Digital tools for researchers | Pascual Pérez-Paredes academic blog

    • Thanks for the comment! Riffyn looks very promising from what I’ve seen. I’ll put it up when it’s more easily accessible.

  16. This is indeed a great collection of tools for researchers – who thought there were so many. I have one more to consider in the “Peer-review publishing” section called http://academickarma.org/ (created by one of my co-workers Dr Lachlan Coin at the University of Queensland, Australia).

  17. I am (and others in other fields) using for immunology (and some related topics) a very nice curation tool Scoop.it.
    http://www.scoop.it/t/immunology
    It allows access to published information and grey literature. It allows to agregate, comment, store, share and find again later selected “serious information”. Obvious application for research, learning and teaching

  18. Pingback: Online tools for researchers | Nader Ale Ebrahim

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  20. One thing that i can not find in the list (may be exist so enlighten me). For the retrieved reviews from conference or journal reviewers, instead of using excelsheet are there a tool for managing that by listing the reviews, assign deadlines to solve, combining related reviews, keep history of all your papers reviews,……

  21. Pingback: 10 additions to the list of digital tools for researchers | Connected Researchers

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  23. Excellent compilation of tools for researchers indeed! I was wondering if you would mind to also add our initiative for sharing and licensing of Biological Research Materials and Related Technologies. We are trying to reach out to scientists to let them know about our open access platform at: http://biomedusa.org
    Thank you for the great resource.

  24. Dear Dr. Crouzier I feel very disappointed that you did not include our open access platform for sharing and licensing of biological research materials : BioMedUSA (http://biomedusa.org) into your collection of digital tools for scientists. Not to mention that you went the extra mile and even removed my note where I asked for it. I am quite puzzled what is your censorship based on? A word of advice would be kind, even when removing my comments from your blog.

    • Hi Vivienne,

      Thanks for your posts! Your last post got lost in the ton of spam this website gets every day. It was never censored, it simply did not get a chance to go through the approval process. I’m very sorry about that.

      BioMedUSA does seem like a great ressource for scientists! We definitely need more platforms like yours than enable researchers to open up their research by sharing samples/materials. I will add this in the next update.

      • Thank you very much Thomas for your response and action. I suspected something was amiss as it seemed counter intuitive. Apparently, we both act in the same social purpose to provide helpful tools for researchers, and I repeat: your resource is an excellent one. The more I appreciate including our free platform for sharing biologicals in your listings.
        Thumbs up!

        Viv

    • Thanks Armin, I’ve made the corrections. The Libre platform seem to be at the late stage of beta testing. But if you have more information about whether the project is abandoned, please share.

  25. Pingback: 4 more digital tools for researchers! | Connected Researchers

  26. I would like to reuse the information contained on this website on our La Trobe University eResearch website – to show digital toolkits that are available to researchers. Would it be ok to use your website in this manner? Many thanks Emma

  27. Dear connected researchers,

    i’m working on Research Lab Tools, we develop android applications for Science.
    We have apps for lab analysis automatization.

    Our apps on Google Play (Play Store)
    *Colorimeter (Measure: RGB, CIE Lab*, Total color difference, Chroma and HUE, this app use smartphone cam to measure.)
    https://play.google.com/store/apps/details?id=com.colorimeter

    *Titratable acidity (This app can perform calculations for acidity, save and export excel full spreadsheet file.)
    https://play.google.com/store/apps/details?id=calc.calculadoradeacidez

    *Color analysis (This app can convert RGB to CIE Lab*, Chroma and HUE. Also, you can export all convertions to Excel file and see converted list of colors.)
    https://play.google.com/store/apps/details?id=com.color.coloration

    If someone have interest on our apps, please visit our Blogger:
    http://researchlabtools.blogspot.com.br/

    Find us on Facebook
    https://www.facebook.com/researchlabtools

    Google Play
    https://play.google.com/store/apps/developer?id=Research+Lab+Tools

  28. Can I use some of your summary here to put on my website? I would like to let more people in my network know those tools but I need to cut off some of the unrelated links. Of course, I will cite this site for more resources! Thanks.

    • Hello,
      Thank you for your question. Glade to know this ressource could be of help to you and your colleagues!
      I would prefer a direct link to Connected Researchers. You can link the specific section you need. If that really doesn’t work for you, you can copy the ressource an refer to this website.

  29. Hello,
    Greate list ! I suggest ISIDORE a scientific search engine for A&H from France with french data but enrichments en english, french and spanish. With 3 millions of record, It’s an important tool too.
    Best,
    Eve.

  30. Pingback: 6 digital tools for researchers added to the list. | Connected Researchers

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  35. Thomas – you are very very hard to contact directly by email (why?). I am not on Twitter. Your expertise would be useful here:

    https://docs.google.com/document/d/1x2RpivCbqZh53XoTvQM6iiFs6R9qip5RLUoeB1Cwt_0/edit#

    This will evolve into a clear “roadmap to digital scholarship” to be presented to funders, in order to develop interoperability standards and consolidate some of the huge number of projects you have listed. Soe of us can’t wait for the next generatin to reap all the benefits!

    • Hello. Thanks for your question. Sure! You can use the content of this website for academic purposes (presentation, report, publication) if you correctly reference the site. If you wish to provide this ressources, please simply link this website.

  36. Greetings!

    Sorry to be contacting you this way, but I couldn’t find an e-mail address…

    Back in May, I sent you an offer to receive a review copy of my book “Writing for Science Journals”, but I did not receive a reply. I am writing once more to see whether this opportunity interests you, or whether you would prefer that I not contact you again about this book.

    Details of the book are available in my signature. The review copy is available in EPUB and PDF formats.

    Thanks for your time. Sincerely,

    ————————————————————————
    Geoffrey Hart (geoff@geoff-hart.com / ghart@videotron.ca)
    Fellow, Society for Technical Communication (STC)
    Manager, STC Scientific Communication SIG, 2000-2005
    Past President, STC Montreal Chapter
    Web: http://www.geoff-hart.com
    blog: http://blatherskite.dreamwidth.org/
    Twitter: @diaskeuasis
    ————————————————————————
    Writing for Science Journals: Tips, Tricks, and a Learning Plan
    http://www.geoff-hart.com/books/journals/journal-book.htm
    ————————————————————————
    Effective Onscreen Editing, 2nd edition:
    http://www.geoff-hart.com/books/eoe/onscreen-book.htm
    ————————————————————————

  37. Pingback: Five new tools added to the toolbox! | Connected Researchers

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  39. Hello to all
    It is very good and fantastic page.
    I have a question. I am a general physician. I have many works that till I have not time to publish them. But now for a qualification in the university for clinician scientist I want to apply but they wanted me to give papers published in more than 1 impact factor in web of sciences. I need help for urgent publication of my work. Can you help me?
    Thanks

    • Hi Amin,
      Thanks for your comment. There are a number of ways you could publish your results. Where you will publish depends on many factors. In what field are your potential readers? Do your readers have access to journal subscription, or would it be best to publish in an open access journal? Can you afford to pay the author’s fees (article processing charge)?

      Just make sure to avoid the predatory journals that will accept your article without any serious peer review in exchange for money (a list is available here http://scholarlyoa.com/publishers/ )

  40. Many factors will help you decide. I discuss criteria for the choice of journals in Chapter 3 of my book on writing for journals (http://www.geoff-hart.com/books/journals/journal-book.htm). To publish in journals with a high impact factor, your research must be world-class. In many cases, it is more practical and effective to publish in journals where your important work will reach doctors and researchers who will benefit the most from your research. I agree with Thomas that you should not submit to journals with weak peer review. A ruthless peer review can be painful, but it is important to ensure that you publish only the highest quality of work. This is particularly important since you are a doctor: human lives depend on the quality of your work.

  41. can i get help regarding my project by linking and inter connecting with respected scholars on this platform?i am currently going through my MS research in clinical pharmacy from china..thanks for consideration

  42. great resource!

    please look at “read” by QXMD? it’s available for computer, android and ipad, and i’ve found it incredibly useful to organize my own journal reading, apart from discovering interesting articles. Link: http://www.qxmd.com/apps/read-by-qxmd-app

    I stumbled on this page because I was looking for a tool that would collate notes from the literature. A more user-friendly version of the “characteristics of included studies” section in revman, if you know what I mean. does this exist? do any of the citation managers have this functionality? Would be grateful for a pointer.

    Also, have heard great things about redcap. although it’s much more than a tool, so i don’t know whether that’s why it doesn’t feature on this list.

    Cheers

    Vijay

    • Thanks for your comment and for pointing out QXMD! I will look into it.
      I am not sure if you are looking for something more sophisticated than a simple notebook integrated into a pdf viewer? If that is all you need, several reference managers or pdf viewers have these. I’m thinking of Paperpile (https://paperpile.com) and ReadCube (https://www.readcube.com) for instance.

  43. Thanks. I’ve not tried either of those. was hoping for cross-referencing/sorting/filtering by type etc–something that combines spreadsheet capabilities with a readable interface. have been making do with excel, but was looking out for something better.

    will look at paperpile/readcube, which other people have been praising as well. 🙂

  44. Pingback: My Favorite Digital Scientific Tools | SciTech Connect

  45. This is a fab summary and resource of useful websites for scientists and digital resources. I would like to add another – Ximbio (www.ximbio.com) – which is a website created to enable the sharing of research tools within the global life science community.

  46. Pingback: My Favorite Digital Scientific Tools | SCI-TECH

  47. Hi Guys,

    I created a service called Pith.li (http://www.pith.li) that allows you highlight the most important parts of online articles and store them in a personal archive.
    We aim at storing the essence of articles. Feel free to have a look and add it to the listing.

    Best regards,
    Johan
    Co-founder Pith.li

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  55. Castor EDC is a mobile-friendly, affordable electronic data capture system for clinical trials, built by researchers, for researchers. We believe in autonomous researchers who can manage their study themselves. Features include audit trails, user management, form building, randomisation, remote capture (patient surveys) and much more.

    Castor doesn’t strive to maximise profits, but wants to make professional data management accessible to researchers all over the world. Small studies are free in Castor EDC! With Castor you can start building your study immediately, and through any web browser.

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  60. Fantastic resource – thank you for compiling it! Can I just point out that ‘F1000’ mentions with regards OA publishing, paper repository, and peer review is actually ‘F1000Research’ and the description isn’t quite correct as that describes our qualitative metric and literature awareness tool F1000Prime. Can I suggest you put something like ‘Open science publishing, using immediate publication followed by transparent peer review’ or something similar?

    Thank you again for creating and maintaining such a valuable resource.

    • Dear Rebecca,
      Thank you so much for your comments. It is important that we get these details right. I have made a few changes, but please do tell me if you have more comments. Thanks for visiting!

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  62. Hi

    The ELN section does not include the LabCollector ELN & LIMS. This ELN is directly aimed at university labs that need both more control than an off the shelf ELNs and also need the ELN connected to instruments and LIMS.

    The company is also staffed by PhD scientists with relevant lab experience.

    thanks,
    James

  63. Pingback: Nine more digital tool added ot the list | Connected Researchers

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