Friday, 19 December 2014

Digital tools for researchers | Connected Researchers

 Source: http://connectedresearchers.com/online-tools-for-researchers/




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.
  • 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.
  • EvidenceFinder – Enriches your literature exploration by suggesting questions alongside your search results. (blog post)
  • F1000 – 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.
  • 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 Search engines and curators.
  • 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.
  • PubPeer – Search for publications and provide feedback and/or start a conversation anonymously.
  • ReadCube – Read, manage & discover new literature.
  • Scicurve – Transforms systematic literature review into interactive and comprehensible environment.
  • Sciencescape – Innovation in the exploration of papers and authors.
  • Scientific Journal Finder - Search engine, which recommends a list of journals based on title and abstract of scientific manuscript.
  • Scizzle – Curator that automagically finds new and relevant research papers. (blog post)
  • Sparrho – Personalised 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.
  • 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.
  • 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.
  • Kaggle – Connect with organisation in need of data prediction algorithms through open competitions for the best code. (blog post)
  • LabRoots – Social network for researchers.
  • Linkedin – Professional networking site for all.
  • 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.
  • ResearchGate – Social network for researchers.
  • ScienceExchange – Marketplace for shared lab instrumentations.
  • SocialScienceSpace – Social network to bring for social scientists
  • Zombal – Connects the scientific community globally for scientific outsourcing
Outreach
  • AcademicJoy – Sharing research ideas and story in research and innovation.
  • I Am Scientist – A science outreach education and engagement activity.
  • nanoHUB – Centralized platform for computational nanotechnology research, education, and collaboration.
  • Publiscize – Empowering scientists to free science and make their research available to everyone.
  • ScienceGist – Simplified summaries of scientific papers. (blog post)
  • SciVee – Science video sharing platform.
  • 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.
  • Kaggle – Platform for data prediction competitions.
  • 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
  • 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. 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.
  • ELabInventory – Web-based laboratory inventory management system designed for life science research laboratories
  • 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.
  • 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.
  • Quartzy – A free and easy way to manage your lab.
  • Quip – Combines chat, documents, spreadsheets, checklist, and more to collaborate on any device.
  • 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.
  • 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.
  • Sumatra – Automated electronic lab notebook for computational projects.
Outsourcing experiments

  • ScienceExchange – Marketplace for shared lab instrumentations.
  • Transcriptic – A remote, on-demand robotic life science research lab with no hardware to buy or software to install.
  • Zombal – Connects the scientific community globally for scientific outsourcing
Find and share samples

  • Addgene – Plasmid sharing platform
  • 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.
  • 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.
  • Benchfly – Video protocols and video platform for scientists.
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.
  • 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.
  • Galaxy Project – Web-based platform for data intensive biomedical research.
  • GenePattern – Genomic analysis platform that provides access to hundreds of genomics tools.
  • GenomeCompiler – Genetic design platform allowing researchers to manipulate and design everything from single genes to entire genomes.
  • 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.
  • Pegasus – Platform that help workflow-based applications execute.
  • Plotly – Online tool to graph and share data.
  • 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.


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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.
  • 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
  • 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.
  • Fidus Writer – Online collaborative editor especially made for academics who need to use citations and/or formulas.
  • Penflip – Collaborative writing and version control. (blog post)
  • SciGit – Change tracking solution for effortless collaborative writing. (blog post)
  • ShareLaTex – Collaborative on-line editor for for Maths or Sciences.
  • WriteLaTex – Online collaborative LaTeX editor.
  • Stackedit – Markdown editor based on PageDown, the Markdown library used by Stack Overflow.
  • Typewrite – A simple, real-time collaborative writing environment.
  • Poetica – Get clear feedback, wherever you’re writing.
  • Quip – Combines chat, documents, spreadsheets, checklist, and more to collaborate on any device.
Manuscript Services and writing assistant tools (to come)
  • Writefull – Provides feedback on your writing using data from the Google Books database. (blog post)


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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.
  • F1000 – Leading biomedical experts helping scientists to discover, discuss and publish research.
  • 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
  • Edanz’s journal advisor – Personal guide that recommends the tools and services you need to get published.
  • Journal Guide – Find the best journal for your research. (blog post)
  • 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

  • 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.
  • Libre – Participative reviewing platform
  • Paper Critics – 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.
  • Publons – Record, showcase, and verify all your peer review activity.


Digital tools for researchers | Connected Researchers

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