Researcher Tools

“One only needs two tools in life: WD-40 to make things go, and duct tape to make them stop.” -- G. M. Weilacher, American humorist

Good research takes time.  You select a topic, you design an experiment, you conduct your experiment, you observe the results, and you analyze the results. Whoo! You’re done! Next topic, please.

If only it were that simple.  There is so much work to be done before and after the experimental work you enjoy. Wouldn’t it be nice if there were tools to make all the drudge work less onerous?

Fortunately, such tools exist … and many of them are free.

One of the best lists of tools we have found is a Blog called Connected Researchers (http://connectedresearchers.com/online-tools-for-researchers/). It is produced by Dr. Crouzier, a researcher experienced in the fields of biomaterials and biopolymers.

The list of tools listed on the site appears below.

TIP: Visit Connected Researchers and take some time to explore … not every tool will be for you.  But the four or five that you do select will save you tons of time.

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Digital tools for researchers
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)
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.
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.
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 – 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
Managing 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
Research 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.
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.
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.
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.
Trelliscience – A digital platform that connects you to the rest of the scientific community, ran by the AAA.
Outreach
AcademicJoy – Sharing research ideas and story in research and innovation.
AcaWiki – Summarizing academia and quasi-academia, one document at a time.
DrawScience – Take science articles, make pictures.
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.
SciWorthy – A science news site for the everyday person to better understand science.
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
Here 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.
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
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.
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.
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.
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.
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.
Fundraising/Grantwriting
Grant Forward – Search engine for research grants.
Pivot COS – A database which includes funding opportunities from all disciplines.
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Write
Writing 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.
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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Publish
Open 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
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 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
New 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.
Publons – Record, showcase, and verify all your peer review activity.
source: http://connectedresearchers.com/online-tools-for-researchers/
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