Sunday, 14 September 2014

Online tools for researchers


Online tools for researchers

Here you will find a list of online
“web 2.0″ tools, designed for researchers. The list will be updated
progressively as this blogs explores the different services out there.

I – Crowdsoucing Research - 
New tools specifically designed for crowdsourcing research are developing rapidly. For example, here are a few funding-based crowdsourcing sites (crowdfunding):

Other crowdfunding seeks active participation of the public or of
other researchers to accomplish specific tasks. Thses site are part of a
movement called citizen science:

  • SciStarter - Have users participate in various scientific experiments.
  • Socialsci – A survey service tailored for researchers. (blog post)
  • Zooniverse - A large collection of ongoing citizen science projects.
  • Project Noah - Participants can help explore and document local wildlife.
  • SETI@home - Help find E.T
  • Folding@home - Give some of your CPU time to help research on protein folding.
  • Kaggle - Harvests the power of crowdsourcing to solve problems in need of data modeling. (blog post)
  • Ubiome – Explore your micro-biome and help researchers understand micro-biome/disease correlation. (blog post)

 II – Social Networking Sites for Researchers - 
network sites seem to come in at least 4 different flavors: site that
offer tools to manage your references, tools to increase your online
presence and ease networking, tools to exchange and engage in new
collaborations and more site that are specialized in specific scientific
fields. Keep in mind that this classification is not exclusive since
all have overlapping functionalities.

Reference managers orientated:
  • Mendeley -  2 million-user mark passed in 2012
  • CiteUlike - Sponsored by SpringerLink.
  • BibSonomy  - Initiative from the University of Kassel, Germany.
  • Connotea  - Sponsored by Nature Publishing group (discontinued March 11)
  • Zotero - Great open source reference manager
Networking orientated:
Social exchange orientated:
  • ResearchGate - The 2 million-user academic social network
  • MyScienceWork  – Soon 5 languages for this European orientated network.
  • UnitedAcademics - Connects science to society.
  • Colwiz - Collective Wizdom from Oxford (UK)
  • Labroots - Pioneer int the science social networking site business.
  • BiomedExperts -  Bringing experts together
  • AcademicJoy - A more personal approach to research
  • ScienceOpen - Research and publishing network (blog post)
Specialized social network:
There are probably many more out there. Please feel free to comment or contact me if you know of any that are not listed here.

 III – Sharing Science (data, figures, code, samples…) -
One important aspect of the open science movement,
is making your research always more accessible. This means thinking of
new ways to communique scientific research, and online tools to share
scientific related materials will certainly. So brows bellow and share

  • Figshare - Share papers, figures.
  • GitHub – Great repository for open source code. Also comes with tools needed to manage your project.
  • OpenWetWare - Share detailed protocols for biologists and bioengineers
  • SciVee - Share videos of protocols and talks
  • Benchfly – View and share videos of laboratory protocols, tips, tricks and techniques. (blog post)
  • SlideShare - Share slide presentations
  • MyExperiment - Share scientific workflows
  • DataCite - Helps you find and cite data
  • Zenodo -  is a publicly funded repository for research results. Offer 1gigabyte of free space
  • arXive- repository for pre-prints of manuscripts in the fields of physics
  • PeerJ Preprint
    – Deposit your preprint paper for free. Accepts research in the field
    of biological sciences, medical sciences, and health sciences
  • SampleOfScience
    - Online platform designed to promote collaboration between scientists
    by stimulating the dissemination of scientific samples. (blog post)
  • GlobalEventList lists scientific and medical events from around the world.
  • Benchling – Manipulate genetic sequences online. Track changes, store and share. (blog post)
  • Protocols - Share and discover protocols . (blog post)
  • Addgene – Share and deposit plasmids.

- IV Lab and Research Management Tools - 
Research laboratories can
be organizational mess when it comes to ordering, inventory, recording
of experimental data or equipment management. Luckily  there’s an
increasing collection of great online tools out there that helps you
manage a lab. Here’s a few, some of which will be featured by a blog
post in the upcoming weeks:
  • LabGuru - One of the most comprehensive web-based lab and research management tool. Free for personal use.
  • Quartzy -  Another very mature lab management service. Completely free!
  • ELabInventory - A commercial web-based tool for inventory management.
  • Life technologies Lab Management Tool -  A free tool for lab equipment management  (blog post)
  • Sparklix - A free web-based electronic lab notebook equipped with  a set of tools to manage your data
  • Labarchives - A free  web-based electronic notebook software (25 Mb of free storage included)
  • Labfolder -
    An online digital lab notebook where users can write, draw and assemble
    reports of their latest experiments, that they can then safely store in
    the cloud. (blog post)
  • Hivebench – Online electronic lab notebook with protocol and inventory management
  • CellKulture – (Private Beta version) Free electronic lab notebook for tracking cell and tissue cultures. (blog post) Discontinued in September 2014 (blog post)

 V – Producing research (data analysis, writing, publishing)  -
There’s a lot of great tools out there
that can help you produce great research, from analyzing data, to
writing and publishing your scientific papers. More and more tools will
also focus on helping you communicate your research through new media,
mostly online (blog, twitter, open source, paper repository…)
Working with data:
  • – Online tool to analyze data, plot beautiful graphs and share all of that with the world.
  • WebPlotDigitizer – Web-based tool to extract data points from figures. (blog post)
Collaborative writing:
  • SciGit - Collaborative writing for scientists made easy. (blog post)
  • Penflip – Collaborative writing and version control with this GitHub for writers. (blog post).
  • Rubriq - Offers
    a rigorous peer-review service for your biological and medical
    sciences-related manuscript before their submission to publishers (for a
    fee). (blog post)
  • American Journal Experts - Online service that will help you through all step of a paper preparation (for a fee).
  • ACS ChemWorx -
    A hybrid tool from the American Chemical Society that allows reference
    management, storage of pdf in the cloud and tools to help write and
    publish in ACS journals.
  • WriteLaTex –  Free collaborative LaTeX editor that that lets you create, edit and share your LaTeX documents.
  • ShareLaTex - Real time collaboration around LaTeX documents
  • Authorea -Collaborative writing tool for scientific articles. (blog post)
  • Paperpile – A browser-based reference manager, with perfect integration with google docs and drive. (blog post)
  • Writefull – A small application that uses Google Books and Web Search to help you write. (blog post)
Publishing support:

  • Edanz’s journal advisor - A
    free online journal selection service. The tool analyzes your abstracts
    and suggests a list of adapted journals ranked by matching score.
  • Journal Guide
    – Analyzes title and abstract to find the perfect journal for your
    paper. Compare and comment on journal cost, aims and scope, open access
    policies. (blog post)
  • RoMEO - Gathers the copyright and self-archiving policies of over 2200 journals. (blog post)
  • Runmycode - Allows
    you to create a companion website for your publication. The site can
    host a cloud-based version of your code that users can run at will. (blog post)
Measuring your impact:
The good old citation number has been the standard metric for impact
for years. How do you know how impactful your research is in the
research 2.0 era? These services provide a new evalutation of research,
in part by considering the online ecosystem. This alternative metrics
has been named “Article Level Metrics” or “Altmetrics” (alternative

  • ImpactStory - Evaluates impact of articles by tracking bookmarks, twitts, blog posts and social network posts. (blog post)
  • PlumAnalytics - Tracks over 20 sources to provide alternative analysis of research impact
  • PLOS Article-Level Metrics - PLOS’s alternative metrics
  • Altmetric -Directly originating from the altmetrics movement, provides article level altmetrics
  • ScienceCard - Early altmetric software (development on hold at the moment)

 VI – Find expertise -
Whether it’s a biology lab needs to find a
software engineer, or a chemistry lab that needs to access to the latest
mass spectrometry instruments and analysis, a whole range of online
services have emerged these past years help you connect to experts and
  • ScienceExchange - “An eBay for science” says This service helps researchers find and use shared equipment facilities around the US.
  • Assaydepot - A network of both public and private research services exchange.
  • Zombal - A
    scientific freelancer platform  Deposit request for research project to
    be done, or come find a job and “transform your scientific expertise
    into cash”.
  • 1degreebio - Find independent review on life science products and service provider
  • Direct2experts - An impressive directory of experts from biomedical institutions around the USA.
  • Biomedexperts - Connects biomedical researchers throughout the world through networks of co-authors.
  • Expertnet - A portal of expertise across Florida’s universities.

 VII – Find, read, organize and discuss papers -
A good chunk of the researcher’s work is to
find the right papers, then to understand and discuss them to generate
new ideas.  A series of tools have been developed to help in that
  • PubPeer - An online community that uses the publication of scientific results as an opening for fruitful discussion. (blog post)
  • Pubmed Commons – Pubmed’s commenting plateform, limited availibility. (blog post)
  • JournalLab – Find and discuss papers. Journal Lab also allows figures to be discussed. (blog post)
  • Publons - specialized in physics orientated manuscripts. Comment and review paper published on the pre-print repository arXiv and other top physics journals (Applied physics letters, Nature, PRL…)
  • EvidenceFinder - Search engine that digs deep into the full text of articles to find facts related to your search queries. (blog post)
  • Google Scholar - Beyond being a great publication search engine like other (pubmed, scifinder, Scirus…), google scholar also implemented researcher profiles and publication suggestions based on your interrest.
  • Pushpin -
    This service includes a classic social network interface, with
    profiles, publication list but also makes recommendations regarding who
    you should follow and what papers might be interesting to you. (blog post)
  • Pubget – Search engine for life science PDFs. Pubget finds and displays the PDFs directly in its interface.
  • PubChase, a tool to search, organize, store pdf, and discover biomedical research both in browser and mobile. (blog post)
  • ReadCube,
    is platform that helps you organize, find new paper and manage your
    pdfs. It also includes a pdf reader with enriched content (including
    links to references, altmetric data and much more)
  • ScienceGist, is a platform that allows users to transcribe the abstracts of top scientific papers in simplified english. (blog post)
  • Scizzle, an aggregator for scientific articles to easily organize, share and collaborate through an user-friendly and clean look. (blog post)
  • Peer Evaluation -
    Allows authors to upload data, articles and media and have them openly
    accessible and available for review and discussion by peers.
  • Peerage of Science -
    Has the particularity of bridging the independent peer-review process
    with direct access to publishing in partner journals if successful with
    review process.
  • Paper Critics - Connects to Mendeley accounts, this tool offers researchers to give and receive feedback about their scientific production.
  • Libre - Participative reviewing platform. This tool is not launched just yet, so be on the lookout for updates.
  • LazyScholar - Chrome extension that saves time when looking for the full texts of scientific papers. (blog post)
  • Sciencescape – Browse networks of papers linked by fields, ranked by Eigenfactor. (blog post)

Online tools for researchers | Connected Researchers

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