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Reference management with mendeley


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This is an introduction to reference management with Mendeley. This presentation was made to participants of the H3ABioNet Introductory Bioinformatics workshop held in Accra, Ghana on 28 March, 2014.

This is an introduction to reference management with Mendeley. This presentation was made to participants of the H3ABioNet Introductory Bioinformatics workshop held in Accra, Ghana on 28 March, 2014.

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  • Mendeley was named after Dmitri Ivanovich Mendeleev, who developed periodic table, and Gregor Johann Mendel (described as the father of modern genetics) who demonstrated that inheritance of certain traits in pea plants followed specific patterns. The founders found existing reference management tools too cumbersome, clunky, and expensive — they cost hundreds of Euros, required a lot of manual data entry, and wouldn’t even store the metadata and the PDFs together!
  • Mendeley is available for all major OS platforms. Mendeley mission is to help you manage and share your research data as you choose.
  • Mendeley account upgrade costs range from $4.99/month – $9.99/month.
  • Mendeley supports 6693 citation styles for thousands of journals.
  • Mendeley importer supports 53 websites currently. Mendeley can import BibTeX, RIS and EndNote™ XML files so you can easily transfer your library from EndNote™, Papers and Zotero. Mendeley also allows you to “watch” folders. Choose a folder on your computer to “watch” so that when you next add papers to that folder, they are also automatically added to your Mendeley library. You can also drag and drop pdf links directly into your Mendeley Desktop library.EndNote is a commercial reference management software package developed by Thomson Reuters. RefWorks is a web-based commercial reference management software package.
  • Organizing your PDFs doesn’t have to be a chore.Mendeley allows you to identify recently added papers, add favorites in a click and store them in multiple folders.
  • Journal club discussions can now be extended through Mendeley groups and the sharing of references and opinions.The public groups in Mendeley are great for creating online bibliographies. I use these to create bibliographies on commonly requested areas of research. By joining / following groups you may be able to identify potential collaborators by scanning the member profiles of groups that interest you.
  • Access your papers anytime, anywhere from your Desktop, web or mobile. Install Mendeley on an unlimited number of computers for free so you can seamlessly access your library at home, office or on campus. Access your Mendeley library through any internet browser by signing into Now your library is even available on computers that don’t have Mendeley installed. Mendeley Web synchronises with Mendeley Desktop and acts as a central server which stores users' library data.
  • Mobile apps allow you to access and view your library on the go. Download the Mendeley app for iPad and iPhone from AppStore in itunes. The iPad and iPhone apps are generally more functional than the Android apps because they are developed by the core Mendeley team. Other android clients for Mendeley include; Droideley, Referey. Available at the Android Market / Google Play.Mendeley apps for Android platform are limited in their functionality – most are charitable efforts. Two apps worth mentioning are Droideley and Scholarly.
  • It does a great job exactly where I need it, i.e. storing and sorting my papers; searching within my collection; suggesting articles and, of course, making references in the text.
  • Mendeleyyoutube channel: website contains videos, tips and tricks on how to get the most out of Mendeley.Mendeley was purchased by the Elsevier publishing company in 2013.[10] The sale led to debate on scientific networks and in the media interested in Open Access,[11] and upset members of the scientific community[12] who felt that the program's acquisition by publishing giant Elsevier, known for implementing restrictive publishing practices, the high prices of their journals[13] (see The Cost of Knowledge) and publicly supporting the SOPA bill, was antithetical to the open sharing model of Mendeley.[14] David Dobbs, in The New Yorker, described Elsevier's reasons for buying Mendeley as two-fold: to acquire its user data, and to "destroy or coöpt an open-science icon that threatens its business model."[14]
  • Transcript

    • 1. Reference Management with Mendeley by Setor Amuzu H3ABioNet Associate
    • 2. Outline • History & Introduction • Features – Reference manager – Add & Organize – Read and Annotate – Collaborate – Backup, Sync, Mobile • Summary 13/05/2014 H3ABioNet Workshop 1: Day 5 2
    • 3. History Mendeley's cofounders (from left to right): Paul Foeckler, PhD, Victor Henning, PhD and Jan Reichelt, PhD 13/05/2014 H3ABioNet Workshop 1: Day 5 3 • Founded in 2007 by 3 PhD students Motivation A tool for: 1. Content Discovery 2. Document management 3. Authoring 4. Collaboration
    • 4. What is Mendeley? • A FREE reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research. • Consists of: Mendeley Desktop, Mendeley Web, Mobile • Available for: 13/05/2014 H3ABioNet Workshop 1: Day 5 4 Linux
    • 5. Reference manager • 2GB free online storage, 1 private/invite-only group with 100MB shared web space • Easily download and install Mendeley Desktop in a few clicks. • Install MS Word Plugin. Compatible with: OpenOffice 3.2 (Windows only), BibTeX, MS Word for Mac, MS Word for Windows 13/05/2014 H3ABioNet Workshop 1: Day 5 5
    • 6. Reference manager - Citations and Bibliographies • Search and select your citation style from over 6000 citation styles, or create your own style. • Easily insert citations and bibliography from Word. 13/05/2014 H3ABioNet Workshop 1: Day 5 6
    • 7. Add documents • Import papers, web pages and other documents into your library from websites. E.g. Nature, BMJ, PLoS • Import from existing software such as EndNote™, Refworks and Zotero. 13/05/2014 H3ABioNet Workshop 1: Day 5 7
    • 8. Organize documents • Identify recently added documents, add favourites, and store your documents in multiple folders. • Comprehensive search with advanced search operators. E.g. “title:”, “author:”, AND, OR, “published_in:” etc. 13/05/2014 H3ABioNet Workshop 1: Day 5 8 Search for… To find articles that have… author: Albert Albert in list of authors
    • 9. Read & annotate PDFs • Navigate through multiple PDFs • Annotate using sticky notes or highlighter pen • Share annotations with others in a private group • Save annotations within PDF & print them 13/05/2014 H3ABioNet Workshop 1: Day 5 9
    • 10. Collaborate, Discover & Network • Collaborate with colleagues online • Create online profile, post comments & browse news feeds • Add contacts, create & join online groups & search over 400 million research papers. 13/05/2014 H3ABioNet Workshop 1: Day 5 10
    • 11. Backup, Sync & Mobile • Free online storage to backup your digital library • Install Mendeley on an unlimited number of computers for free • Access library from any computer with desktop app or directly from Mendeley Web 13/05/2014 H3ABioNet Workshop 1: Day 5 11
    • 12. Backup, Sync and Mobile - Mendeley on Mobile Platforms iOS Android 13/05/2014 H3ABioNet Workshop 1: Day 5 12 Download the iPhone and iPad app for FREE. Scholarley is a 3rd party android app. It is still under development and currently available for free.
    • 13. Summary • Automatically generate bibliographies • Easily import papers from other research software • Collaborate easily with other researchers online • Find relevant papers based on what you’re reading • Access your papers on the go via web, and mobile apps 13/05/2014 H3ABioNet Workshop 1: Day 5 13
    • 14. Reference 13/05/2014 H3ABioNet Workshop 1: Day 5 14
    • 15. Questions 13/05/2014 H3ABioNet Workshop 1: Day 5 15