• Full Name Full Name Comment goes here.
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  • I am one of the founders of Docear, which is a new software for organizing, creating, and discovering academic literature. Today, we released version 1.0 of Docear after a ~2 year beta phase. If you are interested in reference management, you might want to have a look at Docear. The three most distinct features of Docear are:

    1. A single-section user-interface that differs significantly from the interfaces you know from Zotero, JabRef, Mendeley, Endnote, ... and that allows a more comprehensive organization of your electronic literature (PDFs) and the annotations you created (i.e highlighted text, comments, and bookmarks).

    2. A 'literature suite concept' that allows you to draft and write your own assignments, papers, theses, books, etc. based on the annotations you previously created.

    3. A research paper recommender system that allows you to discover new academic literature.

    And Docear is free and open source and available for Windows, Mac, and Linux. More information can be found in our Blog, including a detailed explanation of what makes Docear superior to Mendeley, Zotero, etc. (at least in our opinion :-) ). If you don't like reading, there is also a 6 minute introduction video on our homepage http://www.docear.org ;-)

    In case you are using a BibTeX based reference manager such as JabRef (and you don't want to switch to Docear), you might at least be interested in Docear4Word http://www.docear.org/software/add-ons/docear4word/overview/. Docear4Word allows you to insert references and bibliographies from BibTeX files to MS-Word documents. Hence, it makes writing papers much easier, since e.g. JabRef has no own MS Word add-on.

    Finally, I would like to point you to a recent Blog post I wrote about what makes an evil reference manager. Maybe the post helps you deciding which reference manager to use (even if it's not Docear). http://www.docear.org/2013/10/14/what-makes-a-really-really-bad-reference-manager/
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  • Thanks I think all the recommended changes have been made. June 5th, 2013 (DG)
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  • Thanks for taking some of the suggestions above to update the chart (sorry about the formatting, it looked nice when I typed it). Unfortunately, it looks like Zotero lost Duplicate Detection in this version. We also reverted back to 100MB free storage for Zotero and 1GB free for Mendeley (it should be 300MB and 2GB respectively). Lastly, for mobile versions, I would definitely add ZotPad (for iPad). It has many more features and is more actively maintained than Zandy. You could leave Zandy in of course, but if I had to pick which one to mention, I would definitely choose ZotPad. There's also web based Zotero Reader btw https://secure.zoteroreader.com/
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  • The update from the previous version could have been more thorough. I don't have much to say about RefWorks, but here are some things that caught my eye (mostly about Zotero)

    Comparison Chart:
    * Mendeley is at 1.8.4 now. 1.3.2 is over a year old. I'm not too familiar with Mendeley, but I'd be surprised if it hasn't changed in that long.
    * Zotero can be portable not only because it has a web interface, but because you can install it in Firefox Portable. http://www.zotero.org/support/kb/portable_firefox
    * # of citations: I'm not sure what the 2000+ publications is supposed to mean, but the entry should be pretty much identical to Mendeley's, since they use the same exact styles.
    * This one is brand new, but Zotero now has even better support for Google Docs and Scrivener via the RDF/ODF-Scan plugin http://zotero-odf-scan.github.io/zotero-odf-scan/
    * While Zotero does not have an integrated PDF viewer/annotator, it does not restrict you from using whichever software you like. And the ZotFile plugin will extract (standard) annotations from PDFs. http://www.columbia.edu/~jpl2136/zotfile.html
    * AFAIK Zotero's metadata webscraping is unmatched in the industry in coverage, accuracy, and completeness. And like the Mendeley entry says, Zotero has had the Snapshot feature for a long long time.
    * One quite important thing missing from the chart is the part where Mendeley has pretty strict limits on the size of your private groups (3 people unless you get their premium plan http://bit.ly/10JwzmV).

    I don't think the rest of the document has even been touched for this 'update' Pros/Cons:
    * As mentioned above, I'm not sure what import problems you've experienced, but I'm certain they have since been fixed. If any problems do arise, Zotero fixes them in a matter of days (and often hours).
    * Zotero integrates with all browsers (including mobile) via Bookmarklet, just like Mendeley does. Mendeley's entry says it integrates with Firefox and IE (though it supports other browsers too)
    * The statement about Mendeley generating citations and bibliographies in Word, OpenOffice, Google Docs, LaTeX, and **any other text editor** makes it sound like it integrates with these better than other software. AFAICT, the best you can do is copy-paste pre-formatted citations in plain text http://bit.ly/10fH3Y4 Which is fine, it's just not a Pro over the competitors, which almost all of them can do the same.

    Under the more detailed description of Zotero you write 'Open source, extensible web-based social media tool (shareware really)'. Zotero is definitely _not_ Shareware https://en.wikipedia.org/wiki/Shareware

    I know I'm being quite one-sided here (towards Zotero), since it's the manager I know best. I'm sure there are some details omitted here about Mendeley that have changed (for the better) too.
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  • 1. RefWorks, Zotero & Mendeley: Three Way Comparison 2013Features RefWorks 2.0http://www.refworks.com/Zotero 4.0http://www.zotero.org/Mendeley 1.8.4http://www.mendeley.com/Mission “Online reference managementtool” “See it. Save it. Search it. Cite it.”“Organize research, collaborate &discover knowledge…”Cost Subscription required $$$ Free, open-sourceFree desktop & web interface(owned by Elsevier)Ease of use Average (some users like 1.0 more) Mostly easy,some software quirksMostly easy,social groupsWebaccessibleYes Yes integrates with mostbrowsersYes (same as Zotero)Import/exportfromdatabasesYes, some require text download Yes list of databases Yes list of databases supported(COinS)DownloadpdfsYesYesYesSource links Yes Yes Yes# of citationstyles ~thousands of styles 6400 styles available 6400 styles availableLinks to web Yes Yes YesFormatreferencesWrite-N-Cite for Word/OpenDocstry One Line cite viewCite while you write (CWYW) &rtf-scan feature Cite while you write (CWYW)DuplicaterecorddetectionYES YES YESExtractmetadataNoYesYesPDF markup/annotationNoNoYesWeb scraping Uneven Good scraping feature (someinconsistencies)Excellent (web page snapshot too)Sharing Yes Yes YesCompatibility /mobileversionYesView cites on Web; Android userstry Zandy & ZotpadiPhone & iPad compatibleNotes100mb but can increase 300mb free storage 2 GB free storageThis handout was developed using this wiki entry: see RefWorks, Mendeley and ZoteroDean Giustini, UBC Biomedical Branch Librarian, June 20131
  • 2. RefWorks 2.0 – pros/consPros• Refworks 2.0 is fully supported by most academic libraries• If an academic library subscribes, support is usually good• Use RefWorks to create & share bibliographies; organize folders; attach full text• Access anywhere and via mobile devices• Try RefGrab-It to capture pdfs and webpages• Import citations from RSS feedsCons• RefWorks does not have social features like some newer tools• Its functionality is not the best• You cannot extract metadata from pdfs, so it won’t help if you have a library of pdfsZotero – pros/consPros• Support for Google Docs & Scrivener via RDF/ODF-Scan plugin http://zotero-odf-scan.github.io/zotero-odf-scan/• Now has a stand-alone program for metadata grabs and IE workaround using pluginZotero Bookmarklet (works with iOS devices)• Easy to use bibliography feature; PDFs, notes and images can be attached• Organize citations of any depth in tree into collections; create bibliographies• Zotero integrates with your browser; working in groups; import feature in address bar• Integrates OK with word processors such as Pages, NeoOffice, Google Docs• RDF, TEI, Wikipedia citation templates; COinS, MARC, RDF, unAPI, Browser• Zotero imports directly from a webpage to the library; more convenient than traditionaltwo-steps of saving citation and importing it into library• Try the web-based Zotero Reader https://secure.zoteroreader.com/Cons• Interface: size limitations• Some cumbersome notes features• Keeping interface open limits webpage visibility• Zotero occasionally has difficulty importing citation criteria correctly (but rare)This handout was developed using this wiki entry: see RefWorks, Mendeley and ZoteroDean Giustini, UBC Biomedical Branch Librarian, June 20132
  • 3. Mendeley pros/cons ‘at a glance’ http://mendeley.comDetails Description of Mendeley 1.3.2Cost Free for basic usage (Elsevier purchased Mendeley in 2013 & may monetize it)Premium model http://support.mendeley.com/Storage & team plans https://www.mendeley.com/upgradeDesktop and web versions Sync desktop & website applicationSynching of desktop application to web account NOT automaticMetadata extraction fromPDFs• Drag & drop PDFs into Mendeley Desktop• Detects subject keywords in PDF• Cross-checks your research library against external databases: CrossRef,• PubMed, arXiv, or Google Scholar, DOIs & unique identifiers• Vancouver style, APA, MLA stylesheets (more than 6300+)Share References References can be shared by creating “public” or “shared” (restricted) collectionsMobile support iPhone, iPod Touch, iPadDirect import/export Bookmarklet to import http://www.mendeley.com/import/Citation styles • 6500+ styles (as of May 2013)DOI Pulls all citation details (e.g., metadata)Duplicate record detection Detects duplicatesPDF markup/annotation Annotate, attach notes in PDFsCite/create bibliographies Generate citations and bibliographies in Word, OpenOffice, Google Docs, LaTeX,and any other text editorImporting from & sync withother ref managersImports your existing BibTex, RIS, and EndNote libraries; Browser bookmarksCitation style clipboard http://www.mendeley.com/citationstyles/Browsers Works with Firefox and IESocial networking Yes, private groups, followers, etc.Sharing and collaborationfeaturesGroups, embed papers into your websiteThis handout was developed using this wiki entry: see RefWorks, Mendeley and ZoteroDean Giustini, UBC Biomedical Branch Librarian, June 20133
  • 4. RefWorks 2.0: http://hlwiki.slais.ubc.ca/index.php/Bibliographic_citation_software• Web-based reference manager, widely-used in Canadian academic libraries• Accessible from UBC computers; create your own personal database• Import & store citations, format bibliographies & import citations from RSS feeds• link to files (e.g., PDFs, word documents, Excel spreadsheets)• add new citations by importing or manual entering; share citations for collaborative projects• Go to: https://refworks.scholarsportal.info and “Sign up for an individual account”Interface overview• References: add references with pull-down menu• Search: search for citations by access point (i.e. author, descriptor, journal name)• Bibliographies: create bibliographies• Tools: download plugins e.g. RefGrabIt and Write-N-Cite• Tutorial: http://www.refworks-cos.com/refworks/tutorials/basic.htmlCreating & organizing features:• Select Folders and choose Create …• Give your folder a name; rename or delete as necessaryThis handout was developed using this wiki entry: see RefWorks, Mendeley and ZoteroDean Giustini, UBC Biomedical Branch Librarian, June 20134
  • 5. Importing references:• Search PubMed and select citations; choose Send to and select File MEDLINE• Save file as pubmed_result.txt (use “Send to” “File” option)• In Refworks click on References …then Import• From Import Filter/Data Source pull-down menu, select “NLM Pubmed”• Create Folder you want to add references to import pubmed_result.txt file• Use RefGrab-It to capture webpage content.• Download plugin within RefWorks under “Tools”Searching your reference collections:• Your references are all searchable. Choose “Search” then, “Advanced. Ignore “Search Name”• Change your search field from “Descriptors” to “Anywhere” and choose folder to search• Type a keyword into the search box and click on “Search.”Annotating references, adding PDFs & other files:• Click on “Edit” to add comments, keywords, or attachments to a reference• Note the “Attachment” option. Note the “User” fieldsCreating footnotes & citations in papers:• Download Write-N-CiteZotero 4.0: http://www.zotero.org• Open source, extensible web-based social media tool: "See it. Save it. Sort it. Search it. Cite."• download plugin for Chrome, Safari & Firefox: http://www.zotero.org• Zotero sits at bottom of browser, far right• enhances ability to be social through new Zotero Groups• annotate, tag and organize citations; use notetaking with autosave for enhanced descriptions• gather, organize and cite sources (papers, fulltext pdfs, web pages, images & other objects)• use Collections and Groups to store and share items• to start Zotero on your desktop, click the icon in the lower right of browser• Preferences allows you to install plugins to search text of PDFs and add metadataInterface overview:• iTunes-like interface “window pane” appears at the bottom of your browser; collections and groups arelisted on the left; titles are in the center; metadata at the right column• “My Library” (left column) contains ALL items; click a folder to see citations in that folderThis handout was developed using this wiki entry: see RefWorks, Mendeley and ZoteroDean Giustini, UBC Biomedical Branch Librarian, June 20135
  • 6. • Add Notes and Tags to individual itemsAdding items to Zotero:• Click icon in browser address field• Websites such as library catalogues and book vendors that display a “book” icon are indicating Zotero;tool will recognize items and add them to your collection• Add items manually by clicking on the green “New Item” iconSearching:• Use basic search or advanced via magnifying glass icon; search text, tags, terms, etc.• Save searches by clicking magnifying glass icon and clicking on “Save Search”Adding attachments• Example: Highlight an item in the middle column, right click and choose “Add Attachment/AttachStored Copy of File.”Create bibliographies in Zotero• download Zotero plug-in to add citations while you write ; create bibliographies: highlightreferences; choose Generate Bibliography from Selected Items and select style type needed• Choose Copy to Clipboard and paste the bibliography into a document• Choose Preferences/Advanced to access fulltextSynching & sharing your Zotero library• Save & back-up items, notes and metadata to Zotero server; access from other desktops.• To save attached files, you are limited to 100 mb of space. More space is available for a fee.• Use “Group Settings” in your Zotero online account to add members to groups you want to share. Besure to register with Zotero to access these options.Mendeley: http://www.mendeley.com• Mendeley is a free social document manager (but not open source like Zotero)• Byline: “Organize research, collaborate and discover new knowledge…”• Two components: 1) downloadable desktop application & 2) web interface (hosted at Mendeley)• Easy import, index, annotation, collaboration and backup for your documents• Citations created with metadata in pdf files; imports documents and extracts metadata• Create Collections to store documents and citations; share with others• Plugins for creating bibliographies and scraping webpages; web snapshot featureThis handout was developed using this wiki entry: see RefWorks, Mendeley and ZoteroDean Giustini, UBC Biomedical Branch Librarian, June 20136
  • 7. • A research network of other users to share and discover ideas• Share references, and engage in collaborative tagging of documentsImport to MendeleyManage your citations & pdf files in Mendeley using CollectionsThis handout was developed using this wiki entry: see RefWorks, Mendeley and ZoteroDean Giustini, UBC Biomedical Branch Librarian, June 20137
  • 8. This handout was developed using this wiki entry: see RefWorks, Mendeley and ZoteroDean Giustini, UBC Biomedical Branch Librarian, June 20138