zotero bachelor thesis

Formatting your Thesis and Dissertation:Tools,Tips and Troubleshooting

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What Is Zotero?

Zotero is a citation manager or reference manager tool to store, manage, and cite bibliographic references such as books, articles, webpages, videos, and more.

Use Zotero to collect and organize information and sources; download and save full-text PDFs; and generate bibliographies, full citations, and even in-text citations while you write!

This very brief video explains what Zotero is and shows you how it works:

• Zotero Quick Start Guide Basics on installing Zotero; organizing, collecting and citing your resources, and collaborating with others.

• << Previous: Using Citation Managers to organize your research
• Next: Troubleshoot Word formatting issues >>
• Last Updated: Aug 9, 2024 9:18 AM
• URL: https://libguides.lib.fit.edu/formattingyourthesisanddissertationtoolstipstroubleshooting

• University Libraries
• Research Guides
• Zotero Basics
• Citing and References

Zotero Basics: Citing and References

• Getting Started
• Adding Sources
• Organizing Sources
• Collaborating with Zotero
• Additional Help

Zotero allows you to quickly create standalone bibliographies, insert citations directly into documents, and automatically generate bibliographies from those citations. Over 8,000 citation styles are supported.

Standalone Bibliographies

Standalone bibliographies are useful if you need to create a bibliography that is not associated with text that contains in-text citations, like an annotated bibliography, or if you wrote a paper using in-text citations that are not linked to your Zotero Library. You can create standalone bibliographies from an entire collection or from individually selected items within a collection.

Cite an Entire Collection:

• In the Zotero desktop application, right click on the collection you want to cite.
• Select Create Bibliography from Collection.
• Don't see the style you want? To add styles, click the "Manage Styles..." link below the citation style box, then click the "Get additional styles..." link and search for the style you want to add.
• "Citations" will format your items as in-text citations.
• "Bibliography" will format your items as a full reference citation.
• Under Output Method, select the Copy to Clipboard option.
• Paste your bibliography into a word processor document.

Cite Individual Items:

• In the Zotero desktop application, open the collection containing the items you want to cite.
• Select the item you want to cite (hold the Ctrl button to select multiple). Selected items will be highlighted.
• Right click on one of the highlighted items.
• Select Create Bibliography from Items.

Word Processor Plugins

• Google Docs
• Microsoft Word

Google Docs works with Zotero to help you quickly add properly formatted citations and bibliographies to your documents.

Google Docs - Cite While You Write:

• The Google Docs plugin is bundled with the Zotero Connector and should be automatically installed when you download the Connector .
• Open your Google Docs document and the Zotero desktop application. Both need to remain open while using the Google Docs plugin.
• In Google Docs, the Zotero button is located in the top tool bar.

Add In-Text Citations:

• Place the cursor where you want the in-text citation to be added.
• From the Zotero drop down menu, select Add/Edit Citation.
• The document's citation style can be changed later on.
• As you type, items from your library will appear. Select the correct item.
• Once selected, the item will display in the search bar in the format that will be added to your document.
• Multiple items can be included in the same in-text citation. Add all the items you want to cite to the search bar.
• To edit the in-text citation (i.e. omit author name or add page number), click on the formatted citation in the search bar.
• Once you have added and edited your citations, press the Enter key. Your formatted in-text citation will be added to the text.

Note: If you have a large number of items in your library, you might prefer Zotero's classic Add Citation view, which allows you to view all of your items without using the search bar. Follow these classic view set up instructions to make the switch. For help using classic view, see Zotero's Using the Classic View Citation Window documentation.

Add a Bibliography:

To create a bibliography, you must have at least one in-text citation in the document that is linked to your Zotero library.

• Place the cursor where you want the bibliography to be added.
• From the Zotero drop down menu, select Add/Edit Bibliography.
• The bibliography will be automatically generated in your selected citation style.
• If you add or remove in-text citations from your document, select Refresh from the Zotero drop down menu to update the bibliography.

Word's Zotero plugin can be used to easily add citations and bibliographies to your Word documents, with minimal disruption to your workflow.

Word - Cite While You Write:

• The Word plugin is bundled with Zotero and should be automatically installed when you use Zotero for the first time.
• Open your Word document and the Zotero desktop application. Both need to remain open while using the Word plugin.
• In Word, select the Zotero tab from the top tool bar.
• From the Zotero tab, select the Add/Edit Citation icon.
• From the Zotero tab, select the Add/Edit Bibliography icon.
• If you add or remove in-text citations from your document, select the Refresh button in the Zotero tab to update the bibliography.
• << Previous: Organizing Sources
• Next: Collaborating with Zotero >>

How I Use Zotero to Organize My Research

How I use Zotero to Organize My Research

By Marcy, a Writing Coach

When I started graduate school, one of the most common pieces of advice I received was to pick a citation management software and stick to it.

It took me four years before I finally followed this advice.

The truth is, I had tried to use Zotero before, but frankly, I didn’t understand the hype. Now, I’ve been using Zotero for a year and a half, and I wish I had started sooner. What made me do such a big 180 on using Zotero? Mostly, discovering that it does so much more than just generate citations . Specifically, there are three main features in Zotero that turned me into a convert: its ability to store all of my research in a singular location, its tagging feature, and its notetaking and integrated PDF software.

Storing my research in a central repository

Before I started using Zotero, whenever I downloaded a new text, I had to create a new folder, download the relevant PDF, and move the PDF to the correct folder. It also created issues when I used a text for different topics. For example, if I originally read a text for my English 666 class, I would store it in my English 666 folder. Afterwards, if I wanted to use it again, I’d have to remember where I’d originally read the text or move it to the appropriate place.

With Zotero, my system is a lot more streamlined. Today, I started working on the section of my dissertation introduction that discusses archives in Latin America. After searching through the UNC libraries, I found a source that looked useful to me, so I used my Firefox Zotero Plugin to download the article I needed directly to Zotero.

Within Firefox, I can choose which of my Zotero folders I want to save to. Since this article is for my introduction, I selected the “Introduction” option from the dropdown bar.

My newly-downloaded article now appears automatically in my Zotero desktop app, and it also includes all of the bibliographic information I need.

But what happens if I decide to cite the same article later in my fourth dissertation chapter? The good news is, it’s easy to reuse a source and still stay organized.

I haven’t created a folder for my fourth dissertation chapter, so I’ll start there by clicking the “Add collection” button in the top left-hand corner and giving the collection the name “Chapter 4 research.”

Now that I have my new folder, I can either drag and drop my article into my newly-made “Chapter 4 Research” folder, or I can right-click the source, click “Add to Collection,” and then select “Chapter 4 Research.”

Now, this source appears in both folders (with the PDF), so I can easily access the same source from two different locations.

Now that I have all of my sources in the same place, I use Zotero to help me wade through my research. I’m currently writing the introduction to my dissertation, and I already have over 50 sources in Zotero!

To help me stay organized, I like to give each source I download a tag that tells me what subsection of my research it relates to. For example, I know that one of the major sections of my dissertation introduction is about archives, so I tag all of those sources as “archive.”

To create a tag, I click on my source and then click the “tags” tab in the right-hand side of the page. Then, I click “add” and I write whatever word or phrase I want–in this case, archive.

Once I tag my articles, I can easily filter my sources by typing in the tag in the bottom-left corner and selecting the relevant term. Now, instead of having to wade through 50+ sources, I have around 10 sources.

I also use tags to help me remember which articles I need to include in my Works Cited. While I’ve downloaded every article that might be of interest to me, I won’t end up using all of them in my Introduction. So, whenever I use a source for the first time in my writing, I go back to Zotero and add the tag “include in works cited.” I’ll even use tags to help me filter through which articles I’ve already read and which articles I still need to read!

Note-taking

Once I’ve tagged my sources, I’m ready to start reading and taking notes on my source. To read my source, all I need to do is double click on the source and the PDF appears in a new window in Zotero.

Within Zotero’s PDF editor, I take notes by highlighting and adding sticky notes in the PDF. To highlight or add a sticky note, I just use the bar at the top of the PDF.

While I can take notes within the PDF by adding a sticky note, I can also add notes that appear in the main window. When writing my Introduction, I’ve mostly relied on my PDF annotations and I haven’t taken as many notes. However, for my second chapter, I used the notes feature extensively, typically writing brief summaries and to record my reaction to a source.

What I like about keeping notes this way is that it shows up in the main interface of Zotero. So I can quickly click on different sources to read my notes and jog my memory. This comes in handy when I’m writing and I remember an argument that I’ve read, but I can’t remember which source made the argument. Rather than opening 50 PDFs manually, I use the tags to narrow my search down to a subset of articles. Once I’ve narrowed it down, I can quickly browse through my notes without ever having to leave Zotero’s main screen.

Zotero has been a lifesaver by helping me work more efficiently and strategically. Now, all that’s left for me to do is actually write my introduction…

• NPS Dudley Knox Library
• Research Guides

Citation Guide

• Zotero Examples
• Examples & Rules
• Examples & Rules
• BibTeX Code
• BibTeX Code ≤ v2.6
• Other Styles
• Generative AI

  APA: Zotero Examples

   For NPS theses, papers, and publications: to cite properly, follow these examples and apply the essential rules .

Select  American Psychological Association (APA) 7th edition  for the citation style in Zotero and in Word.

If a source type does not appear in the Zotero examples, consult the examples page.

Always check your output against the Citation Guide example .

For each source, ensure that your document has at least one in-text citation that has not been manually edited (i.e., put in signal-phrase format) to maintain the connection between Word and Zotero.

Book > Audiobook

Book Chapter in Edited Book > One author, two editors

Book section > three authors, one editor > from the introduction, forward, preface, etc., electronic book > chapter with doi or url.

Edit the in-text citations: remove the [ p. ] if you use a locator other than a page number.

In-text Citations

(Bonds, 2014, p. Chapter 3, para. 1)

Electronic Book > From a book provider (Kindle)

Edit the reference entry: remove the [ . ] after the title.

Reference Entry

Krishnan, A. (2008).  War as business: Technological change and military service contracting .  [Kindle DX version]. https://www.amazon.com

Electronic Book > From a library database

Book > print > one author, book > print > two authors, with edition number, book > print > three authors, class notes > published, lecture > published (online), presentation or workshop, computer program / software > hard copy, computer program / software > online, conference proceedings (online), conference proceedings (print), conference proceedings > paper presented at conference > unpublished, data set > published, data set > unpublished and retrievable, encyclopedia.

Edit the first in-text citation: add the full name of the organization and place the acronym in brackets. Edit the reference entry: replace the acronym with the full organization name.

First In-text Citation

( Department of Labor [ DOL ] , 2008)

DOL Department of Labor . (2008).  The construction industry under the Fair Labor Standards Act (FLSA)  [Fact sheet]. https://www.dol.gov/agencies/whd/fact-sheets/1-flsa-construction

Edit the first in-text citation: add the full name of the organization and place the acronym in brackets. Edit the reference entry: replace the acronym with the full organization name and add the full date.

( Department of Defense [ DOD ] , 2005)

DOD Department of Defense . (2005 , December 19 ).  Information assurance training, certification, and workforce management  (DOD Directive 8570.01-M). https://www.esd.whs.mil/Portals/54/Documents/DD/issuances/ dodm/857001m.pdf

( Joint Chiefs of Staff [ JCS ] , 2017)

JCS Joint Chiefs of Staff . (2017).  Countering air and missile threats  (JP 3-01). https://www.jcs.mil/Portals/36/Documents/Doctrine/pubs/jp3_01_pa.pdf

Field Manual / Military Regulation

( Department of the Army [ DA ] , 1994)

DA Department of the Army . (1994).  Sniper training  (FM 23-10). https://www.bits.de/NRANEU/others/amd-us-archive/fm_23-10%2894%29.pdf

Government Report > CRS Report

Government report > gao report, government report > strategy document / other government report.

Instruction

( Office of the Chief of Naval Operations [ OPNAV ] , 2019)

OPNAV Office of the Chief of Naval Operations . (2019 , May 5 ).  Navy Safety and Occupational Health program for forces afloat (OPNAVINST 5100.19F). Department of the Navy. https://www.secnav.navy.mil/doni/Directives/05000%20General%20Management%20Security%20and%20Safety%20Services/05-100%20Safety%20and%20Occupational%20Health%20Services/5100.19F.pdf

Edit the reference entry: add the full date.

Takai, T. M. (2013 , March 28 ).   Adoption of the national information exchange model within the Department of Defense  [Memorandum]. Department of Defense. https://dodcio.defense.gov/Portals/0/Documents/2013-03-28%20Adoption%20of%20the%20NIEM%20within%20the%20DoD.pdf

Handbook > Online

Handbook > print, journal article > online > with doi or url, journal article > online > from a library database, journal article > print, legal > bill / resolution > federal enacted, published in congressional record.

Edit the reference entry: remove the [ , ] after the date.

S. Res. 438, 114th Cong., 162 Cong. Rec. 2394 (2016) , (enacted).

Legal > Bill / Resolution > Federal unenacted

Legal > code of federal regulations, legal > congressional hearing > full hearing, legal > congressional hearing > testimony within a hearing, legal > court case decision > lower court.

Edit the reference entry: add the pages or paragraphs cited.

Lessard v. Schmidt, 349 F. Supp. 1078 , 1092–1104 (E.D. Wis. 1972). https://scholar.google.com/scholar_case?case=16374362071956566586

Legal > Court Case Decision > Supreme Court

Legal > executive order > basic format, legal > executive order > extended format, legal > federal acquisition regulation (far), legal > public law > u.s. code.

Edit the first in-text citation: add the full name of the statute and place the acronym in brackets. Edit the reference entry: replace the acronym with the full statute name.

( National Environmental Policy Act [ NEPA ] ,1969)

NEPA  National Environmental Policy Act , 42 U.S.C. § 4331 (1969).

Legal > Public Law > U.S. Statutes at Large

Magazine article > online > doi or url > no author, magazine article > online > from a library database.

Edit the reference entry: after the year, add the month(s) (and day if applicable).

Katz, F. (2020 , January–March ). You're grounded for life.  Parenting Highlights Quarterly ,  112 (1), 22–27. ProQuest

Magazine Article > Print

Map > google map, multimedia > film, multimedia > podcast.

Edit the reference entry: add [ (Host). ] after the host's name.

McBracket, D. (Host).  (2020, January 7). Taking the sigh out of citation (No. 846) [Audio podcast episode]. In  Team Citation presents.  Komodo Studios. https://www.komodo-studios.com/podcasts/10486/firstnamelastlastnamefirst.html

Multimedia > Video

Newspaper article > online > doi or url > author given, newspaper article > online > doi or url > no author, newspaper article > online > from a library database, report > research report / think tank report / white paper.

Edit the reference entry: list the first six authors followed by [ … ] and then the last author.

Dixon, L., Clancy, N., Miller, B. M., Hoegberg, S., Lewis, M. M., Bender, B. , Ebi nger, S., Hodges, M., Syck, G. M., Nagy, C., &  . . . Choquette, S. R. (2017).  The cost and affordability of flood insurance in New York City  (Report No. RR1776-NYCEDC). RAND. https://www.rand.org/pubs/research_reports/RR1776.html

Report > Technical Report > Author given (online)

Report > technical report > organization as author (online).

( National Toxicology Program [ NTP ] , 2012)

NTP National Toxicology Program . (2012).  Toxicology and carcinogenesis studies of trimethylolpropane triacrylate (technical grade) in F344/N rats and B6C3F1/N mice (dermal studies)  (Report No. TR-576). National Institutes of Health. https://ntp.niehs.nih.gov/go/tr576abs

Report > Technical Report > Author given (print)

Secondary / indirect source.

Cite in your text or format the in-text citation as shown in the Citation Guide example.

Social Media

Edit the in-text citations: delete the handle.

(Babygiraffe [@babygiraffehaslastlaugh] , 2020)

Thesis / Dissertation > From a commercial database > Dissertation

Thesis / dissertation > from an institutional archive > dissertation, thesis / dissertation > from an institutional archive > thesis, unpublished work > accepted for publication (online), unpublished work > not submitted for publication (print), unpublished work > submitted for publication (online), website / webpage > author given, website / webpage > organization as author.

( Federal Bureau of Investigation [ FBI ] , 2017)

FBI Federal Bureau of Investigation . (2017, April 6).  Forging papers to sell fake art.  https://www.fbi.gov/news/stories/forging-papers-to-sell-fake-art

Website > No date given

Website > janes example.

Working Paper / Occasional Paper

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• Last Updated: Jul 29, 2024 10:16 AM
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Citing sources.

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• Avoiding Plagiarism

Getting Help

Visit Zotero's Support Center . 

Using Zotero

• Getting Started
• Organization
• Adding References
• Finding Full Text

Setting Up Zotero

Zotero is a free "open source" citation manager. There are three steps to setting it up. Their downloads page gives you access to the first two.

• Installing desktop software (automatically downloads into Word as well)
• Installing browser connection
• Creating an online account at Zotero

Desktop Software

• If you are using a PC, set up Zotero desktop by downloading and then running the program
• If you are using a Mac, download the .dmg file and drag it to Applications , then run Zotero from Spotlight, Launchpad, or the Applications folder

Browser Connection

• For both Mac and PC users, you will also need to install a connector to bridge the connection between your browser and installed desktop software

Online Account

Go to Zotero and register for an account online

Help and Documentation

• See the Zotero Documentation and Forums pages for more information and technical support.
• This 6-minute YouTube video is a concise "first look" at how Zotero works.
• A Heavy Duty step by step video from Grad Coach. Use the nav buttons in the description to jump to different parts. 
• You may also find Zotero guides from Oregon State and/or Georgia State helpful.

Understanding the Homescreen

Note that the folder organization appears on the left, while the folder contents appear in the middle. The metadata for the selected item will appear on the right.

Creating Collections

Zotero will allow you to create collections and sub-collections from the folder organization pane. A single item is allowed to be in multiple collections at once. Click the folder icon in the task bar to create and name a new collection.

Adding Tags to References

Add tags to your citations with a keyword of your choosing to make them more easily findable. Creating tags allows you to search your library with the keyword.

To add a tag to an item, select the Tags tab in the metadata pane. You must have an item selected in the folder contents pane. Click Add to add a tag.

To search tags, use the search box in the task bar.

Removing Duplicates

Zotero cannot detect duplicates within a selected folder. Instead, it will identify duplicates within your entire library. If you have multiple projects, the duplicates will reflect them all.

We recommend creating a separate Zotero library for a dedicated project which will need accurate duplication numbers. Contact your informationist for further information, or transfer your citations to another citation manager to perform duplication.

Sharing Citations with Others

You can create Groups in Zotero in order to collaborate with others. It is important to note that the amount of storage available for a group account is dependent on the group owner's individual storage limit in their Zotero library. There is no limit to the number of users in a group.

• Once you log in, choose a name for your group.
• For group type, choose Private Membership in order to both share PDFs and maintain privacy.
• You will then be asked to customize permissions for the group type.
• Under Member Settings, you can invite members and update roles.

Once you have synced your Zotero desktop to your online account, you will see your group(s) folders under Groups on the Zotero desktop window.

Manually Adding References

You can manually add an item by clicking on the green plus icon in the task bar of your Zotero desktop software. Select the appropriate item type and then fill out the fields.

You can also add PDFs to your Zotero account. Zotero will look for their metadata from the internet.

• Drag and drop the PDF into the middle of your Zotero homescreen or click Store Copy of File under the green plus icon
• Once added to Zotero, you will see its icon as a PDF symbol
• Right click on the item and select Retrieve Metadata for PDF

Importing from the Web

Use the browser connector that you installed from Zotero to capture an item from the web and add it to your library

Importing from Databases

Zotero can import a variety of formats. The most commonly used are RIS, PubMed XML, and EndNote XML. Imports will automatically create a new folder which you can rename. Zotero can also import a library from another citation manager when a correct format is chosen. It is recommended to use the RIS file format for this purpose.

To import, from the Zotero desktop software, go to File and Import . Select the file you'd like to import and follow the prompts.

Creating a Bibliography

Create a bibliography by exporting a bibliography from a selected item or folder.

Right click on the selected item and choose Create Bibliography from Items... . Then choose

your desired citation style and output.

Using Zotero in a Word Document

Downloading the Zotero desktop software will automatically install Zotero into your word processing program. Select the Zotero tab from your word processing program to display your options.

Accessing Full Text from Hopkins

• From top navigation menu, go to: Edit --> Preferences --> Advanced
• Open URL Section
• Select either "Custom" or "Johns Hopkins" from the drop-down list.
• Add the link below in the Resolver field.

Resolver: https://catalyst.library.jhu.edu/discovery/openurl?institution=01JHU_INST&vid=01JHU_INST:JHU

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• Last Updated: Sep 13, 2024 10:57 AM
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• 5 Steps to Using Zotero
• Adding the Browser Connector
• Creating an Online Account
• Syncing to Online Account
• Browser Add-on (Connector)
• Search Results List
• Google Scholar
• RIS / other file formats
• Manually Add a Source
• Collections / Folders
• Moving / Deleting Sources
• PDFs, Images, & Other Files
• Creating & Sharing Groups
• Modifying Source Records
• Select, Change, Add a Style
• Insert In-text Citations
• Create Bibliographies
• Remove Zotero field codes
• Troubleshooting Plug-in
• Transferring from Other Platforms
• Export Zotero RDF file
• Export an RIS file
• Source Management Comparison Chart
• Zotero Plug-in not Visible
• Error Messages
• Unexpected behavior

Citing and References

Once you have sources in your Zotero Library, you can now add in-text citations and bibliographies to your research paper, thesis, dissertation, book chapter, book, or article.

When you installed the Zotero Desktop app, the Word plug-in was automatically added to Microsoft Word.

This section covers how to do the following.

• Select, Change, Add a Style - Step by step instructions on selecting your preferred style whether APA or specific to a journal.
• Insert an In-text Citation ,
• Add a Page Number , and
• Omit an Author's Name .
• Add a Bibliography in a Word Document ,
• Creating a Bibliography from a Zotero Collection , and
• create Annotated Bibliographies .
• Remove Zotero field codes Learn how to remove the Zotero field codes for submission to a publisher or thesis / dissertation repository.
• Troubleshooting the Plug-in

Download MS Office for Free

As an ISU student, you can download the Office Suite to your Mac or PC for free.

Ask me for help

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Advanced Research & Doctoral Dissertation

• Introduction
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• Zotero Quickstart Guide
• Start with Keywords
• Transition to Citations
• Searching by Methodology
• Reading Articles
• Constructing the Lit Review
• Referencing Other Dissertations
• Publishing Your Dissertation
• Introduction to Zotero
• Installing Zotero & Connectors
• Saving References to Zotero
• Zotero & Google Docs

Zotero is an open source application that collects, manages, and cites research sources. It's easy to use, connects with your web browser to download sources, and best of all it's free.

To use Zotero, you'll need to install the Zotero application and connector components.  This enables your browser to save citations to Zotero.  Once you've watched the tutorial below, go ahead and install both pieces on your personal computer. 

Once you have Zotero and the connector installed, you can start importing references to your account. Watch the tutorial below to learn how to save several different types of sources. 

One of Zotero's best features is its ability to write citations and create bibliographies. The Zotero menu will automatically appear in your Google Docs editor after you install Zotero. Watch the tutorial below, to learn how easy it is to use Zotero while you write your thesis. As with any citation software, you will still need to proofread the formatted citations for accuracy and style. 

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• Last Updated: Aug 29, 2024 3:04 PM
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• Research Guides
• Create Citations & Bibliographies
• Add Sources to Zotero

Choose a Word Processor

Create a citation, select a citation style, edit citations, create bibliographies.

• Organize Your Zotero Library
• Annotate & Take Notes
• Share & Collaborate
• Store & Back up Your Files
• Zotero on iPad and iPhone
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Using Zotero with a word processor allows you to make use of Zotero's ability to automatically track and format citations/footnotes/endnotes within your written document according to a chosen citation style. Zotero works with  Microsoft Word, LibreOffice , and Google Docs .

You can follow Zotero documentation to switch from one word processor to another within the same document.

• In your Word/LibreOffice/Google Docs document, place the cursor where you'd like to add a citation.
• Select the Zotero tab. The first time you use Zotero with Google Docs, you will be prompted to give permission to link your Google Docs account with your Zotero library to allow them to communicate with each other. 

• The first time you do this in a document, you will be asked to choose a citation style. Select a style from the list and click OK.
• A small window or bar should appear. Search for or select the item you'd like to cite, enter page numbers if relevant, and click OK. 
• The citation/footnote/endnote should appear in your document, correctly formatted.
• For suggestions of how to cite difficult or unusual documents, see HKS's Ask a Librarian Zotero answers . 
• If you want to cite multiple sources together, click on the Multiple Sources button to select multiple items together. 
• To add text to the beginning or end of your citation, use the Prefix and Suffix boxes. 

Video on Using Zotero with Microsoft Word

The first time you insert a citation in a document you will be required to choose a citation style.

You can change the citation style at anytime via the Document Preferences button in the Zotero menu in Word. 

If you do not see the style you want listed, you can add more citation styles to your library .

To make changes to your citation, place your cursor within the citation (1) and then click the Zotero Edit Citation button (2).

In the pop-up window, make the desired changes (e.g., adding page numbers) and click OK. 

Your citation will automatically refresh and display the edits you made. 

Correct Errors

All metadata errors in a citation should be corrected in Zotero, not in Word/LibreOffice/Google Docs.

Only use the Zotero Edit Citation function in the Zotero toolbar if you are making changes like those depicted above.

After you have gone into Zotero and updated the citation, use the Zotero Refesh button in Word to update your document.

This section will cover several different ways to create bibliographies with Zotero:

• Bibliography from Citations : You can create a bibliography from all the works you have cited in your paper, using Word/LibreOffice/Google Docs. This may be particularly useful for citation styles that use a shortened note or author/date form. 
• Annotated Bibliography : You can create annotations of works and automatically append the annotations to your bibliography entries.
• Standalone Bibliography : You can create a bibliography directly from works in your Zotero library without using Word/LibreOffice/Google Docs.

Create Bibliography from Citations 

After adding citations to your Word/LibreOffice/Google Docs document, click Add/Edit Bibliography.

Zotero will insert a fully-formatted and alphabetized bibliography of all references cited in your document, using the citation style you had previously chosen: 

Note that this bibliography will only contain articles, books, etc. that you have cited in your document. If you would like to add items to your bibliography that you have not cited in the document , place the cursor into the bibliography and click Add/Edit Bibliography again.

You will now see a pop-up window similar to the one you see when adding citations. The area on the right (1) contains all items already included in your bibliography; the area in the middle (2) shows all items in the Zotero collection selected in the area on the left (3). From the middle area, select the item(s) you would like to add to your bibliography, then click on the green right arrow between the middle and right areas. 

Click OK. The additional item(s) should now show in your bibliography: 

Annotated Bibliographies

• APA: Download the style "American Psychological Association 6th edition (annotated bibliography with abstract)."
• Chicago: Download the style " Chicago Manual of Style 17th edition (note, annotated bibliography)."
• Open your Zotero Library and select the item that you want to annotate.
• In the "Info" tab on the right-hand pane, w rite the annotation in the "Extra" field.
• Repeat this step for each item that you want to include in the annotated bibliography.
• Open your word processing document and follow the standard process for inserting a citation into your document.
• When prompted to choose your citation style, select the Annotated Chicago or APA style that you just downloaded.

Standalone Bibliographies 

You can quickly create standalone bibliographies with Zotero in three different ways.

• Creating a bibliography from a Zotero Collection .
• Creating a bibliography from select items in your Zotero library .
• Creating a bibliography of select items with drag-and-drop (known as Quick Copy in Zotero parlance) .

Note that bibliographies created with any of these three methods are static. In other words, changes you make to a citation in Zotero will not be reflected in these bibliographies; they will be simple Word/LibreOffice/Google Doc documents. 

Creating a bibliography from a Zotero Collection 

Creating a bibliography from select items in your Zotero library 

• In Zotero, select the items you would like to include in your bibliography (holding down the CTRL [Windows] or Command [Mac] keys while clicking on items with your mouse). (If you would like to select items from different collections, select them from the My Library view.) 
• Right-click (control-click on a Mac) on any of the selected items; then select Create Bibliography from Items . 

Proceed as described under Creating a Bibliography from a Zotero Collection . 

Creating a bibliography of select items with drag-and-drop

• In Zotero, select the items you would like to include in your bibliography (holding down the CTRL [Windows] or Command [Mac] keys while clicking on items with your mouse). If you would like to select items from different collections, select them from the My Library view.
• Drag and drop the selected items into a Word document. The items will be formatted into a bibliography according to the citation style you have selected under the Export section of Zotero Preferences. 
• << Previous: Add Sources to Zotero
• Next: Organize Your Zotero Library >>

Except where otherwise noted, this work is subject to a Creative Commons Attribution 4.0 International License , which allows anyone to share and adapt our material as long as proper attribution is given. For details and exceptions, see the Harvard Library Copyright Policy ©2021 Presidents and Fellows of Harvard College.

Managing your Zotero library effectively

Is your zotero library growing wild.

If you’re looking at this unit of the course, you may be in a place where you’ve got the basics of Zotero down — how to add or import items , how to use the Zotero Connectors to add items from a web browser, and how to use Zotero to generate citations and bibliographies in Microsoft Word — but you’re wondering what else you can do with the software. If your collection of citations has begun to grow beyond 30 to 50 items, it may start to feel a little disorganized.  So how do Zotero’s built-in organizational features work together to create a coherent system for taming and managing all your research content and course materials?

That’s what this unit is all about. In it, we take an in-depth look at the three main systems Zotero uses to organize content: collections , tags , and related items . After modules that look at each of these features in detail, we show you an add-on for Zotero, called Zutilo , that can be used to make an easier time of managing items in bulk (copying and pasting tags, editing item information, adding new keyboard shortcuts, and more). Here’s what you’ll find in this unit:

• An introduction to collections, tags, and related items
• collections
• related items
• Instructions for using Zutilo to make tagging and item data much easier to manage in bulk

We recommend going through the modules in order, so why not start with the introduction to collections, tags, and related items ?

Learning Objectives

Upon completion of this chapter, you will be able to:

• Contrast the use of collections, tags, and related items for managing Zotero content
• Manage tags and related items easily using the Zutilo add-on

A features used to show that two Zotero items are connected in some way. Related Items appear on the "Related" tab of an individual Zotero entry's information pane. The nature of the relationship can be arbitrary. For example, chapters of the same book; linking a journal article to other articles it mentions; etc.

Unlike tags and collections, you cannot search for related items. This feature is just a nice way for to illustrate connections between Zotero items that are of interest to you.

Software that provides additional functionality for Zotero. These are also referred to as plugins or extensions.

A list of available add-ons for Zotero is maintained here: https://www.zotero.org/support/plugins

An add-on for Zotero that provides a large set of utility functions and allows you to create keyboard shortcuts for many actions. The name is a combination of "Zotero" and "utility."

You can download Zutilo from here: https://github.com/wshanks/Zutilo/releases

Mastering Zotero by Kris Joseph is licensed under a Creative Commons Attribution 4.0 International License , except where otherwise noted.

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WashU Libraries

How to choose: zotero, mendeley, or endnote.

• Gathering Citations
• Switching among tools
• Writing your paper

Chat with a librarian or reference assistant

Match Your Workflow

You cannot go wrong choosing any of the tools, but it helps if you take a few things into consideration before starting. Remember that you can switch between the tools, it just becomes less convenient the longer you use a tool and the more file attachments you collect.

Some reasons to choose Zotero:

• It gathers citation records for non-PDF and PDF content. Zotero's single-click capture works with many databases and websites, and works well with many catalogs, including WU Classic, MOBIUS, and WorldCat (FirstSearch interface)
• You can also enable the retrieval of PDF metadata, which allows you to create citation records just from dragging a PDF into Zotero.
• Zotero has built in PDF reading and annotation tools . (newly added feature 3/2022)
• Zotero is open source and cannot be acquired by a company.
• *Pricing structure: Zotero follows the "freemium" model:  300 MG for the free version with additional storage available for purchase
• For continuously updated Zotero information, downloading, and excellent help pages, and forums, check their website:  https://www.zotero.org/support/ .
• WUSTL Libraries has a helpful Zotero guide .  In addition, the Libraries have more support available for the Zotero program.  To make an appointment for help, see Zotero Help appointment button on your left.

Some reasons to choose Mendeley:

• Your research content is primarily contained in PDF files: Mendeley has an integrated PDF viewer and can create citation records just from importing a PDF file. Mendeley.org has the strongest website and community platform.
• Mendeley’s PDF viewer has excellent, easy-to-use, built-in capability.  You may also edit with another Mendeley user simultaneously.
• Mendeley is owned by the for-profit publishing company Elsevier.
• *Pricing structure: Mendeley follows the "freemium" model:  2 GB for the free version with additional storage available for purchase
• For continuously updated Mendeley information and excellent help pages, check their website:  https://www.mendeley.com/guides .

Some reasons to choose EndNote:

• Zotero and Mendeley are relatively young tools when compared to EndNote. EndNote X9 offers some additional features that might be necessary for your discipline and work flow.
• There are two versions of Endnote -- a stand alone desktop program and EndNote Online, a cloud-based version. If you want to use both, they can be synced so that you have the same references (from a single desktop library) in both places.
• However, EndNote X9 is not free but can be purchased with a significant educational discount through the Washington University STS. Currently, EndNote for WUSTL students for $24.  For purchasing information, go here: https://sts.wustl.edu/sas-mathematica-and-endnote-for-students/ .
• For additional info, help pages, and videos about Endnote X9, check their thorough company guide: EndNote X9: https://clarivate.libguides.com/endnote_training/users/enx9
• To establish your free Endnote Online account use the following steps:
• Go to the  Web Of Science    from a computer connected to the campus network
• Click the Products link at top right of page. EndNote will be one of the options
• Click register on the pop up window
• Storage limit: EndNote online via the Web of Science provides 2GB of storage with upgrade packages available.
• Scroll down on this website to see a comparison of the two EndNote options: https://endnote.com/product-details/basic/
• This guide at WUSTL’s Becker Medical School is also a helpful resource.

Related Guides

• Zotero & ZoteroBib by Kris Helbling Last Updated Sep 6, 2024 1633 views this year
• Citing Your Sources & Writing Styles by Services *Research & Liaison Last Updated Sep 6, 2024 2122 views this year
• Next: Gathering Citations >>
• Last Updated: Sep 6, 2024 11:42 AM
• URL: https://libguides.wustl.edu/choose

Best Tools For Thesis Writing: Dissertation and Academic Writing Tools

In the quest to master the art of thesis writing, selecting the right tools is crucial. This comprehensive guide introduces the best tools available for thesis writing, each tailored to enhance different aspects of the writing process.

From advanced language proofing to efficient reference management, these tools are designed to streamline your workflow, ensure academic integrity, and elevate the quality of your thesis. Discover how each tool can transform your thesis writing experience, making it more efficient and effective. 

Best Tools For Thesis Writing

Grammarly – Language Proof Your Thesis

Grammarly is not just a grammar checker; it also cater to various aspects of academic writing, from ensuring the originality of content to assisting with the intricacies of formatting and citation.

Grammarly integrates with word processing software like Microsoft Word and Google Docs. It facilitates real-time editing and proofreading, allowing students to refine their thesis statements and arguments as they write. 

The tool’s compatibility with online sources is a boon for literature reviews, streamlining the process of integrating various studies and reports into a cohesive narrative.

It works with many reference management software, ensuring that all bibliographical entries are error-free and consistently formatted. These includes: 

One of the lesser-known features of Grammarly is its ability to suggest rephrases for overused or unclear phrases, a common issue in lengthy academic pieces like dissertations or theses. This aids immensely in maintaining a clear and engaging narrative throughout the writing process.

Additionally, for students working with LaTeX for technical writing or complex document formatting, Grammarly’s ability to check the clarity and readability of text, when used in conjunction with a LaTeX editor, is invaluable.

Grammarly’s free version is robust enough to handle the basics of grammar, spelling, and punctuation. However, for a more in-depth analysis like vocabulary enhancement and advanced grammar checks, the premium version steps in.

Turnitin – Remove Plagiarism From Your Academic Writing

Turnitin is far more than just a plagiarism checker; Turnitin offers a suite of features that profoundly enhance the writing and research process.

One of Turnitin’s standout features is its ability to compare submitted work against an extensive database of academic papers, offering peace of mind to those concerned about inadvertent plagiarism in their dissertation writing.

This comparison includes a thorough check against online sources, making it a robust tool for literature reviews.

Turnitin’s integrates with word processing software like Microsoft Word and Google Docs. This way, you get real-time plagiarism detection, ensuring that all citations and references are accurately credited, a crucial aspect in academic integrity.

The software is also invaluable in managing the format and citation style of a thesis.

Whether it’s APA, MLA, or Chicago style, Turnitin helps ensure that your bibliography and in-text citations are correctly structured, thus avoiding common errors in academic writing.

Additionally, Turnitin’s feedback and grading tools are a boon for educators and students. They allow for detailed comments and suggestions, which can be crucial in refining a thesis statement or rephrasing sections for clarity and impact.

This feature is particularly beneficial in the revision phase of thesis writing.

Suppose you use reference management software like:

In this case, Turnitin’s compatibility ensures a seamless integration, making the management of bibliographies and citations more efficient.

This integration is especially helpful in disciplines requiring extensive reference management, such as in technical writing or legal studies.

Microsoft Word – Base For Your Thesis Writing 

Microsoft Word, offers a plethora of features tailored for the rigorous demands of thesis writing and dissertation crafting. It’s more than just a word processor; it’s a comprehensive tool designed to streamline the writing process for students and researchers.

Microsoft Word’s template feature can be a game-changer for academic writing. You can set up a standard format for your thesis, including predefined styled for:

• Subheadings, and

This not only saves time but also helps in maintaining a professional look required for academic submissions.

One of the lesser-known yet incredibly handy features is the ability to create and manage citations and bibliographies.

Compatible with reference management software like Mendeley, Zotero, and EndNote, Word simplifies the process of citation, crucial in avoiding plagiarism and ensuring proper acknowledgment of sources.

For those dealing with extensive research papers, Word’s navigation pane is a boon. It allows easy mapping and reorganization of sections, crucial in maintaining a coherent structure in your thesis. 

Word’s Review feature is invaluable for collaborative writing. It allows for tracking changes, inserting comments, and even comparing different versions of a document. This is particularly useful when multiple revisions are involved in the thesis writing process.

Freemind – Outline Your Dissertation

FreeMind, a mind mapping software, is an innovative tool that’s increasingly being utilized in the realm of academic writing, particularly for thesis and dissertation preparation.

This free, open-source software offers a dynamic way to organise:

• Research, and

At the heart of FreeMind’s utility is its ability to help students and researchers create visual outlines for their academic projects. This is particularly advantageous during the initial stages of thesis writing, where organizing a vast amount of information and ideas can be overwhelming.

FreeMind allows users to create nodes for each main idea or chapter of their thesis, to which they can add sub-nodes for more detailed points or references. This hierarchical structure makes it easier to map out the entire thesis, providing a clear overview of the project.

For graduate students embarking on extensive literature reviews, FreeMind can serve as a tool to categorize and link various sources and theories.

This not only aids in avoiding plagiarism by keeping track of citations but also helps in synthesising information from different sources cohesively.

Additionally, FreeMind’s compatibility with various word processing tools, like Microsoft Word and LaTeX, ensures that the transition from mind mapping to actual writing is seamless.

Its ability to export maps in multiple formats allows for easy integration into other software used in the writing process.

FreeMind’s real-time collaboration feature is a boon for those working on joint research papers or dissertations, facilitating brainstorming and idea-sharing among team members.

This feature, along with its intuitive interface, makes FreeMind a valuable asset in the toolkit of academic writing tools, enhancing both the efficiency and quality of academic writing projects.

ChatGPT – Best AI Writing Assistant

ChatGPT is based on advanced AI technology, and can be used to assist in various aspects of academic writing. This makes it a valuable asset for students and researchers.

In the context of thesis writing, ChatGPT can be utilized for brainstorming ideas, generating outlines, and even providing suggestions for thesis statements.

Its ability to process and generate text based on user prompts makes it an excellent tool for drafting initial versions of academic documents.

For those engaged in the laborious process of writing a dissertation, ChatGPT offers real-time assistance in:

• Rephrasing sentences,
• Enhancing clarity, and
• Suggesting alternative ways to present complex ideas.

For researchers conducting literature reviews, ChatGPT can help summarize articles, providing quick insights into their content. This is particularly useful when dealing with a large volume of literature.

However, it’s important to note that while ChatGPT is a powerful tool, it should be used to complement traditional research methods, ensuring accuracy and credibility in academic work.

ChatGPT’s versatility extends to its compatibility with various software tools used in academic writing, such as Microsoft Word, LaTeX, and softwares like Mendeley, Zotero, and EndNote. This compatibility streamlines the writing process, from initial research to the final draft.

Canva – Software Tools For Graphics

Canva, primarily known for its graphic design capabilities, is increasingly finding its way into the realm of academic writing, particularly in the visual presentation of complex data and information.

This tool, with its user-friendly interface, offers a fresh approach to creating visually appealing elements for theses, dissertations, and research papers.

In the process of thesis writing, Canva can be used to design compelling graphics, such as infographics and charts, which are essential in representing data in a more digestible format.

This is especially beneficial in fields where visual data presentation can significantly enhance the understanding of complex topics.

Canva’s vast library of templates and design elements allows for the creation of professional-looking graphics without the need for advanced design skills.

For graduate students working on dissertations, Canva provides an array of options to create layouts for posters or presentations, often required for thesis defenses or academic conferences.

The tool’s drag-and-drop feature simplifies the process of designing these materials, making it accessible even for those with limited graphic design experience.

For those concerned about plagiarism and citation, Canva can aid in creating original graphics, ensuring that your academic work remains unique and authentic.

While it doesn’t replace traditional writing software, Canva complements them by adding a visual dimension to academic writing, enhancing the overall impact and readability of scholarly work.

Zotero – Citation Tools For Writing

Zotero has become a cornerstone tool for academic writing, especially in the fields of thesis and dissertation writing.

As a comprehensive tool designed for students, researchers, and academic writers, Zotero simplifies the process of managing research materials, such as: 

• Organizing, and

One of the standout features of Zotero is its ability to seamlessly integrate with browsers. This allows users to easily add sources from the web to their Zotero library with just a click.

For thesis writers who rely heavily on online sources for their literature review, this feature is a significant time-saver.

Zotero’s ability to automatically extract citation information and store it in an organized library simplifies the management of research sources.

Zotero offers robust support for various citation formats. Whether it’s:

• Chicago, or

Zotero can generate bibliographies and in-text citations in the chosen format, directly integrating with word processors like Microsoft Word and Google Docs. This integration is particularly beneficial for maintaining consistency in citations throughout a lengthy academic document.

Furthermore, Zotero stands out for its collaboration features. It allows users to share libraries with others, making it a useful tool for co-authored research papers or group projects.

The real-time syncing feature ensures that all members of a research group have access to the latest resources and references.

Zotero’s compatibility with PDF management tools and its ability to index the content of PDFs for easy searching adds another layer of efficiency. For graduate students and thesis writers, this means quick retrieval of information from a vast collection of saved research papers.

Wrapping Up: Best Academic Writing Apps And Tools

In conclusion, the journey of thesis writing is made significantly smoother with the aid of these versatile tools. From Grammarly’s meticulous language polishing to Zotero’s efficient citation management, each tool offers unique capabilities to enhance your academic writing.

By integrating these resources into your workflow, you can focus more on the content and quality of your thesis, ensuring a well-crafted, professionally presented final document. Embrace these tools to unlock your full potential in academic writing and research.

Dr Andrew Stapleton has a Masters and PhD in Chemistry from the UK and Australia. He has many years of research experience and has worked as a Postdoctoral Fellow and Associate at a number of Universities. Although having secured funding for his own research, he left academia to help others with his YouTube channel all about the inner workings of academia and how to make it work for you.

Thank you for visiting Academia Insider.

We are here to help you navigate Academia as painlessly as possible. We are supported by our readers and by visiting you are helping us earn a small amount through ads and affiliate revenue - Thank you!

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How I wrote my Thesis in Markdown using Ulysses, Pandoc, LaTeX, Zotero, and GitHub

September 27, 2019 | 7 min read

I'm a big fan of Ulysses for writing. Using the simple Markdown syntax, it is easy to concentrate on writing content without any unnecessary distractions. Because of that, I also wanted to write my bachelor's thesis in Markdown with Ulysses.

Did I build this workflow to procrastinate from actually writing my thesis? Maybe 😅

But in the end, I found it to be a smooth experience that helped me finish the thesis more quickly.

However, there are some features that Markdown does not provide out of the box, which are necessary for writing a thesis. Namely, generating tables of content, reference management and citations, cross-references, and equations. So, I looked for ways to fill in those gaps.

This article requires a basic understanding of using the command line and is mainly focused on macOS users. For installing required software, Homebrew is recommended

Project Structure and Version Management with Git

As a developer, I'm used to using Git in my projects, committing changes, and being able to see a log of everything I did. As I wanted to open-source my thesis anyway, I decided to use Git with GitHub for it as well.

My project structure is fairly simple. All content and content-related files are located in a src folder. This is what it looks like in my project folder:

If you want to explore the project structure, visit my thesis repository .

Ulysses to Markdown

Ulysses uses a syntax that extends Markdown's usual spec. They call it "Markdown XL". To process your text, you need to get it out of Ulysses. You could just add an external folder to Ulysses and work with that, but that disables a lot of features, like easily inserting images, iCloud sync, the ability to split your content into multiple sections, etc., that make Ulysses great.

An easy workaround is exporting your content as a TextBundle . A TextBundle is essentially a folder that contains your content as a Markdown file and all assets like images that your text contains. I exported my thesis into the Git repository every time I finished a section.

Reference Management with Zotero

A good thesis needs good sources and managing them all by hand is tedious and error-prone. This is where Zotero comes in. Zotero is a free and open reference management software that supports a variety of export formats. Using its Chrome extension, it's easy to add new sources.

To make Zotero compatible with our workflow, you need to install the Better BibTeX extension. This extension enables Zotero to automatically create and update a bibliography file that we can later integrate into the other tools.

To create the bibliography file, click Export , select Better BibLaTeX and check Keep updated . You can now save this file in your project folder next to your exported TextBundle.

Zotero to Ulysses

To make it easier to insert references from Zotero into Ulysses, I created an Alfred workflow that provides a simple shortcut to do that. In Ulysses, just press ⌘ + ^ and Zotero will show you a search window where you can search for the reference you want to insert. When you've got your references, press enter and Zotero will insert the reference into your document.

You can download this workflow here . Of course, you can change the shortcut or the way it behaves in Alfred.

Inserted references look like [@knapp2019] , where knapp2019 is the reference key from Zotero. If you want to provide a page, you can just add it to the reference: [@knapp2019, pp. 20-24] . This is Pandoc syntax, but more on that in the next chapter.

Typesetting with Pandoc and LaTeX

Pandoc is a useful utility for converting different markup formats between each other. In our case, we need to convert Markdown to LaTeX. In addition to converting markup formats, Pandoc supports processing citations and cross-references using plugins.

If you just want to compile your document to a PDF with a template, you can skip to the next section.

You can install Pandoc and required extensions using Homebrew:

To convert your text to LaTeX, use the following command inside the TextBundle:

This will generate a standalone ( -s ) TeX file containing the converted text and all packages that are required to compile it. To work with LaTeX files, you need the MacTeX package. To install it do that, run:

This will install all required packages that you need to work with LaTeX. Please note that this package is quite huge at about 4 GB.

To compile the generated LaTeX file to a PDF, run the following command:

This will take a few seconds depending on the size of your document and create a PDF called text.pdf . The created PDF already contains a generated bibliography and looks nice. However, you might want to customize it so it fits your or your university's style.

Templating in LaTeX

Creating a template in LaTeX is easy and chances are that there's already a good template for your university or other styles that you can use.

In my case, I used a template by Manfred Enning for the style of my university, FH Aachen .

Create a new index.tex file in the template directory and insert the template here. There are only three important things you need to make sure.

First, the template must include the text.tex file generated by Pandoc. To include it, insert the following line where the content should be placed:

Second, LaTeX needs to know where referenced images are stored. For that, insert the following line before the beginning of the document:

Third, if you use references, you need to tell LaTeX to import them and where to place them. To do that, add the following lines to the start of your template:

Then, add the following line where you want to insert the bibliography:

If you want to add a table of contents, a list of tables, or a list of figures, you can add these lines:

For an example of what this template file could look like, take a look at my template on GitHub.

Now, to compile your document to a PDF using the template, you need to compile your Markdown file to LaTeX again, but this time without the standalone ( -s ) flag. If you've skipped the typesetting step, you can now skip to the next section. Otherwise, run this command:

Then, switch to the template directory and run the following command:

This will create an index.pdf file containing your styled document.

Streamlining the Workflow with Docker

The last steps all seem like a lot of work that you don't necessarily want to do every time you want to compile your document to PDF. To make it all easier, I've created a Docker image that does all the work for you.

If you don't already use Docker, you can install it by running:

To compile your document using Docker, just run:

This image will then convert your Markdown to LaTeX, make sure all images are in a supported format, compile everything to a PDF, copy it to the output directory and clean up any files that have been created during the compilation – LaTeX creates a lot of files.

Automating the Build Process with GitHub Actions

If you want to automatically let GitHub build the PDF on every release you create, add this file to your repository. Now, every time you create a release on GitHub, your document will automatically be compiled to a PDF and the result will be attached to the release like this .

This process takes a few minutes but since it runs automatically in the background, it doesn't really matter.

Tips for Using LaTeX Syntax in Markdown XL

Using Pandoc with the plugins described above allows you to use special syntax for specific LaTeX commands.

Named References

Named references can be added to figures, tables, equations, and sections. For figures, place {#fig:referenceName} directly after an image in Ulysses (no whitespace allowed). You can now reference the figure with @fig:referenceName .

The concept works the same for the other categories. Named sections, for example, work like this:

You can now reference that section using @sec:referenceName .

Writing equations in Markdown XL is as easy as creating a new Raw Source Block ( ~~...~~ ) and adding a math block with the equation inside of it. For example:

Labelled Tables

To create a table with a label, you can place the label below the table after a colon like this:

Wrapping Up

The presented workflow might look a bit complicated, but it works well once it's all set up. I didn't need to worry about layout issues or how my text would be formatted later and could just write in my favorite editor, an environment that I'm already used to.

Since the content is written in Markdown, it can easily be published to other mediums, like blogs, ebooks, and more. This makes it super flexible.

Feel free to contact me @leolabs_org if you have any questions or suggestions.

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Support for Master's Thesis Type and full Bibtex format

I imported my bibtex collection into Zotero and realized that Zotero does into distinguish between Master's and PhD Thesis types of documents.

• kiselev March 19, 2009 edited March 19, 2009 1. Different Thesis types are cited differently: @MastersThesis{ 2. Regarding Zotero notes and files entries when exported to BibTeX: 1) there should be at least correct representation of them in Bibtex (without ???) - so it will be possible to correct those entries in JabRef. Now you cannot open those entries there. 2) Now to exclude those entries when exporting to Bibtex I have to tag them with a special tag "extra" and put this condition in Search - not very smart ! Anyway Bibtex tab would make life easier for me and I believe for others - it is a standard way for representing references. I believe that Zotero still will be primarily used by those who knows what Bibtex is. Those who does not need this tab - not gonna use it. Thanks !

Please also take a look how categories are represented in Biblioscape GUI - a tree of checkboxes - it is a very convenient representation for managing tags or categories.

• kiselev March 19, 2009 edited March 19, 2009 Biblioscape supports hierarchies of categories which can be though as collections but not tags in Zotero. Bibsonomy supports hierarchy of tags as syntax, but lacks of proper graphical representations of those hierarchies. I like Zotero for good usability, but would like to have some freedom with Bibtex - there is nothing bad for Zotero to be a good Bibtex tool as well! Thanks !

1. Different Thesis types are cited differently: @MastersThesis {

Anyway Bibtex tab would make life easier for me and I believe for others - it is a standard way for representing references.

Those who does not need this tab - not gonna use it.

Anyway Bibtex tab would make life easier for me and I believe for others - it is a standard way for representing references. I believe that Zotero still will be primarily used by those who knows what Bibtex is.

• madpower March 11, 2010 Hi! > Can you show me a formatted bibliography where different thesis types are formatted differently? Please, have a look at http://www.ads.tuwien.ac.at/publications/bib/pdf/prandtstetter-PhD-09.pdf You will see in the References at the end of the document that there are master's theses and phd theses differentiated through the words "master's thesis" and "phd thesis". BTW: these are set automatically by BibTeX and not inserted by the user!!! With respect to BibTeX: There are sciences where BibTeX and LaTeX is the standard - mainly computer sciences and all other sciences incorporating a lot of formulas in papers. So please, do not say that only a negligible mass of people uses BibTeX. BTW: Large publisher as Springer and Elsevier support LaTeX and BibTeX with their own style files making the complete publishing process much easier. br, Matthias

You will see in the References at the end of the document that there are master's theses and phd theses differentiated through the words "master's thesis" and "phd thesis".

• madpower March 12, 2010 > Really, I think that it's a bug that BibTeX models these as distinct fields Maybe one can argue that BibTeX is missing a "simple" thesis field but I rather think it is a bug that any type of thesis in Zotero is exported as @phdthesis using the BibTeX-exporter. This is definitely not correct. I hope someone related in developing this exporter will take notice of this anyhow. For now, I have to rethink whether Zotero is usable (for me) since unfortunately I have items which are phd theses and others which are master's theses but BTW I have no other thesis type (although there might be a lot of others) in my list of about 300 publications. greetings, Matthias

Maybe one can argue that BibTeX is missing a "simple" thesis field but I rather think it is a bug that any type of thesis in Zotero is exported as @phdthesis using the BibTeX-exporter. This is definitely not correct.

• madpower March 12, 2010 Sorry, if someone misunderstood my comment: I do not expect any develoepr to invest time if s/he is not interested in. But I think that one of the goals of any such system is that as much people as possible use it. So, if BibTeX is not correctly supported (e.g. import BibTeX and then export it again leads to different outputs) users using BibTeX will unlikely use Zotero. It is as easy as this. For example, one solution would be that the "Type" field is used as identification. Eg. type "phd" leads to @phdthesis , type "master" leads to @masterthesis and any other type leads to @misc (since there is no solely @thesis in BibTeX). I thought that such a solution is "obvious". Sorry. BTW: Saying "BibTeX introduces a silly data model" is wrong and shortminded. BibTeX is open in such a term that if you want your special entrytype (eg. @bachthesis for bachelor theses) then write it and extend your style file for correctly formatting this entry. This is done in about 15 minutes of work. Anyhow, you will notice that in many, many years of existing BibTeX no-one ever thought that such an entry type is really important - otherwise it would already be included in a "standard" BibTeX installation. Each BibTeX-implementation will however ignore unknown types without any error messages, i.e. you can add your own fields/types in public bib-files while others (having not your extended BibTeX-version) can still use it. regards, Matthias

For example, one solution would be that the "Type" field is used as identification. Eg. type "phd" leads to @phdthesis , type "master" leads to @masterthesis and any other type leads to @misc (since there is no solely @thesis in BibTeX). I thought that such a solution is "obvious". Sorry.

• ajlyon March 12, 2010 As I stated before, I certainly think that this could be improved in the BibTeX export translator ( https://www.zotero.org/trac/browser/extension/trunk/translators/BibTeX.js ). I think that it should be possible to treat some of the unambiguous cases (M.A., M.S. and some more -> @mastersthesis , everything else -> @phdthesis ). Since the two @XXXthesis types are treated similarly in most styles, this shouldn't cause issues. Even so, I'm a little afraid of trying to handle this using too clever of logic in the export translator, since this choice of which type to output is being made by guessing, and incorrect guesses can be very confusing for users who are creating items that are, to Zotero, of the same type. As for the design of BibTeX's theses and BibTeX in general, the flexibility that it provides is great for its intended purpose-- authoring by a number of computer-savvy authors using an openly extensible document authoring system. That's not the same as Zotero's model, and it's not a model for robust bibliographic data interchange. I think it should be feasible to tweak the BibTeX.js translator so that items that @mastersthesis items it imports will export back to @mastersthesis items, using the Type field as noted. This would require changes to both import and export, since the translator doesn't appear to populate Type on import on the basis of the choice of @XXXthesis .

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