LaTeX, BiBTex, LyX, Zotero: Starter's Guide


Political Science/Social Science Publishing using LaTex and LyX

BiBTeX bibliography and citations management using Zotero Standalone, Zotero for Firefox, ZotFile, Lyz, and JabRef

  1. Download MikTex, the background program where the magic actually happens. This is where LaTex runs from and does the work in the background. You should have to only seldomly go into MikTex to deal with packages. (See step below)
  2. Install MikTex. You must do this before you install Lyx in step 3.
  3. Download LyX and choose one of the "Installers" (so 2.1, or 2.2 for most) Lyx is the user interface system, the program most similar to Microsoft Word that uses MikTex to produce what you want: that academic and professional looking final PDF product. You can also use LyX to produce that purple, generic looking PowerPoint everyone uses in Political Science.
  4. Install Lyx. When prompted, you should not download MikTex. You have already installed it. During Lyx installation, Lyx will automatically detect MikTex.
  5. Download Zotero Standalone (scroll down), which will manage your citations for use in LyX. There are two parts to Zotero, the standalone, which allows you to manage your bibliography off-line and this automatically syncs with your account (which you set up in Step 4) and with the Zotero for Firefox online interface (step 6) which you can access anywhere around the world.
  6. Go to www.Zotero to register an account. 
  7. Open Firefox, download Zotero for Firefox. Enter your login (same from step 4). You can also download this by going to Firefox and clicking on "Tools" > "Add-ons." In the top right corner "Search for Add-ons." Search for "Zotero."
  8. Create a folder where you will keep your bibliographies. The extension (like .pdf, .doc, .xls) for these bibliographies are ".bib".
  9. Download Master.bib (also linked below) and Zotero.bib below into your bibliography folder. For all political scientists, many of the most common citations are in Master.bib, from James Stimson, which I have already cleaned up and modified. Zotero.bib carries most rational choice, international security citations, which I created.
  10. Let's go back to Zotero Standalone and enter your citations. Click the Settings (looks like a "wheel") button, and import. One by one Import  Master.bib and Zotero.bib from your bibliography folder. 
  11. Press sync (the green arrow button on the top right).
  12. Going back to Firefox (restart it), the "Zotero" button should be on the bottom right. See it? Awesome.
  13. In Firefox,  Click on "Tools" > "Add-ons" and in the top right corner "Search for Add-ons." Search for "ZotFile", which will help manage your PDF attachments.
  14. Restart Firefox again.  Click on "Tools" > "Add-ons" and "Extensions." You should see both Zotfile (step 11) and Zotero (step 5) downloaded in your list of extensions.
  15. Still in Firefox, set up your VPN for access through UCSD so you can easily download documents from JSTOR and most academic journals hassle free.
    • On Firefox, open the Tools menu and select Options.
    • Click the Advanced icon.
    • Click the Network tab.
    • Click Settings.
    • Select Automatic proxy configuration URL.
    • In the text field, enter http://webproxy.ucsd.edu/proxy.pl
    • Click OK to close the window. 
    • Click OK again to close the Options window and save your settings.
    • Close and restart Firefox.
    • From now on, every time you use Firefox, the first time you attempt to access a UCSD-restricted website, you will need to enter your UCSD network username and password, and click OK.
  16. In Firefox,  Click on "Tools" > "Add-ons" and in the top right corner "Search for Add-ons." Search for "Lyz", which will help manage your citations online and cite directly from Firefox to your document. 
    • Restart Firefox.
  17. Open LyX (from step 4).  Create a new document! 
    • Start experimenting. Don't fuss around with too much. The major difference between LyX and Microsoft Word is that "What You See Is NOT What You Get"... remember, LyX is not the program that makes your text professional and academic-looking, it's MikTex. So, not until you press "Control" and "D" simultaneously to view your document, MikTex is not running yet. 
    • How to start? LyX makes it easy and also formulaic, it's like an outline.
    • On the top left there should be a box "Standard"
    • Click to change to "Title" (on the bottom, under the heading "Front Matter")
    • Type your Title. C
    • Create a new line
    • Continue down that list (the box on the top left) and go down all the fields under the heading "Front Matter"): Author, Date, Abstract, etc... 
    • When you're done with the Front Matter stuff, then start with "Section" and go down all the fields under the heading "Section") 
    • Press Control D to preview.... your first LaTex document! Congratulations! Ok, now stop it.
  18. Let's now insert our bibliography into our Lyx Document. 
    • Scroll down to the very bottom of that LyX document, where you will enter your bibliography.
    • On the Menu bar, click Insert→Lists & TOC→BibTeX Reference.
    • A gray box will be opened up and click Add → Browse and find your Bibliography folder to insert your "Master.bib" and "Zotero.bib" files one by one.
        On the Style box, choose "apsr".
      1. On Content, select "All cited references" (so even though your document has access to everything in  "Master.bib" and "Zotero.bib" it will only show those you actually cited.
    • Press "Control" "D" so the system updates your bibliographies.
    • Go to menu, Documents > Settings > Bibliography 
      • Under Citation Style, select "NatBib" and Author-year
      • Next to Processor, choose "BibTex"
    • Let's test your bibliographies. 
      • Go to somewhere in your document where you want to insert a citation. 
      • On the Menu bar, click Insert→Citations.

      • All the citations from "Master.bib" and "Zotero.bib" should be there on the left. 
      • Click on any citation. 
      • Press "Add" and it will be added to the right side of the window.
      • If you want to cite multiple works, keep on clicking citations on the left and pressing "Add"
      • On the bottom of the Citations box under "Formatting", you can choose what style to put them in. (For example, if you are inserting a parenthetical citation, choose the parenthetical style. For political science, it's usually (Author Year) with no comma.)
    • Go back to LyX (your word processor),  press "Control D"
      • Scroll down to where you inserted your citation from step 21. Showing up? Check.
      • Scroll down to where you inserted your bibliography from step 18. Are the works you cited in Step 21 showing up on the bottom of your paper? Check. 
    • Now, since   "Master.bib" and "Zotero.bib"  are static and non-changing, you always want to add new stuff and add to your bibliography, right? Recall "LyZ", (step 16) helps you directly cite something online from Firefox to your document, so you need to create a tunnel from LyZ to Firefox. That tunnel is called LyZ, the "LyXServer path." As any good LyZ tunnel-maker will know, you need a portal on both sides -- Zotero on Firefox AND in LyX. 
      • In LyX go to menu, Tools > Preferences > Paths and in the box next to "LyXServer pipe", type “\\.\pipe\lyxpipe” (without quotations) for Windows. Mac users can use “~/.lyxpipe”.
    • Go to Firefox (restart it before you do this) and click the "Zotero" button on the bottom right.  
      • If prompted, insert your log-in information from step 4. All the citations from Master.bib and Zotero.bib should be in there. It may take a while to load. Yes? Great!
      • See image below. Click to enlarge.
        • On the Zotero bottom half of your Firefox screen, on the top, there should be a "LyZ" button. Click  the button and go to "Settings"
          • In the box next to Lyx Server, enter "\\.\pipe\lyxpipe" (no quotes)
          • Check the "Create Cite key" box.
          • Next to City Key, enter "author year" (no quotes). Do not capitalize "Author"
          • Next to Export Format, select "BibTex"
    • Let's test our LyZ tunnel.
      • Go back to Firefox and go to JSTOR.org, you should be prompted to enter your UCSD proxy information.
        • On jstor.org, if you see "Your access to JSTOR provided by your UC campus library..." on the top right, you have set up your VPN on Firefox correctly.
        • Search for any article that interests you. 
        • On your URL bar (where you enter "jstor.org") in your JSTOR results page, you should see a yellow or blue colored document icon on the far right. 

        • See image below. Click to enlarge.
        • Click on it and choose which citations you want to save to your bibliography. Things you click and save on Firefox automatically syncs with your Zotero for Firefox and Zotero Standalone. 
      • Go back to the Zotero bottom half of your Firefox screen (you can always "X" this out and close it and reopen it by click "Zotero" on the bottom right of FIrefox.) On the top right of Zotero in Firefox, Click on the green arrow button. The citations you downloaded from JSTOR should now appear in your Zotero list of citations. 
      • Go back to LyX and choose a place where you want to test and use the new JSTOR citation.
      • Go back to Firefox and on Zotero, right click one of those new JSTOR citations, and select "Cite in Lyx"
        • You will be asked to either create a new database. 
        • Go to the Bibliographies folder where you stored  "Master.bib" and "Zotero.bib" 
        • Type a new database name. Let's name it "LyZ", after our tunnel (*.bib extension is automatically added if you don’t provide it) and press OK. 
        • The citation is added into the BibTeX database you have just created and inserted into the LyX document. 
      • Your citation should appear in the LyX document now.
    • Go back to LyX and Insert the new, (the third .bib file) BibTeX database into LyX document. Still remember how to do this? I don't.
        • Scroll down to the very bottom of that LyX document, where you entered your bibliography.
        • Double click your existing bibliography.
          • A gray box will be opened up and you should see your two previously inserted .bib files, "Master.bib" and "Zotero.bib" 
          • Click Add → Browse and find your Bibliography folder to insert your "Lyz.bib" file.
        1. Press "Control" + "D". This is important
        2. Does the JSTOR citation you inserted from Firefox in step 24 show up in your LyX document? Awesome.
          • Just like how you inserted your other citations in step 21, you can go back and use that JSTOR citation from Lyz.bib again by going to LyX, clicking on the Menu bar, and then Insert→Citations.
          • You can always use the search function under  Insert→Citations since you now have 1000+ citations.
        3. When you have new citations you want online, again: 
          • Like before, go back to Firefox and go to any academic site (list of sites supported by Zotero automatically).
            • You may be prompted to enter your UCSD proxy information.
            • On your URL bar in your results page from an academic site, you should see a yellow or blue colored document icon on the far right. Click on it and choose which citations you want to save to your bibliography. Things you click and save on Firefox automatically syncs with your Zotero for Firefox and Zotero Standalone. 
          • New instructions: Go back to the Zotero bottom half of your Firefox screen.
            • On the top right of Zotero in Firefox, Click on the green arrow button. The citations you downloaded from JSTOR should now appear in your Zotero list of citations. 
            • Your Step 28 citations should now show up along with all the Lyz.bib, Master.bib, and Zotero.bib ones 
            • Before you insert your Step 28 citations, you need to first Click the "LyZ" icon and click "Update BibTex". Remember, you saved your last citations into the new file Lyz.bib. Since you want to use a new citation, you need to add it to the Lyz.bib file first!
            • Now, you can go to your LyX file and scroll to where you want to enter the new citation.
            • Press Control D in LyX.
            • Go back to Firefox and right click your new citation and press "Cite in LyX"
            • Your new citation should now appear in Lyx.

        ċ
        Master 4.bib
        (368k)
        Jeffrey Kwong,
        Jul 5, 2012, 2:08 PM
        ċ
        Zotero.bib
        (676k)
        Jeffrey Kwong,
        Jul 5, 2012, 2:08 PM
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