BibTex is a program that reads entries from a database of citationsbased on the output of LATEX andthen makes a bibliography file thatLATEX can insert into thedocument. There is lots to say about BibTex (and some good manuals that doit well) but here are some essentials I have found useful and not coveredin the books. (There is a lot to say and learn about LATEX too).
Download FileZilla Client for Mac OS X. The latest stable version of FileZilla Client is 3.51.0. Please select the file appropriate for your platform below. Using the built-in SSH client in Mac OS X. Mac OS X includes a command-line SSH client as part of the operating system. To use it, goto Finder, and selext Go - Utilities from the top menu. Then look for Terminal. Terminal can be used to get a local terminal window, and also supports SSH connections to remote servers. For client versions up to 8.2.1175.0 (8.2 Patch 3) or all installations on OSX 10.4 and 10.5: Download the corresponding BES Client package file to the Mac computer. Open the disk image by double clicking the DMG file (eg: BESAgent-8.2.1310.0-BigFixMacOSX.dmg) to mount it. Run the BESAgent Installer Builder.
Finding the material for a BibTex database is a chapter of itsown, covered at least briefly at http://www.sci.utah.edu/~macleod/litbase
There is a repository ofbibtex files available for use at the SCI Institute.
Quick Links:
There are a suggestions when using BibTex:
- The standard way to show citations in the text is as ``[N]' where N is the reference number in the bibliography. We often use a style and a package called as usepackage[super]{cite} in the LaTeX file that writes them as superscripted numbers. This style is also smart enough to find sequences of numbers and compress them, e.g., text1,2,3,4,5,9 becomes text1-5,9.
- Enter refs as you go and do not leave them all to the last minute! This makes for unnecessary stress when we need it least. Give us your refs in whatever form you have and we can get them entered now.
- If you are part of SCI (or otherwise smart and organized), please note the key naming conventions we use. You can find these in the SCI Bibtex tips web page.
The default location for the Bibtex files for a document are in the samedirectory as that document. A slightly better solution is to have adirectory that holds all your Bibtex files and then hard-wire the commandsin LateX to find those files.
A better way (the best way?) is to store all your Bibtex files in oneplace in your computer, ideally managed through a system like Subversion,and then to tell the Bibtex program where to look. How this works dependson the operating system and the Bibtex application, of course, but here aresome typical examples. I found a lot of this information at this web site by Julien Dutant .
- Unix, in all its flavors.
This is the simplest but not the most common, sadly. The solution requires, of course, on an Environmental variable, which users typically set in a start script like .bashrc (for the Bash shell). This bit of code also sets the TEXINPUTS environment variable, which is also helpful when one has some style files that are stored in a common directory and need to be available to all LaTeX files. ${HOME} is a built in variable that is set to be a user's home directory so this bit of code sets my LaTeX directory to ~macleod/tex/latex and my Bibtex directory to ~macleod/litbase/bibtex. - TexShop on the Mac (OSX)
TexShop is based on TexLive and TeXLive requires a pre-set location, i.e., you cannot adjust this location and must store all .bib files in this place. The files go in
or subfolders of this directory.Of course, this directory is not directly visible in the modern versions of Mac OSX and the Finder, thus protecting users from all this tedious detail? To access the ~/Library directory, either use a terminal or use the 'Go' command in the Finder but hold down the the option key to see this directory in the list. Here is what the result should look like:
Once visible, you can maneuver to the texmf/ directory and then add the necessary bibtex/bib directories and store bibtex files there.
I like to keep things in the same (visible) place for all programs that use bibtex so I have created a link between this standard location and the place TexShop wants to see things. This is a Terminal command so use with the usual care: You should then see something like the following (again from a terminal window): A above, this assumes my bibtex files are all in my directory.
- WinEdt
In the control menu: Menu > Options > Executions Modes..
A window opens with several tabs. In the 'Console Applications' tab, you find a list of commands. Select bibtex, and add to the 'Switches' field:
NIH requires public disclosure of journal articles supported by NIHfunding and all such articles receive a code called the PMCID as part ofthe PubMed system. As an NIH funded researcher, you MUST include this codeevery time you cite such a reference, especially in progress reports,proposals, and biosketches.
To support this code in BibTeX, I have created a slightly modifiedversion of one of the most common BibTeX style files (.bst), which isavailable here.
To use this new style file,
- Add a field called 'pmcid' to each BibTeX reference that contains the PMCID string, which you can locate by searching for the papers in the PubMed system.
- Modify your bibiographystyle command to look (something) like this:
To edit a BibTex file, you can use any editor but emacs has lots ofgreat support for this process. The ones I like are Nelson Beebe's emacstools found at www.math.utah.edu/pub/emacs/, in particular bibtoolsand bibtex-support.
Here is what my .emacs contains to access these:
Note that these commands assume a subdirectory called emacs/lispin which the require lisp code (.el or .elc files) isavailable.
There are some other fun software tools that can make life easier withBibTex. Most are in the public domain in one form or another and I haveincluded links where I had them--if the links fail, use Google and pleaselet me know (macleod@sci.utah.edu).
5.1 EndNote
EndNote is notreally a program that works on BibTexfiles but it does manage citationswell and it has some support for BibTex that can make it useful.
See endnote.html for moredetails on how to convert between Endnote and BibTex.
5.2 bibclean
The goal of bibclean is to clean up syntax and layout errors in BibTexfiles so that all entries have a nice, clean look that is consistent. Theprogram will also reveal some errors in the file, which can be veryhelpful! To get bibclean, surf on over to
www.math.utah.edu/pub/bibclean/and thank Nelson Beebe for making this available.
Here are some direct links that might be helpful
- Initialization file for bibclean, keep this somewhere that bibclean can find it.
One of the many arguments to bibclean essential for SCI databases, ifonly because it is the convention we had adopted:which I actually alias to bibclean so that I don't forget!
5.3 Mendeley
The free literature databased program Meddeley has support for Bibtex output.
5.4 Converting from Word bibliography to BibTex
This is truly amazing! There is a website called hubmed.orgthat will convert from Word document text that you copy to the web pageinto Bibtex files! It actually works.
This program is some sort of search engine interface to Pubmed and itmanages to parse the text and propose matches for each entry in thebibliography. I am really impressed with this tool!
5.5 Testing a BibTex file
There is a simple way to test a BibTex file for completeness usingLATEX and the bibtex commands fromyour own computer. Testing is a good plan, especially if you do it afterediting the file and not when you are in a hurry and have to build adocument using the file.
To test a BibTex file, make a LaTeX file, call it testbib.texwith the following contents:where ``sci' is the name of the BibTex file to test.
Then runand the output will list all the errors or warnings resulting from tryingto parse the file sci.bib. Some of the output will be warningsthat you can ignore but other errors can be fatal the next time you use thefile.
5.5 BibDesk
BibDesk is a Mac OSX program to edit and manage your bibliography. It willkeep track of both the bibliographic information and the associated filesor web links for you. Read more atbibdesk.sourceforge.net/.
5.6 JabRef
JabRef is a new cross platform,open source program to edit and manage your bibliography. It performssearches and downloads articles (assuming they are open access) and seemsto have a lot of customlization options. It claims to integrate well withmany LaTeX systems/editors, including eXstudio, LyX, Kile, LatexEditor,Emacs, Vim, and WinEdt.
NOTE:
Between mid October 2019 and mid February 2020 everyone in the Army was migrated to use their PIV Authentication certificate for Email access. You no longer use the Email certificate for Enterprise Email or any CAC enabled websites
Mac users who choose to upgrade (or already have upgraded) to Mac OS Catalina (10.15.x) will need to uninstall all 3rd Party CAC enablers per https://militarycac.com/macuninstall.htm AND reenable the built in smart card ability (very bottom of macuninstall link above)
If you purchased your Mac with OS Catalina (10.15.x) already installed, you can skip the uninstall part above and follow the instructions below.
6 'high level' steps needed, follow down the page to make this a painless systematic process
| 1. | Is your CAC reader 'Mac friendly'? |
| 2. | Can your Mac 'see' the reader? |
| 3. | Verify which version of Mac OS you have |
| 4. | Figure out which CAC (ID card) you have |
| 5. | Install the DoD certificates |
| 5a. | Additional DoD certificate installation instructions for Firefox users |
| 6. | Decide which CAC enabler you want to use (except for 10.12-.15 & 11) |
Step 1: Is your CAC reader Mac friendly?
Visit the USB Readers page to verify the CAC reader you have is Mac friendly.
Visit the USB-C Readers page to verify the CAC reader you have is Mac friendly.
'Some, not all' CAC readers may need to have a driver installed to make it work.
NOTE: Readers such as: SCR-331 & SCR-3500A may need a firmware update (NO OTHER Readers need firmware updates).
Information about these specific readers are in Step 2
Step 2: Can your Mac 'see' the reader?
Plug the CAC reader into an open USB port before proceeding, give it a few moments to install
Step 2a: Click the Apple Icon in the upper left corner of the desktop, select 'About This Mac'
Step 2b: Click 'System Report..' (button)
Step 2c: Verify the CAC reader shows in Hardware, USB, under USB Device Tree. Different readers will show differently, most readers have no problem in this step. See Step 2c1 for specific reader issues.
Step 2c1: Verify firmware version on your SCR-331 or GSR-202, 202V, 203 CAC, or SCR-3500a reader. If you have a reader other than these 5, Proceed directly to step 3
Pdf to excel 3.1 serial key. Step 2c1a-SCR-331 reader
If your reader does not look like this, go to the next step.
In the 'Hardware' drop down, click 'USB.' On the right side of the screen under 'USB Device Tree' the window will display all hardware plugged into the USB ports on your Mac. Look for “SCRx31 USB Smart Card Reader.” If the Smart Card reader is present, look at 'Version' in the lower right corner of this box: If you have a number below 5.25, you need to update your firmware to 5.25. If you are already at 5.25, your reader is installed on your system, and no further hardware changes are required. You can now Quit System Profiler and continue to Step 3.
Step 2c1b-SCR-3500A reader
If you have the SCR3500A P/N:905430-1 CAC reader,you may need to install this driver, as the one that installs automatically will not work on most Macs. Hold the control key [on your keyboard] when clicking the .pkg file [with your mouse], select [the word] Open
Step 3: Verify which version of MacOS do you have?
(You need to know this information for step 6)
Step 3a: Click the Apple Icon in the upper left corner of your desktop and select 'About This Mac'
Step 3b: Look below Mac OS X for: Example: Version 10.X.X.
Step 4: Figure out which CAC (ID Card) you have
(You need to know this information for step 6)
Look at the top back of your ID card for these card types. If you have any version other than the six shown below, you need to visit an ID card office and have it replaced. All CACs [other than these six] were supposed to be replaced prior to 1 October 2012.
Find out how to flip card over video
Step 5: Install the DoD certificates (for Safari and Chrome Users)
Go to Keychain Access
Click: Go (top of screen), Utilities, double click Keychain Access.app
(You can also type: keychain access using Spotlight (this is my preferred method))
Select login (under Keychains),and All Items (under Category).
Download the 5 files via links below (you may need to <ctrl> click, select Download Linked File As.. on each link) Save to your downloads folder
Please know.. IF You have any DoD certificates already located in your keychain access, you will need to delete them prior to running the AllCerts.p7b file below.
https://militarycac.com/maccerts/AllCerts.p7b,
https://militarycac.com/maccerts/RootCert2.cer,
https://militarycac.com/maccerts/RootCert3.cer,
https://militarycac.com/maccerts/RootCert4.cer, and
Double click each of the files to install certificates into the login section of keychain
Select the Kind column, verify the arrow is pointing up, scroll down to certificate, look for all of the following certificates:
DOD EMAIL CA-33 through DOD EMAIL CA-34,
DOD EMAIL CA-39 through DOD EMAIL CA-44,
DOD EMAIL CA-49 through DOD EMAIL CA-52,
DOD EMAIL CA-59,
DOD ID CA-33 through DOD ID CA-34,
DOD ID CA-39 through DOD ID CA-44,
DOD ID CA-49 through DOD ID CA-52,
DOD ID CA-59
DOD ID SW CA-35 through DOD ID SW CA-38,
DOD ID SW CA-45 through DOD ID SW CA-48,
DoD Root CA 2 through DoD Root CA 5,
DOD SW CA-53 through DOD SW CA-58, and
DOD SW CA-60 through DOD SW CA-61
NOTE: If you are missing any of the above certificates, you have 2 choices,
1. Delete all of them, and re-run the 5 files above, or
2. Download the allcerts.zip file and install each of the certificates you are missing individually.
Errors:
Error 100001 Solution
Error 100013 Solution
You may notice some of the certificates will have a red circle with a white X . This means your computer does not trust those certificates
You need to manually trust the DoD Root CA 2, 3, 4, & 5 certificates
Double click each of the DoD Root CA certificates, select the triangle next to Trust, in the When using this certificate: select Always Trust, repeat until all 4 do not have the red circle with a white X.
You may be prompted to enter computer password when you close the window
Once you select Always Trust, your icon will have a light blue circle with a white + on it.
The 'bad certs' that have caused problems for Windows users may show up in the keychain access section on some Macs. These need to be deleted / moved to trash.
The DoD Root CA 2 & 3 you are removing has a light blue frame, leave the yellow frame version. The icons may or may not have a red circle with the white x
| or | DoD Interoperability Root CA 1 or CA 2 | certificate | |
| DoD Root CA 2 or 3 (light blue frame ONLY) | certificate | ||
| or | Federal Bridge CA 2016 or 2013 | certificate | |
| or | Federal Common Policy CA | certificate | |
| or | or | SHA-1 Federal Root CA G2 | certificate |
| or | US DoD CCEB Interoperability Root CA 1 | certificate |
If you have tried accessing CAC enabled sites prior to following these instructions, please go through this page before proceeding
Clearing the keychain (opens a new page)
Please come back to this page to continue installation instructions.
Step 5a: DoD certificate installation instructions for Firefox users
NOTE: Firefox will not work on Catalina (10.15.x), or last 4 versions of Mac OS if using the native Apple smartcard ability
Download AllCerts.zip, [remember where you save it].
double click the allcerts.zip file (it'll automatically extract into a new folder)
Option 1 to install the certificates (semi automated):
From inside the AllCerts extracted folder, select all of the certificates
<control> click (or Right click) the selected certificates, select Open With, Other..
In the Enable (selection box), change to All Applications
Select Firefox, then Open
You will see several dozen browser tabs open up, let it open as many as it wants.
You will eventually start seeing either of the 2 messages shown next
If the certificate is not already in Firefox, a window will pop up stating 'You have been asked to trust a new Certificate Authority (CA).'
Check all three boxes to allow the certificate to: identify websites, identify email users, and identify software developers
or
'Alert This certificate is already installed as a certificate authority.' Click OK
Once you've added all of the certificates..
• Click Firefox (word) (upper left of your screen)
• Preferences
• Advanced (tab)
• Press Network under the Advanced Tab
• In the Cached Web Content section, click Clear Now (button).
• Quit Firefox and restart it
Option 2 to install the certificates (very tedious manual):
Click Firefox (word) (upper left of your screen)
Preferences
Advanced (tab on left side of screen)
Certificates (tab)
View Certificates (button)
Authorities (tab)
Import (button)
Browse to the DoD certificates (AllCerts) extracted folder you downloaded and extracted above.
Note: You have to do this step for every single certificate
Best Bibtex Client For Mac Versions
Note2: If the certificate is already in Firefox, a window will pop up stating: 'Alert This certificate is already installed as a certificate authority (CA).' Click OK
Note3: If the certificate is not already in Firefox, a window will pop up stating 'You have been asked to trust a new Certificate Authority (CA).'
Check all three boxes to allow the certificate to: identify websites, identify email users, and identify software developers
Once you've added all of the certificates..
• Click Firefox (word) (upper left of your screen)
• Preferences
• Advanced (tab)
• Press Network under the Advanced Tab
• In the Cached Web Content section, click Clear Now (button).
• Quit Firefox and restart it
Bibtex Convert
Step 6: Decide which CAC enabler you can / want to use
Only for Mac El Capitan (10.11.x or older)
After installing the CAC enabler, restart the computer and go to a CAC enabled website
NOTE: Mac OS Sierra (10.12.x), High Sierra (10.13.x), Mojave (10.14.x) or Catalina (10.15.x) computers no longer need a CAC Enabler.
Try to access the CAC enabled site you need to access now
Mac support provided by: Michael Danberry