1 Maurisar

Lyx Bibliography Manager For Mac

Reference management for LaTeX users : a toolbox

Recommended software

JabRef is the reference management software recommended by the Library for people writing papers in LaTeX. It runs on Linux, Mac OS X and Windows and integrates well with LaTeX editors such as Kile, WinEdt, Emacs, etc.

BibDesk is a good alternative for people working under Mac OS X, as it integrates somewhat better in the workflow.

Import references

Attention: automatic import saves time by removing the need to copy-paste references into your reference management software but you still need to review each imported reference to ensure that there were no errors or lost information during the import.

Last update: April 2009. This page is currently under revision.

JabRef

BibDesk

ISI Web of Knowledge

 
  1. Select the records to export
  2. Click on the Save to EndNote button
  3. Save as file
  4. From within JabRef, use the File->Import (ctrl-I) function
  5. Set Files of Type to ISI
  6. Check the imported references, then OK
  1. Select the records to export
  2. Click on the Save to EndNote button
  3. Save as file and open with BibDesk
  4. Check the imported references
  5. Drag and drop the references from the imported file into your database

or

  1. Use the inline search box for ISI from within BibDesk: Searches -> Web of Science SCI
  2. Check for quality, then click the Import button on relevant results

Warning: the inline search box does not query all databases.

EngineeringVillage

 
  1. Select the records to export
  2. Click on the Download button
  3. Select the BibTeX format
  4. Save as file and open with JabRef
  5. Check the imported references
  6. Copy the downloaded records into your database (ctrl-C, ctrl-V)
  1. Select the records to export
  2. Click on the Download button
  3. Select the BibTeX format
  4. Save as file and open with BibDesk
  5. Check the imported references
  6. Drag and drop the references from the imported file into your database

Scopus

 
  1. Select the records to export
  2. Click on the Output button
  3. Select Export format: RIS format
  4. Select Output: Abstract format
  5. Save as file
  6. From within JabRef, use the File->Import (ctrl-I) function
  7. Set Files of Type to RIS
  8. Check the imported references, then OK
  1. Select the records to export
  2. Click on the Output button
  3. Select Export format: RIS format
  4. Select Output: Abstract format
  5. Save as file and open with BibDesk
  6. Check the imported references
  7. Drag and drop the references from the imported file into your database

PubMed (Medline)

 
  1. Select the records to export
  2. Select Display: XML in the drop-down menu
  3. Select File in the rightmost drop-down menu
  4. Save as file
  5. From within JabRef, use the File->Import (ctrl-I) function
  6. Set Files of Type to Medline
  7. Check the imported references, then OK

or

  1. Use the inline search box for Medline from within JabRef: Web Search -> Search Medline (F5).
  2. Select the records to export, check for quality, then OK

Warning: the inline search box does not query all databases.

  1. Select the records to export
  2. Select Display: MEDLINE in the drop-down menu
  3. Select File in the rightmost drop-down menu
  4. Save as file and open with BibDesk
  5. Check the imported references
  6. Drag and drop the references from the imported file into your database

or

  1. Use the inline search box for PubMed/Medline from within BibDesk: Searches -> PubMed
  2. Check for quality, then click the Import button on relevant results

Warning: the inline search box does not query all databases.

Ovid

 
  1. Select the records to export
  2. Select Fields: Complete Reference
  3. Select Result Format: Ovid
  4. Click the Save button
  5. Save as file
  6. From within JabRef, use the File->Import (ctrl-I) function
  7. Set Files of Type to Ovid
  8. Check the imported references, then OK

Not available :-(

Use JabRef to convert the references to BibTeX until a better solution is found.

CSA Illumina

 
  1. Select the records to export
  2. Click Save, Print, Email
  3. Click the Save button
  4. Save as file
  5. From within JabRef, use the File->Import (ctrl-I) function
  6. Set Files of Type to CSA
  7. Check the imported references, then OK

Not available :-(

Use JabRef to convert the references to BibTeX until a better solution is found.

Infoscience

 
  1. Select the records to export
  2. Select Export: BibTeX on the right-hand side
  3. Save as file and open with JabRef
  4. Check the imported references
  5. Copy the downloaded records into your database (ctrl-C, ctrl-V)
  1. Select the records to export
  2. Select Export: BibTeX on the right-hand side
  3. Save as file and open with BibDesk
  4. Check the imported references
  5. Drag and drop the references from the imported file into your database

NEBIS

 
  1. Select the records to export
  2. Click Mail/Save
  3. Select Predefined Format: EndNote, RefMan, ProCite, etc.
  4. Leave the other fields blank
  5. Save as file
  6. From within JabRef, use the File->Import (ctrl-I) function
  7. Set Files of Type to RIS
  8. Check the imported references, then OK

Reference import not available yet :-( Use JabRef to convert the references to BibTeX until a better solution is found.

or

You can set up an inline search box using the Z39.50 protocol. To do this

  1. Choose Searches -> New Search Group...
  2. Select Type: Z39.50
  3. Select Server: Other and fill up the following information

A note on inline search functionnalities

For many databases, you can search directly from within the reference management software (inline search)

Warning: this should not be used for extensive litterature research, since inline search typically does not query all available databases.

Always do your litterature research on the web, and export relevant results in your reference management software. Inline search tools should only be used to retrieve known references.

Cite while you write (CWYW)

Windows: Set up CWYW using WinEdt and JabRef

A button push selection to WinEdt (ctrl-L) is available on the JabRef toolbar (also works with other editors, such as LyX, Kile, Emacs, etc.)

Linux: Set up CWYW using JabRef

In order for this to work, you have to set up a LyX pipe (even if you don't use the LyX editor). On your home directory, create a .lyx folder, and an empty file called lyxpipe in it. Then, configure both JabRef and Kile to use this file as the LyX pipe. In JabRef, go to Options -> Preferences -> External programs and set the Path to LyX pipe field.

When all is set, use the same procedure as under Windows (see above).

Mac OS X: Set up CWYW using JabRef

In JabRef, select the references you want to cite, then choose Edit -> Copy \cite{BibTeX key} (⌘-K). Paste it (⌘-V) in your editor (e.g. TexShop).

Mac OS X: Set up CWYW using BibDesk

In BibDesk, select the references you want to cite, then choose Edit -> Copy (⌘-C). Paste it (⌘-V) in your editor (e.g. TexShop). To specify what should be copied when hitting ⌘-C (\cite string, whole reference etc.), go to BibDesk -> Preferences -> Citation and choose Default format: TeX cite command.

Resources

 

All our best wishes for a successful thesis ! -- The Library team

Categories: Mac, Mac, JabRef, lyxpipe, TeX

<< | Page list | >>

This is a HOWTO for LyX/Mac, a full-featured native implementation of LyX on the Mac OS X.

Download

LyX/Mac is available as a binary for Mac OS X 10.4 and later. (Note additional prerequisites below.) The download page is here.

For users who prefer emacs-like modifier key bindings, there is additional information on customizing these keys, including patched binary versions.

Gatekeeper

"LyX" can't be opened because it is from an unidentified developer.

With Mac OS X Mountain Lion a new feature is active: the Gatekeeper. It's there to help protect your Mac from malware and misbehaving apps downloaded from the Internet. An app that is delivered by an unknown developer � one with no Developer ID � will be blocked. To get a developer ID one has to buy a license from Apple with yearly costs. Because there is no support for open source programs like LyX by Apple the application is not signed. (In case you are GPG user we provide gpg signatures, see Download Checksums & signing section).

Fortunately there is an easy way to start LyX without disabling Gatekeeper:

1. Don't open the application with a double click. Click it while pressing the Control-key instead.

2. Choose Open

3. Another window is opened. There you choose open again. That's it.

More information is available here (the Apple documentation).

Mac

Prerequisite

You need a TeX installation. The easiest option is to use MacTeX. The .dmg file for a complete MacTeX installation is very large (> 1 GB), but it is a very complete distribution and installs right out of the box. MacTeX includes all the components necessary for TeX to work, and includes the bibliography managing program BibDesk.

Users with slower download speeds might want to download BasicTeX, a much smaller distribution, linked from the MacTeX page.

Useful Helper Programs

Previewers

LyX/Mac uses the system default viewers, and should require no configuration for PDF and HTML.

To specify a non-default GUI viewer use or in Preferences -> Outputs -> File formats -> filetype -> Viewer.

Spellcheckers

As of LyX/Mac 2.0, spellchecking support is included by default.

Bibtex tools

Envelopes

To print envelopes, install envelope in /usr/local/bin and make it executable. While you're writing a letter in LyX, do File -> Export -> Custom -> ASCII and give as the command; it will parse the address from the letter and print an envelope, including the USPS barcode.

OmniGraffle converter

OmniGraffle is a great software for creating diagrams under Mac OS X (in particular, it works very well with LaTeXiT so that you can easily insert math formulae into diagrams). As it doesn't have a command line mode, you can use an AppleScript in order to insert ".graffle" files directly into LyX.

  • Put og-export.scpt somewhere on your disk (e.g. in ).
  • In order to use it, go to LyX preferences, add an OmniGraffle file format (just type for the editor), and then add converters:
    • converter:
    • converter:
    • converter:
  • Note that currently, LyX doesn't work with OmniGraffle packages (e.g. diagrams including images). This problem will hopefully be solved in the future (see this bug for details).

On screen quality of included PDF files

When you include a PDF graphic in a LyX file, it will appear crisp in the typeset PDF file of your document, but the version you see in the LyX window can be quite ugly. Lyx converts PDFs to PNG to show them in this window, and the default conversion method can choose quite a low definition for these bitmaps. A quicker and better solution would be to include a converter that uses the program that comes with OSX (it is a command line tool that you can use in the Terminal for converting a graphic file between different formats). To create this converter, you should open the Preference menu item in the LyX menu, and go to the File handling tab, then the Converters item. Here we will use the item as a template. When you choose this item, the bottom boxes are filled and you can read a command that starts with in the converter box. We will first change the item on the right to (you should have this possibility in the combo that opens when you click on EPS), and change the converter command as consequence, by replacing the complete command by:

You can also increase the value if the generated bitmaps look too small on your screen (please first check that Lyx shows them at 100% of their size). When you finish setting these parameter, click button next to the top converters list (if not, you will loose the new converter), then click . If you open a new file containing PDF graphics, they should be much better looking and crispier now. If you want to change these values later, you should come to the same screen, select this converter, change the parameters in the converter box, and click before leaving this screen.

Beyond basics

PdfSync and SyncTeX -- Forward Search and Reverse Search

LyX allows, using a suitable viewer such as Skim.app, to navigate quickly between a particular place in a LyX document to the corresponding place in the rendered PDF document (forward search) and from a particular place in the PDF back to the corresponding place in the LyX document (reverse or inverse search). However, some set-up is needed before this functionality is available.

  • Please note that there are more up-to-date instructions using SyncTeX on this wiki at http://wiki.lyx.org/LyX/SyncTeX where the free OS X PDF viewer Skim.app is used. (Skim is highly recommended for this use.)
  • Please note also that there are new instructions about reverse search in Additional Features Manual.

PdfSync is similar to reverse DVI search but is for the (now more common) method of directly producing pdf files. If you use the program Skim as your previewer you can COMAND-SHIFT-click in the previewed pdf file which causes the cursor to move to that point in LyX.

  • In LyX > Preferences > File Handling > File formats > PDF (pdflatex), in the Viewer setting select "Custom" and then enter in the viewer setting. Then click Save.
  • In Skim > Preferences > Sync select LyX.
  • Include in the preamble of your LyX files.
    Troubleshooting PdfSync
    Make sure that the .lyxpipe.in and .lyxpipe.out files do not exist when LyX is not running. (They are normally deleted when LyX quits, but if LyX crashes, they remain and prevent LyX from communicating with PDFView.) Their location can be found in LyX > Preferences > Paths.

Version Control

  • Please note that there are new instructions about version control in Additional Features Manual.

Version control is useful for managing large documents, or documents with multiple authors. In order to implement it, you need to have RCS (Revision Control System) installed. This is a standard part of Xcode. The simplest way to get version control working, is to install the Xcode Tools package contained on the OS X install DVD. See the Mac Version Control page for more information.

Interaction with X11.

Xfig or X-windows previewers like xdvi or gv can be used with LyX/Mac if you modify your file. For details, see the environment.plist page. Alternatively, you can change the viewer for postscript or dvi with or . Note that X11 must be running first for either of these to work.

DVI viewers

By default, LyX will generate PDF files. If for some reason you prefer to create and view DVI files, some set-up hints are provided on the Mac-DVI page.

Pipes

Name in Path Problem (JabRef)

Programs such as JabRef communicate with LyX via pipes, which are sometimes named incorrectly by default (e.g., they assume that the pipe is in a directory that has a space in its name, such as , but other programs often cannot deal with spaces in paths). You may need to fix the lyxpipe path in both LyX and JabRef in Mac OS X.

To fix the LyX pipe in JabRef, open JabRef and go to and in "Path to LyX pipe" enter . Close JabRef.

Then open LyX, go to , and in "LyXServer pipe" enter . Reconfigure. Close LyX.

The next time you run LyX and JabRef, you should be able to push citations directly from your BibTeX bibliography in JabRef into LyX. If anything goes wrong, JabRef will return an error message, and you will have to redefine the pipe. You might try the following: (1) change the LyXServer path in LyX -> Preferences -> Paths back to ; (2) recreate the directory by entering in a terminal session, ""; and (3) restart LyX.

Known issues

  1. Due to limitations in the Qt/Mac library, interface languages other than English modify the organization of the toolbar menus and it may not be possible to directly enter some special characters into the document preamble (you can copy them to the preamble).

Please report any other bugs to the appropriate LyX mailing list. A web gateway is also available.

The information on this page is believed to be accurate, has been used successfully on many systems and sites, and has benefited from the comments and suggestions of many users. Due to the variations in individual systems, this information and the various files and code available on this page are conveyed as is with no warranty of any kind.

More information

This group contains the following pages:

Categories

MacJabReflyxpipeTeX

Leave a Comment

(0 Comments)

Your email address will not be published. Required fields are marked *