Setting up webdav server for sysbio

# Ordinary users should NOT read what follows.
# See also http://www.howtoforge.com/how-to-set-up-webdav-with-apache2-on-ubuntu-9.04
mkdir /home/www/secure/webdav-sysbio
touch /home/www/secure/webdav-sysbio/index.html
# Add the following to apache sites conf:
        <Directory /home/www/secure/webdav-sysbio/>
        Options Indexes MultiViews
        AllowOverride None
        Order allow,deny
        allow from all
        </Directory>
        Alias /webdav-sysbio /home/www/secure/webdav-sysbio/
        <Location /webdav-sysbio>
        DAV On
        AuthType Basic
        AuthName "zotero-sysbio"
        AuthUserFile  /etc/apache2/webdav-sysbio-passwd.dav
        Require valid-user
        </Location>
# Generate password file:
htpasswd -c webdav-sysbio-passwd.dav zotero-sysbio
chown root:www-data webdav-sysbio-passwd.dav 
chmod 640 webdav-sysbio-passwd.dav
# Restart apache service

Setting up Zotero client

 Installing Zotero

If you are new to Zotero, go to http://www.zotero.org/download/ and click Zotero for Firefox link. Follow the installation instructions, and finally, restart Firefox.

Zotero GOTCHAS

When you get SSL certification error messages, you have to copy .mozilla/firefox/*.default/cert_override.txt file to .zotero/zotero/*.default/ directory.

Setting up Zotero for Sysbio

Press Ctrl-Alt-Z to open Zotero frame. Click Action, select Preferences and go to Sync tab where use the following credentials to configure the Zotero client.

Zotero sync server
  Username: iocbio
  Password: <ask around, Marko and Pearu would know>
File syncing
  Select WebDAV
  URL: https://sysbio.ioc.ee/webdav-sysbio/
  Username: zotero-sysbio
  Password: <same as above>

To merge your Zotero database (in case you have one) to Sysbio Zotero database, you have to collect all your references under the <your name> folder. Then update local database with Sysbio database by clicking Sync button. In the first time it may take several minutes to download Sysbio references and PDF files. Note that more than 1.8GB will be used for PDF files. To finalize the merge, move the <your name> folder to /home folder in Zotero.

 Zotero for LaTeX/BibTeX users

While Zotero provides interfaces to Word and OpenOffice applications, see http://www.zotero.org/support/word_processor_plugin_installation, then the BibTeX support is not so great. We have created a software, zotero2bibtex, that creates bibtex file from local Zotero database. In addition, it normalizes journal and publisher names.

Installation of zotero2bibtex

cd svn/sysbio/software/zotero2bibtex
svn update
sudo ln -s `pwd`/zotero2bibtex.py /usr/local/bin/zoter2bibtex

To enable RefTeX in Emacs, add the following lines to ~/.emacs file:

(autoload 'reftex-mode               "reftex" "RefTeX Minor Mode" t)
(autoload 'turn-on-reftex            "reftex" "RefTeX Minor Mode" nil)
(autoload 'reftex-add-to-label-alist "reftex" "RefTeX Minor Mode" nil)
(add-hook 'LaTeX-mode-hook 'turn-on-reftex)

Usage of zoterO2bibtex

Go to the directory of your latex document and run

zotero2bibtex

This will create zotero-iocbio.bib file to the current working directory. In latex, use

\bibliographystyle{plain}
\bibliography{zotero-iocbio}

To update zotero-iocbio.bib with recent changes from Zotero client, rerun the zotero2bibtex program.

zotero2bibtex is being developed continuously. In addition to get latest bug fixes and new features, zotero2bibtex needs to be occasionally updated with new journal information and unicode-latex connection support. So, before running  zotero2bibtex, it is recommended to update zotero2bibtex from svn. In case of svn update conflict, choose "mine conflict" by default unless you know about the conflict.

Advanced usage of zotero2bibtex

Every time you run zotero2bibtex, it will retrieve reference information from the local Zotero database.

When new articles have been added, there is a change that our journal database does not have the corresponding journals. To update the journal database, open svn/sysbio/software/zotero2bibtex/data/ltja_iocbio.txt file and follow the instructions in the file header. In short, you have to check whether out journal database contains the journal, but the journal name is misspelled, for example. If this is the case, then insert the ISSN number to the beginning of the corresponding line and rerun zotero2bibtex. If not, then fill in the missing parts in the line (but don't touch the last field, see the file header for more information).

Similarly, when new books are added to Zotero database, then you might need to update publishers database, located in svn/sysbio/software/zotero2bibtex/data/ltpa_iocbio.txt.

If you have updated the local iocbio databases then commit your changes to svn repository.

While running zotero2bibtex, it may show some error messages about missing keys, for example. These errors should be fixed in Zotero client and then rerun zotero2bibtex.