## Monday, November 15, 2010

### Ubuntu and LaTeX Update: Ubuntu Releases and Bibliography Management (Mendeley Desktop and BibTeX)

Ubuntu Update:

So it has been a few months since switching to Ubuntu from Windows...and I haven't looked back. It is working out great and I love it. However, it is not perfect and I still need windows to do a few things, like my timesheet program and play some old games. This is easily done by either dual boot (install Windows first, then Ubuntu) or using a virtual machine installation software like WINE or Virtual Box. I don't really like WINE because it only displays or uses an XP version of Windows, and I didn't really find it useful or user friendly.

Ubuntu Releases:

Ubuntu releases new versions every six months. The latest went from 10.04 LTS to 10.11. The LTS versions are Long Term Support versions while others are not. For the best quality and less hassle in making sure everything works fine, I believe the developers recommend sticking to the LTS versions for stability.

The Ubuntu developers name their releases in a alliterated fashion, usually after animals.

https://wiki.ubuntu.com/Home

Releases

This is THE definitive place for members of the Ubuntu community to discuss ideas and store team-related information.

Released (Current & Stable)

Dapper Drake

6.06 LTS

June 1, 2006

Supported until June 2011 (Server)

Hardy Heron

8.04 LTS

April 24, 2008

Supported until April 2011 (Desktop) or April 2013 (Server)

Karmic Koala

9.10

October 29, 2009

Supported until April 2011

Lucid Lynx

10.04 LTS

April 29, 2010

Supported until April 2013 (Desktop) or Supported until April 2015 (Server)

Maverick Meerkat

10.10

October 10, 2010

Supported until April 2012

To be Released

Version

Release Schedule

Support Date

Natty Narwhal

11.04

April 2011

Supported until October 2012

Some like the often releases (like me, I get bored quickly sometimes) while others don't because they think it is too hasty and buggy. It's like I said before it's mostly up to personal preference.

LaTeX Update:

Well on to LateX. Haven't looked back on this either. Love, love, love LaTeX. At first it might seem a little antiquated and/or intimidating, but this is a superior alternative to Word, OpenOffice, or any other word/document processor. I love the freedom, independence, and best of all it's free as in beer and . It is not totally unorganized, in which I mean LaTeX was written to automatically take care of many formatting issues I constantly run into with Microsoft's Word. Writing papers and theses are a breeze, and LaTeX probably is best for longer documents like these. Formulas, sections, fonts, figures, are easy and wonderful once you get the hang of it. I don't have to worry about Word crashing, or EndNote not working, or MathType giving me problems.

Now Latex is not perfect, and it is a learning curve, but I recommend it to anyone who writes scientifically. No more worrying about Word moving figures or whatever it does on its own. You have full control.

Bibliography Management: A Little on Mendeley Desktop and BibTeX

Now bibliographies, as I understand it today, are worked by BibTeX. I just learned something that I would like to quickly pass along. I use Mendeley Desktop to store my reference library information. There are others like Zotero, etc., and I chose MD because I like the way it looks and how it operates to store information. It is personal preference. My advice is to briefly try and look at many as you can then choose ONE and STICK with it. MD is not perfect either, but has a good community and is active in developing its software for updates. Other reference library software include JabRef and KBibTex for LaTeX/BibTeX users. I will try to review the software at a later time in more depth.

More on BibTeX here:

http://www.bibtex.org/

http://en.wikipedia.org/wiki/BibTeX

Now MD has a export feature to export your reference in a BibTeX format. Beware that MD is far from perfect in this, and you will need to manually do some tweaking. For example, MD has a field or category called institution so that you can, as I do it, store the authors' affiliation information. MD exports this as institution or organization which refers to the publisher so you will have to manually change it to the appropriate BibTeX field of affiliation. Also, for conference locations MD exports city as address (publisher) when it should be the field location. So this isn't so bad to do every time you export one reference, but is quite overwhelming when you already have hundreds of exports and have to manually correct them like me, :(, :). Just be consistent with your Bibtex and MD listings and maybe MD with one day be more consistent with BibTeX. For example, I prefer in MD to have the authors' full name if possible, but in BibTeX the generated bibliography doesn't look good with full names plus I don't have all the full names so I prefer to use just initials for first and middle names.

Also, I would make two all reference listings in BibTeX. One for where the titles of papers are capitalized and one where they are not because journals require different preferences (whether caps or not). This will save you lots of time genereating the bibliography for certain papers. I would also make a separate BibTeX file for each paper, thesis, report you write so you only have the necessary references to look at and not your complete list.

BibTeX Links for Fields and Referencing

Here are some links to BibTeX fields and reference labels:

From:  http://en.wikipedia.org/wiki/BibTeX

BibTeX uses a style-independent text-based file format for lists of bibliography items, such as articles, books, and theses. BibTeX bibliography file names usually end in .bib.
Bibliography entries each contain some subset of standard data entries:

• address: Publisher's address (usually just the city, but can be the full address for lesser-known publishers)
• annote: An annotation for annotated bibliography styles (not typical)
• author: The name(s) of the author(s) (in the case of more than one author, separated by and)
• booktitle: The title of the book, if only part of it is being cited
• chapter: The chapter number
• crossref: The key of the cross-referenced entry
• edition: The edition of a book, long form (such as "first" or "second")
• editor: The name(s) of the editor(s)
• eprint: A specification of an electronic publication, often a preprint or a technical report
• howpublished: How it was published, if the publishing method is nonstandard
• institution: The institution that was involved in the publishing, but not necessarily the publisher
• journal: The journal or magazine the work was published in
• key: A hidden field used for specifying or overriding the alphabetical order of entries (when the "author" and "editor" fields are missing). Note that this is very different from the key (mentioned just after this list) that is used to cite or cross-reference the entry.
• month: The month of publication (or, if unpublished, the month of creation)
• note: Miscellaneous extra information
• number: The "(issue) number" of a journal, magazine, or tech-report, if applicable. (Most publications have a "volume", but no "number" field.)
• organization: The conference sponsor
• pages: Page numbers, separated either by commas or double-hyphens.
• publisher: The publisher's name
• school: The school where the thesis was written
• series: The series of books the book was published in (e.g. "The Hardy Boys" or "Lecture Notes in Computer Science")
• title: The title of the work
• type: The type of tech-report, for example, "Research Note"
• url: The WWW address
• volume: The volume of a journal or multi-volume book
• year: The year of publication (or, if unpublished, the year of creation)
In addition, each entry contains a key that is used to cite or cross-reference the entry. This key is the first item in a BibTeX entry, and is not part of any field.

### Entry Types

Bibliography entries included in a .bib file are split by types. The following types are understood by virtually all BibTeX styles:
article
An article from a journal or magazine. Required fields: author, title, journal, year Optional fields: volume, number, pages, month, note, key
book
A book with an explicit publisher. Required fields: author/editor, title, publisher, year Optional fields: volume, series, address, edition, month, note, key
booklet
A work that is printed and bound, but without a named publisher or sponsoring institution. Required fields: title Optional fields: author, howpublished, address, month, year, note, key
conference
The same as inproceedings, included for Scribe compatibility. Required fields: author, title, booktitle, year Optional fields: editor, pages, organization, publisher, address, month, note, key
inbook
A part of a book, usually untitled. May be a chapter (or section or whatever) and/or a range of pages. Required fields: author/editor, title, chapter/pages, publisher, year Optional fields: volume, series, address, edition, month, note, key
incollection
A part of a book having its own title. Required fields: author, title, booktitle, year Optional fields: editor, pages, organization, publisher, address, month, note, key
inproceedings
An article in a conference proceedings. Required fields: author, title, booktitle, year Optional fields: editor, series, pages, organization, publisher, address, month, note, key
manual
Technical documentation. Required fields: title Optional fields: author, organization, address, edition, month, year, note, key
mastersthesis
Master's thesis. Required fields: author, title, school, year Optional fields: address, month, note, key
misc
For use when nothing else fits. Required fields: none Optional fields: author, title, howpublished, month, year, note, key
phdthesis
A Ph.D. thesis. Required fields: author, title, school, year Optional fields: address, month, note, key
proceedings
The proceedings of a conference. Required fields: title, year Optional fields: editor, publisher, organization, address, month, note, key
techreport
A report published by a school or other institution, usually numbered within a series. Required fields: author, title, institution, year Optional fields: type, number, address, month, note, key
unpublished
A document having an author and title, but not formally published. Required fields: author, title, note Optional fields: month, year, key

From: http://texblog.wordpress.com/2007/08/09/how-to-use-a-bibtex-file/

BibTeX offers a whole list of entry fields, entry types and different bibliography styles.

Entry fields (standard):
• address: Publisher’s address (usually just the city, but can be the full address for lesser-known publishers)
• annote: An annotation for annotated bibliography styles (not typical)
• author: The name(s) of the author(s) (in the case of more than one author, separated by and)
• booktitle: The title of the book, if only part of it is being cited
• chapter: The chapter number
• crossref: The key of the cross-referenced entry
• edition: The edition of a book, long form (such as “first” or “second”)
• editor: The name(s) of the editor(s)
• eprint: A specification of an electronic publication, often a preprint or a technical report
• howpublished: How it was published, if the publishing method is nonstandard
• institution: The institution that was involved in the publishing, but not necessarily the publisher
• journal: The journal or magazine the work was published in
• key: A hidden field used for specifying or overriding the alphabetical order of entries (when the “author” and “editor” fields are missing). Note that this is very different from the key (mentioned just after this list) that is used to cite or cross-reference the entry.
• month: The month of publication (or, if unpublished, the month of creation)
• note: Miscellaneous extra information
• number: The “number” of a journal, magazine, or tech-report, if applicable. (Most publications have a “volume”, but no “number” field.)
• organization: The conference sponsor
• pages: Page numbers, separated either by commas or double-hyphens
• publisher: The publisher’s name
• school: The school where the thesis was written
• series: The series of books the book was published in (e.g. “The Hardy Boys”)
• title: The title of the work
• type: The type of tech-report, for example, “Research Note”
• url: The WWW address
• volume: The volume of a journal or multi-volume book
• year: The year of publication (or, if unpublished, the year of creation)
Entry fields (non-standard):
• affiliation: The authors affiliation.
• abstract: An abstract of the work.
• ISBN: The International Standard Book Number.
• ISSN: The International Standard Serial Number. Used to identify a journal.
• keywords: Key words used for searching or possibly for annotation.
• language: The language the document is in.
• location: A location associated with the entry, such as the city in which a conference took place.
• LCCN: The Library of Congress Call Number.
• mrnumber: The Mathematical Reviews number.
In addition, each entry contains a key that is used to cite or cross-reference the entry. This key is the first item in a BibTeX entry, and is not part of any field.
Entry types:
• @article
An article from a journal or magazine.
Optional fields: volume, number, pages, month, note, key
• @book
A book with an explicit publisher.
Optional fields: volume, series, address, edition, month, note, key
• @booklet
A work that is printed and bound, but without a named publisher or sponsoring institution.
Optional fields: author, howpublished, address, month, year, note, key
• @conference
The same as inproceedings, included for Scribe (markup language) compatibility.
Optional fields: editor, pages, organization, publisher, address, month, note, key
• @inbook
A part of a book, which may be a chapter (or section or whatever) and/or a range of pages.
Required fields: author/editor, title, chapter/pages, publisher, year
Optional fields: volume, series, address, edition, month, note, key
• @incollection
A part of a book having its own title.
Optional fields: editor, pages, organization, publisher, address, month, note, key
• @inproceedings
An article in a conference proceedings.
Optional fields: editor, pages, organization, publisher, address, month, note, key
• @manual
Technical documentation.
Optional fields: author, organization, address, edition, month, year, note, key
• @mastersthesis
A Master’s thesis.
Optional fields: address, month, note, key
• @misc
For use when nothing else fits.
Optional fields: author, title, howpublished, month, year, note, key
• @phdthesis
A Ph.D. thesis.
Optional fields: address, month, note, key
• @proceedings
The proceedings of a conference.
Optional fields: editor, publisher, organization, address, month, note, key
• @techreport
A report published by a school or other institution, usually numbered within a series.