Biblios - Bibliography and Research Tools

March 2006
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A blog tracking tools and technology for researching and writing papers, articles and dissertations.

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This Blog Has Moved

I have been fighting off comment and trackback spam and have been finally driven to move to another tool. It is with great sadness that I leave my beloved PyDS and PyCS (python rules!) tools. This weblog has been moved to and is now being driven by WordPress.

I have imported the posts from this site have not been able to get the comments. I trust this site will stay available.

posted at 18:57:52    #

New Bibutils Release

Chris Putnam has released v3.7 of his bibutils bibliographic conversion utilities. Up until now, the suite of tools did a nice job of converting from BibTeX, RIS, and Endnote to MODS. Now it adds the ability to go from MODS back to those formats. What this means is it provides a sort of universal translator, allowing one to go, for example, from BibTeX to RIS by way of MODS.

posted at 11:32:16    #

Related project: BiblioX

BiblioX is "an attempt to create a XML-based system for formatting bibliographic citations and references using XSLT. The recommended Document Type for storing bibliographic information is MODS, the Metadata Object Description Schema. Development is centered around this format, although examples in other formats are included for comparison." BiblioX offers (experimental) support for DocBook, MODS & TEI XML schemata.


posted at 00:05:20    #

Bibster: peer-to-peer bibliographic management and searches

Bibster is a Java-based system which assists researchers in managing, searching, and sharing bibliographic metadata (e.g. from BibTeX files) in a peer-to-peer network.

The advantage of the system is it provides the possibility to search on a distributed peer-to-peer network using Semantic Web technologies. It provides an easy way to share data with other researchers.

posted at 00:03:12    #


Thanks to Mark Grimshaw for the pointer to the new home for WIKINDX on sourceforge.  WIKINDX is a free web based (php / apache / mysql) bibliography management system.  Very cool.  They have just recently released 2.0 RC1.  Looks very interesting, and since it is multi user ... al sorts of different usage patterns are possible.  Take a look!

Mark also pointed me to a bibliography resource I hadn't see before ... Bibliophile  (RSS/ATOM).

Bibliophile is an initiative to align the development of bibliographic databases for the web. It aims to promote standards, discussion among users on necessary features and a variety of specific solutions for different fields of research.

The cool thing is that the site is really a blog that aggregates content from member projects.  Subscribed!



Bibliophile now has a Wiki!

posted at 02:28:16    #

Bibtex Processor for the MoinMoin wiki

Here is a processor for MoinMoin that renders bibtex files into the wiki - it appears to require bibtext2html.


posted at 01:37:04    #

bib2xhtml 2.12

Here is a new release of bib2xhtml 2.12:

bib2xhtml 2.12 bib2xhtml is a program that converts BibTeX files into HTML (specifically, XHTML 1.0). The conversion is mostly done by specialized BibTeX style files, derived from a converted bibliography style template. This ensures that the original BibTeX styles are faithfully reproduced. Some post-processing is performed by Perl code. This is an update of the bib2html program written by David Hull in 1996 and maintained by him until 1998.

posted at 01:32:48    #

Putting Visio diagrams into LyX/LaTeX

Today I was again faced with a need to put a Visio diagram into a LaTeX document via LyX...

posted at 04:17:04    #

Biblioz 0.1 released - Zope Based Bibliography Management

Looks like there is a budding effort to build a bibliographic management tool on top of Zope. From the announcement:

Biblioz - A first step towards a framework for organising bibliographic references.

Provides - BookRef, JournalRef and BookChapterRef (arche)types, BibliozTool for rendering each of the Bibioz content types to specific citation formats, and AmazonTool for fetching details from Amazon webservices (which can be used to autopopulate BookRefs)

posted at 13:33:52    #


It is amazing how much content that was only available to me as a student by browing the stacks and periodical archives in the university library is availabe for free over the internet. This changes research methods dramatically. I don't need to be located close to the campus anymore.

For example here is FreeFullText, a list of all the journals whose content is available for free on the 'net. provides direct links to over 7000 scholarly periodicals which allow some or all of their online content to be viewed by ANYONE with Internet access for free (though some may require free registration). The issue(s) which are available for free are indicated for each title on the alphabetical periodical lists. The design of this site is optimized for users seeking specific articles for which they already have the citation. If some of the articles you need are not available for free online, you may obtain them for a fee through a document delivery service, such as Pinpoint Documents. If you wish to "search" for articles on a particular topic, please use a bibliographic database such as PubMed. This site does not attempt to list ALL periodicals on the Internet, only those which offer free full-text content. Titles will be removed from this list if they cease to offer any free full-text content.

posted at 12:49:04    #


When I was working on several papers in my senior year of University, I developed a research tool that allowed for structured note taking which was cross referenced to my bibliography. Essentially, it was an automated version of the old 3 x 5 cards to track my bibliography and notes for a paper. It worked fairly well, although I dropped the project because at the time the amount of work I had to do to manage the database component was too much.

Enter now the idea of combining a bibliographic database with a blog/wiki for note taking. This is an idea from darcusblog that I think has tremendous potential.

I've come to the conclusion that weblogs, wikis and bibliographic databases ought to blur together. Weblogs provide a good way to distribute content (including one's own notes), and wikis a superior way to author linked structured content.

The potential for effortless autolinking for citations a la wiki has me drooling!

Source: darcusblog
posted at 21:29:36    #

Serendipity Strikes! Weblogs and Personal Research

I have had a passing interest in academic publishing, bibliography management and research tools for the humanities. Recently I have taken up my hobby again and wanted to get caught up in the field. So I have been tracking various feedster queries for the last month looking for good blogs about those topics. Today I hit pay dirt. Feedster churned up a post to Clay Reddings Blog entitiled Bibliography creation and XML.

Now, I haven't yet absorbed his comments yet, but his entry pointed me to Bruce DArcus blog which is a treasure trove of thinking around what bibliography management tools should look like today. I find his WikiBibBlog idea facinating (combines a wiki, a blog and a bibliographic database). From there, there are all kinds of links into the topic.

This really shows the value of something like feedster. It may not be as comprehensive as Google, but what it can do is provide a link to an intial blog which in turn links to others etc. And that allows you to find something far more important than just a static page somewhere. You can find an active community talking and publishing around your search topic. Feedster is an amazing personal research tool.

posted at 21:10:24    #

Jabref 1.4

There is a new release of the JabRef bibliography management tool available.

This version adds command line import and export functionality, advanced search, custom export filters, and several small additions and fixes.

posted at 17:58:24    #

A quest for the Holy Grail of technical documentation - Chris Karakas

Chris Karakas has put together a huge resource on publishing with Lyx and SGML. This is a tremendous resource.

A method for single-source publishing using LyX and SGML is presented: LyX is used as a comfortable graphical SGML editor. Once the document is exported to SGML from LyX, it undergoes a series of transformations through sed and awk scripts that correct the SGML code, compute the Index, insert the Bibliography and the Appendix and take care of the correct invocation of openjade, pdftex, pdfjadetex and all the other necessary programs for the generation of HTML (chunked or not), PDF (with images, bookmarks, thumbnails and hyperlinks), PS, RTF and TXT versions. All aspects of document processing are handled, including automatic Index generation, display of Mathematics in TeX quality both online and in print formats, as well as the use of bibliographic databases with RefDB. Special care is taken so that the document processing is as transparent to the user as possible - the aim being that the user writes in LyX, then presses a button, and the lyxtox script does the rest.

posted at 17:52:00    #

wiki-wiki of the LyX community!

Lyx has a wiki! Marvelous. Includes a section on About using BibTeX with LyX

posted at 22:12:16    #

Begin to use JabRef as BibTeX manager

Just ran across this reference to JabRef. Taking a quick look at it, it may be better than the Bibdb tool I had used before. Certainly looks a lot nicer and it seems to work with Lyx as well ... interesting

Source: Results For: bibtex
posted at 18:53:52    #

Research and Authoring Tools for the Humanities

My mother is working on her Ph.D. and has asked me to work with her on setting up a research suite of tools for managing bibliographies, related research, paper and article authoring. It will also likely be used to manage and produce her Ph.D. dissertation if we are succesfull.

It has been about 14 years since I completed my degree and the academic world has changed substantially. Whereas I spent a lot of time in the periodical stacks and the various journal indexes, all that is now done online ... without ever darkening the door of the library.

This shifts the tools emphasis away from 3 x 5 cards for bibliographic information to tools that automatically download the data from the online library and even produce bibliographies, integrate into Microsoft Word.

Some examples of tools are Reference Manager, End Note and Pro Cite which are all from Thomson ISI Researchsoft. These tools are all mature and widely supported by online research databases. The trouble is that your research is then locked up in their proprietary databases or online services.

I am exploring a different option. The standard bibliographic data format in the sciences is bibtex and the standard environment for authoring and publishing seems to be Latex based on Don Knuths Tex for typesetting. These two standard tool sets are tightly integrated. So my first run at this is to setup the following tools as an integrated research and authoring suite:

  • Miktex for Latex/Tex support on Windows

  • Lyx for Latex authoring environment

  • BibDB for Windows as the bibtex bibliography database manager.

It would be nice to hear from anyone who is currently using such a setup for writing and research management.

posted at 15:31:12    #
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