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Wikindx facilitates academic writing in a browser

By Frank Tuzi on May 27, 2008 (4:00:00 PM)

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Anyone interested in writing academic and research papers knows that the process includes researching existing works, planning a research study, collecting and analyzing the results, and writing up the findings. In such papers, reference and citation information is essential. GPL-licensed Wikindx lets you store bibliographic references, quotations, and notes in a database, from which you can easily insert appropriate citations into a paper using its built-in Web-based word processor.

The written papers can be formatted to adhere to the major research writing formats, such as APA, MLA, Chicago, and Turabian. In other words, Wikindx can manage all of your reference materials, include them in research papers, and format the papers according to research specifications.

Even more impressive is that Wikindx runs entirely through a browser, and allows multiple users to share data input. People can also work offline in a text file or a word processor and add changes back in to Wikindx when they reconnect to the Internet.

Setup

In order to use the Wikindx system, you must set it up on a server, but that's a straightforward process. It requires a Web server like Apache, the middleware language PHP, and a database like MySQL. Wikindx will not create a database, so make sure you create one before you run the setup script. You can create a MySQL database by using phpMyAdmin, by entering mysqladmin create databasename at the command line, or by entering mysql from the command line and typing create databasename. After making the database and uncompressing the Wikindx file, save the uncompressed folder in a Web-accessible location on your server. Restart the Web server and point the browser to the new Wikindx server location. Wikindx will ask a few simple questions to complete the setup process, then move you to the newly installed Wikindx front page.

Setting up the server is the easy part. Installing data and using Wikindx effectively is a longer and much more time-consuming process. Once the system is up and running, you must fill it with bibliographic information, annotations, and comments. The majority of your information is probably in word processor documents, paper-based journals, and online classroom tools, which you must enter manually.

Add bibliographic information to the Wikindx system by selecting Resource -> New from the menu to invoke a series of windows to input the resource. Wikindx supports about 40 types of resources, including articles, books, book chapters, Web sites, and conference proceedings. You can enter authors, or select any that are already in the system from a dropdown list. The final page allows you to input metadata for the resource, such as keywords, abstracts, personal notes, and categories. You can store metadata in an unlimited number of categories. For example, if my Wikindx site contained hundreds of resources about geology and I wanted to find articles related to carbon 14 dating, I could search for carbon 14 dating, and resources that included carbon 14 as a keyword or category would appear on the search list results page. This final page also allows you to input an abstract and personal notes about the resource, and is thus a great place to enter notes that you plan to use for a paper.

Although entering resources is time-consuming, Wikindx has a few modules to speed the process. It provides a Firefox add-on that marks BibTeX text on Web pages for easy copying and pasting into Wikindx, and another that allows users to import Amazon.com book resource information.

Wikindx allows multiple people to participate in the inputting process. Wikindx administrators can set up usernames and passwords. Users can add resources to the site for all to view, or write papers that only owner can view. Users can create bibliographies, which are lists of resources on a specific topic. They can search or browse the database and can export bibliographies in a number of formats, such as RTF and HTML.

Not only can Wikindx information be available to all authorized users, but the administrator can allow any site visitor read access to the database. Wikindx defaults to read-only permissions for global users, but organizations that cannot legally make their sites public or which desire greater control and privacy can add security via the Web server by adding a .htaccess file in the main Wikindx folder or user directives in a Wikindx directory container in the Apache configuration file.

Writing a paper

Once you or your team has entered your resources in the database, Wikindx becomes a powerful tool for writing scholarly papers with references. Wikindx includes an online WYSIWYG word processor in which users can create, edit, and save documents. You can use bold, italic, or underlined text, change font size and type, and employ bulleted lists, pictures, section breaks, and tables. When you've finished up in Wikindx you export the paper to an RTF file. You can then import, finalize, and polish the paper in an external word processor, where you can determine line spacing, paper size, and bibliographic formatting.

To begin a paper, select Papers -> New paper from the menu. The browser loads the WYSIWYG editor and a standard toolbar. Included in the standard toolbar is an Insert Citation Tag button which, when pressed, opens a search window to let you find and select a desired citation. After you select the desired reference, the search window closes and returns you to the paper, with the citation tag added at the insertion point. The citation is a tagged code, not the actual citation information. Wikindx replaces the tag when the author exports the paper. During the export process, writers can select the paper format (e.g. APA, MLA), line spacing, footnote formation, page numbering, and long quotes layout (e.g. single spaced, double spaced, indented).

While writing papers online, authors should save their work often, since network connections do sometimes fail and there is no autosave function. I have on more than one occasion lost some of a paper because I clicked off my Wikindx site before I saved the paper.

After finishing a paper, you must export it to an RTF file. The toolbar includes a save and export button that opens an export window, which allows you to select options such as paper format and line spacing and save the paper to a local computer. Exporting the paper from Wikindx also locks the online version of the paper. Subsequent views will list the paper but will not allow editing. If you desire to re-edit the paper, you have to click the save button and save it with the same or different name.

Wikindx administration

Wikindx administrators are responsible for initial system configuration and security. They also manage resource keywords and categories, users, themes, and resource importing. Categories and keywords are metadata that help define what a resource is about and what the contents is related to. Managing keywords and categories can be a daunting task for a single administrator, which is why the project offers a plugin to allow users to manage them. Administrators can allow anyone to register or manually add users to control editing powers.

Wikindx provides a few themes for the appearance of the Wikindx site; administrators can also create their own.

Users can also participate in some administrative duties. Users can create and manage groups and group bibliographies; group bibliographies allow members of a group to add or delete bibliographic entries to the group bibliography.

Wikindx can function in a number of languages, and can be converted to other languages with little work. Wikindx was created with language localization in mind. All of the menus and application messages are in a few language files that can be edited for any language.

One drawback of Wikindx is that it lacks a spell-checker, and for some reason, Firefox's spell-checker does not function with Wikindx. However, that's not a big burden since writers will export their paper and view it again in a standalone word processor.

Wikindx is a great application for anyone or any group writing research materials such as scholarly papers, research documentation, and annotated bibliographies. It is well suited to either group or individual work.

Frank Tuzi is an associate professor of linguistics and technology.

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on Wikindx facilitates academic writing in a browser

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LaTeX

Posted by: Anonymous [ip: 128.146.172.220] on May 27, 2008 07:17 PM
If you plan on having a career in academics, you won't regret learning LaTeX. Sure it's a steep learning curve, but you only learn it once.

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Re: LaTeX

Posted by: Anonymous [ip: 62.78.253.74] on May 28, 2008 04:14 AM
LaTeX is good for typesetting -- but one still needs an editor for writing. In my opinion it is better to use a real word processor for writing and LaTeX for typesetting. But best solution is to use a real word processor for writing, and let the publisher do the typesetting.

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Re(1): LaTeX

Posted by: Anonymous [ip: 24.5.210.198] on May 28, 2008 04:31 AM
Publishers get layout wrong sometimes & some won't typeset your review papers.

If you don't want to learn LaTeX, you can use LyX or other GUIs.

If you don't mind learning it, any text editor will do (meaning you can write ANYWHERE & could use your preferred editor instead of the clunky one included with an office suite).

Writing in LaTeX enables "plugins"; easy separation of textual content, media content, and styling; easy version tracking/diffing; etc.

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Re(2): LaTeX

Posted by: Anonymous [ip: unknown] on May 28, 2008 07:49 AM
Text editors are not good for writing books or papers unless one can tweak and tinker with macros etc. For example, it took me too long to find out how to get a decent word-wrapping out of Emacs. It was driving me crazy... Also Bibtex sucks for humanities. In more ways than I can think of.

BTW, I have never ever seen a publisher or journal in humanities that accepts articles in LaTeX. It is either .doc or .rtf -- so one has to convert the manuscript from LaTeX to a normal format anyway.

Writing with a modern word processor also enables easy separation of content and styling. In addition, modern word processors have decent spellchecking and grammar check -- those can easily incredible amount of time spent in proofreading.

Just my 5 cents -- after having written my first (and last) book in with Emacs in LaTeX and having converted it to rtf for proofreading before handing it to the graphic designer.

LaTeX might be _the_ solution for mathematicians, astronomians, people in IT etc. But it is far from perfect solution for people in humanities or social sciences.

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Re(3): LaTeX

Posted by: Anonymous [ip: 24.5.210.198] on May 28, 2008 01:58 PM
"Text editors are not good for writing books or papers unless one can tweak and tinker with macros etc."

Most popular text editors do have very powerful macro support & can use regular expressions & easily use external programs. I don't think that the popular word processors are better in these departments.


"Also Bibtex sucks for humanities. In more ways than I can think of."

Just because you use LaTeX does not mean that you need to use BibTeX. There are numerous other more modern approaches (or you can use a reference manager that writes LaTeX directly). There are certainly some in the humanities who use LaTeX in some form (either directly or by using it for typesetting XML documents).


"BTW, I have never ever seen a publisher or journal in humanities that accepts articles in LaTeX."

This is simply not true. Any that also publish math/science will accept LaTeX. Certainly the book publishers all accept it.


"Writing with a modern word processor also enables easy separation of content and styling."

They do enable it, but I wouldn't call it "easy" to get cross-references, to apply wholly new styles, etc. It is certainly not "easier" than LaTeX.


"In addition, modern word processors have decent spellchecking and grammar check -- those can easily incredible amount of time spent in proofreading."

Text editors and LaTeX GUIs can feature these too.

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Wikindx facilitates academic writing in a browser

Posted by: Anonymous [ip: 190.47.69.30] on May 27, 2008 09:11 PM
I recommend also Bibus.
Regards,
suribe

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Wikindx facilitates academic writing in a browser

Posted by: Anonymous [ip: 201.17.255.253] on May 27, 2008 11:35 PM
sounds fantastic. references should appear in a shared database ("repository") ideally!

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Re: Wikindx facilitates academic writing in a browser

Posted by: Anonymous [ip: 59.136.56.137] on May 28, 2008 05:10 AM
And the great things about this app is that dozens of people working in a similar field can benefit from each other. As every participant adds more bibliographic datato the Winindx database, more references, abstracts, notes and comments get shared by the group.

Years ago - I learned the benefits of annotated bibliographies. This system takes the annotated bibliography 2 steps further because these entries are indexed and searchable and the building of this annotated bibliographies is a group effort that can benefit the group and the greater community



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Wikindx facilitates academic writing in a browser

Posted by: Anonymous [ip: 128.250.6.244] on May 28, 2008 02:30 AM
or there is aigaion, which provides similar functionality.
http://www.aigaion.nl/

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aigaion (re: was Wikindx facilitates academic writing in a browser)

Posted by: Anonymous [ip: 24.5.210.198] on May 28, 2008 03:14 AM
"or there is aigaion, which provides similar functionality."

Does aigaion have any wiki features?

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Re: aigaion (re: was Wikindx facilitates academic writing in a browser)

Posted by: karnesky on May 28, 2008 03:57 PM
As far as I know, Aigaion is really only a bibliography manager. It does have a great notes system that allows you to refer to other references, but I don't think you'd really want to write an article in Aigaion.

Media wiki and refbase together or either uniwakka or wikindx alone are more suitable for online writing, though.

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MediaWiki + refbase

Posted by: Anonymous [ip: 24.5.210.198] on May 28, 2008 03:12 AM
Wikindex looks like it could be an o.k. reference manager and an o.k. wiki, but I just can't used to the interface.

MediaWiki is an outstanding wiki (used by Wikipedia) & has a lot of plugins. Still, it lacks centralized reference management.

There are multiple citation plugins for it, but I have grown to like refbase. The integration could still use improvement, but t isn't perfect, but it also works with Endnote, BibTeX, etc. so the flexibility is worth it.

http://www.mediawiki.org/wiki/MediaWiki
http://refbase.sourceforge.net/

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Re: MediaWiki + refbase

Posted by: karnesky on May 28, 2008 03:53 PM
You're correct that we still have work to do on this integration. You might also want to check out PIRA to see how refbase could be integrated with a WYSIWYG editor. It seems to have been for a class project or something, but they did a good job--it lets you write your paper & will perform contextual literature searches based on what you have written. MediaWiki and others are probably much better for real authoring work, but it give you an idea of what kind of integration is possible:

http://pira.isrl.uiuc.edu/

I don't think word processors and LaTeX tools are going anywhere, though. wikindx, refbase, and many of the reference managers listed at:

http://en.wikipedia.org/wiki/Comparison_of_reference_management_software
http://bibliophile.sourceforge.net/projects.php

work with these more conventional tools.

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Questions

Posted by: Anonymous [ip: 24.5.210.198] on May 28, 2008 03:29 AM
As noted, your review was interesting, but it does leave questions:

"Wikindx defaults to read-only permissions for global users, but organizations that cannot legally make their sites public or which desire greater control and privacy can add security via the Web server by adding a .htaccess file in the main Wikindx folder or user directives in a Wikindx directory container in the Apache configuration file."

Would this mean two logins (one for the http server & one for wikindx)?


"While writing papers online, authors should save their work often, since network connections do sometimes fail and there is no autosave function. I have on more than one occasion lost some of a paper because I clicked off my Wikindx site before I saved the paper."

Is there some magic to fix this? I'm used to autosave & could not stand this limitation? Firefox extension? Or would that not work because:

"One drawback of Wikindx is that it lacks a spell-checker, and for some reason, Firefox's spell-checker does not function with Wikindx. However, that's not a big burden since writers will export their paper and view it again in a standalone word processor."

I thought the firefox checker works with every textarea?

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Re: Questions

Posted by: Anonymous [ip: 59.136.56.137] on May 28, 2008 04:13 AM
my version of Firefon 2.0.0.14 on Fedora 8 has the spell checker, but the textareas used in Wikindx do not get checked. Could be a javaschipt issue

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Re(1): Questions

Posted by: Anonymous [ip: 24.5.210.198] on May 28, 2008 04:25 AM
In firefox 3.0b5/Ubuntu, the spell-checker works on the textarea for papers.

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Re: Questions answered

Posted by: Anonymous [ip: 59.136.56.137] on May 28, 2008 04:18 AM
Would this mean two logins (one for the http server & one for wikindx)?

Wikindx has its own internal login capability. Apache also has it - so yes two can be used. to access the website, Apache security can be implemented. If using the read-only settings, all visitors can access without logging in and writers & reference contributers log in to contribute.

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Re: Questions-Autosave & Answer

Posted by: Anonymous [ip: 59.136.56.137] on May 28, 2008 04:21 AM
"While writing papers online, authors should save their work often, since network connections do sometimes fail and there is no autosave function. I have on more than one occasion lost some of a paper because I clicked off my Wikindx site before I saved the paper."

Is there some magic to fix this?

there are no quick fixes from the user side. there are no extensions or server side possibilities. The only solution I could imagine is to add that functionality to the Wikindx application. It can be done - but it needs to be added to Wikindx. Perhaps you can suggest that to them?

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LaTeX isn't just for typesetting!

Posted by: Anonymous [ip: 89.1.211.203] on May 28, 2008 09:34 AM
Latex encourages you to focus on structure and content, not on visual layout; in my experience, my writing is much better and faster with latex than with a word processor.

Regarding latex in the humanities: most linguistics journals accept latex, and there are latex macros for almost any kind of thing linguists have to deal with. (but still, most linguists use Word, for the same reason they use Windows...)

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Re: LaTeX isn't just for typesetting!

Posted by: Anonymous [ip: 59.136.56.137] on May 28, 2008 11:16 AM
Wikindx - unlike LaTeX - does not focus on formatting or structure - it enables the management, sharing, & insertion of bibliographic data and any associated notes that users add. This app is much more web 2.0 - users can participate, collaborate and take advantage of the work of others who have added to the bibliographic database. The system can become a knowledge base for any specific field of study.

LaTeX is great - but the point here is not structure - it is collaborative efforts to build up a searchable bibliographic system whose entries can be easily dorted and added to writing.

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Re(1): LaTeX isn't just for typesetting!

Posted by: Anonymous [ip: 24.5.210.198] on May 28, 2008 03:17 PM
"Wikindx - unlike LaTeX - does not focus on formatting or structure"

This is a limitation of wikindx, not a feature. There seems to be no way to apply real styling information, so that documents look good and meet publisher requirements.

There is also no semantic markup--you have to apply bold/underline/etc. manually like the bad old days.


"This app is much more web 2.0 - users can participate, collaborate and take advantage of the work of others who have added to the bibliographic database. The system can become a knowledge base for any specific field of study."

Yes and no. This might be web 1.5, as users can do some content creation. But it lacks many features that people expect from web 2.0: there's no clean AJAX interfaces which make this experience anything like using a desktop word processor. There's no auto-save! Other wikis have semantic markup, embed microformats, and aren't limited to legacy formats like RTF.

UniWakkaWiki may be a little closer to web 2.0 if you want a single wiki+reference manager that is "LaTeX-like." It has mathml/latex/asciimath, and opendocument/LaTeX export & supports jmol, etc.

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Re(2): LaTeX isn't just for typesetting!

Posted by: Anonymous [ip: 59.136.56.137] on May 28, 2008 03:27 PM
"there's no clean AJAX interfaces" & "aren't limited to legacy formats like RTF." - excellent points!!

Perhaps Wikindx looking into adding these features?

Don't know UniWakkaWiki - but will check it out - Thanks

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Wikindx facilitates academic writing in a browser

Posted by: Anonymous [ip: 134.220.244.41] on June 04, 2008 08:38 AM
Firstly, thank you very much Frank for your positive review on my software WIKINDX.

A couple of points you might be interested in:

1. The author states: "Exporting the paper from Wikindx also locks the online version of the paper. Subsequent views will list the paper but will not allow editing. If you desire to re-edit the paper, you have to click the save button and save it with the same or different name."

That shouldn't be the case and I haven't heard of that behaviour before. I've just tested this on the wikindx test drive and it performs as I expect: create a paper, save it, open it from the list, edit it and the next save keeps the same name and writes over the previous version of the file unless you choose to rename it.

2. As the author of this article has also written an article on Moodle, you may be interested to know that there is a Moodle filter for WIKINDX: http://moodledev.yeovil.ac.uk/moodle/course/view.php?id=2.

3. The author doesn't mention bibtex and Endnote bibliography imports which, if you already have bibliographies in those common formats, dramatically reduces the time taken to populate the wikindx.

4. Users are not limited to the pre-supplied bibliographic styles, administrators can create new styles.

5. I write in both technical and humanities styles. In the latter, e.g. APA, context-sensitive in-text citation formatting is one of the major strengths of the word processor. For example, wikindx recognizes that authors' names have already appeared in a sentence in which the citation has been added and will not add the name(s) to the citation. Wikindx will recognize the author has been cited previously in the paper and, if the style requires it, will use ibid, op cit etc. in footnotes or endnotes. Just some examples of the context-sensitive citation formatting.

6. Wikindx has a plug-in system allowing users to write and add plug-ins in PHP to extend wikindx's functionality. A variety of plug-ins already exist including PubMed search/import.


Responding to a couple of the posts here:

1. The paper does not use a textarea, it uses an iFrame which is probably why the firefox spell-checker does not work. It relies on the Midas engine in the Firefox and other browsers (not Opera and some versions of Konqueror) so in many respects I am limited as to the functionality that can be supplied.

2. I have racked my brains about autosave. If anyone can come up with the answer, please let me know (contact via my sourceforge email on the SF wikindx site please).


Wikindx development proceeds but, as I now have a real job instead of having plenty of time to work on wikindx while doing my PhD, the pace has slowed somewhat (wikindx has also matured since I started it over 4 years ago). I'm hoping to do some work on a v4 over summer (European) and hope to make the following changes:

Main:
1. Update to PHP5.
2. Add a more sophisticated templating engine such as Smarty.
3. Make wikindx far more modular than it currently is and, in the main download, include only the core functionality, off-loading other functionality (e.g. the word processor) to plug-in modules. I'm hoping this will encourage more plug-ins to be developed and it will also ease the load on translators who need only localize the core messages.

Potential:
1. Search/import across multiple wikindices.
2. Allow multiple authors to author the same paper.
3. Allow for a choice between WYSIWYG paper views and more Latex structural views.
4. Export to more formats such as PDF, TeX.
5. Add some AJAX functionality.
6. Full-text searches through attachments.


I am only one person -- though I have had help through the years, approx. 95% of the programming is my work. I have less time to work on wikindx these days and future expansion will start moving into areas in which I lack expertise. Adding multiple authoring to papers is a case in point. I suspect it will use some pure wiki technology -- rollbacks, contributor comparisons etc. -- with which I am unfamiliar. Same for TeX and PDF outputs and AJAX integration. I always welcome developers with open arms to this open source project. If you feel you can help, please contact me through my SF address on the project website.

Thanks,

Mark Grimshaw

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Wikindx facilitates academic writing in a browser

Posted by: Anonymous [ip: 72.72.207.230] on June 07, 2008 03:56 AM
worked with bibus for a while - but zotero does it all. Really - it's too easy to use - beats endnote the sock off. Zotero is a nice large developer base too

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Wikindx facilitates academic writing in a browser

Posted by: Anonymous [ip: 72.94.151.156] on June 13, 2008 04:50 PM
Frank...
Jean Keiser here... Are you still in Japan? Email us at bjkeiser@cheerful.com.

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