Research

Firefox

Firefox is a web browser that can be customized to become an indispensable tool for the researcher.
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Firefox Plugins

Zotero

, the essential research tool

If you lend any credence to the recent lawsuit (thankfully it was dissmissed) brought against Thomson Reuters and George Madison University, then Zotero is basicaly like EndNote®. I have never used EndNote®, but from what I know, many of the features that are important to me in Zotero are absent in EndNote®.

  • Cataloguing and Referencing
    • Cataloguing:
      • Zotero is organized like a catalog. It collects records of items and organizes them. A record can technicaly be of almost any item, from written works to physical artifacts, and Zotero comes with many item types that will be used in the research world.
      • Zotero will recognize library catalogues and other record databases and will then display an icon in the location bar of firefox. Clicking on this icon will cause Zotero to download and save this record.
      • Records may include such information as the creator, date, title, description, and abstract. All of the entries in these records can be searched with both a simple and advanced search tool.
      • Subcollections can be created to organize copies of records from the master record collection (My Library). You can also turn complex searches into special subcollections that will always contain all matching records from the master collection.
    • Referencing:
      Zotero can export selections of records as bibliographies in most common bibliographic formats.
  • Document Review
    • Any file, such as a document or image, can be "clipped" to a record and viewed in firefox if there is a viewer plugin for that file type. Files associated with on-line records, like the PDF copy of a journal article, will automatically be clipped to the record when zotero downloads it. Zotero can search .doc, .pdf, and .ps files using the built in search tools.
    • Zotero can generate a report of a selection of records which will be viewed as a web page in Firefox. This allows you to rapidly review information like the titles and abstracts in the selection of records.
    • Zotero can generate an animated time-line of a selection of records which will be viewed as a web page in Firefox. The time-line can be set at various time scales and scrolled. Clicking on an entry in the time-line pulls up the record represented by that entry in Zotero.
  • Annotation
    • Sticky Notes:
      Any file clipped to a record can be annotated with sticky-notes (the notes appear on the document) if there is a viewer plugin for that file type in Firefox.
    • Notes:
      Notes can be created in the Zotero database as stand-alone notes or notes clipped to a record. The notes can use varios types of standard formatting, such as bold, italic, underline, centering, etc.
  • Peer Collaboration:
    Lastly, and possibly most importantly, Zotero can sync its database with a central server, allowing many researchers in even a widely scattered peer group to collaborate and share their information quickly. There is a Froglab peer group for Zotero. Contact me if you wish to join it.
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Searching Plugins

Add to Search Bar

The Firefox search bar allows you to use web-based search engines without visiting their search page. With this plugin you can right click in any text entry box on a web page and add it to the search bar as a search engine.
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Searchbastard

Searchbastard is a powerful set of search tools for using web-based search engines. Features like simultaneously searching with many search engines and quick searches triggered by a single key stroke make it an indispensible tool.
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Find In Tabs

One of the features that make a modern web browser powerful is the use of "Tabbed Browsing" which allows you to have many pages open simultaneuosly. This can be useful for keeping reference pages open, search multitasking, site preloading, simultaneous document review, etc. All modern text manipulation applications also have a "find" capability which allows you to search the text for strings or expressions. The Find In Tabs plugin changes the standard find feature in Firefox to search simultaneously in all open tabs. The search gives you a list of occurences, each of which can be clicked to display the location of the occurence in Firefox.
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Tabhunter

The power of "Tabbed Browsing" is much attenuated if it is difficult to locate and identify tabs. Tabhunter allows searching through tabs by the name of the tab or the web page it displays.
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Tab and Session Plugins

Session Manager

The power of Firefox can be much enhanced with the addition of "Sessions". Sessions save the state of Firefox including history, text data and cookies, even in the case of a Firefox or system crash. A session is like a period of discrete, directed activity. For instance, finding and reading the daily news from multiple sources might be one session. Checking on-line collaboration and social networking accounts, like Facebook and Zotero, might be another. Thus, the work done in firefox can be divided into functional units, allowing for simple multitasking of many different but complex activities.
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Tree Style Tab

This extension organizes tabs like folders. Any tab opened from another tab (parent tab) is attached to the parent tab like a subfolder of the parent. Tab organization of this sort makes it much easier to navigate complex sessions that involve many tabs.
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Tab Scope

Tab Scope creates thumbnail images of web-pages that pop up when the pointer hovers over a tab. The preview images actually have clickable active links, and the image size and properties are configurable. This can make Tabbed Browsing and Session Management much more intuitive for user.
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Document Production

OpenOffice

OpenOffice is a suite of appications similar to Microsoft Office®. It works on Microsoft Windows®, Macintosh, and Linux platforms.
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Abiword

Abiword is a free word processor which can read and write many document formats. Some prefer it to OpenOffice Writer, which is also a word processor. It works on Microsoft Windows®, Macintosh, and Linux platforms.
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LyX

If you create a lot of documents that include complex formatting such equations or chemistry symbols you might want to use a text document processor such as LyX. LyX uses Latex which is great for laying out documents that will be printed. You can include images and other graphics and export to PDF and Postscript, HTML, and other formats. This application also works on Microsoft Windows®, Macintosh, and Linux platforms.
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SeaMonkey©

SeaMonkey© is an "all-in-one internet application suite" which includes a web browser, mail and news (usenet) reader, chat client, and composer. The composer allows the simple and intuitive creation of web pages and provides integrated web-authoring tools. It runs on Microsoft Windows®, Macintosh, and Linux platforms.
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PortableApps

PortableApps allows Microsoft Windows© users to put applications on a portable device and run them from it. This allows the user to use their own applicatins and configurations for these applications on many different computers which run Microsoft Windows®. Applications which have been made portable include Firefox, OpenOffice, Abiword, instant messengers, and many others. You can get PortableApps as a suite which includes many applications or you can download the individual applications you choose.
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Froglab FirefoxPortable

This is Firefox Portable with some of the Firefox addons and the Froglab Zotero database. Simply unzip the contents into any folder, a thumbdrive, the desktop, or any other location, and run FirefoxPortable as usual. The directory is protected, so contact me if you wish to obtain it.
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