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To prepare a bibliography please use the Chicago Manual of Style which is commonly used by historians. A list of the most common material you will use when preparing a research paper can be found here.

Suggestions for citation management software:

Licences für Citavi Team and Endnote are available free of charge for students of the University of Cologne.

Comparison of Bibliographic Software by the Technische Universität München

Zotero is an extension (or add-on) to the Firefox browser, which enables users to save information on books, articles, vidoes, and other material from within the open browser window. One click saves metadata from the site by recording available citation information. Zotero also allows users to save attachments to these citations, making it possible to store PDF files of articles, screenshots from a web page, or user-generated notes. Once added, the bibliographic information can be exported directly into Microsoft Word and Open Office.
(Developed by the Center for History and New Media)

Mendeley is a free reference manager and academic social network that can help organize research, collaborate with others online, and discover the latest research.

Omeka is a Web-publishing tool dedicated to displaying information and archival material in an attractive, easy-to-use format. It's a free and open source form.

Scribe is a notetaking application designed with historians in mind.
(Developed by the Center for History and New Media)

Web Scrapbook is a clipping file for the Internet. Into that file you can place images, excerpts, and whole web pages that you find while you surf the web or that reside on your computer. In addition, you can annotate these items, sort them into folders, and add memos to those folders. Unlike a bookmarks file or favorites list that is stored by your web browser on your computer’s hard drive, you can access items you save to the Web Scrapbook from any computer connected to the Internet.
(Developed by the Center for History and New Media)