Two Free Academic Software Tools
1) Docear (pronounced “dog ear”)
Academic Literature Suite of Applications
“Docear is the complete solution for searching, organizing and creating academic literature such as assignments, theses, books and research papers. Just as an office suite bundles the applications essential to the professional environment, Docear integrates the essential applications of a researcher. These include an academic search engine, file manager, PDF reader*, mind mapping and note taking tool, reference manager, paper drafting, and word processor*. While the components are integrated, they are still replaceable so that if you don’t like Docear’s reference manager, you can simply use another one.
“Docear has two unique features that no other currently available tools offer. Firstly, Docear lets you import PDF annotations (including bookmarks, comments and highlighted text). This allows a document’s most important information can be easily organized. If more information is required than the bookmark or comment itself provides, Docear can open the PDF on the page the bookmarks points to. Secondly, all information is structured in a mind map which we believe to be much more effective and efficient than a simple list or social tags.”
Free mind mapping and knowledge management software
“Freeplane is a free and open source software application that supports thinking, sharing information and getting things done at work, in school and at home. The core of the software is tools for mind mapping (also known as concept mapping or information mapping) and using mapped information. Freeplane runs on any operating system that has a current version of Java installed. It can be run locally or portably from removable storage like a USB drive.”
These separate projects have tight integration: http://www.docear.org/faqs/what-has-docear-to-do-with-freeplane/