The process of researching is more than just performing experiments in the laboratory. It is also the constant search for pertinent information and techniques as well as dissemination of results that assist others. It is not always straightforward for students to learn how to use research tools appropriately. These links and software are important resources that I use and have my undergraduate and graduate students use as well.
Finding and Organizing Articles and Sources
The ISI Web of Knowledge is an excellent starting point for researching scholarly information. This also allows you easily to move backwards and forwards in time through references to find important and relevant material. Since BYU has a subscription, I recommend using it. It is also integrated with BYU's journal subscriptions which make it particularly easy to find journal articles from many different sources. Additional information available through the ISI are journal impact factors and individual citation metrics for authors.
JabRef is a tool that allows you to organize your sources in an easily accessible and searchable manner. It also allows you to embed links to your PDFs or the original online content. It stores the information in BibTeX format so it is particularly useful when used in conjunction with basic LaTeX or LyX. It can be a bit slow because it is written on a Java platform but it is quite useful.
Writing Scholarly Work
While Word is useful for dashing off the quick document here and there, to properly cite, link, and prepare mathematically intense work, better options are available.
LaTeX, embodied in a particularly useful form, MikTeX, can be downloaded and is the standard in technical writing. It is extremely powerful and will typeset your information in book-ready format.
Built on top of the LaTeX or MikTeX base, LyX is a powerful editor for LaTeX and integrates extremely well with BibTeX. While I started writing in LaTeX many years ago, I find that the interface through LyX is much easier and very powerful, especially because it can handle any type of image file. The citation tools are particularly powerful when integrated with JabRef. I can easily find and locate the appropriate paper I am trying to cite in LyX. My opinion is that LyX is finally a tipping point for the widespread use of LaTeX because of its ease of use. For the user that has grown up with Word-type products, LyX is a natural stepping stone into the LaTeX typesetting world.
If you need to manipulate the TeX directly, then using TeXnicCenter is a good editor for line by line changes. I use this to finish formatting work for submission to a journal that accepts LaTeX.
Figures are some of the most important tools to illustrate important points and ideas as well as present data. Thus, it is important that they are clear and easily viewed. In general, for reproduction, you want to use a vector-based art program to finalize the figures. This is problematic when using Word documents which convert them to bitmaps and is the reason that many journals require you to upload figures separately from the main body of the text.
MATLAB is an excellent program to create figures. However, it is usually important to modify the text or add indicators and arrows to the figures that are generated. I usually export to Adobe Illustrator and then modify the text appropriately there. However, I have also used a combintation of other software to do this.
Inkscape is a powerful vector-based graphics editor that can easily create high-quality figures for publications. Inkscape has many features that are comparable to Illustrator. I have used it in conjunction with the plot2svg command in MATLAB which works extremely well. You do have to consider whether you will be using color or different line styles/symbols so the publication and presentation format you are targeting is important.
To dash off a simple figure in eps format, OpenOffice.org Draw is also a good solution.
Many times you may want to perform a quick check on assumptions that you are making for a proposed experiment or device. Many commerical packages are out there and can give you accurate results for a variety of structures and configurations. I find that a simple tool for some basic work and to teach students about simulations is the Maxwell SV package.