The last years I have switched back and forth between Linux (mostly SuSe) and Windows. I have ended up with Windows, and this page is a summary of which tools you might install and use if you are a Windows user entering our group. If you prefer Linux, I suggest you ask Patrick :-).
LaTex is the most elegant and easy to use typesetting system for scientific writing and publishing. If you are familiar with HTML, latex works pretty much the same way. You need a text editor to write your document, and when you want to watch the result of your writing you have to compile the document (from a .tex file to a .dvi file) and convert it to for example a pdf or a ps file. To get LaTex to run properly under Windows you need to download Miktex and WinEdt.
WinEdt is a very good editor for writing latex documents (or any other documents!). WinEdt is shareware, is free to download, install and use, but you will be annoyed with some pop-ups to make you remember that you should pay for the editor if you like it.
TeXnicCenter is a feature rich integrated development environment (IDE) for developing LaTeX-documents on Microsoft Windows (Windows 9x/ME, NT/2000/XP) freely available under GPL. I have not used it myself, but it's a good editor, and it's free!
JabRef is an open source bibliography reference manager. JabRef has (at least) two very nice features: (1) it is linked to the medline database, which contains most of the neuroscience papers. From medline you can download all information about desired papers (authors, journal, year, etc.), and store it in your own private database. This database can, of course, be linked to your electronic version (pdf) of the paper. (2) The file format JabRef uses in its database is BibTex, thus it is really easy to use as a reference manager in combination with latex. And, in addition, JabRef works perfectly in combination with WinEdt. If you want to have a reference in your thesis, just click the WinEdt icon in JabRef, and your marked paper will be referenced in you open WinEdt document and put into your bibliography.
Note that many journals have their own preferred latex template which you can download from the journal's homepage. They also have their own bibliography style, which can be downloaded from LaTeX Bibliography Styles Database. When writing thesis, ask older students which latex-template you should use. Use templates! You should not do everything from scratch when you write a latex document.
LaTex uses the eps format for graphics. So, when you do simulations etc, save the files (if possible) in eps format. If you want to include other graphics filetypes in your LaTex document, you have to convert them. I use Adobe Illustrator for converting, but there are free alternatives, like Gimp. However, there are some pitfalls when converting. In Adobe, after you have chosen Save As EPS, you get some EPS Options. Make sure that none of the options are checked, e.g. Include Document Thumbnails should NOT be checked.
MATLAB is my preferred simulation tool when it comes to numerical simulations and programming. Note, however, that this is a licensed (and quite expensive) tool, and be aware of the very nice and freely available clone, Octave.
Mathematica is the tool I use when I do analytical mathematics. This is also a licensed (and expensive!) product.
NEURON is a programming tool for simulating activity in neurons and networks of neurons. If you want to learn how to use this tool, I made a webpage with advices on how to approach the subject. (link here - or use the link of the left menu)
Comsol multiphysics (also licensed!) was earlier called FEMLAB, an acronym for the Finite Element Modeling
Laboratory. This is an advanced software package for
modeling and simulation of any physical process you can describe with partial differential equations. I have used it quite a bit when teaching electricity and magnetism (and quantum mechanics). Exercises (in 
)