Saturday, March 13, 2010

Useful Software for Geology Majors

If you're studying geology and are a computer geek, I have some ideas that you may not have thought of. But knowing how resourceful most computer geeks are, I am sure you have found similar things.

OSXStereonet
OSXStereonet can take input planes and lines (e.g., strike/dip, trend/plunge) and take care of important calculations often made on a stereonet.  It can do a cylindrical and conical best-fit, find poles to all planes, generate Kamb contours, and much more.  This software is a must for all geology majors and professionals.  OS X only.

Mendeley

Mendeley is not open source, but it does use a few open sourced libraries such as QT.  But that isn't important.  What is important is that it helps you manage journal articles for writing research papers in a very natural way. It automatically extracts metadata from downloaded PDFs and fills in the bibliographic details.  If the software thinks it doesn't have everything, it'll prompt you.  But best of all, it has a built in PDF reader that allows for highlighting and note taking... plus those same PDFs can be uploaded to Mendeley servers for syncing with other computers!  Or, share your bibliography using the Mendeley website.  It can also create a customizable organized directory tree of all the papers you have loaded into it.  I use it to categorize articles, take notes,  and export references to BibTex.  Others may want to use it to cite while you write in documents.  What is key with this software is that it does not get in my way!  With software like this, who needs Dark Age software like EndNote or an amazingly cluttered desktop? For OSX, Windows, and Linux.

Anki

Anki replace Mnemosyne as my favored flashcard software.  Mnemosyne has not seen a release in over a year.

Anki is open source software  and is flash card program that uses algorithms that prevents wasting time on cards you know. It schedules cards based your rankings.  It allows you to use LaTeX and paste in arbitrary raster images from the clipboard.  Must have for those that need to memorize material.  It is cross-platform.

mhchem

Mnemosyne lets you modify the LaTeX preamble. So you can add packages which can make inputing cards much faster. I use the package mhchem. It typesets chemical equations or formulas using input that is very natural for most people familiar with chemistry. It aligns numbers in equations very nicely. Get it and typeset your flashcards using that package. Its documentation is a very easy read.

LaTeXiT

LaTeXiT is for MacOSX. What better way to put your favorite TeX formulas into most any other OSX software. It is really fantastic. Double joy when you find that Grapher that comes with OSX can give LaTeX formatting for formulas that you used to generate graphs! Of course GNUPlot is probably necessary for your research papers. If you have OSX Snow Leopard, follow these instructions to compile GNUPlot.

The Periodic Table

The Periodic Table is a OSX Dashboard widget. It isn't a must have but damn is it convenient to find out very quickly ion charges and atomic mass! Now where is a good isotopes widget? ;-)

PDF-XChange Viewer

PDF-XChange Viewer is for Windows but free. Unlike Adobe Acrobat Reader (for the vast majority of PDFs I have used), but like OSX's Preview, it can do annotations. For slideshow heavy courses where the professor posts before lecture, this is a must have. It also has drawing tools and a highlighter. Be careful though as some PDF readers might get confused with abundant annotations and stack them atop each other and refuse to let you rearrange them.


Inkscape

Inkscape is the de-facto open source software for creating vector-based graphics.  It's for MacOS X, Windows, and Linux.  However, you need the latest XQuartz environment for MacOS X for it to run.  If you need to redraft infinitely scalable sketches from your field book, look no further.  But if you can afford Adobe Illustrated, or your department has it on their lab computers, I suppose you might be better off.  But at least, with this, you can work on diagram-based assignments at home.  Inkscape can also be a terrific way to create forms for use in the field.  It export to PDF.

Adobe Illustrator
This software needs no introduction.  If you're having problems with Inkscape, picking up an academic license of Illustrator might be a worthwhile solution.  Illustrator is great for finishing off maps exported from ArcGIS.  It can also help you draw various things handy to structural geology such as balanced cross sections and strain ellipses.

rsync

On OSX v10.4 and greater, use rsync -aE /Volume/thumbdrive /Users/username/somebackuplocation regularly to backup your thumbdrives without copying data that has not changed. -E might not be useful copying off a FAT32 thumbdrive but it is there in case OSX can actually use those file attribute data on the HFS+ side. Definitely use it if you're backing up to a HFS+ external drive or vice versa. -a is archive mode which sets a bunch of flags that ensures you get a quality backup.  But, timemachine is rather nice, too.  It's really an overglorified, but awesome, rsync :-)


synctoy

Synctoy is software for Windows.  It is an easy to use method to sync files between disks, flash drives, networks, and so on.  If you operate Windows, and maintain files on a fallible flash drive, you better keep backups on your other computers.  Synctoy makes backups faster by only copying files that are new or have been updated.

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