Class 1: Introduction (Draft)

Welcome to Research Tools, Fall 2011. This course is designed to familiarize you with software and processes to facilitate collecting, managing, and processing scientific data. You will also be learning ways to manage the writing process: managing references, tracking changes in your documents, building papers, and group writing. The class will be a success if some of these tools make the rest of your research career more productive and enjoyable.

The syllabus will be updated as the course progresses. The schedule is not currently set and will be starting to be updated soon.

Classes will have audio recordings that will be published. You are welcome (and encouraged) to make your own recordings of the lectures.

• Where: Rm: 142, Chase Ocean Engineering, University of New Hampshire
• When: Tuesdays and Thursdays 11:10-12:30

This is a hands on class. You will be in front of a computer during class throughout the semester. Please feel free to use the computer to take notes or use instant messanger or Internet Relay Chat (IRC) to discuss the course material, but do not use the computers for non-class related topics.

All of the technologies have been chosen to be readily available and likely to be around for many years to come. You will gain experience with the following (do not worry if you have not heard of some or all of these). Because this is a one semester class, we will not be able to go into depth on these topics, but this should provide the foundation for you to learn more when you need or want to.

Note: this is not the order that we will cover the material and we might not get to all of these in class.

• Security
  • How to manager large numbers of passwords
• Linux, the "BASH" shell (command line), and VM Ware virtual machines
• The Python programming language and Matplotlib for creating graphs
• Structured Query Language (SQL) for simple databases, the SQLite database engine, and the SQLite Manager Firefox Plugin
• eXtensible Markup Language (XML) for data and ISO metadata
• The EMACS text editor and the "org-mode" text format
• LaTeX and HTML formats for publishing writing
• Bibtex journal reference format. Jabref and Zotero software for managing references
• Mercurial (hg) distributed version control system (DVCS)
• Generic Mapping Tools (GMT) and MB System for reading multibeam sonar data.
• QuantumGIS (QGIS), GDAL and Proj.4 for general GIS tools
• Google Earth, Google Fusion Tables, and NASA World Wind
• Internet Relay Chat (IRC)
• Collecting data from serial ports and over the network (TCP and UDP)
• Mediawiki based wikis
• GeoMapApp

Topics that I would like to cover, but probably will not be able to get to:

• R for statistical analysis
• GRASS - a large GIS system
• Octave (an open source subset of Matlab)