ACHS Class Information

Class Descriptions and Prerequisites

The classes at ITC-ACHS are designed for persons doing medical and biological research at the University of Virginia. All examples and demonstrations reflect this design. All microcomputer classes assume a basic operational knowledge of either the Windows95/NT or Macintosh operating systems. ITC classes are available for training in these areas.

Introduction to FreeHand

This course is designed for the user who has little or no experience in using FreeHand. Students will be learning the use of the basic tools associated with FreeHand as well as how to insert and manipulate images and text to create figures, banners and posters. The use of color within FreeHand as well as printing problems and solutions will also be discussed. All examples in the course will relate to creating and annotating medical images and figures for use in publication and presentation.

Introduction to ImageQuant

This course is designed for those who are new to the Molecular Dynamics gel analysis software known as ImageQuant. The course provides a general overview of the ImageQuant package and demonstrates how to use ImageQaunt to analyze 1-dimensional protein gels.

PhotoShop

The ACHS Photoshop workshop is designed specifically for researchers putting together figures for grants, publications, and posters. The objective is hands-on learning of effective ways to do common tasks. The course focuses primarily on printing images (not web graphics). This four-hour afternoon workshop begins with a 20 minute introduction to the Photoshop workspace (which should be review), jumps into how to "clean up" a fresh scan and put two images on a page, and then ends with repairing a tear in a gel. This course is not an introduction to Photoshop. It assumes that participants have used Photoshop and wish to fine-tune their skills. It does not count toward the ITC web certification program available through ITC-Training.

Prerequisites: ITC Photoshop Fundamentals course, or having used Photoshop to put together at least three figures. If you have any questions about the course content or whether the course will benefit you, please contact Stacey Hughes via email or telephone.
sah4j@virginia.edu Phone: 982-4025

Introduction to Unix, Parts I and II

These courses are not currently being offered at ACHS.

This course is intended as a general introduction for those who are new to UNIX. It will provide the basic tools you need to use the powerful sequence analysis and other programs that are available in UNIX. Highly recommended for those who want to do sequence analsis with the GCG package. For further information you may also refer to the class handouts which are document ACHS-304 and document ACHS-305. The course will cover the following topics:

  1. User interfaces available on ITC Unix machines.
  2. An overview of the Unix file structure.
  3. Basic UNIX commands for file manipulation and printing.
  4. A short description of file permissions.

Introduction to GCG using SeqWeb

For those who are new to sequence analysis. This course is intended for those who have never used GCG. It will provide a gentle introduction to the most powerful sequence analysis package available. After completion you should be able to run most GCG programs. For further information you may also refer to the class handouts which are document ACHS-306 and document ACHS-310. The following topics will be covered:

  1. Starting GCG and getting help.
  2. An overview of the basic abilities of the program package.
  3. The GCG sequence format and how to reformat sequences.
  4. How to use the sequence editor.
  5. Running a typical GCG programs and setting the program options.

Intermediate Sequence Analysis using SeqLab

This course will focus on multiple sequence analysis and is intended for those who have done some sequence analysis, but would like to do more advanced work. Some basic knowledge of GCG is assumed. This course is strongly recommended for those who want to do the PHYLIP course. For further information you may also refer to the class handout which is document ACHS-307. The course includes the following:

  1. Specifying multiple sequences and using list files.
  2. Multiple sequence format (MSF) files.
  3. How to specify MSF files for alignments and editors.
  4. The multiple sequence editor (Lineup). How to proofread, modify and annotate sequences.
  5. Dealing with difficult alignments. The effects of program parameters and how to force alignments.
  6. How to prepare sequence alignments for publication with Microsoft Word and PageMaker.

Phylogenetic Analysis

This course is an introduction to the PHYLIP phylogenetic package and assumes a knowledge of sequence analysis and a UNIX text editor, such as Pico, EMACS, Vi, or Jove. Participation in the Multiple sequence analysis workshop is highly recommended. For further information you may refer to the class handouts which are document ACHS-309 and document ACHS-311.

  1. A short overview on the different types of phylogenetic analysis and commonly used terms.
  2. How to initialize the package and to set up your directory with all the necessary files.
  3. Formatting input files.
  4. Transferring files between GCG and PHYLIP with READSEQ.
  5. Running parsimony and distance matrix programs and interpreting results.
  6. Bootstrapping and statistical significance.

 

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