Catalog Course Description
General Description
Course Syllabus
Course Outline
Required Texts
Known hard copy typos
Known html typos
Disclaimer
Return to VADMS Instructional Activities
Catalog Course DescriptionMolecular Biology Computer Techniques 4 (2-6) Prereq BC/BP 364 or 563; GenCB 301. Computer analysis of protein and nucleic acid sequence, secondary structure prediction, protein folding, homology searches and uses of databases. Cooperative course taught by WSU, open to UI students (MMBB 578).
General DescriptionThis course is a lecture/laboratory course with emphasis placed on acquiring bioanalytical computing skills. Students are given hands on experience using the computer in either a sequence analysis or molecular modelling track and then are expected to apply their skills to their own project of interest.
The course is organized as follows: 3 one hour lectures per week for the first 10 weeks of the semester plus at least one three hour lab session for the same time period. The rest of the time is dedicated to the semester project. The time spent in lab escalates as the semester progresses.
Each student is given the necessary account(s) on VADMS platforms in which to carry out their assignments. They use local resources as well as INTERNET ones to complete their tasks.
Course Syllabus
Course OutlineBC/BP 578 is mainly a laboratory course enhanced by lectures. See the syllabus section for a listing of lectures. The following is a listing of brief summaries of each week's activities with a link to the actual exercise. Those weeks with links whose description doesn't include information on the size of the document are not available yet.
Lab Manual for weeks 1 - 3
Week 1: A tour of the
computing resources available to you in this course. [49K doc with 1 gif]
Author: Susan Jean Johns
Week 2: A basic introduction to the computing platforms on which this course will be taught. Items covered include background information on computers, the nature of the computing resources to be used, and instructions on using the text editor. Also included Unix for Beginners. [73k doc with 1 gif, 28k doc] Author: Susan Jean Johns
Week 3: Learning about the concept of databases and how they are organized. Discovering the databases in the VADMS system and learning how to gather information from them. Exploring the nets for more biocomputing databases. [55k doc] Author: Susan Jean Johns
Lab Manual for weeks 4 - 6
Week 4 - molecular modelling
Learning about entering data for various uses. Exploring data formats
and how to use them. [117k doc with 3 gifs] Author: Susan Jean
Johns
Week 4 - sequence analysis Learning about entering data for various uses. Exploring data formats and how to use them. [81k doc with 1 gif] Author: Susan Jean Johns
Week 5 - molecular modelling Learning about the ways to estimate protein secondary structures and the usefulness of these techniques for other purposes. [49k doc] Author: Susan Jean Johns
Week 5 - sequence analysis Unknown DNA: Rational Probe Design and Analysis -- the "Guessmer." How to design and analyze oligonucleotide probes and primers for discovering genes in organisms where they have not been identified when the gene's encoded protein sequence is known in other organisms. [110k doc with 3 gifs] Author: Steven M. Thompson
Week 6 - molecular modelling Learning about advanced data entry techniques. Exposure to recognizing and correcting data input problems. Modification of data files for specialized needs. Modification of MacroModel minimization output files to take into account solvent effects. [78K doc with 1 gif] Author: Susan Jean Johns
Week 6 - sequence analysis DNA Sequencing: The GCG Fragment Assembly Package (FAS) -- getting your fragments into the computer and assembled into a continuous sequence. [53k doc with 0 gifs] Author: Steven M. Thompson
Lab Manual for weeks 7 -9
Week 7 - molecular modelling
Learning about determining the physical characteristics of molecules on
the computer. Coloring the determined secondary structure of a molecule.
Creating and using alpha carbon traces and the superpositioning of
molecules. [41k doc] Author: Susan Jean Johns
Week 7 - sequence analysis Gene Finding Strategies: After the Sequencing's Done, What Next? How are coding sequences recognized in genomic DNA? Searching by signal versus searching by content -- transcriptional/translational regulatory sites and exon/intron splice sites; "nonrandonmess" and codon usage -- understanding the concepts and differentiating between the approaches. [115k doc with 3 gifs] Author: Steven M. Thompson
Week 8 - molecular modelling Learning about doing measurements on molecules and docking them together. [38k doc] Author: Susan Jean Johns
Week 8 - sequence analysis Advanced Database Similarity Searching: What's available, the methods and the algorithms -- motifs, hashing techniques and heuristics, dot matrix analysis, multiple sequence alignments, and profiles. [160k doc with 3 gifs] Author: Steven M. Thompson
Week 9 - molecular modelling Homology Modelling: combining seqeunce analysis and molecular modelling skills to explore the theoretical modelling of unsolved sequences based on solved ones. [102k doc with 0 gifs] Author: Susan Jean Johns
Week 9 - sequence analysis Estimating protein secondary structure and physical attributes: Learning about various methods and the usefulness and limitations of these predictions. [112k doc with 6 gifs] Author: Susan Jean Johns and Steven M. Thompson
Lab Manual for week 10
Week 10 - molecular modelling
Learning about data visualization techniques using Molscript
software. Recognizing desired structural data elements and combining them
with PDB formatted data files from different sources for use in the
software. [55K doc with 0 gifs] Author: Susan Jean Johns Also
included is the MolScript v1.4
documentation [86k doc with 0 gifs].
Week 10 - sequence analysis SeqLab and Molecular Evolutionary Phylogenetic Inference: How GCG's SeqLab Graphical User Interface (GUI) to the Wisconsin Sequence Analysis Package can be used to develop and refine input for programs from PHYLIP (PHYLogeny Inference Package) and how to use the available molecular evolution inference tools to ascertain and draw phylogenetic trees. [339k doc with 15 gifs] Author: Steven M. Thompson and Susan Jean Johns
Required TextsThe following lab manuals are required for BC/BP 578:
lab manual for weeks 1-3, ISBN 0000044733
new: $6.80
lab manual for weeks 4-6, ISBN 0000044741
new: $14.35
lab manual for weeks 7-9, ISBN 0000044768
new: $15.05
lab manual for week 10, ISBN 0000044776
new: $10.90
Known hard copy typos The following is a listing of the typos found in the BC/BP 578 manuals sold through the Bookie for the spring 97. This is not a complete list.
Week 2:- the printing instruction given at the bottom of page 11 should read as follows:
% lpr (your lastname).txt
Known html typos The following is a listing of the typos found in the BC/BP 578 html versions of the manuals for the spring 97.
DisclaimerThe materials presented here are unique to the Washington State University campus. They require the assignments made on the VADMS computing platforms in order to work properly. They are only presented here as examples of instructional materials in biocomputing education field.
In the html versions of these materials a colored bar serves as a divider between such items as the cover page and the rest of the text, the background materials and the actual exercise, the exercise and any appendixes or other included materials. [It has been noted that not all printers produce the gif images as they were intended to be.]