In the fall of 2003, Matt DeJongh from the Computer Science department and Maria Burnatowska-Hledin from the Biology and Chemistry departments co-taught an introductory course in bioinformatics at Hope College (see article in Transformations). This course was designed to bring together computer science majors and biology majors to teach them the basics of bioinformatics and engage them in research projects. The goals for the course were:
We were particularly interested in giving the students a cross-disciplinary experience, so that the computer scientists could learn the language of the biologists, and vice versa.
The two textbooks chosen for this course were:
The course was structured as a 3-hour lab, meeting once a week in a computer lab. Each week the students were responsible for some reading and exercises from one or both textbooks prior to coming to the lab. During the lab, we spent 1 hour or so lecturing on background concepts in molecular biology and computer science, then we gave students lab work involving bioinformatics exercises and programming assignments. During the latter part of the semester, the students used the lab time to work in interdisciplinary teams on research projects under our supervision and that of other faculty.
The following documents contain the lab exercises assigned to students. They are intended to complement their reading and work in Bioinformatics for Dummies, and serve to familiarize the students with existing bioinformatics concepts and tools. Answer keys are provided for the Formal Response Questions in each lab exercise.
| Document | Description | Reading | Answer Key |
|---|---|---|---|
| Lab I Word PDF | This lab contains introductory material about HIV, which is used as a uniting theme through all the labs. It also introduces the use of PubMed. | Chapters 1 and 2 | Word PDF |
| Lab II part 1 Word PDF | This lab introduces GenBank records for DNA sequences, and LocusLink records for information associated with genetic loci. | Chapter 3 | Word PDF |
| Lab II part 2 Word PDF | This lab demonstrates the use of whole genome browsers, including the NCBI genome browser, TIGR, Ensembl, and the UCSC and Vista browsers. | Chapter 3 | Word PDF |
| Lab III Word PDF | This lab discusses DNA sequence analysis, including screening for vectors, analyzing the nucleotide composition, and finding genomic repeats. It also introduces the BLAST tool for similarity searches. | Chapters 5 and 7 | Word PDF |
| Lab IV Word PDF | This lab shows procedures for analyzing RNA and doing phylogenetic analysis using RNA. | Chapter 12 | Word PDF |
| Lab V Word PDF | This lab discusses protein sequence analysis, including alignments using BLAST, and the prediction of physico-chemical properties such as molecular weight. | Chapters 4, 7 and 8 | Word PDF |
| Lab VI Word PDF | This lab continues with protein sequence analysis, stepping through searches for motifs and conserved domains, and prediction of secondary protein structure. | Chapters 6 and 11 | Word PDF |
| Lab VII Word PDF | This lab continues with protein sequence analysis, stepping through prediction of tertiary protein structure. | Chapter 11 | Word PDF |
| Lab VIII Word PDF | This lab continues with protein sequence analysis, stepping through multiple sequence alignment and iterative BLAST searches. | Chapters 7, 9 | Word PDF |
| Lab IX Word PDF | This lab describes phylogenetics analysis. | Chapter 13 | Word PDF |