Usage Policy: You may link to these resources and download PowerPoint
presentations for personal use. Copying and including these materials
on other web pages is prohibited except when approved by SWBIC.
Courses & Tutorials
Bioinformatics -
Many detailed PowerPoint presentations suitable for introductory
upper division or graduate courses in bioinformatics. The
presentations are organized for lecture or reference, with an
index describing their use. The course materials emphasize
bioinformatics applied to DNA and protein sequences and protein
structures. The analysis tools described are accessible through
freely available Internet resources. Other topics like molecular
phylogenetics and PCR primer design are also introduced, and some
of the materials would also be suitable for use in genetics or
genomics courses. These materials were developed by Dr. R. L.
Bernstein of San Francisco State University while on sabbatical
at SWBIC and will be presented in his bioinformatics course at
SFSU. SWBIC resources and presentation materials have been
incorporated into the slides.
Bioinformatics
& Genome Analysis [NMSU, MolBio 470 Spring 2001]
- This course introduces the basic concepts of the discipline of
bioinformatics and introduces basic computational tools and methods that are
used in the organizing and analysis of data. It includes an introduction
to large-scale DNA sequencing methods, and the methods and algorithms used to
perform analyses such as alignments, homology searches, and advanced
searching techniques. In addition the course will present basic computational
tools such as use of the WWW, Unix fundamentals, file management, and
database concepts.
Computational Management of Molecular Biological Information -
This basic bioinformatics course was authored by Dr. Narayanan B. Perumal
from Florida State University for the SWBIC web site. The course is
presented in lecture notes format with accompanying laboratory
exercises and will provide a good overview of the fundamentals
of Computational Molecular Biology. Links to a large number of
bioinformatics related resources on the Internet are provided
within the course modules.
Genome Sequencing, Fragment Assembly, and the use of Consed, Phred, and Phrap
- A PowerPoint presentation on genome sequencing methods
with a focus on how sequence fragments are assembled.
Topics include: review of DNA structure, polymerase chain reaction,
sequencing chemistry, raw sequence data, shotgun sequencing approach,
and treatment and assembly of sequence fragments.
The methods used by Phred and Phrap for base calling,
sequence quality determination,
and fragment assembly are treated extensively,
including computer science techniques used by these programs.
Authored by Oliver Hampton (SWBIC graduate student employee),
Phuc Nguyen, and Alessandro Dal Palú
(NMSU Computer Science graduate students).
-[Prepared using Microsoft Power Point 2000. It may
be viewed on-line or downloaded and viewed locally using Microsoft Power
Point.
Tutorial in Molecular Biology
- A set of tutorials on retrieving a gene sequence or a family of gene
sequences, constructing a family of aligned protein sequences, and displaying
the 3-dimensional structure of a protein.
Soil Bioremediation
- A PowerPoint presentation giving reviews and case histories of four major
bioremediation processes: bioventing, land treatment, slurry phase treatment,
and composting.
-[Presentations have been prepared using Microsoft Power Point 97. They may
be viewed on-line or downloaded and viewed locally using Microsoft Power
Point.
Introduction to Environmental
Engineering
- A course covering principles in environmental engineering and science:
physical chemical systems and biological processes as applied to pollution
control.
