SWBIC Educational Resources
Courses & Tutorials

SWBIC Educational Resources  >> Courses & Tutorials

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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 Pal� (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.