IBEST - news and events - Summer 2005
IBEST in the News
Monday, May 16 2005.
UI Graduate First to Earn Bioinformatics And Computational Biology Degree
IBEST weekly discussion group
The IBEST discussion group meets every week in the UI Commons. Download a copy of the summer 2005 calendar (pdf 40K), or contact James A. Foster, foster@cs.uidaho.edu, IBEST Director.
The public is welcome.
BCB Handbook
The BCB Handbook is now here! This document answers any questions students may have regarding admissions, requirements, and degree procedures for the BCB graduate program.
For more information download the BCB Handbook (pdf 52K)
Student activities
The BCB Journal http://emerson.hungry.com/bcbjc/»
The BCB Journal Club is intended for graduate students studying Bioinformatics and Computational Biology (BCB) at the University of Idaho, although anybody with an interest in the material is welcome to participate.
Selected papers from the IBEST community
Dr. Steven J. Brunsfeld Steven Brunsfeld»
“Evidence for a glacial refugium in the northern Rocky Mountains”
The mesic coniferous forests of the Pacific Northwest are divided into coastal/Cascadian and northern Rocky Mountain segments, which are isolated from each other by the arid Columbia River Basin. Many plant and animal species have a disjunct distribution between the coastal and inland mountains, whereas other species are endemic to one region. As part of a larger effort to test hypotheses on the phylogeography of the region, we have begun to analyze species with both endemic and disjunct distributions. We are using molecular genetic data to test hypotheses on whether Rocky Mountain mesic forests are the result of ancient vicariance and subsequent survival in river canyons south of glaciation.abstract»
Dr. Holly A Wichman Holly A Wichman»
“Experimental evolution recapitulates natural evolution”
Genomes of the closely related bacteriophages ΦX174 and S13 are 5386 bases long and differ at 114 nucleotides, affecting 28 amino acids. Both parental phages were adapted to laboratory culture conditions in replicate lineages and analysed for nucleotide changes that accumulated experimentally. Of the 126 experimental substitutions, 90% encoded amino-acid changes, and 62% of the substitutions occurred in parallel in more than one experimental line.paper (pdf 311kb)»
Selected lectures from the IBEST community
Dr. Larry J. Forney Larry Forney»
Sample lectures from Biology 111, Evolution/Diversity of Life
This course has two objectives. The first objective is to explain and
illustrate various aspects of chemistry and biology that are common to all organisms, and to provide a fundamental understanding of eukaryotic and prokaryotic cell structure and function. A second objective of the course is to help students better grasp the mechanisms and consequences of adaptive evolution. The lectures, laboratory exercises, and assignments will emphasize the following aspects of evolutionary biology:
- Lab 7: Clarifying Monet (pdf 100kb)»
- Perhaps when most people take a walk through a garden or a park or the countryside, they see a pleasant blend of greens, along with the colorful blooms of flowers. To plant systematists, however, these scenes are not only aesthetically pleasing, but present a great challenge. There are over 1/4 million species of plants currently recognized, and with many tropical areas of the world poorly documented, there are likely thousands more species yet to be discovered. The challenge plant systematists face is to discover the evolutionary relationships of the world’s plants, and subsequently classify the world’s species of plants based on how closely they are related to other plants. To do so, a variety of information is used, including morphological data, genetic data, ecological data and even fossil evidence.more…
- Lab 8: Life is Full of Chances (pdf 120kb)»
- “Mutations” are changes that occur in the sequence of nucleotides that comprise DNA. A change in the sequence of nucleotides in DNA will result in a change in the sequence of the corresponding messenger RNA (mRNA) if and when the DNA is transcribed. When the mutant mRNA is used as a template for the synthesis of a protein, (a) a protein with a new amino acid sequence can be produced, (b) the synthesis of the protein can be prematurely terminated, or (c) the sequence of the protein can remain unchanged.more…
- Lab 9: Mistakes Happen (pdf 104kb)»
- The word “mutation” tends to have a negative connotation, but mutations are essential to all forms of life. Without mutations, species would not be able to adapt to changes in the environment, and evolution would not occur. The variation in the genomes of individuals within a species provides the genetic material upon which natural selection acts. Although there are a number of enzymatic systems that cells use to repair certain types of mutations, they are unable to repair, and it would be unwise to suppress, all mutations. Accordingly, each species has evolved to have a mutation rate that ultimately benefits the species as a whole.more…
Links suggested by IBEST members
Interesting links for students interested in Bioinformatics.
- Biotext» Prof. Marti Hearst UC Berkeley
- “New methods and tools are needed to improve how bioscience researchers search for and synthesize information from textual descriptions of bioscience research. We are building a flexible, efficient, platform-independent database system infrastructure specifically geared towards supporting the advanced and particular search needs of bioscience researchers. We are using this infrastructure to support the development and deployment of statistical approaches to natural language processing, which will identify entities and relations between them in bioscience texts. This will in turn facilitate more effective search and synthesis. We are working with bioscience researchers to develop intuitive, appealing, interfaces for using these facilities to perform efficient and effective searches. The resulting system will support new ways of asking scientific questions of the underlying databases, and new tools for assembling the pieces of biosciences puzzles.”
- What is Bioinformatics?»
- Sponspored by the National Center for Biotechnology Information this site introduces you to the field of Bioinformatics.
- National Institutes of Health»
- Founded in 1887, the National Institutes of Health today is one of the world’s foremost medical research centers, and the Federal focal point for medical research in the United States. The NIH, comprising 27 separate Institutes and Centers, is one of eight health agencies of the Public Health Service which, in turn, is part of the U.S. Department of Health and Human Services.
- The Human Genome Project»
- Genomic Research began with The Human Genome Project (HGP), the international research effort that determined the DNA sequence of the entire human genome, completed in April 2003.
Selected sites from the Scout Report»
The Changing Face of Medicine»
The Changing Face of Medicine is a new exhibit at the National Library of Medicine that explores “the many ways that women have influenced and enhanced the practice of medicine.” The online version of the exhibit is quite extensive, and includes a resources section with downloadable lesson plans, a lengthy list of suggested reading, and a students’ guide to a career in medicine. There are four groups of lesson plans for various grades (K-2, 3-4, 5-8, and 9-12). Topics covered include human senses, the circulatory system, adolescent health, and medical careers. The site also offers four online interactivities — fun, multimedia features “that use games and learning modules to bring issues of science and medicine to life.” [RS]
the scout report, October 31, 2003
A Revolution in Progress: Human Genetics and Medical Research»
The DeWitt Stetten, Jr., Museum of Medical Research at the National Institutes of Health presents this online version of the new exhibit, “A Revolution in Progress,” which offers a comprehensive look at genetic research and its contribution to medical science. Readers can really cover some ground with this Web site, with pages upon pages devoted to a wide range of topics including genetic diseases, genes and drugs, the Human Genome Project, ethics and genetics, and more. Not overly familiar with genetic concepts? The Genetic Basics area of the site provides a solid and easy-to-follow introduction to the field. There is also a cartoon guide to genetics for kids. [RS]
the scout report, June 27, 2003
Bioinformatics.org»
Bioinformatics.Org is a nonprofit academic organization that is committed to promoting the free exchange of biological information. This Web sitecurrently hosts 48 research projects, along with free software and news. The Frequently Asked Questions section provides an overview of the field of bioinformatics, other resources, and career information. Even though free, registration is required to access some sections of the site.
the scout report, February 8, 2002
