Bioinformatics and Computational Biology Tools

BioCyc
The BioCyc Knowledge Library is a collection of Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism, with the exception of the MetaCyc database, which is a reference source on metabolic pathways from many organisms.

Biology Workbench
A web-integrated access portal to numerous databases and analysis tools

Centre of Bioinformatics at Peking University
Bioinformatics Resources and Services

ConSurf
A server for identification of conserved regions in proteins by surface mapping of phylogenetic information.

Human Genome Project information
A large suite of web sites provided by the U.S. Department of Energy with information and resources on the Human Genome Project from research, medical, ethical, and educational perspectives. Includes primers on the Human Genome Project.

Molecular Visualization Freeware
Eric Martz, U. Massachusetts -Amherst

• Chime
  browser plug-in
• RasMol
  stand-alone

National Center for Biotechnology Information
NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information to researchers and the public.

Protein Explorer
A protein visualization tool, useful in conjunction with several Biology Workbench applications. Protein Explorer is a RasMol-like interface implemented in Chime, but the Protein Explorer can offer much greater assistance and automation. Thus, the Protein Explorer can make visual exploration of protein structure much more accessible to novices, occasional users, or nonspecialists, as well as making it much more convenient than RasMol, even for experts. See in particular Lesson Plans for Molecular Visualization and DNA Structure: An Interactive Animated Nonlinear Tutorial for Protein Explorer educational materials.

UK Human Genome Mapping Project Resource Centre
Bioinformatics Resources and Services

Bioinformatics Links Directory
The Bioinformatics Links Directory features curated links to molecular resources, tools and databases.

Bio-Web
The Bio-Web provides links to cell and molecular biology news, books, tools and resources.

Bioinformatics/Computational Biology
Reports, Lectures, Essays

Lecture on Molecular Evolution
A great introductory text about life from the beginning, and how molecular biology can and is revealing new secrets. By David Nelson, U of Tennessee - Memphis)

About Bioinformatics
A great text about the beginnings of bioinformatics.

Modeling of Biological Systems
This workshop report, from the National Science Foundation, touches biological modeling on a much broader level, dealing with ecology, evolution, and organismal biology, but also molecular and cellular biology.

NCBI Education
A portion of the NCBI site of special interest to educators and students.

NIGMS Computing Life
This website, from the National Institution of General Medical Sciences, introduces you how scientists use computers to advance our understanding of biology and human health.

Computing for Molecular Biology
Lloyd Allison, Monash University. A good explanation of the theory behind computational molecular analysis, even gives a non-technical introduction. Provides some codes for sequence alignment.

Bio-5495
A great resource!! Michael Zucker, Washington University. If you ever wondered just how computational molecular biology was done, this series of lectures will introduce you to the various schools of thought.

Elementary Sequence Analysis
A fantastic starting point!! Brian Golding, McMaster University. This is a great resource for anyone just starting off in computational biology. It begins with an introduction to computer science, basically, and discusses the different sequence databases and how to search them. Sequence selection, alignment, distance matrices, phylogenies, pattern analysis. It's all here!

BioComputing Hypertext Coursebook
Georg Fuellen, University of Bielefeld. Another excellent introductory set of comp bio lectures.

Comparing Genomes in Terms of Protein Structure
Mark Gerstein & Hedi Hegyi, Yale University

Bioinformatics Resources
Stanford University. Links to agencies, societies, archives, centers, databases, conferences, courses, genome centers, genome databases, and protein structure servers.

Comp Bio references
U. of California, Santa Cruz. Links to UCSC resources, a protein-prediction contest, conferences and journals, online courses and texts, and many other miscellaneous, unclassified pages.

Comp Bio Courses
Hongping Liang, Radford University. Computational biology courses, genome analysis, promoter and regulatory elements, gene finding tool, algorithm for sequence analysis, molecular modeling, biological databases and software, bioinformatics resources.

Center for Biological Sequence Analysis
Technical University of Denmark. A huge number of links to databases, protein structure predictions, sequence and structural similarity searchers, alignment and phylogeny tools, universities, journals, newsgroups.

Bioinformatics Course Information
UK HGMP Resource Centre

The Biology Project
U. of Arizona. An excellent and fun look at biology as a whole. "Lectures", activities, quizzes, and much, much more!

SMETE Digital Library
Gateway to a comprehensive collection of science, math, engineering and technology (SMET) education content and services to learners, educators, and academic policy-makers.

National Science Digital Library
Program to build a digital library for education in science, mathematics, engineering and technology, funded by the National Science Foundation (NSF) Division of Undergraduate Education.

SciCentral
A lot of resources related to all sciences, not strictly to biology. Links to courses, labs, papers, special features, you name it. Really take a long look!

The Tree of Life
A collaborative web project, produced by biologists from around the world. On more than 2000 World Wide Web pages, the Tree of Life provides information about the diversity of organisms on Earth, their history, and characteristics. Each page contains information about one group of organisms.

Biology, Medicine, and Other Sciences

BioQUEST
A BSW partner project, the BioQUEST Curriculum Consortium actively supports educators interested in the reform of undergraduate biology and engages in the collaborative development of curricula. See in particular BEDROCK and Bioinformatics and Biology Education.

UIUC-Hughes Biotechnology Education and Outreach Program
Another initiative in biology education, sponsored by a grant from the Howard Hughes Medical Institute and housed at the University of Illinois at Urbana-Champaign, devoted to training teachers and students in biotechnology concepts and hands-on experiments. The program offers workshops and curriculum support to teachers. The program also offers equipment loans to teachers wanting to conduct molecular biology laboratories with their classes.

American Museum of Natural History Seminars on Science
Six-week, online distance learning courses for K-12 educators on a variety of topics, including Genetics, Genomics, Genethics.

Dolan DNA Learning Center
The world's first science center devoted entirely to public genetics education and an operating unit of Cold Spring Harbor Laboratory. Provides curricular activities, workshops, online tutorials, etc. on molecular biology topics.

BioWeb
BioWeb is a collaborative website produced by faculty members from 14 different University of Wisconsin System universities and centers, with the hope to pool resources to improve the quality of biology education at all of the UW-System institutions.

BioLEARN
An on-line collection of biology education activities created for and by Wisconsin high school and middle school biology teachers. Each activity is organized by sub-discipline, has been proven in Wisconsin classrooms and evaluated according to a rubric by BioLEARN team members.

MdBioLab
An initiative between MdBio, Inc., the University of Maryland Biotechnology Institute (UMBI), and The Institute for Genomic Research (TIGR). MdBioLab will travel to high schools throughout the state of Maryland, spending one week at each institution.

Sci-Tech Library Newsletter
Oriented for librarians, but a rich source of news and info for educators and professional scientists as well. By Stephanie Bianchi.

HighWire Press
"Library of Science and Medicine." Electronic access to a huge body of scientific literature.

Nature
One of the leading scientific research and news journals, the Nature website gives access to some of its content free of charge.

PubMed
Free open access to MEDLINE, the premiere index of biological and medical literature, sponsored by the National Center for Biotechnology Information.

Online Mendelian Inheritance in Man (OMIM)
A catalog of human genes and genetic disorders developed for the web by the National Center for Biotechnology Information. The database contains textual information and references. It also contains copious links to MEDLINE and sequence records in the Entrez system, and links to additional related resources at NCBI and elsewhere.

SciCentral.com
A portal to breaking scientific research news from many leading sources. Links to courses, labs, papers, special features, and more. A great source!

ScienceDaily Magazine
A magazine and Web portal devoted to science, technology, and medicine. ScienceDaily is unique in that the magazine's articles are selected from news releases submitted by leading universities and other research organizations around the world.

Education

The Inquiry Page
To find out more about inquiry-based teaching and learning, visit the Inquiry Page, a blossoming community of educators interested in supporting inquiry learning.

Genome: The Secret of How Life Works
This web site contains informative and interactive content for anyone with a genome: students, teachers and parents. Tour the Genome Exhibit, test your knowledge and learn more!

HiCE
The Center for Highly Interactive Computing in Education Investigation Station, at the University of Michigan. Develops learner-centered technology and curricula that address major needs of schools today, enabling all students to learn and enabling students and teachers to engage in serious intellectual inquiry around authentic, meaningful, motivating, mindful-learning experiences. See also HiCE's Palm Pages, a collection of handheld device (Palm) applications for classroom exercises, along with instructions for each.

LESTER
Learning Science and Technology Repository is an online community and database focused on innovations in learning science and technology. LESTER profiles innovative LST research projects, researchers, organizations, and funding sources.

Technology-supported Inquiry Environments for Teaching and Learning
A seminar course offered Spring 2002 at UIUC, coordinated by Dr. Umesh Thakkar. Site has links to class lectures, information on a variety of educational technologies for science teaching, class projects, etc.

"Teachers' biology training put to test in mock murder trial," from The Tennesseean (Nashville)
Nice, short article on one teacher's biology class efforts.

Bioinformatics for High School Women

Digital Knowledge Research Collaborative

Illinois Learning Standards

National Science Education Standards

The WebQuest Page
This site is designed to serve as a resource to those who are using the WebQuest model to teach with the web. By pointing to excellent examples and collecting materials developed to communicate the idea, all of us experimenting with WebQuests will be able to learn from each other.

Organizations and Institutions

The Shodor Education Foundation
The Shodor Foundation is a non-profit research and education organization dedicated to the advancement of science and math education, specifically through the use of modeling and simulation technologies. Included on this site are instructional resources and software ready to be used in the classroom.

Illinois Science Teachers Association (ISTA)

National Association of Biology Teachers (NABT)

National Education Association (NEA)

National Science Foundation (NSF)

General

The Open Directory
"The Open Directory Project is the largest, most comprehensive human-edited directory of the Web. It is constructed and maintained by a vast, global community of volunteer editors . . . As the Internet grows, so do the number of net-citizens. These citizens can each organize a small portion of the web and present it back to the rest of the population, culling out the bad and useless and keeping only the best content." Check out the Bioinformatics Education section.

Creative Commons
a movement to allow IP creators to reserve "some" rights to their work while still allowing most kinds of public access. This site may be of interest to those writing tutorials, software, and other educational materials, and we encourage BSW authors to consider making use of these kinds of licensing arrangements if they have concerns about maintaining control over their work.