IGERT NIMBIOS NSF

SCALE-IT Biology Curriculum Workshop June 22-26, 2009

This page will contain resource used at the workshop and participant projects that can be found following the workshop.


Resources

      Participant Projects           E-science Resources             Tools              Educational Links


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If you have question email to sje@sbb.uvm.edu

Participant Projects

    1. Extreme Genes: Extremes in Human Transcript and Protein Sizes
    2. The mystery of the enolase pocket
    3. Alcohol and Asian Flush: Breaking down the structure of the enzyme ALDH2
    4. Do HIV-1 Sequence Trees have similar structures in AIDS Paitients?
    5. The Crash!!!!! HIV-The Silent Killer
    6. Sequence/Structure Variability in the Major Histocompatibility Complex Protein Class I alpha chain.
    7. Understanding HIV / AIDS from a Bio-Math Perspective
    8. Classroom Pearls for Life Sciences and Mathematics Students
    9. A Devil of a Disease

4H Sharing

Biology in a Box
http://eeb.bio.utk.edu/biologyinbox/
Biology in a Box is a fun and challenging way for entire K-12 schools to enhance their life sciences curriculum

Biology Scholars
http://www.biologyscholars.org/
Life sciences professional societies have established the Biology Scholars Program to enhance biologists understanding and practice of evidenced-based teaching and learning

KEEP toolkit
http://www.cfkeep.org/
A set of web-based tools that help teachers, students and institutions quickly create compact and engaging knowledge representations on the Web

BS in Bioinformatics
http://www.ist.unomaha.edu/?p=und/bio
Mark Pauley's development of a integrative program in bioinformatics

Mark Pauley's CCLI for Integrating Bioinformatics in the Life Sciences
http://ccli.ist.unomaha.edu/
Includes week long modules for introducing bioinformtics in various courses

Tree Thinking PubMed link
http://www.ncbi.nlm.nih.gov/pubmed/16284166
Don't forget to also download the Supplement material (quizes)

Computing Life
http://publications.nigms.nih.gov/computinglife/
Published by the National Institute of General Medical Studies Find out how biomedical engineers, mathematicians, physicists, and biologists use computers to answer important health-related questions (free booklet).

Human Microbiome Project (HMP)
http://nihroadmap.nih.gov/hmp/
Within the body of a healthy adult, microbial cells are estimated to outnumber human cells by a factor of ten to one. These communities, however, remain largely unstudied, leaving almost entirely unknown their influence upon human development, physiology, immunity, and nutrition. To take advantage of recent technological advances and to develop new ones, the NIH Roadmap has initiated the Human Microbiome Project (HMP) with the mission of generating resources enabling comprehensive characterization of the human microbiota and analysis of its role in human health and disease.


E-science Resources: Data Collections and Analysis Tools

American Journal of Undergraduate Research
http://www.ajur.uni.edu/
A refereed journal for undergraduate research in the pure and applied sciences, mathematics, engineering, technology, and related areas in education

ASM MicrobeLibrary
http://www.microbelibrary.org/
Peer-reviewed resources for teaching undergraduate microbiology

CaseIt!
http://caseit.uwrf.edu/caseit.html
Framework for collaborative case-based learning via open-ended molecular biology computer simulations with cases based primarily on genetic and infectious disease

CELLS alive!
http://www.cellsalive.com/
Film and computer-enhanced images of living cells and organisms for education and medical research

CIteSeer Scientific Literature Digital Library
http://citeseerx.ist.psu.edu/
Digital library focusing primarily on the literature in computer and information science

DOAJ: Directory of Open Access Journals
http://www.doaj.org/
This site covers free, full text, quality controlled scientific and scholarly journals

GAPMINDER
http://www.gapminder.org/
Unveiling the beauty of statistics for a fact based world view

Gordon Research Conference on Visualization in Science and Education
http://www.grc.org/programs.aspx?year=2009&program=visualiz
Meeting every other year to discuss visualization in science and education.

ImageJ
http://rsbweb.nih.gov/ij/
Free software for image processing and analysis.

Kimball's Biology Pages
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/
Online biology textbbook

MathDL: The MAA Mathematical Sciences Digital Library
http://mathdl.maa.org/
MAA Reviews, Classroom Capsules, Notes and more!

MERLOT (Multimedia Educational Resource for Learning and Online Teaching
http://www.merlot.org/merlot/
Peer reviewed online teaching and learning materials

OER Commons
http://oercommons.org
Free-to-use teaching and learning content from around the world!

SENCER: Science Education for New Civic Engagements and Responsibilities
http://www.sencer.net
Building civic capacity by connecting the science of learning to the learning of science

SOURCEFORGE.NET
http://sourceforge.net
Find and build open source computer resources

The Journal of Young Investigators
http://www.jyi.org
Undergraduate, peer-reviewed science publishing

The Virtual Cell
http://www.ibiblio.org/virtualcell/
Examine cells


Tools

Biology Workbench
http://workbench.sdsc.edu       Getting Started with the Biology Workbench (PDF)
The Biology WorkBench is a web-based resource for analyzing and visualizing molecular data developed at NCSA (the National Center for Supercomputing Applications). Undergoing continued development at the San Diego Supercomputer Center, the innovative Biology WorkBench integrates access to many tools within a simple graphical user interfacse.Database searching is integrated with access to a wide variety of analysis and modeling tools, all within a point and click interface that eliminates file format compatibility problems.

Biology Student Workbench
http://peptide.ncsa.uiuc.edu/

The Biology Student Workbench consists of curricular materials centered around molecular biological investigations, links to educational, scientific, computational, and informational resources, and communication tools to bind together a contributing community of educators. It is designed to give a transparent introduction to the use of the Biology Workbench for learning and teaching biology at all levels.

SIB Homepage (Student Interface to the Biology Workbench) and other Bioinformatics information
http://deltas.animal.uiuc.edu/sibdoc/index.html

Bioinformatics Education section of the Open Directory project.
http://dmoz.org/Science/Biology/Bioinformatics/Education/
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. Instead of fighting the explosive growth of the Internet, the Open Directory provides the means for the Internet to organize itself. 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.

Case It!
http://www.uwrf.edu/caseit/caseit.html
Case It! is a National Science Foundation-sponsored project initiated by members of the BioQUEST Curriculum Consortium and based at the University of Wisconsin-River Falls and Michigan State University. The goal is to provide a framework for collaborative case-based learning in molecular biology using interactive computer simulations, and to have high school and university students from around the world participate via Internet conferencing.

The ConSurf Server
http://consurf.tau.ac.il
Server for identification of functional regions in proteins.

GeneDoc
http://www.psc.edu/biomed/genedoc

GeneDoc is a full featured multimple sequence alignment editor and shading utility.

The Inquiry Page
http://inquiry.uiuc.edu/
This is a dynamic virtual community where inquiry-based education can be discussed, resources and experiences shared, and innovative approaches explored in a collaborative environment. You can search a growing database of inquiry units, and you can also build your own inquiry units. You can see pictures of inquiry-based activities and learn more about some of our partners who use inquiry methods. Learn how to assess and evaluate inquiry-based education or look for more inquiry resources to support what you're doing.

John C. Herron's Evolution Simulation Software for Evolutionary Analysis
http://faculty.washington.edu/~herronjc/SoftwareFolder/software.html

National Center for Biotechnology Information (NCBI)
http://www.ncbi.nlm.nih.gov
Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease.

NCBI Education
http://www.ncbi.nlm.nih.gov/Education/

OMIM™ Online Mendelian Inheritance in Man
http://www.ncbi.nlm.nih.gov/omim/
This database is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center for Biotechnology Information. The database contains textual information, pictures, and reference information. It also contains copious links to NCBI's Entrez database of MEDLINE articles and sequence information. The OMIM Morbid Map, a catalog of genetic diseases and their cytogenetic map locations arranged alphabetically by disease, is now available.

Protein Data Bank
http://www.rcsb.org/pdb/
The Protein Data Bank is a worldwide archive of three dimensional structural data of biological macromolecules. The PDB collects, validates, and distributes as widely as possible the experimental models of proteins. The management of the PDB is the responsibility of the Research Collaboratory for Structural Bioinformatics (RCSB). The vision of the RCSB is to create a resource based on the most modern technology that facilitates the use and analysis of structural data and thus creates an enabling resource for biological research. The RCSB PDB is supported by funds from the National Science Foundation, the Department of Energy, and the National Institutes of Health.

Protein Explorer
http://molvis.sdsc.edu/protexpl/frntdoor.htm
(PE) version 2.0 enables visualization of macromolecular 3D structure with exceptional ease of use. Visual analysis of proteins, nucleic acids, and ligand interactions can be done largely from menus, buttons, and forms, with context-sensitive help and color keys displayed automatically. PE employs the Chime plugin that is derived from RasMol, and PE understands all RasMol commands. However, PE enables visual analysis to considerable depth without learning a single RasMol-style command, and it is much more powerful than RasMol. PE enables easy selection of portions of a molecule, to apply different rendering or coloring schemes, and to hide selected moieties. In addition it has one-click routines to map sequence to structure, show contact surfaces (overview of noncovalent bonds to any moiety), solvent-accessible surfaces, cation-pi interactions, and salt bridges. Advanced routines simplify finding noncovalent bonds, and coloring a protein by conservation/mutation from a multiple protein sequence alignment. Websites can include hyperlinks to Protein Explorer that prespecify molecule(s). Adopted by the Protein Data Bank as a 3D structure viewer. Authored by Eric Martz, using MDL Information Systems' Chemscape Chime freeware. PE is freeware for Windows or Macintosh.

SeqPup
http://iubio.bio.indiana.edu/soft/molbio/seqpup/About-seqpup.text
SeqPup is a biological sequence editor and analysis program. It includes links to network services and external analysis programs. It is usable on common computer systems, including Macintosh, MS-Windows and X-Windows.

SWISS-PROT
http://www.expasy.ch/sprot/
SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotations (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases

Tree Finder
http://www.treefinder.de/
TREEFINDER computes phylogenetic trees from nucleotide sequences. Using the widely accepted Maximum Likelihood method, it supports six popular models of sequence evolution up to the general time reversible model with Gamma distributed rates among sites. All model parameters including the rate heterogeneity can be estimated from the data. A genetic tree search algorithm explores tree space for the likeliest trees, having a good chance to not being trapped in local optima of the likelihood surface. Its exhaustiveness is accomodable to the users patience.


Workshop Links

Future Workshop Opportunities
http://www.computationalscience.org/workshops/summer07/index.html

Open Educational Resources
http://oercommons.org/

NCBI Mini Courses
http://www.ncbi.nlm.nih.gov/Class/minicourses/
NCBI bioinformatics mini-courses are either problem based, such as "Identification of Disease Genes" or NCBI resource based such as "BLAST Quick Start". The courses are 2 hours in length with first hour devoted to an overview that is followed by a one hour hands-on session. The courses are free and NCBI is beginning to offer the mini-courses at extramural institutions as well. In these cases, NCBI pays for the travel expenses of the instructors.

Web links for Investigative Case Based Learning
http://bioquest.org/icbl/asmcue2005

CancerQuest
http://www.cancerquest.org
Designed to educate the layperson about the biology of cancer and cancer treatments. Note interactive visualizations.

BioMed Central
http://www.biomedcentral.com/
Publisher of a collection of peer-reviewed, Open Access microbiology/infectious disease journals.

The Public Library of Science
http://www.plos.org/
The Public Library of Science (PLoS) is a non-profit organization of scientists and physicians committed to making the world's scientific and medical literature a freely available public resource.

Genome Biology
http://genomebiology.com
Serves the biological research community as an international forum, both in print and on the web, for the dissemination, discussion and critical review of information about all areas of biology informed by genomic research.

Faculty of 1000
http://www.f1000biology.com/
A new online research service that will comprehensively and systematically highlight and review the most interesting papers published in the biological sciences, based on the recommendations of a faculty of more than 1000 selected leading researchers.

Teach The Earth
http://serc.carleton.edu/teachearth/topics.html#teaching
Using visualizations and datasets and models, interactive lectures, fields labs, quantitative literacy, petrology, structural geology, designing courses and much more

Free Medical Journals
http://freemedicaljournals.com/
Dedicated to the promotion of free access to medical journals over the Internet.

NIH AIDS Research and Reference Reagent Program
http://www.aidsreagent.org/
Free resource of more than 6,500 biologicals and chemicals for the study of HIV and others. To register with the AIDS Reagent Program, you must be a Principal Investigator, Laboratory Director, or equivalent (public or academic institution), or a Director of Research or equivalent (private or for-profit institution).

Transferrins Page
http://www.chatham.edu/undergraduate/bio/lambert/transferrin/transferrins.htm
A Project BEDROCK exploration site managed by Lisa Lambert.

Free Human Genome Project Booklet
The Human Genome Project (HGP) has created a free, downloadable publication covering what is known so far about this subject. The publication is available at http://www.ornl.gov

Genetic Science Learning Center

http://gslc.genetics.utah.edu/

Transposon Bank
http://ctcworldsrv1.tc.cornell.edu/people/cmaher/bioquest/index.html
This site assists individuals in learning about transposable elements (TEs) and their effects on everyday lives. It features examples from the worlds of garden peas, the critically important food crop rice, and the interrelationships between a commercial crop, cotton, its pest, and current management strategies.

Bioweb - Scott Cooper
http://bioweb.uwlax.edu/GenWeb/Molecular/molecular.htm
BioWeb is a collaborative website produced by faculty members from 14 different University of Wisconsin System universities and centers. By pooling our resources we hope to improve the quality of biology education at all of the UW-System institutions.

Bioinformatics Module
http://bioquest.org/bioinformatics/module/
A number of linked investigations and tutorials that are in the developmental phase by the Biology Student WorkBench project collaborators.

Molecular Evolution - David R. Nelson
http://drnelson.utmem.edu/evolution.html
Lecture on Molecular Evolution I

David Sheppard's materials
http://www.udel.edu/Biology/sheppard/bosbu/BostonBioinformatics.html
Lessons designed for use with SeqWeb, a sequence analysis program licensed for use by GCG. Files are in PDF format and can be printed to any printer using Adobe Acrobat Reader.

Looking into Glycosidases: A Bioinformatics Resource for Biology Students
Editable Word Doc (2.3 MB)     PDF Version (1 MB)
Utilizing strategic molecular investigations, bioinformatics, and visualization tools in undergraduate biology is supported here by a number of scenarios for investigation. Several introductory molecular problem spaces are featured with appendices on the glycosidases, resources, internet tools, and selected literature. NOTE: None of these scenarios comes with a solution. We generated many supportable hypotheses while working on the problems and hope you will enjoy similar success! Written by Ethel Stanley and Keith Stanley.

The EdGrid Project
http://bioquest.org/bioinformatics/EdGrid/
The Educational Grid (EdGrid) Biology Student Workbench (BSW) project is a growing collection of enhancements to the Biology Workbench including tutorials and inquiry-based materials, all of which help students and teachers conduct meaningful investigations in molecular biology. The project specifically addresses a pre-service teacher audience, and it supports the use of the inquiry-based learning and teaching approach to science education.

Action Bioscience
http://www.actionbioscience.org/
ActionBioscience.org is a non-commercial, educational web site created to promote bioscience literacy. the web site provides articles by scientists, science educators, and science students on issues related to seven bioscience challenges: environment, biodiversity, genomics, biotechnology, evolution, new frontiers in science, and bioscience education. In addition, the web site provides educators with original lessons and resources to enhance bioscience teaching.

USGS
http://fresc.usgs.gov/index.html
The USGS Forest and Rangeland Ecosystem Science Center provides research and technical assistance in support of sound management and conservation of biological systems in the western United States.


Other Resources

Highwire Press - Stanford
http://highwire.stanford.edu/
Stanford University Libraries' HighWire Press began in early 1995 with the online production of the weekly Journal of Biological Chemistry (JBC), the most highly cited (and second largest) peer-reviewed journal. As of October 2002, HighWire now produces 342 sites online.

Net Center for Plant Genomics
http://plantgenome.sdsc.edu/
A collaborative effort between the National Science Foundation (NSF), the San Diego Supercomputer Center, and the Plant Genome Research Program has resulted in this online resource for sharing plant genome information. Users can perform a more general Web literature search, or search a group of databases for nucleotide sequences. The site provides additional information such as other related NSF projects and job openings in plant genomics. The entire site is directed toward a specific and advanced audience. Annotation from the Scout Project .

Molecular Information Agent
http://mia.sdsc.edu/
This Web search tool from the San Diego Supercomputer Center allows users to "search the internet to find all current information for a molecule of interest." Molecular Information Agent (MIA) thoroughly searches several online biological databases and removes invalid links from the search results. In order to complete a search, users must complete a brief registration. Because the search function takes a few minutes to generate results, the registration allows users to choose to either save the query and return later to view the results, or have the results emailed to them. This site may prove to be a time saving tool for those users who desire up-to-date information on molecules of interest. Annotation from the Scout Project.