Download Introduction to the WWW and biological

Worksheet for Bioinformatics 1
ACTIVITY: Learn to find biological information from the WWW
Exercise 1 Search engine and biological databases
Objective: To use search engines and biological databases
(1) Common www search engine
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Google (http://www.google.com), search for “maize leaf mutants”
Google scholar (http://scholar.google.com), search for “maize leaf mutants”
Google images (http://images.google.com), search for “horse coat color”
Q: What do we find?
(2) Biological databases
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MaizeGDB (http://www.maizegdb.org)
⇒ Search for mutations we learned in class “albino”, “tangled”, “zebra stripe”
Q: What information can we get for these mutations?
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EMBL-EBI (http://www.ebi.ac.uk/2can)
⇒ Go to “Basic Biology > Organisms and cells”
Q: What can we find inside a cell?
⇒ Go to “Basic Biology > Molecules of life > DNA”
Q; Why do we need DNA?
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EMBL-EBI Karyn’s genome (http://www.ebi.ac.uk/2can/genomes/genomes.html )
⇒ Go to “Eukaryotes” and look up human, maize, horses
⇒ Go to “Bacteria” and look up E. coli, H. pylori
Q: What is a genome?
Q: List reasons for sequencing the genome of these organisms:
o Human (Homo sapiens)
o Maize (Zea mays)
o E. coli
o H. pylori
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Worksheet for Bioinformatics 2
ACTIVITY: Learn to use biological databases and tools from the WWW
Exercise 1 Case study
Objective: To use combinations of databases and tools to study a specific topic
1) Find descriptions of different coat colors in horses
⇒ Online Inheritance in Animals (OMIA), http://omia.angis.org.au
2) Identify the gene(s) involved in specifying “cream coat color” in horses. What is
the function of the protein? Find examples of other genes involved in making horse
coat color.
⇒ NCBI Nucleotide,
http://www.ncbi.nlm.nih.gov/sites/entrez?db=Nucleotide
⇒ NCBI PubMed, http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed
3) Study genetic diseases such as diabetes, and the genes involved.
a. Where can we find the diabetes genes in the human genome, and what is its
function?
⇒ Try searching at:
• NCBI Genome,
http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome
• Online Mendelian Inheritance in Man (OMIM),
http://www.ncbi.nlm.nih.gov/sites/entrez?db=OMIM
b. Find examples of other human genetic diseases. What are the symptoms of
the disease? How are they inherited?
⇒ Example of a simple recessive genetic disease, cystic fibrosis. Find more
information at
• Your Genes Your Health, http://www.ygyh.org/cf/whatisit.htm
⇒ Try searching for other examples of human diseases that have a genetic
basis.
• Your Genes Your Health, http://www.ygyh.org
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Worksheet for Web development 1
ACTIVITY: Learn to make a simple web page
Exercise 1 Create a simple web page
Objective: To learn to create HTML file using Microsoft Word.
⇒ What is HTML?
• Check out HTML on Wikipedia (http://en.wikipedia.org/wiki/HTML)
1. Open Microsoft Word. Create a new file by going to:
o File > New > Blank Document
2. In the file:
• Describe your background and about yourself.
• Provide picture(s).
• What did you learn from this workshop?
• Make a Punnett square for your favorite gene.
3. Save file as type “Web page”. File will automatically be saved with an .htm or. html
extension.
4. Open file with Web browser (e.g. Internet Explorer) to check out your web page.
(optional) Exercise 2 Use of basic HTML tags
Objectives:
To learn HTML file contains the “head” and “body” sections,
To learn the use of basic html tags for line paragraphs “p” and line breaks “br”
⇒ Follow workshop online resource to practice use of tags in HTML file,
http://maize.tigr.org/cellgenomics/outreach/workshop2007/web_exercise1.html
http://maize.tigr.org/cellgenomics/outreach/workshop2007/web_exercise2.html
(optional) Exercise 3 Explore the use of additional HTML tags
Objective: To learn the use of html tags for text, images and links
⇒ Go to public online resource to add more HTML tags to your html file,
http://www.w3schools.com/html/
• Text formatting, creating lists, adding links to other web sites
• Changing background color, HTML color
• Adding images, creating tables
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