Exploring Bioinformatics and Computational Biology (BIOS 3170)

1. Gene alignments: antibiotic resistance Protein alignments: function of CFTR protein Exploring Bioinformatics and Computational Biology (BIOS 3170) Manipulating genetic data: genetic disease Sequence assembly: human genome Bioinformatics and Computational Biology (BCB) Agent-based models: foraging ants Gene prediction: prokaryotic gene discovery This course provides hands-on experience through a sequence of BCB modules. Mathematical models: infectious disease Microarrays: zinc-induced gene expression Structure prediction: drug design

2. email: sandefur@uncp.edu web: http://www.unc.edu/~sandefur twitter: oshehoma Dr. Conner I Sandefur,Visiting Assistant ProfessorSPIRE Postdoctoral Scholar BA Computer Science, George Washington University, Washington DC PhD Bioinformatics, University of Michigan, Ann Arbor, Michigan

3. On your computer, navigate to http://bio3170bioinformatics.wordpress.com/

4. 5 minute exercise: course/syllabus question formation • In your group: • Introduce yourselves to each other • Select a spokesperson to introduce your group members and ask your questions • Come up with 3 questions about the course that you feel are important (examples: aspects of the syllabus, assignments, project, etc.) Use your Guided Question to help spark discussion (if you need it) Up next: class discussion

5. This course provides hands-on experience through a sequence of BCB modules. Gene alignments: antibiotic resistance Protein alignments: function of CFTR protein Exploring bioinformatics: Nova Scotia Niemann-Pick Disease Manipulating genetic data: genetic disease Sequence assembly: human genome Bioinformatics and Computational Biology (BCB) Agent-based models: foraging ants Gene prediction: prokaryotic gene discovery Mathematical models: infectious disease Microarrays: zinc-induced gene expression Structure prediction: drug design

6. Exploring bioinformatics: Nova Scotia Niemann-Pick disease “Niemann-Pick disease is an inherited condition involving lipid metabolism, which is the breakdown, transport, and use of fats and cholesterol in the body. In people with this condition, abnormal lipid metabolism causes harmful amounts of lipids to accumulate in the spleen, liver, lungs, bone marrow, and brain.” http://ghr.nlm.nih.gov/condition/niemann-pick-disease http://en.wikipedia.org/wiki/Niemann-Pick_disease,_type_C Navigate to http://www.ncbi.nlm.nih.gov/omim

7. Web Exploration Questions: Nova Scotia Niemann-Pick Disease (NS-NPD) • OMIM: Is NS-NPD causes by a defect in a single gene, or is more than one gene involved? • OMIM: What gene(s) are involved in NS-NPD? What is known about the normal function(s) of the gene(s)? • OMIM: What chromosome(s) is/are the gene(s) located on? • OMIM: Would this disease be considered dominant or recessive? • GENE INFOUCSC: How many nucleotides are there in the gene responsible for NS-NPD? • GENE INFOUCSC: How many amino acids are there in the protein it encodes?

8. E-Lab Notebook Entry #1 is due Thursday, August 28 http://bio3170bioinformatics.wordpress.com/category/e-notebook-entry-1/