Introduction to Bioinformatics - COIN81
Below is an outline of the twelve course topics in COIN81. Depending on your interests and abilities, you may decide to invest more time on some topics and less on others. Your assignments should document / chronicle your path through these topics. Week 12 (BioPerl and XML) are advanced topics and are optional material for this course.
Week one - What is bioinformatics? Molecular biology review. Web technologies review. NCBI tour. Introduction to genomic websites - NCBI, industry sites, consortiums, literature sites, resource (link) sites. Casual lecture / workshop will cover assignment one. Date is TBA, most likely Wednesday evenings.
Lab 1 - Required reading: Commercialization of Bioinformatics and Molecular Genetics Primer (DOE). Other reading TBA (various listservs or very current publications in bioinformatics, biotechnology, and / or bioengineering).
Week two - Introduction to NCBI (PPT) and NCBI resources, NCBI mission, BLAST, UniGene, retrovirus and whole genome resources.
Lab 2 - NCBI tour, using BLAST, BLASTn, BLASTp, BLASTx, when to use translated BLAST. Determining putative protein domains. Start assignment two. Take time to practice as much with BLAST as you can.
Week three - GenBank, EMBL, DDBJ - searching GenBank, NCBI data model, genome and proteome resources, EMBL, and DDBJ.
Lab 3 - Locating genomic entries from BLAST and other data inputs. Exporting genomic data into other file formats.
Week four - UniProt, Swiss-Prot, EMBL protein resource, references / citations, PDB and PIR references, links to GenBank entries, links to protein resources. Introduction to sequence alignment techniques, and other protein comparison and analysis tools. Proteins and Proteomics - PPT
Lab 4 - Explore UniProt, Swiss-Prot, EMBL, and ExPASy resources, physical properties and molecular weights of unknown sequences. ClustalW and other alignments.
Week five - Protein Structure Modeling SWISS-MODEL Protein Data Bank Archive of .pdb files. Structures determined by X-ray, NMR Protein Structure Exercise - PPT and protein structure exercise.
Lab 5 - Theoretical structure search, searching “Molecule of the Month”. Using SWISS-MODEL first approach for structure determination. Protein structure exercises. Protein project assignment three. (Combine UniProt, Swiss-Prot, PIR, Pfam, Swiss-Model, and PDB resources).
Week six - Phylogenetics, HIV mutation, and SARS
Lab 6 - You'll use Biology Workbench and swami to study HIV mutation, retroviral proteins, and the emergence of SARS. This is a three part lesson. After completing these exercises, you are ready to submit assignment four.
Week seven - Phylogenetics and Avian Influenza Virus.
Lab 7 - Investigate Avian Influenza Virus using scenario based lesson. You may add this work to assignment four.
Week eight - SNPs and Haplotypes
Lab 8 - Investigating dbSNP and Perlegen to explore SNPs and haplotypes. Complete the SNPs and Haplotypes exercises. You will describe this work in assignment five.
Week nine - Microarrays and gene expression.
Lab 9 - Tour of Affymetrix portal, optional webinars on microarrays and gene expression.
Week ten - Systems biology and metabolic pathways.
Lab 10 - Tour of KEGG pathways database and NCBI pathway searcher. Using pathway and enzymatic information. Webinars and BioCYC.
Week eleven - Synthetic Biology (PPT) and Digital Cells (PPT).
Lab 11 - Explore SyntheticBiology.org, Synthetic Genomics. Read paper on Venter's artificial organism, and explore the J. Craig Venter Institute (JCVI.org).
Week twelve - BioPerl and XML for bioinformatics.
Lab 12 - Optional work for advanced studies. Work on BioPerl problems, and develop a small XML model.