What to expect?
- check An overview of some of the major techniques used in bioinformatics
- check Hands-on experience with some of its most popular algorithms
- check Demonstratation on visualization packages for bioinformatics algorithms
- check Hands-on exercises using open source tools to understand the common bioinformatics tasks
- check Exposure to topics, examples, and problems that can be added to the repertoire of projects for CS1/CS2, data structures and algorithms, and other CS courses, including bioinformatics
When and Where?
date_range Friday, February 23, 7:00 pm - 10:00 pm
room Room 303, Baltimore Convention Center, One West Pratt Street, Baltimore, Maryland 21201
Workshop Guide
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transformTranscription and Translation CS1, CS2
Biology Motivation Transcription/Translation Algorithm Transcription/Translation Algorithms Hands-On Exercise ONE: Human Traits
TWO: Investigating Inherited Diseases
HandsOn_Sequences.txt
Sample Programs translation.py
find_substitution.py
Protein_wildtype.txt
CDS_mutant.txt
Protein_mutant.txtArticles "What is Bioinformatics?" by Luscombe et al. -
line_styleMotif Detection CS2, Algorithms, Other
Biology Motivation Motif Detection Algorithm Motif Detection Algorithm: PWM Hands-On Exercise THREE: Constructing Position Weight Matrix
FOUR: Scoring Short Sequences using a Position Weight MatrixSample Programs create_PWM.py
Donor_MOG.txt
score_oligo.pyArticles "Modeling Regulatory Motifs" by Sridhar Hannenhalli -
Additional Materials
Motif Detection (Long)
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spaPhylogenetic Tree Construction CS2, Algorithms, Other
Biology Motivation Phylogenetic Trees Algorithm UPGMA Algorithm Hands-On Exercise Landmarks of the HIV-1, HIV-2, and SIV genomes
FIVE: The Origins of HIV
env_protein_sequences.txt
gag_protein_sequences.txt
pol_protein_sequences.txtSample Program UPGMA.py Articles "Phylogeny for the Faint of Heart: A Tutorial" by Baldauf -
low_priorityPairwise Sequence Alignment Algorithms, Other
Biology Motivation Pairwise Sequence Alignment Algorithm Dynamic Programming for Sequence Alignment Hands-On Exercise SIX: PAX6
zebrafish_pax6_protein.txt
PAX6_seqs.txtSample Program seqalignment.py
notes: (1) install NumPy, (2) only one alignment is printedArticles "Identification of Common Molecular Subsequences" by Smith and Waterman
Biology Background
Do you want to learn enough biology to be able to appreciate bioinformatics?
Yes? Do the following in the given order:
Read some interesting facts about the Human Genome Project (1990-2003) whose primary goals were to discover the complete set of human genes and make them accessible for further biological study, and determine the complete sequence of DNA bases in the human genome.
The slides are organized in the following way: the 3 states of DNA, RNA, Protein are discussed first, then the transitions between states are introduced: transcription from DNA to RNA, followed by translation from RNA to Protein.
Go through a review of the two transitions: transcription from DNA to RNA and translation from RNA to Protein.
This is a longer version of item 2 above. Make sure to cover the slides up to page 1.12.
Use this sheet as a guide to the biology terms one has to understand to appreciate bioinformatics. Do you know them all?
Ready for some problem solving? Try these interesting problems.
If you want to know more, choose "Central Dogma of Molecular Biology" and enjoy.
NOVA program. Requires Quick Time or Real Video Plug-in. Recommended segments: 1, 2, 6, 9, 10, 12, 13, 14, and 16.
Do you want to know more? Please get in touch with me via email for additional links and pointers.