A talk on my bioinformatics work using Ruby given at ROROSyd on 8 October 2013
Semi-Japanese version: http://www.slideshare.net/agrimm/hiv-talk-for-programmers-english-draft
3. What's AIDS?
Disease caused by HIV
If untreated, damages the immune system
Damage of immune system can cause death
4. What’s HIV?
Virus
Cannot live independently
Hijacks the cells of living creatures to reproduce itself
Genome is 9749 letters long
Human genome is 3 billion letters long
Has two copies of the genome
Humans also have two copies of their genome
5. Impact of AIDS
Prevalence Annual deaths
Worldwide 35 million 1.5 million
Australia 18,000 100
Japan 8,100 100
6. What am I studying?
Two types of mutation
Point mutation
Recombination
9. Why study mutation?
It enables HIV to escape the immune system
It enables HIV to become resistant to drugs
10. Laboratory component
Start with viruses with a known genome
Infect cells with viruses
Let them reproduce for one generation
Determine the sequence of new viruses
None of this done by me!
15. Breaking of assumptions
I used to assume a sequence would be either wild
type or marker type, or a mixture
Now I have to handle wild type or marker type 1 or
marker type 2