Curing AIDS, with programming

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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

Published in: Technology, Health & Medicine
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Curing AIDS, with programming

  1. 1. Curing AIDS, with programming Andrew Grimm
  2. 2. Curing AIDS Understanding HIV, with programming Andrew Grimm
  3. 3. What's AIDS? Disease caused by HIV If untreated, damages the immune system Damage of immune system can cause death
  4. 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. 5. Impact of AIDS Prevalence Annual deaths Worldwide 35 million 1.5 million Australia 18,000 100 Japan 8,100 100
  6. 6. What am I studying? Two types of mutation Point mutation Recombination
  7. 7. Point mutation One letter of the genome changing to another letter
  8. 8. Recombination Swapping equivalent portions of the two copies of the genome
  9. 9. Why study mutation? It enables HIV to escape the immune system It enables HIV to become resistant to drugs
  10. 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!
  11. 11. Analysis component Compare sequences against the sequences of the original
  12. 12. Challenges faced
  13. 13. New questions and analyses Questions lead to new analyses New analyses lead to new insights New insights lead to new questions
  14. 14. Performance Initially only dealt with hundreds of sequences Now deal with millions of sequences
  15. 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
  16. 16. Questions?

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