Curing AIDS, with programming
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This document summarizes Andrew Grimm's research using programming to understand HIV and AIDS. It discusses how HIV hijacks cells to reproduce, causing AIDS if left untreated. Grimm studies two types of HIV mutations - point mutations changing single letters in the genome, and recombinations swapping portions of the two genome copies. Studying mutations helps understand how HIV escapes the immune system and becomes drug-resistant. Grimm analyzes virus sequence data from laboratory experiments to compare original and mutated genomes and gain new insights into HIV, facing challenges as his analyses have expanded to millions of sequences.
Curing AIDS, with programming
- 2. Curing AIDS Understanding (理 解する) HIV, with programming Andrew Grimm
- 3. What's AIDS? • Disease caused by HIV • Unless treated (治療する), damages (損傷する) the immune system (免疫系) • Damage of immune system can cause death (死)
- 4. What’s HIV? • Virus (病毒) o Cannot live (生き残る) independently (単独で) o Hijacks (乗っ取る) the cells (細胞) of living creatures (生体) to reproduce ( 生殖) itself • Genome (ゲノム) is 9749 letters (文字) long o Human (人間) genome is 3 billion (30 億) letters long • Has two copies of the genome o Humans also have two copies of their genome
- 5. Impact (影響) of AIDS Prevalence Annual deaths (死/年) Worldwide (世界的) 35 million (3500万) 1.5 million (150万) Australia 18,000 100 Japan 8,100 100
- 6. What am I studying (研 究)? • Two types of mutation (変異) • Point mutation (点突然変異) • Recombination (遺伝的組換え)
- 7. Point mutation • One letter (文字) of the genome (ゲノム) changing to another letter
- 8. Recombination • Swapping equivalent portions of the two copies of the genome
- 9. Why study (研究) mutation (変異)? • It enables HIV to escape (免れる) the immune system (免疫系) • It enables HIV to become resistant (耐性) to drugs
- 10. Laboratory (実験室) component • Start with viruses with a known genome • Infect (感染させる) cells with viruses • Let them reproduce (生殖) for one generation (世代) • Determine the sequence of new viruses • None of this done by me!
- 11. Analysis component • Compare sequences against the sequences of the original
- 13. New questions and analyses • Questions lead to new analyses • New analyses lead to new insights • New insights lead to new questions
- 14. Performance (性能) • Initially only dealt with hundreds (100s) of sequences • Now deal with millions (100万s) of sequences
- 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. Questions? • RubyConf Australia http://www.rubyconf.org.au • ２０１４年２月 • シドニー • Under the ハーバーブリッジ, with views of the シド ニー・オペラハウス • @rubyconf_au