Curing (医する)AIDS,with programmingAndrew Grimm
Curing AIDSUnderstanding (理解する) HIV,with programmingAndrew Grimm
Whats AIDS?• Disease caused by HIV• Unless treated (治療する), damages (損傷する) theimmune system (免疫系)• Damage of immune system ...
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...
Impact (影響) of AIDSPrevalence Annual deaths (死/年)Worldwide (世界的) 35 million (3500万) 1.5 million (150万)Australia 18,000 100...
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)
Point mutation• One letter (文字) of the genome (ゲノム) changingto another letter
Recombination• Swapping equivalent portions of the two copies ofthe genome
Why study (研究)mutation (変異)?• It enables HIV to escape (免れる) the immunesystem (免疫系)• It enables HIV to become resistant (耐...
Laboratory (実験室)component• Start with viruses with a known genome• Infect (感染させる) cells with viruses• Let them reproduce (...
Analysis component• Compare sequences against the sequences of theoriginal
Challenges (障害) faced
New questions andanalyses• Questions lead to new analyses• New analyses lead to new insights• New insights lead to new que...
Performance (性能)• Initially only dealt with hundreds (100s) of sequences• Now deal with millions (100万s) of sequences
Breaking of assumptions• I used to assume a sequence would be either wildtype or marker type, or a mixture• Now I have to ...
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...
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Curing AIDS, with programming

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"Curing AIDS, with programming", for Hamamatsu.rb . A talk about bioinformatics.

「Curing AIDS, with programming」hamamatsu.rbに。バイオインフォマティクスについて。

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Curing AIDS, with programming

  1. 1. Curing (医する)AIDS,with programmingAndrew Grimm
  2. 2. Curing AIDSUnderstanding (理解する) HIV,with programmingAndrew Grimm
  3. 3. Whats AIDS?• Disease caused by HIV• Unless treated (治療する), damages (損傷する) theimmune system (免疫系)• Damage of immune system can cause death (死)
  4. 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) longo Human (人間) genome is 3 billion (30 億) letters long• Has two copies of the genomeo Humans also have two copies of their genome
  5. 5. Impact (影響) of AIDSPrevalence Annual deaths (死/年)Worldwide (世界的) 35 million (3500万) 1.5 million (150万)Australia 18,000 100Japan 8,100 100
  6. 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. 7. Point mutation• One letter (文字) of the genome (ゲノム) changingto another letter
  8. 8. Recombination• Swapping equivalent portions of the two copies ofthe genome
  9. 9. Why study (研究)mutation (変異)?• It enables HIV to escape (免れる) the immunesystem (免疫系)• It enables HIV to become resistant (耐性) to drugs
  10. 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. 11. Analysis component• Compare sequences against the sequences of theoriginal
  12. 12. Challenges (障害) faced
  13. 13. New questions andanalyses• Questions lead to new analyses• New analyses lead to new insights• New insights lead to new questions
  14. 14. Performance (性能)• Initially only dealt with hundreds (100s) of sequences• Now deal with millions (100万s) of sequences
  15. 15. Breaking of assumptions• I used to assume a sequence would be either wildtype or marker type, or a mixture• Now I have to handle wild type or marker type 1 ormarker type 2
  16. 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

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