curing aids, with programming
DESCRIPTION
"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。TRANSCRIPT
Curing (医する ) AIDS,with
programmingAndrew Grimm
Curing AIDS Understanding (理解する ) HIV,
with programming
Andrew Grimm
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 )
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 genomeo Humans also have two copies of their genome
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
Japan 8,100 100
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 )
changing to another letter
Recombination• Swapping equivalent portions of the two copies of
the genome
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
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!
Analysis component• Compare sequences against the sequences of the
original
Challenges (障害 ) faced
New questions and analyses
• Questions lead to new analyses• New analyses lead to new insights• New insights lead to new questions
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 wild type or marker type, or a mixture
• Now I have to handle wild type or marker type 1 or marker type 2
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