jetpoint meeting @jetbrains on bioinformatics
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JetPoint Meeting
JetBrains BioLabs #jetmeet
6.03.2013
JetBrains
At JetBrains, we have a passion for making people more productive through smart software solutions that help them focus more on what they really want to accomplish, and less on mundane, repetitive "computer busy work".
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BS-seq
ChIP-seq
Illumina27/450K
ChIP-seq
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ChIP-BS-Seq
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Open Data
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Wet Labs problems
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Academic software
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A Farewell to
Bioinformaticshttp://madhadron.com/a-farewell-to-bioinformatics
Fuck you, bioinformatics. Eat shit and die.
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, , A Farewell to Bioinformatcs, .
JetBrains BioLabs
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RNA-directed DNA methylation in Arabidopsis
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SVM + Ada Boost ML. n- . .
Tradeoff:
~ 80%
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Proof of concept AdaBoost
~ 99%
ML !
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ML smRNA
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BS-Seq
, smRNA, PiRNA, lncRNA, etc
,
Illumina450K
Infinium Methylation 450K is a hybrid of two different assays, Infinium I and II.
Due to its design, Infinium Methylation 450K technology generates a dataset that should be viewed as two distinct datasets. Infinium II data are less accurate and reproducible than Infinium I data.
Peak-based correction makes it possible to treat Infinium I and Infinium II data as a single dataset.
Infinium Methylation 450K is one of the most attractive powerful and cost-effective tool currently available for generating quantitative DNA methylomes for health and disease, notably in the framework of large biomarker discovery studies.
Microarray Illumina450k.
Illumina450K
Beta = methylated / (methylated + unmethylated)
Beta .
Illumina450K
+ subset quantile normalization
Beta , Peak-Based correction Subset Quantile Normalization
Illumina450K
SNP-
Subset Quantile Normalization
Batch effects
(genes, gene regions, etc) Mann-Whitney U-test
: NDA
. Laboratory of Stem Cell Biology .
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ChIP-seq
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Poisson Mixture
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Poisson Mixture + HMM
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AIC = 2*freedom_degrees log(likelihood)
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Chromasig
ChIP-Seq - Chromasig
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Chromasig
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Tools
Java
R
Big server computations (Linux)
Confluence, Bamboo, Crucible
Continuous integration, tests
JetBrains
JetBrains BioLabs
LabBook - . . Excel. .
Genome query .
Genestack Platform - universal collaborative ecosystem for bioinformatics research and development. http://genestack.com
, JetBrains .
JetBrains BioLabs
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[email protected]: oleg_s