Team5

For formating in markdown, see here.

Names:

• Stacey Butler
• Michael Livesay
• Robert Rennie
• Sarka Petrickova
• Mary Angelica Tursi

Ideas:

• Genotype/phenotype correlation analysis
• Topological data analysis
• Competitive dynamical models based on stock spacing

Types:

• height vs time, genotype, stock spacing

Algorithms:

• Spectral clustering methods
• Gilpin-Ayala equations
• python mapper
• persistant homology

Data:

• vcf: Read /Team5/Accessing_genome_data.Rmd

file.copy(from = "/data/terraref/sites/genomics/derived_data/ril/gbs/imp_TERRA_RIL_SNP.vcf", to = '~/Team5/Data/')

• genesys: Use shell to download compressed .cvd file, extract, and upload to RStudio

wget https://github.com/pi4-uiuc/Team5/files/1049350/genesys-dataset-bd6e6ee9-7919-11e3-9d0a-5254001a6979.zip

tar -xvf genesys-dataset-bd6e6ee9-7919-11e3-9d0a-5254001a6979.zip

• terraref traits: Read /Team5/terraref_traits.Rmd

• To match vcf and genesys: Read /Team5/match_vcf_genesys.R