Omics Day2 3

Day 2 (9/15)

AtMet metabolomics

• improvement of PVT (https://github.com/afukushima/pvt) metabolome visualization webapp (http://atmetexpress.riken.jp/analysis/)
  • summarizedexperiment (http://bioconductor.jp/packages/3.2/bioc/html/SummarizedExperiment.html)
  • d3 network
  • pathview (http://www.bioconductor.org/packages/release/bioc/html/pathview.html) integration
• Pathway data curation of Arabidopsis metabolites list in AtMet Database (Arabidopsis metabolome database)
  • R package for linkdb RDF client (https://github.com/kozo2/linkdbRDF)
  • maually curate name, IDs (PubChem CID, KEGG, KNApSAcK etc.) (Continuing...)

PIERO Reaction Ontology

• pathview integration with PIEROutil (https://github.com/kozo2/PIEROutil)
• shortest path search with PIEROutil
• Data curation of terminology

Glycomics

• https://github.com/glycoinfo/bh/wiki/day2
• https://github.com/glycoinfo/bh/wiki/day3

Proteomics

day 2

• Discussion about metadata with a wet collaborator.
• Yoshizawa-san and Tabata-san go to Kyushu University to interview Prof. Matsumoto.
• Performance test for uploading a large data file from Nagasaki to Niigata and Mishima.
• flow.js
• HTTP/2

day 3

• Developing jPOST RDF schema and ontology