C2G2 06-13-2013 HML

= Agenda =
 * 1) Show how to upload and access data using Dropbox
 * 2) sftp opening up
 * 3) Dropbox standalone program
 * 4) Dropbox on non network machine
 * 5) Drive
 * 6) Share your files with datascienceresearch@gmail.com
 * 7) Need to come up with documentation and program for uploading and sharing. We currently have Java programs that can do just this, but we need to clean them up.
 * 8) Demonstrate Trinity
 * 9) Add additional options
 * 10) Add downstream checking/quality checks
 * 11) Demonstrate Trans Abyss (not online yet)
 * 12) Show how you can access our literature. There is a really good illumina short read assembly paper.
 * 13) Blast2Go
 * 14) Build local database to speed it up? - Yes
 * 15) Need specific gene ids, gene symbols - write a wrapper
 * 16) Ion proton (Chapman)
 * 17) http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Sequencing/Semiconductor-Sequencing/proton.htmlJonthan
 * 18) Trimmomatic tool with single reads
 * 19) Create project page for individual projects

Follow Up from Meeting on 6/7: Annotation Tools for Non-Model Organisms (B2G wrapper) TransAbyss Wrapper Dropbox Storage Account Information

Project Timeline Updates: Shrimp Transcriptome (Jill): Fastq files in hand by 6/14 PM. Overview: Pooled sample of normoxia, hypoxia, and hypercapnic hypoxia treated shrimp (n = 51 shrimp); hepatopancreas; total RNA sent to NCSU GSL; Stranded Library (Encore Complete RNA-Seq DR Multiplex Systems 1–8); 2 lanes, 100bp SR, HiSeq2000 Shrimp RNAseq (Jill): normoxia, hypoxia, hypercapnic hypoxia (4 and 24 hrs) total n = 54; barcoded; details TBA