Since June 2013 I have been using IPython as my lab notebook. This page is meant to serve as the forward facing access portal for the public (those not interested in the .pynb files). Anyone can download all the files (zip file, project on GitHub) to view (and execute) in IPython. Below are links to some active project entries rendered in the IPython Notebook Viewer.
BiGill_RNAseq
BiGill_Tran_Elements
BiGill_array
BiGo - methratio error
BiGo_GFF_dev
BiGo_RNAseq
BiGo_larvae
BiGo_larvae_2
BiGo_larvae_methylkit
BiGo_methratio
BiGo_methratio_mito
BlackAb_Annot
CC_ampk
EY_methratio
LT_C1q
OlyO_Chi_Exp
OlyO_GonadExp
OlyO_PacBio
OlyO_transcriptome
OsHV_host
Ruphi_OA_RNAseq
TJGR_CpG_binding
TJGR_CpG_islands
TJGR_Methylation_GenomeSnapshot
TJGR_Mgo_Expression
TJGR_OysterGenome_IGV
TJGR_ProteinAnnot
TJGR_pearl
UW_SoftwareBootcamp
Tools
In addition to using IPython as platform for documenting my work, I am beginning to develop automated workflows in IPython. Here is my first attempt. It takes a fasta file and provides a graph showing representive GO terms.
Before IPython?
Between 2010 - 2013 my notebook platform of choice was Evernote. You can access the notebook ..