nii

New Informatics Initiatives
//(in order of priority//)


 * run the following through pipeline (with documentation)**

4 Paired-End Gonad Libraries []

[] [] [] [] [] [] [] []


 * - Setup public facing iPython Notebook install on hummingbird.**

I would like to setup IPython notebook server on hummingbird that could access and run remotely. http://ipython.org/ipython-doc/dev/interactive/htmlnotebook.html

[]
 * - Install implement De-novo assembly / RNA_seq pipeline locally....**

using DH3 BB3 as models [|- see sheet f]or raw data.


 * - Setup full installation of Galaxy.**

Currently we have Galaxy server running on genefish.fish.washington.edu. It functions but is missing several tools / dependancies. http://wiki.galaxyproject.org/Admin/Get%20Galaxy

We would like something more robust with complete complement.

Essentially I think we would like the production environment install on bigfish. http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer

It might be just easier to upgrade what we have?


 * - De Novo assembly of //Ostrea lurida// transcriptome**

combine all into master transriptome

Below is reads we have to date:

Version 1 raw reads (used in http://goo.gl/roshW) [] []

OA larval data [] [] [] []

Single End Gonad data [] [] [] []

4 Paired-End Gonad Libraries []

http://eagle.fish.washington.edu/whale/Friedman_Oly_broodstock/full/filtered_108A_Male_Mix_AGTCAA_L004_R2.fastq.gz http://eagle.fish.washington.edu/whale/Friedman_Oly_broodstock/full/filtered_108A_Male_Mix_AGTCAA_L004_R1.fastq.gz http://eagle.fish.washington.edu/whale/Friedman_Oly_broodstock/full/filtered_108A_Female_Mix_GGCTAC_L004_R2.fastq.gz http://eagle.fish.washington.edu/whale/Friedman_Oly_broodstock/full/filtered_108A_Female_Mix_GGCTAC_L004_R1.fastq.gz http://eagle.fish.washington.edu/whale/Friedman_Oly_broodstock/full/filtered_106A_Male_Mix_TAGCTT_L004_R2.fastq.gz http://eagle.fish.washington.edu/whale/Friedman_Oly_broodstock/full/filtered_106A_Male_Mix_TAGCTT_L004_R1.fastq.gz http://eagle.fish.washington.edu/whale/Friedman_Oly_broodstock/full/filtered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz http://eagle.fish.washington.edu/whale/Friedman_Oly_broodstock/full/filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz


 * - Examine Oly PacBio Data**

Data @

http://eagle.fish.washington.edu/whale/index.php?dir=Pat%2F

Complete
- Transfer Coordinate System from Genome to Transcriptome Solution: []