The predominance of this module will be exploring the how genomic technologies provide insight into pathogen dynamics and host response.

Databases

NCBI
JGI
Sigenae
OrthoDB

matzLab
crassostreome

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Software

Galaxy
https://main.g2.bx.psu.edu/
-Please obtain account and explore tutorials

Sequence Analysis tools @ NCBI http://www.ncbi.nlm.nih.gov/guide/sequence-analysis/
- ie BLAST, PrimerDesign

Google Docs (Drive)
https://drive.google.com

Geneious
http://www.geneious.com/
-Free version available - consider Pro Trial during later half of class.

CLC Sequence Viewer http://www.clcbio.com/index.php?id=479
-Free multi-platform

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My Favorite Gene Projects

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Data Servers

• armina - http://aquacul4.fish.washington.edu/~steven/armina/?M=D
• asteroideae - http://goo.gl/KtGtf
• anquilla - https://www.dropbox.com/sh/1mi9bp4sf87mbaz/FqOsFy_-tN
• aluterus - https://www.box.com/s/c89fb23f427a68c33289
• Catalyst ShareSpace (read and write access)

Galaxy Public / Shared Histories

• https://main.g2.bx.psu.edu/u/sroberts320/h/bio533
• https://main.g2.bx.psu.edu/u/sr320/h/databases
• https://main.g2.bx.psu.edu/u/sroberts320/h/bio533-workfile

Exercises and How-to

• Visualizing assemblies (mapped reads) in Galaxy