Below is the the KEGG pathway for the Wnt Signaling Pathway in purple sea urchins (green). I have added all the contegs found significantly enriched in the Pycnopodia  transcriptome. They are in the red and blue […]

The Wnt pathway! http://web.stanford.edu/group/nusselab/cgi-bin/wnt/reporters. Play the video to see a baby Zebrafish expressing Tcf/Lef-miniP:dGFP.

My post today will be covering the weekend as well as today, […]

Here is my IPython notebook from the 8-12-14. I went through all the steps to enrichment. The files are now organized under my folder on maxine.

An update on my non-class related research, but very relevant to the work we are doing on the sea star transcriptome.

The tides were low last week so the sea star survey team went out to get the end of summer […]

Yesterday I got the results back from the qPCR that I sent out at the start of the class. This was a very interesting set of samples. It included clams from several sites with sea star wasting disease and a set of […]

Paper on using next gen sequencing to find viruses in insects

Sijun_etal_Viruses2011_NextGenerationSequencingInsectVirusDiscovery

This mornings post is an summery of the work I did on Friday and finished up over the weekend. There was a lot of coding and great visualizations! Lauren gave us a WGCNA tutorial. Below is the R […]

1. Open my notebook in the mirrored maxine

2. Copy the ULR of the notebook into http://nbviewer.ipython.org/

3. Now, copy the nbviewer ULR for the notebook into the quotes in the code below and add to the post.

Some pretty pictures from today. These are showing the genes differentially expressed in the exposed vs. the non-exposed sea stars. The immune response is lighting up clearly. After making this I worked on coding […]

This is not really a week in review video, but it goes along with the weeks topic of sea star wasting disease so I thought it could go here. I will post another for last week.

Here is the story of SSWD research […]

Fantastic lecture and lab today on how to begin working with transcriptomic data. We are working with the data generated from the spring sea star experiment. We learned to use Ipython to track work flow […]

Data from the YSI taken at Picnic Cove on Shaw Island, WA. Each reading was taken off the bottom by few inches. The site was moderately infected with the laby. There were more blades with lesions at the site then […]

Date
Site
Transect
Meter
Z. marina density (non flowering)
Z. marina density (non flowering)

7/24/14
False Bay
Shallow
0
0
0

7/24/14
False Bay
Shallow
25
18
2

7/24/14
False […]

Great lecture today on the Pacific Coast sea star wasting disease epidemic by Drew Harvell. We are really starting to put the pieces together and have a better handel on the outbreak, due to great collaboration […]

Week 1 video posted!

Got to learn about pathogenic protists yesterday (bitter crab syndrome!) and transcriptions. In our free time we set up a sea star disease […]

Our understanding of immunity in invertebrates is limited by the tools developed to study it at this time. Today we had lectures from Carolyn and Steven on the host response to stress and infection, showing how […]