KNOW YOUR PATH…Python, Coral, and ISH

What an eclectic day with a common theme: PATH!

IPython NB was conquered today, as I was able to successfully install it once realizing a very important thing… the PATH needed to be rerouted. See below for the details on how to do that if interested.

In addition, the ISH group continued with the ISH protocol for both Sea Star and Coral samples. Test PCRs worked well for most of the samples, all coral except for 16S Eubacteria ones (*which turned out were never tested, because the wrong primers were used, ooops) and the Ehrlichiae primers were problematic even after a second run. We’ve gotten probes successfully attached and amplifying on the coral samples, however Sea Star has had a few more hurdles and did not amplify with the probes (see images below). SO we may have to go back to the drawing board for those and figure out what our path is going to be for the next few days.

photo2  photo1 (3)photo1 (2)

Also, we’ve begun to examine coral slides from various diseases and health states. They are absolutely beautiful, but they’re also really difficult to examine. Feast your eyes!

BTV 028 BTV 027 BTV 026 BTV 025

How to load IPython on your computer:

  • install Anaconda (
  • then check when it is and whether anaconda in correctly configured for your path
  • cvvvv:/ collin$ pwd


    cvvvv:/ collin$ export PATH=/anaconda/bin:$PATH

  • then update Anaconda and IPython (

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