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Roberts Lab Documents

Home Page: http://sr320.github.io/LabDocs/

R 0.01% Perl 0.03% HTML 0.16% Shell 0.01% Jupyter Notebook 99.79% Perl 6 0.01%

labdocs's Introduction

LabDocs

This is the former space for the Roberts Lab lab resources. As of 20170828, it will no longer be updated, but will not be deleted. Primary use of this repo will return to Steven Roberts as a personal Lab Docs repository.

To access actively maintained Roberts Lab repositories now exist here: Roberts Lab GitHub Organization

This new repository contains all of the info that exists here, but has been updated and reorganized.

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emmats mgavery che625 jldimond jheare kubu4 jmuil maiderjustel eugeniocarpizo jvlf edlopez78 gitter-badger grace-ac laurahspencer shellywanamaker john2912 pariswu1988

labdocs's Issues

Define Purchasing Protocol

Define how purchasing is done - going to github?
keeping form?
I think last week wrong item was purchased because user did not provide part no.

Docker talk Tuesday

Ben Marwick, Assistant Professor of Archaeology, joins the All-Campus Reproducibility Seminar Series on Feb 10th, 1:30pm in the WRF Data Science Studio Meeting Room, 6th floor Physics/Astronomy Tower. He will give a talk titled:

"Doing Reproducible Research with Docker"

Other Sequencing options

via ScienceExchange

https://www.scienceexchange.com/services/illumina-ngs

code NY2015 for 15% off your next Illumina NGS order.
If NGS is not the service you're looking for, send me a note and I'll connect you with our free, concierge specialist, who can source your entire project

Linux box

Twice today software installs failed which I think would have worked on Linux- painless means to see if this is viable option going forward?

Maybe dual boot genefish? Or greenbird?

Purchasing: Drives

Please order 3 of these on 62-4106

and one of these

SeaGrant Preproposal

Update readme.md

update to include description to each file.

Set up bu script for nightingales sheet

Oly Bisulfite Sequencing

OlyO samples movement

Oyster bay

Plan for OlyO microsats data

Cnidarian Sequencing

Lets get something in this month..

In terms of organisms that would be easily accessible, I would suggest either Aiptasia pallida or Anthopleura elegantissima, both anemones. Aiptasia is becoming the lab rat of choice for folks studying the molecular and cell biology of cnidarian-dinoflagellate symbiosis. It's a tropical species that is nearly circumglobal, and is also the bane of the tropical reef aquarium keeper's existence due to it's ability to hitchhike with live rock and spread throughout an aquarium. But these characteristics happen to make it great for biologists who want an easy-to-keep model organism. It's also versatile because it can live without symbionts entirely or be successfully infected with a range of symbiont genotypes, which is generally the exception rather than the rule among symbiotic cnidarians (which has also lead to some criticism regarding its appropriateness as a model for cnidarian symbioses). They could probably be collected for free from an aquarium or an aquarium store; otherwise you can buy them from Gulf Marine Specimen in Florida. The advantage of the latter option is that you could be more certain of their origin.

Anthopleura is also a really interesting anemone because it associates with two entirely different symbionts, and can also live symbiont free. It has a long history as a model organism--going back to the 1960s when it was essentially the first species in which the nutritional role of dinoflagellate symbionts was confirmed. And it's local, easy to keep, and I have some in the sea table at Shannon Point right now. The only downside I see to them is that the coral and symbiosis research communities are less interested in temperate species because, well, they aren't tropical and that's where all the buzz is.

I suppose you could also get some coral material from an online supplier. But they would not provide much taxonomic information (which can be tricky if you only have a fragment) or geographic information, so not ideal. But if you want to wait a few more months, there's a good chance I'll be going to Belize this spring (May or June) and could probably bring back some fixed material. That reminds me that it would be good to talk sometime about preservation methods for my field work to ensure that I get good material for RNAseq and bisulphite sequencing--this will be important to know since field conditions, and even marine lab conditions, are very basic.

What's the overall goal? This may also factor in to which species would be the best...