Creating the Processing Pipeline

The early stages of my research have been comprised of creating a pipeline of computer scripts that can process the large amounts of genomic data I have. Because the files I’m dealing with are incredibly large (10gb text files) none of the data cleaning and processing can feasibly be done by hand. I’ve tried several strategies to do this, and after weeks worth of failed attempts, I was able to get the major file processed and broken down into much more reasonably sized files that I now have to work on further to fully process to the point where I can use them to create a phylogeny.

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Almost done!

Me and a giant wild grape vine

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A Walk in the Park

A typical day of fieldwork generally starts around 9:30am, by which time the heat and humidity has already set in. Sometimes I meet a volunteer, usually a longtime Richmond resident who has kindly volunteered to show me around their favorite park and its plants, but mostly I head out by myself. With me, I carry a checklist with all the species I’ve seen so far, a waterproof notebook where I record the details of each collection, a pocket magnifier, and an nearly antique vasculum, found in an old Millington cabinet. A vasculum is a cylindrical, metal container used to hold fresh plant specimens.

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James River Flora


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Winding Down Field-Work

The start of this summer’s research has been so busy because we do the bulk of the data collection in the field before July. So, while I’ve been establishing methods for plant tissue preservation and practicing with them, we’ve also spent time at Blandy Experimental Farms and this upcoming weekend we are headed to Presequile National Wildlife Refuge, for our last weekend of field-work. The most exciting part of getting ready for field work for Presquile is that it is an island so we have to anticipate all of our needs for both lodging and data collection, so the pressure is really on! I’m also kind of hoping to have some spare time to do a little bird watching because I bet it is amazing in the early morning. The flowers on the milkweed at our Yorktown site are starting to bloom, and it is really drawing the butterflies out which is so fun to look at when it starts to get really hot in the middle of the day and it may be easy to get distracted, so fingers crossed they are also blooming at Presquile. I’ll be checking back in with photos from the next research trip and some lab updates in a week or two!