17 Ağustos 2015 Pazartesi

13th of August to 14th of August: Primer Design Narrative Part 2

In these last two days of our internship we finished up our primer design code and starting wrapping up our internship. We also had a special final day on the 15th, which my colleagues have detailed on their own blog entries. Before diving into our daily narrative I would like to leave you with the state of the room at the end of the 13th of August, a gloomy looking place without the home decorations we had installed at the beginning of the internship. But a lot of good memories were born in this room, so lets round up on a good note.


To kick off the second half of our last week we began by looking over the code that Mr. Ahmet had written last night along with Mr. Osman and how we could solve the problems that had arisen since last night. As always we made sure to comment our code so others can understand our code along with helping us get a refresh of our own code much faster. Below is the flow of the entire coding we have done, laid out on our board to make sure we are up to date with how it functions.

The only thing left to do in this section was to combine all of our sequence parsing and filtering code into one document, making sure to comment along the way. Unfortunately we hit a pothole as we couldn’t seem to find any primers under our ideal primer length of 500, even though by all rights we should have. The struggle to fix our code took quite a bit of time and in the end we had to delete one of the oldest functions we had that was no longer relevant to our current coding scheme.

After celebrating our victory with some Counter-Strike we moved on to work on our code some more by rearranging some existing functions and adding in the heterodimer removal function. Finally at the end of the effort we were greeted with a huge list of good primers that could we could. However too much of a good thing can be bad, because now we had too many primers. While waiting for our verification code to finish running (it would take a couple hours) we finally managed to watch The Internship. After the movie Mr. Ahmet made some optimization changes to the code to speed up the process immensely. And on that victorious note we ended the night by starting to clean out our room as we were nearing the end of our internship.


Today the early birds among our group had breakfast at Erciyes Börek while waiting for the others to show up. After everyone was gathered we had a look at the Cytoscape visualization Mr. Ahmet had cooked up. Below is the work in progress of visualizing the interactions the primers have with each other.

Then Mr. Ahmet talked about developing an algorithm to find “triangles”of primary primer connections, then adding them into a list. After they are stored in some way we can look at the triangle primer connections with other triangles. It sounds confusing but the overall goal is to find the primers with no web-like connections to other primers, which means we can use these primers in multiplex PCR as they will not interfere with all the other primers in the same PCR tube. A couple hours went into writing the code to find the connections among the primers, along with some new Python coding we hadn’t done before like “isinstance” being used.

We took a short lunch break to eat some delicious yağlama that Ms. Aysegul had made for us. After rounding up with some dessert we found out that we could fit 6 of our exon primers into one tube. Below are the relevant triangles merged into a hexagon (visualized in Cytoscape).

We took a short break playing some Counter-Strike before relocating to Starbucks to close of our internship. At Starbucks we evaluated each other on our performance and how we thought the general atmosphere of the internship was like. Everyone even got a farewell mug signed by Mr. Ahmet himself.

We made plans to meet tomorrow one last time to eat breakfast at Mr. Ahmet's house to truly wrap up and conclude our internship adventure.

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