Generating Errors and Not Talking to the Microbes

At the height of my frustration earlier this week I would have been happy to tell you that computers in general and one program in particular are demonically possessed and out to drive my blood pressure through the roof. However, a little patience and a lot of stubbornness have gone a long way in solving the problems presented by a pipeline Blair found online. Let me explain: Blair is still looking for a program we can trust to consistently analyze his data. One particular program online seemed to be tailored to what we were looking for, but it does what Blair refers to as “black box magic” – it means that a program doesn’t necessarily show you how it gets from your input to the result. This leads to a number of problems, the key one currently being in that when I get error messages it can be hard to establish what to change. The error messages aren’t helpful either, “Error: lo1” merely gives me the impression my computer is laughing at me (you must admit, it does look like “lol”). There was definitely a period of time where I felt like all I was doing was generating error messages. However, a perusal of the FAQs, tutorials and a series of systematic changes to the file upload method resulted in the successful upload of all the files. I’m still working on understanding WHY the upload worked – from what I can tell I was doing exactly what had failed ten times previously but hopefully an email to the site managers will clear that up as well.

On a different note, Wednesday I got to do some actual lab work instead of just data analysis. The labs in the Marine Science Research Building seem well equipped for just about anything. Blair ran me through a typical procedure for collecting DNA and rattled off a list of things to keep in mind when working with DNA and in sensitive labs in general. One of the big issues is keeping the delicate strands of DNA long enough to get actual data from them, as well as preserving the integrity of the data and not contaminating the samples. Blair works with 90+ samples at a time, so it’s all too easy to see how cross contamination could happen, as well as contamination from everything else that could be floating around the lab. Sometimes Blair is unintentionally hilarious when explaining lab procedures: “You don’t have to close all of the tubes because we’re about to add another solution, but just make sure you aren’t dripping anything around, don’t lead over the samples, try not to disturb the air too much if you can, you know… and don’t talk to the microbes”. I’m not sure how he guessed but he’s on to my little quirks; if he didn’t know before, he definitely does now.

Currently Should Be Reading: College Physics – Young and Geller

Currently Shouldn’t Be Reading: The Ground Beneath Her Feet – Salman Rushdie

Currently Listening To: O Chao de Praca – Banda Prakantar

Posted in 2010-2011, EUREKA

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Alex Iteen is a second year student majoring in Biology. He is interested in bioengineering and synthetic biology. He is currently working in Dr. Fygenson's lab on DNA nanotubes.
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