Industry Placement


Why haven't I been writing regularly?

Simply put I've been working like crazy!

Two amazing things have happened to me this last month and laying the groundwork that has made them happen has been super stressful, rewarding and time-consuming:

  1. I've gotten permission to write a scientific methods paper on all of the work I've been doing this last 6 months
    • I have since written that paper (with a lot of vital help! without which I would have gotten nowhere)
    • It's in a drafting stage and waiting to get feedback, hence I have time to write this!
  2. I applied for and received a research grant from the Genetics Society to do research on QTL mapping of the very phenotypic traits my methodology measures and generates.

Hopefully, I can write more on these soon when more information is not under wraps!

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As a computer scientist, I have always listened in amazement at the seemingly magic things that biologists have told me and thought up a million questions.  Most prevalent in this, is how do DNA, RNA and cells actually work? Where do they come from? Why do we talk about having X chromosomes and yet sometimes refer to DNA as a big long string of AGCT. These are the things that torment me. That make me feel like a small child who has walked into the crazy world of wall street. Information flying everywhere and people yelling incoherent sentences that make me stare in amazement. All the while wondering 'how do these people know what's going on, where is the logic, where does it begin?'.


Well folks, that is my grand question.

Continue reading A Computer Scientists foyer into Cellular Biology

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I haven't had the chance to write a decent post on my current IY for a few weeks, I would say unfortunately but not so as I've been having a blast!

I've been  getting to play with all sorts of hardware that I had no idea about until recently. I got to spend a few days researching methods of creating movement through electronics, magnets and pneumatic (not the thing you get from being too cold, I made that mistake too).

The gif (pronounced with a hard G) above shows one of my little contraptions that  I was extremely excited to build.  It mostly took me a bit to interpret how the wiring of our actuators matched to the inner coils, after that it was 6 wires to a H-Bridge and 4 pins to the arduino to give signals of direction essentially. Here's the code I've been using as a super simple demo just to test the wiring is working (If you haven't played with an Arduino then go get one, super cheap, super easy, super open-source electronics)

I should have probably mentioned by now that there is an actual point of these weight lifting devices, as I mentioned in previous posts load-cells are generally ill-suited to continuous weighing, particularly in environments where the conditions don't like to stay the same. I am attempting to design a cost

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Well this week has been fun!

We started with one of the IBERS researchers bringing round 81 plant pots (pretty hefty ones at that, 6kg each) to the Gravi greenhouse. This meant it was time to setup them all up on the weighing benches (yeah those ones I posted about last time). Once all in position it was time to test the entire system to see if all 81 plant pots would be watered and weighed correctly...

Continue reading First experiment in Gravimetrics

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I've spent the last few days having a crazy, fun-filled, packed, hands-on introduction at work at the NPPC! I literally got started here with running tests, inspecting systems and patching old codebases.

Mainly I've been playing around with, the now a few years old, Raspberry Pi model B's. They're super fragile and hate being tampered with. That's meant that a lot of my time has been testing devices, checking images are not corrupted and re-imaging SD cards.

These Pi's are all part of a large system which controls an automated watering and weighing system for the use with various experiments. Getting this system into a usable state has been fun, but there is quite a bit of urgency as a new experiment is due to start in under 4 days!

One of my little side missions is to test the automated scales that we are using.

These numbers above show some readings I've set up to be taken every minute. I used a known weight of 2Kg and you can see that over time the quality of the scales are diminishing. Which when you play to do this over months... THIS IS VERY VERY BAD FOR SCIENCE EVERYWHERE!

A somewhat longer term project on this that I am hoping to work on is to revamp this system. Currently it is written entirely in Perl which in itself is quite an oddity. I would love to rewire all of the Pi's in use (15+), move them to be closer to their scales they handle and the water they control. I also plan on upgrading these to possible the Pi 3 as they are much more stable and power efficient (due to sleep modes, and handling of random power cuts). Additionally rewriting the software to make use of Python and more friendly clear to understand code, as well as maintain the documentation for it would make me very happy indeed!

Hopefully I will get to update my progress on this again soon!

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