The new year: new research, new things to learn, new things to do

New. Lots of “new” going on at the moment. It’s fantastic.

I’ve recently started my new Comparative Animal Locomotion module at the RVC, and it’s been really interesting so far. A lot of what has been covered so far is old hat, but it’s reinforcing to re-cover and re-learn things I haven’t thought about for a while. We’re just about getting into new things, for instance, scaling finally clicked! Felt like a bit of a eureka moment, and is incredibly simple once the mental approach is sorted out. Did you know that cat bone diameter scales isometrically?

I also started my new lab project for the year: felids, gait transitions and kinematics for now. New challenges (more new things!) present themselves with this project. Due to the nature of studying big cats, there’s some obvious claw and tooth shaped dangers presented. As such, calculating true measurements from the data I have will be different to the way I’ve done it previously, but certainly achievable accurately. It appears tigers don’t trust force plates, and will try to avoid walking on them at all costs – scaredy cats! More on this to come in a future post, hopefully with a few gifs showing the true nature of these oversized moggies.

Finally, PhD application season is here, and I suppose this is the crux of this post, ad something else new to me. I’m currently working on my CV, which is so different to any CV I’ve made in the past. Academic CVs need so much more content in them than the last one I put together, which was for a coffee shop job! I owe a huge thanks to Michelle Reeve and Chris Basu of the Structure and Motion Lab for helping me redraft and refine my CV. Check them out on various social media by clicking their names.

I’ve got my sights set on the PhD I want, now I just have to apply (successfully) and interview (successfully). Things feel very real at the moment, with a lot to juggle between coursework, research, lectures and applications. More PhDs will be advertised soon, so there’s only going to be more to look at. When I look back to two years ago, where I wasn’t entirely sure what I wanted to do with my degree/career, it’s daunting to see how far I’ve come.

So here’s to more productivity, more learning and some success. Until next time, when I hopefully something else new to talk about.

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And so the summer ends

Not as extensive a post as last time, and nowhere near as substantial, but here’s some experiences I’ve had, and some musings about the next few weeks as the summer draws to a close.

This week, I helped out a little more on the giraffe project, helping out where I could with data collection for future work.

It was great to experience data collection on such a large scale! Manual work shovelling sand and lifting slabs of wood made me feel right at home, and was a nice refreshment from time spent in the office. The first day was spent setting up for collection: putting force plates into the steel framework underground, wiring up and protecting and burying the plates. Day two and three were spent collecting, the first of which went perfectly. Day three faced some small technical issues, none of which impacted upon the quality of the data, but I’ve come to the conclusion that without some problems you can’t have been doing real science.

Though only a short week helping out, I had a whale of a time. Now I have a few weeks to relax and enjoy time off before class begins. I’ll be spending tome of that time contemplating a few species I may want to study, and might dedicate a post or two to bouncing ideas around. It’s something I need to be considering now that I’m set on doing a PhD after my undergraduate degree.

Thanks for reading, I’ll be sharing my experiences learning new things this term, and may share my analysis of a few papers I should be dissecting in my class’ journal club! Until next time!

My Summer in the SML

I spent this summer, the second of my undergraduate degree, in the Royal Veterinary College’s Structure and Motion Laboratory, as I undertook a BBSRC-funded Summer Research Experience Placement. The purpose of the REP is to give undergrad students a taste of what research would be like as a career. In my case, I was given the fantastic opportunity to study giraffe locomotion. Mentored by Christopher Basu, a PhD student in the SML, and Professor John Hutchinson, my ten-week project began at the start of July.

First things first, I had some ground work to do. All the data had been collected prior to my placement, though I will be joining Chris next week to collect fresh data for his future work. Giraffes were recorded using high speed video cameras walking parallel to the edge of their enclosure, over concealed force-plates measuring ground reaction forces. I was provided with 3 days’ worth of data in raw video format, which needed laborious converting, cropping into individual trials and rating. And so went the first week.

Once the data was in a useable format, I had the process of deciding how to digitise the trials.  This process allows us to extract numerical data that can be analysed from videos by plotting coordinates on individual frames. Using a digitising script I had previous experience of, within the MATLAB suite, seemed like a good idea. Next was deciding where to plot on the giraffe. 15 points were selected, encompassing the head, neck, and the nearside fore- and hind-limb. I created a profile of reference for each giraffe to ensure consistent digitising. 7 weeks later, and with many lessons learned in my digitising method, it was done. 15 strides ready for analysis.

An example of a trial
An example of a trial

This bought about the opportunity for a new challenge: using MATLAB for data analysis. Having never used any language-based software in the past, I was keen to learn what I could in the short time I had left. Due to the relatively small size of my data set, I was able to do a lot of my analysis in Microsoft Excel, but I did learn enough to compose some plots in MATLAB.

Then came statistical analyses, which I view as the necessary evil in all science. Without stats, results are largely useless, but we’ve never seen eye-to-eye. Thankfully, Excel was able to help me again here with handy regression analysis tools.

I can’t share a lot of what I found, due to the data being as-yet unpublished, but here’s a teaser of my findings! The plot below shows how, at any particular speed, the hindlimbs have a longer duty factor (spend a larger percentage of the time on the ground) than the forelimbs. This is interesting because the forelimbs carry most of the weight in giraffes, so one might expect the opposite trend.

A teaser of some of my findings!
A teaser of some of my findings!

So that’s the science covered, which has been the best experience of my academic life. The chance to have my own research project is hopefully just a taste of what to come from the future, but there’s a long way to go yet. However, there’s more I’ve learnt throughout my summer besides just the science. The most striking of which are the importance of both science communication and networking.

If you don’t communicate your science, who is going to know about it? With the dawn of Twitter and other forms of social media, there’s no reason not to shout from the rooftops about your work. Within both the public and scientific communities, there’s so much happening that no one can keep track of it all. Posting a tweet about cool new findings, showcasing your data collection or asking for solutions to your next problem all help to bring awareness to your work. I’ve been working on keeping a Twitter presence throughout my ten weeks, and it helps keep a driving force there during the monotonous groundwork such as digitising.

Another brilliant feature of Twitter is the range of people you can interact with, which brings us onto networking. Learning as many names and faces as possible seems important. Not only because knowing someone’s name when you meet them is polite, but you never know who the next collaborator or contributor is going to be. Oh, and because finding out what other people are working on is so cool! Within the SML alone, there are so many different projects looking such a wide range of species, it’s staggering to try and think about them all.

In the coming weeks, I’ll be starting the third year of my undergrad degree, incorporating another SML project on felids. Stay tuned to the blog, or follow me on Twitter @averageginge for future updates!

I’m Luke, and this summer, I got to be a scientist.

First post for a month or so, with good reason

It’s been a long time since I last posted, but I made the executive decision that digitising wasn’t a thrilling point of discussion for the next post on my journey, and until yesterday, that has pretty much been all I’ve done.

Until Monday arrived. I gloriously finished digitising. “I’m free of MATLAB!”, I thought, foolishly. For as long as I want to be a biomechanist, I will never be free of MATLAB. But I’m okay with that. With heaps of digitised data stored in .csv files begging to be analysed, I began deciding what I actually wanted to find out. Simple kinematics are a given, and if I manage to debug the code that someone is providing, I might be able to derive some joint angles, which will be great!

With the manageable data set I have, I’m able to do the majority of my analysis in Excel, which although not ideal, does the job. In future I hope to use MATLAB almost exclusively, but learning an entire coding language and analysing my data in the dwindling time I have left on this project is a little optimistic.

Yesterday came my first result. Space calibration, decrypting my first ever Ground Reaction Force data and a multitude of Excel equations has given me a speed, stance/swing times and duty factors. I’m ecstatic. All the hard work has paid off!

Once I’ve collected as much as this as I can, I’m going to write a code to determine theoretical leg lengths, I think. From there, the calibrated space will give me stride lengths, and I’l be able to garner some relative lengths and frequencies too, as well as Froude number.

What’s life without a challenge?

For more constant updates, follow me on Twitter @averageginge (I’ve had that handle for years, it’s not changing).

Oops, it’s been a while…

Oops, it’s been a while…

So I may have not posted in quite a little while long time. Ah well, there’s one here now.

Since we last spoke, a lot has happened. I did the salamander project, lots of digitising and writing up, but I earned a First in that project! The year overall finished as a high 2:1, just like last year. Due to overall disliking the taught content this year, I’m happy with that. Next year I require 72.3% for an overall First Class BSc, so my sights are set.

At time of writing, I’m just starting my third week of my BBSRC funded studentship within the Structure and Motion Lab at the RVC, working on giraffe locomotion. It’s amazing! Giraffes are such funny creatures to look at, when you really pay attention. Despite having never actually met the subject animals (Bashu, Ijuma, Savannah, Willow and Luna from Whipsnade Zoo), their personalities exude through the medium of video, and I may have let slip the odd giggle when reviewing the data.

The timetable I work to now is brilliant. Though flexible, I’m finding myself working to solid, consistent days, and enjoying every minute. It’s the research life for me!

Until the next time I remember to post… Farewell!

An update from the land of 10pm dinners

Wow, what a week! 7 days into the trip to Oviedo, Spain, and I finally have enough downtime to write a short post here about what I’ve learned, besides a little Spanish.

Salamanders are awesome amphibians, capable of some intriguing locomotor gaits. As it happens, the population we have been studying is one of the smaller and slower fire salamander populations, according to Guillermo, a visiting S. salamandra geneticist. Despite this, they still exhibit some great locomotor ability. Who knew salamanders could gallop?!

However, fun as they are, as we near our 160th salamander, I’m growing slightly tired. Apparently this is a very large data set for animal science, which is great for the research. Not so great for the amount of video renaming, converting, cropping and digitising we have yet to do though!

The next best thing about being on a research trip in another country? The food! Great food every day of the week, never leaving the table anything less than fit to burst, and then doing it all over again the next day.

As another evening draws to a close, and my departure looming two mornings from now, I look forward to returning home for data processing. Staying in a 5 star hotel and eating out every night is fantastic, but the return to reality will be refreshing.

Until next time.

So this is what doing science is all about…

This week has been the introduction to what being a scientific researcher means. I know it’s only a second year BSc project, but it is hopefully the start of what is to come.

I’ve had a heath and safety induction. It’s almost a shame that such measures are necessary in today’s society that we must be warned not to touch things on fire. Yet across business, education, life and science, health and safety is at the forefront of our experience.

I’ve also got to grips with some of the software I will be analysing the salamander videos with. Pretty complex stuff! MATLAB is a new package to me, but very clever in its execution. I’m yet to convert the data points I can produce into manipulative, meaningful numbers yet, but that will come during the research.

And, finally, I am endlessly reading and reviewing the literature surrounding salamander biology, ontogeny and locomotion. I expected a mountain to climb, but sifting through an avalanche of white sheets of research feels like fighting an uphill battle. The top is still not in sight, in fact, I may still be at base camp. I’m enjoying it, but using this blog as a momentary reclamation of a free mind, without feeling guilty of being unproductive. As my understanding grows, I’m even more eager to get stuck into the science!

Flights to Oviedo, Spain, are on Wednesday. I’ll hopefully update whilst there. Adiós!