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Giving my revision some structure! (Year 13 2019/20)

Hi, I'm Novasae, welcome to my GYG!
I'm going into year 13 this September and whilst I haven't made a study blog before, I'm hoping that by writing about my study habits I'll find it a little bit easier to remain organised and motivated! I'm in the middle of a Nuffield Research Project right now which has thankfully been keeping me busy over the summer. I'm doing nanopore sequencing, and studying how different DNA fragment lengths impact classification in a "shotgun sequenced" soil sample. I'm aiming to post once a week and to maintain a healthy work-life balance (which in my opinion at least is way more important than just pure revision time, but maybe that's just an excuse for procrastinating)

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About me

What am I studying?

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Future?

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What do I do outside of revision?

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If you notice my post and have your own GYG, please plug it! I'd love to read it! I'm going to go out for dinner now after spending some time reading at the library

(edited 4 years ago)

Reply 1

username3670510

I thought I'd share a little more about my project going into the last week.

There's a few ways we can go about classifying nucleotide reads, but they basically all consist of comparing segments of nucleotides in a read against a database which allows us to decide to a certain degree of certainty what the read belonged to. This has problems in itself as public databases aren't always perfectly curated: one of the biggest examples of this is the Japanese rice fish Oryzias latipes - whoever added the sequence for this fish to the database left tons of adapter sequence (a DNA sequence ligated during library construction that helps the sequencer do its job) and viruses in there, so that it pops up all the time when using certain less strict programs.

I started by using two relatively fast tools, Kraken and Centrifuge but these turned out not to be suitable for our data set. Kraken uses a k-mer based method, which means it splits reads into 31 base long segments, which turned out to have a rather bad effect on the fractions we sequenced with the shortest DNA fragments, meaning that whilst the matches are fairly accurate we can't compare the results between fractions. Centrifuge has the afore-mentioned problem and is equivalent to pulling organism names out of a hat.

Which is why, three days before the conclusion of my time here, I've switched to more sensitive methods that shouldn't be affected too poorly by read length. One that I'm particularly interested in is DIAMOND, a tool that classifies DNA reads by translational BLAST, meaning that it locates gene bodies, translates them into their amino acid sequence, and then looks that sequence up in its database instead. This is immediately much more sensitive, and protein databases tend to be slightly better in their quality (apparently the drug discovery field likes proteins). Also because it's quite targeted, it is reportedly 20,000 times faster than your traditional BLAST search, which an A-Level student may have done on some digested Lambda DNA online. Also, I get to use like 1.5 terabytes of RAM at a time which is more than I will ever get my hands on ever again o.o

Overall this project has gone way quicker than I anticipated and I'm no closer to a poster than I was at the beginning of the summer :tongue:

. As well as the Nuffield celebration I'll be attending the Young Scientist's Journal conference in October to present said poster which I anticipate to be really interesting! There's going to be talks, workshops and all sorts going on.

Reply 2

16CharsIsTooShor

Hi.

I didn't understand what anything you wrote about your project means 😅 but it sounds interesting

Good luck with everything 👍

Reply 3

username3670510

Original post by JustAWxnderer

Hi.

I didn't understand what anything you wrote about your project means 😅 but it sounds interesting

Good luck with everything 👍

That's okay, it's more for me than anything! Thank you!

Reply 4

brainzistheword

Study Forum Helper, Careers Forum Helper

Original post by novasae

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About me

What am I studying?

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What do I do outside of revision?

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Have loved reading your posts so far :heart:

Being a Mental Health Ambassador is amazing! Would definitely like to hear more about the work this involves.

All these GYGs make me want to start another one :beard:

Reply 5

mez_merising

woah your epq sounds craaazy (but in a good way :wink:

)
all the best for y13!

Reply 6

greenapples2

hey, I also want to study natural biological sciences (I'm year 12), could you please tag me!! good luck xx

Reply 7

username3670510

Hi, thanks for all the replies everyone :biggrin:

I've had a very long and tiring couple of weeks but it has all been well worth it. I did my work experience (my school makes us organise some in the first week of September or we're stuck doing MOOCs) at a lab that works with a particular species of Streptomyces. You know the smell that you get just after rain? That's Streptomyces sporulating and releasing a compound called geosmin, and as you could expect the entire lab smelt of it :biggrin:

I won't bore you with the exact details, but I learnt a lot of aseptic technique and got to do loads of microscopy including transmission electron microscopy!

Then since the 9th I've been back at sixth form. I've forgotten everything and I must have done 10 chemistry papers already, and I looked absolutely insane coming out of further maths running around spinning a piece of paper so clearly it's already gone downhill without me realising. We also finally got our predicted grades - mine are A*A*A*A which I'm really chuffed about. I did go to speak to my chemistry teacher who gave me the A which is somewhat pathetic but I wanted to know what I was doing wrong and he just said "don't worry I don't give A*s you're gonna do fine". I also spent like 3 evenings just playing Minecraft until like 8pm but we don't talk about it.

It's also personal statement crackdown time which is really funny because noone has looked at it yet. I keep saying "oh I did this oh I changed that oh can you please take a look for me" but I haven't been given any feedback from any teachers cause my form tutor is responsible for every early applicant in the school (which is 3 for cambridge, and absolutely loads for medicine, and for some reason the cambridge applicants have been pushed to the side for a bit) and I'm really stressed and losing sleep over it because the school deadline is next tuesday. aaaaaa I also sent the school my details to submit my application for the NSAA :smile:

Last bit for @mpaprika - obviously I don't know anything about you or your situation but do what you can to get yourself out there! I must have done so many outreach events at Cambridge but just sign up for everything especially the student shadowing scheme but on top of that drag a friend to masterclasses (that's what I did). There are so many opportunities out there for prospective students. At the open day we literally had a group of 6 people come to the NatSci event at Clare and we were doing interview questions 2 lecturers vs 6 and it was absolutely incredible. I can't believe that so many people missed out on that but it made the experience better for me so their loss I guess!

TL;DR: I have spent way too long working and not having a summer and I have cracked and need to go have a day out somewhere and pretend to be a human

Reply 8

username3670510

I paid for UCAS o.o Still need my sixth form to upload and check my reference and then I can go and be stressed about the next thing. If anybody reading this has tips for the NSAA that would be brilliant - I'm mostly worried about having to learn a bunch of new stuff... I just need to do some papers and crack on really so I'll do that later this week.

Gonna focus much more on studying now that's over but I've still got a poster to finish off early this week or it won't get printed in time which would be super scary. I also have a further decision paper due on Thursday which I'm absolutely going to fail lol, it was by far my weakest unit in the AS exam last year and since then we've added on such fun topics as Simplex algorithm lol

We are doing partial fractions in both normal and further maths at the moment which is super nice and relaxing but we are also doing hyperbolic functions which is the opposite, and in biology is specific immune response and the light independent step which is a lot of remembering. So I just came back from going stationery (I hope I got the right one) shopping to buy more folders. I need to make a tracker for chemistry (if someone has done this before please help) and locate my maths one which is "somewhere".

I also bought a candle since it's getting to that time of year! It's pomegranate scented! I like spending money on candles way too much and I should probably reign it in a bit but they're just so nice!

Reply 9

greenapples2

woo best of luck with UCAS! :smile:

Reply 10

username3670510

Original post by mpaprika

woo best of luck with UCAS! :smile:

Thank you! I'm glad that I got to a point with my personal statement that me and my tutors were really happy with :smile:

Reply 11

username3670510

I amended my personal statement according to the suggestions of my Head of Sixth and am now trudging through a decision paper with no bloody answer booklet. Drawing out billions of tables and graphs is really draining... oh well.