Dr Samantha Pendleton
Engineer of data, ontologies, and clusters.
Thrower of pots, controllers, and eggs.
Applying for a PhD
My experience of the PhD application process tl;dr: be yourself, include things you have learnt (even if not much practical experience), and get some buzz words in the bank (make sure you use them correctly)!
Introduction During my time as a mentor for undergraduates and teaching assistant for Masters students, I have had questions about the PhD application process. Now as a PhD student with a bunch of curated responses, the following post is the advice I gave.
Digital Art
My Digital Artwork This page is a collection of art I digitally developed during the pandemic/my PhD. They are ordered by date (first to most recent). Thank you for scrolling!
Colours
The Rainbow project A set of fun - little - projects developed with Python for the command line interface.
As of 2019 these projects are no longer supported! indigo Simple to-do list: indi-go-ing
indigo is a to-do list tracker (GitHub repo). During my PhD, I often had impromptu meetings which needed my laptop and I found myself unable to multi-task: reading results, listening to others, and trying to write down notes. I usually ended up rushing my notes, which then became unreadable. And so, I made indigo to make my note-taking easier: I can Alt+Tab to switch between the window of results to the window of notes.
Max Perutz Science Writing Award Entry
Weaving webs for smarter science This piece was submitted for the 2019 Max Perutz Science Writing Award. A competition for MRC students to write about their science to the public. It is aimed for students to communicate about their PhD in a way that a wider audience, such as non-scientific individuals, can understand - to help us build our communication skills. How can we do great science if we can’t find useful information? In the UK there are many repositories that have captured vast collections of patient information. These repositories are called Biobanks. Each Biobank contains confidential data corresponding to the health and wellbeing of thousands of patients, including years of health records, doctor’s letters, and importantly, links those records to banked biosamples. Yet, a lack of standardised clinical annotation across these Biobanks leaves gaps in our knowledge which hampers the utility of millions of biosamples, as they can be difficult to find.
Acidoseq: a toolkit for the studying of Acidobacteria sequences
Acidoseq Acidoseq is a tool for studing metagenomic reads, grouping Acidobacteria classified and unclassified reads into subdivisons based on GC content. It is a Python package, designed for Nanopore sequences, available open-source on GitHub with a condensed paper.
This work was a part of my Masters degree (2018), which the dissertation is available to read.
The motivation behind development of this package was due to many of Acidobacteria’s recovered sequences were labelled as “unclassified”.
Masters Dissertation
Metagenomics of Acid Soil: a study of Nanopore long-reads and Acidobacteria tl;dr: check out a summarised version of the dissertation.
Developed a tool to classify unclassified Acidobacteria, acidoseq, which is available to read in more detail in a project page.
Introduction Since I enjoyed my Summer Bioinformatics research position (2017), for my Masters dissertation I hoped to work with Amanda Clare again.
Amanda spoke to the same research group, who had new sequences for me to look at. These reads were derived using Nanopore sequencing from Aberystwyth soil. The output includes ~2 million sequences: made of ACGT basepairs.
Outsider Perspective of a PhD
Witnessing my partner writing their PhD tl;dr: a PhD is an emotional rollercoaster with side effects (sleep talking).
My partner, Sam, successfully passed his PhD Viva, taking ~4.5 hours. He monitored his heart rate and plotted it, seems quite a traumatic event.
This blog post is to acknowledge the stress of a PhD from a friend, partner, and outsider perspective. I hope this post isn’t misunderstood or reflects any selfishness: I am writing to acknowledge this stressful experience.
Lovelace Colloquim 2018
Attending the 2018 Lovelace Colloquim in Sheffield tl;dr: my first conference, very fun!
The BCS Lovelace Colloquium is an annual conference for women and non-binary individuals in computer science and related fields. I submitted an abstract based on the poster from the Bioinformatics research I had done the Summer previously.
This year’s conference (2018) was held in Sheffield, which I was both excited and nervous as I had only ever visited few places in the UK. Due to terrible traffic on the way to Sheffield, I missed the beginning of the social activities (the treasure hunt). But was able to join the group a little towards the end of the evening. I met fellow conference attendees from Aberdeen, Bath, and even new Aberystwyth students.
Summer of Bioinformatics
My first Bioinformatics experience tl;dr: see the research poster.
Introduction Preface: Bioinformatics covers a wide range of areas, e.g. developing complex algorithms to answering complex questions.
Old Poem
Banging Playground WARNING: read at your own cringe. I made this poem when I was 11 years old (2007) for English class. I was notoriously terrible at poems. It’s foggy, we’re drowsy, with the sound of bangs; We’re crawling around the best we can.
Shouting, exploding, and pushing to the limit; It’s raining mud, the sun seems timid.
Sweaty, dizzy, and confused; The youths are rising and all bruised.