- From 2009 to 2016 I was taking a BSc in Health Sciences and Biology with a focus on Molecular and Cell biology and neuroscience. I graduated in 2016.. That's a second degree...
- From 2017 to 2018 MSc in Molecular and Cellular Biology at Sheffield Hallam University in Sheffield... I became more interested in cancers and genomics, and generally the underlying molecular pathways in human diseases.
- From 2018 to 2021 I have been a PhD student at Sheffield Hallam University - with the PhD title "Identification of variants contributing to the risk of schizophrenia using high-throughput sequencing". This is a PhD based in dry-lab/computational biology. I presented some preliminary findings in a poster last year at a (virtual) international conference FENS 2020. And now am writing up... I have completed almost all of the big data work, using R Studio and Linux command-line. The server is a beast - 500GB of RAM, 2 Xeon 32-core processors...
- Last week I took part in Stepik's Bioinformatics Contest 2021 and have qualified for the next round... 5700 people signed up and ~1400 qualified. It's a tough programming contest, but there's a good community of data scientists, bioinformaticians, and software engineers who get involved. I finished the qualification round at position 131, two below the chunk of those at joint 1st position. I put some code up on github for one of the questions (zorgster/bioc21q3). I completed all of the questions in Python (but started out thinking I was going to use Java or C).
- Over the last few years I have completed a few Coursera courses:
- Johns Hopkins University - Data Science specialization. This was a tough course to do alongside a PhD - I progressed slowly - but perseverance paid off in the end.
- DeepLearning.ai's Deep Learning specialization covering Neural Networks, CNNs, and RNNs (LSTM+GRU etc.) - this led to an interest in colouring old photos (colouring by context) and neural style transfer (blending the style of one image into the content of another). I thoroughly recommend this as an introduction to NNs starting with the fundamentals. Andrew Ng is great at explaining things and building it up lesson by lesson.
- Fundamental Neuroscience for Neuroimaging - I had to read a lot about MRI studies in schizophrenia and needed to know more about all of the terminology...
- On and off, I take a look at Algorithms, Part I - just to improve a) knowledge of data structures, algorithms and b) to keep my Java skills going...
- for Christmas I was given a Raspberry Pi 400 - Pi in a keyboard! A hark back to the old ZX81 days.. I haven't had the time to explore it as much as I would like to - once I get the thesis out of the way. I now have a stack of Arduinos and 2x Pis to turn to when I have some spare time.
- 3-4 years back, I helped produce a few video tours for a paper about Japanese sea wall defences - it was finally published 2 years ago in 2019 - Imagining Disasters in the Era of Climate Change: Is Japan’s Seawall a New Maginot Line?. The paper has been cited 4 times to date. I thank Prof. Peter Matanle at SEAS, University of Sheffield for including me as a co-author... It was also a harrowing introduction to the review process - although I was mostly an observer of the process. Peter is talking about a follow-up paper in the future.
My laptop has taken a beating in the last year... constant writing and tapping away during lockdown. The power cable socket wore out and I had to install a replacement.. luckily on a Dell Inspiron 3585 it simply unscrews and unplugs from the motherboard.
Problems to solve... my old Asus laptop hard disk strangely won't boot. The head seems to be stuck. This happened coincidentally - after I used a pen drive which I had imaged an installation disk for Ubuntu. When I closed down the Ubuntu OS, and tried opening Windows again, nothing. Just a high-pitch buzzing from the disk. A bit gung-ho, I opened the disk quickly and pulled the head back. I had access briefly but then the head stuck again. Can an Ubuntu pen drive do that to a HD? Somehow mess up the firmware? It's forming part of the queue of things to look at when I have the time.
It would be nice to get some of the data off that disk...
Some sites used for coding...
https://deepnote.com/ - Jupyter notebook-style Machine Learning workspace.
https://kaggle.com/ - Machine Learning competitions related to actual research
And Family History - I've done a lot of that... 23andMe or AncestryDNA combined with family history tree-building with Ancestry is very effective... but also very distracting, so it's on the sidelines too...
Writing up thesis.... everything must be put on hold - unless it is directly related to the PhD..
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