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Name: Simon Murray

Type: User

Company: Genomics England

Location: London

Welcome! 🌅

Thank you for visiting my GitHub profile!

I thought I would add a little guide to help you navigate my profile more easily.

I have created a contribution guide repository which maps out all the contributions I made to the organisations I have worked for throughout my career.

Skills

Pipeline Development (Nextflow, nf-core, nf-test with a little bit of Groovy and Java)
Containerisation (Docker, Singularity/Apptainer)
Cloud Infrastructure Deployment (AWS EC2, AWS S3)
CI/CD (Git, GitHub actions, GitPod)
HPC Job Scheduling (IBM LSF, Sun Grid Engine)
Downstream scRNAseq analysis (Python, R)
Environment Package Management (conda, mamba)
Experience Training New Bioinformaticians (Unix, Docker and Singularity/Apptainer, HPC architecture, scRNAseq analysis in Python and R)

Career Timeline

Sept 2019 - Dec 2023:
- Cellular Genetics Informatics - I worked as a Bioinformatician with the Cellular Genetics Informatics team at the Wellcome Sanger Institute for four years whilst earning my degree. My job was to support the Cellular Genetics Faculty by developing high throughput scRNAseq analysis pipelines for their research, building containers with docker and singularity to add additional software to Sanger's IBM LSF HPC, fixing faculty built environments managed by conda and aiding faculty to navigate the infrastructure and job scheduler on the Sanger HPC.
Jan 2024 - May 2024:
- Eco-Flow - I worked as a Senior Research Technician - Bioinformatics at UCL as the Technical Lead on the Eco-Flow project. This project is designed to build gold standard nf-core compliant Nextflow pipelines for ecologists at varying universities throughout the UK. The aim is to alleviate the strain they experience when trying to complete high through put analysis on their universities' HPC by providing portable, containerised pipelines.
May 2024 - Present:
- I am currently working as a Bioinformatics Engineer at Genomics England.

Contact

If you wish to contact me please use: simondonaldmurray [at] gmail [dot] com

Have a Nice Day! 🌌

Simon Murray's Projects

bioconvert

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

cellbender_scripts

Scripts that run cellbender remove-background which removes technical artifacts and submit it for execution on compute nodes on a cluster.

clustering_investigation

Multiple scripts that visualize clustering data, generate heatmaps, produce statistics of Seurat data and compare clustering of different algorithms.

conda-package-publish-action

Automatically Publishes Conda Packages To Anaconda

configs

Config files used to define parameters specific to compute environments at different Institutions

contribution-guide

A guide to repositories I have contributed to in my career.

covid-19

Forked repository of Covid19 Outbreak Data

covid-19-outbreak-tool

Script that automatically downloads latest covid19 data, produces plots tracking latest developments before uploading latest data and graphs to a website.

covid19_outbreak

Website produced by covid-19-outbreak-tool hosting graphs tracking covid19 cases, deaths and recoveries. The data can be downloaded from the website.

database_coursework

Script that produces database using sqlite3 and populates it with covid19 testing data.

dbgap_data_extraction

Scripts used to fetch and extra data from the dbgap database before analyzing the data with star fusion and star rem.

dna-pipeline

Nextflow DNA Seq Pipeline that performs: Quality Control, Alignment, Removing Duplicates, Variant Calling and Variant Annotation

dotplot_fasta

A program that produces a dotplot diagram that can compare short DNA, RNA and protein sequences as described below.

Script that curates and explores expression data. This data is then used to train and test machine learning algorithms that then predict cancer in a new dataset. Logistic regression, tree modeling and neural networks were used.

omero_validation

Python script that validates input files ready for OMERO stitching and upload

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

scanpy_soupx

Repo which takes output from starsolo analysis and analyses it with scanpy and soupx

sceasy

A package to help convert different single-cell data formats to each other

simondmurray

Repository for containing my GitHub profile welcome page

statistics_introduction

Script that performs multiple statistical tests on multiple sets of input data and generates statistical plots.

synteny

An nf-core compliant Nextflow pipeline for running synteny analysis.

systems_biology_coursework

GitHub repo for completing systems biology coursework module

test-github-actions

Created and tested GitHub actions used to build, test and publish packages to Anaconda and PyPI for the repo hemberg-lab/sc3s.

test-tower-ci

Testing using GitHub Actions in conjunction with Nextflow Tower

testing_episcanpy

Script running RNA seq steps: normalization, calculating variability, clustering and visualisation with a new package called episcanpy.

testing_sphinx

Scripts that initialize and execute the sphinx software which has been integrated with graphviz to produce custom graphs for website publication.

university-major-project

Evidence of all scripts used in University Major Project for evidencing in University report

updating_adata_colourscheme

Script alters anndata objects to change colour scheme for plotting with cellxgene

utils

Useful bioinformatics scripts including BAM and VCF file naming convention conversion, contain removal, reordering and sorting BAM files and VCF + BAM chromosome comparison.