PhD Conversion Case Study: Tim Noble
04 Jul 2022







I am working in the Data Services group in the STFC’s Scientific Computing Department (SCD). I joined STFC on the PhD conversion programme after working for several years in the biotechnology industry. As part of my role as the Rucio (a data management software) Service manager I work closely with developers, universities, and large physics and astrophysics experiments.

I started my Higher Education by studying Microbiology at the University of Huddersfield, which I chose because of my interest in biology and specifically, viruses. I took part in a placement year, where I worked at the Leeds Institute of Genetics Health and Therapeutics, then worked in a small biotechnology company before completing a masters and PhD in Molecular and Cellular Biology.​​

​​Left to Right Figure 1*, Figure 2** and Figure 3***

Following my PhD, I worked for another small biotechnology company developing nanoclay based therapeutics where I got a wide range of experiences in the lab and out. However, during the early months of the pandemic, I was furloughed. Having had a long-time interest in computers but no experience in programming, I spent my furloughed time learning to code and develop things in Python. I worked on a few personal projects and realised I enjoyed the challenge of writing and developing programs.  I started to look for work in this new field but as an inexperienced coder this was challenging and I was reluctant to completely leave science. When I found the PhD conversation program, it seemed like a perfect fit to build on both his scientific background and my newfound interest in coding and developing.

All successful applicants for the PhD conversion program are integrated with a project, and for me this was developing and taking over the Rucio Data Management Software and service. To integrate myself with the team, and get up to speed, I has took part in various training and worked with developers of the software, sysadmins within SCD, and university site admins.

During the program, I have been supported to develop various skills for e.g. Linux, program development, project management, sysadmin skills, and an overall understanding of many technologies I had not encountered before.

I am now the Service owner for the Rucio software and service working within the Data Services group within SCD and Tier-1. I aim to help researchers to use the powerful data management software, making sure that the software has the features the experiments need to integrate with their workflows, that the service is available and is set up correctly to support the experiment, and making it more accessible to more communities.

Before I started in this role, I didn’t have a lot of experience with program development, and no experience with being a service owner, sysadmin, or with Linux but during my time at STFC I have definitely learned a lot, and look forward to learning more.

I am pleased that I chose to take part in the PhD program, I was interested in computing, but my path before this point didn’t quite align. I enjoyed my time in biology and I do not regret my choices, but I am happy with where I am now.​

​*Figure 1: A heat map of gene expression generated to assess gene expression differences between the cell clusters. The gene expression across the clusters highlighted several different cell populations with different gene expressions. Clusters 0 and 1 being one population, Clusters 2 to 6 being another, 7 another and 8 another. This data implies further that it was not just the top two genes expressed within the clusters which differentiate the clusters from one another. As shown in the key, yellow represents up-regulation, purple represents down-regulation, and black represents no expression.

**Figure 2: Comparing the genes of significance to literature, each of the cluster groups allowed for the identification of the cell cluster groups. The gene expression profiles were used to identify the cell population; resulting in the identification of monocytes, lymphocytes, erythrocyte and CAR cells.

***Figure 3: A schematic of where the potential SSC and CAR cells fiti in the venous sinusoid. The enrichments for the SSC was performed with the STRO-1 and CD146 markers, The SSC while not identified after this work, has shown a close relationship with the CAR cells. A population which shares many characteristics associated with the SSC, and some papers even claiming the CXCL 12/LEPR+ cells are the SSCs. One thing is clear, that further work is needed to narrow the search for these SSCs, but the inclusion of this Drop-Seq data does point towards a pericyte origin, with multi-lineage differentiation capability, and regulatory effercts on the HSC. Despite the incomplete identification of the SSC, this diagram shows the venous sinusoid, and surrounding cells, inlcuding the CAR and SSC working together to regulate the HSC cells, with both the CAR cells and SSC cells are capable of differentiation (represented by the black arrows) into the chondrogenic, osteogenic, and adipogenic lineages. The CAR cells and the SSCs regulate the HSC through CXCL12 interaction with CXCL4.

Contact: Noble, Timothy (STFC,RAL,SC)