More RateSetter info, and PhD thesis

config.toml

@@ -61,7 +61,7 @@ disableHugoGeneratorInject = false
 
   # Home subtitle of the index page.
   #
-  homeSubtitle = "PhD Student and Researcher"
+  homeSubtitle = "Postdoctoral Research Fellow, Researcher, and compute enthusiast"
 
   # Set a background for the homepage
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@@ -112,13 +112,13 @@ disableHugoGeneratorInject = false
   [params.footer]
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+    copyright = false
     author = true
 
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       #"Powered by <a href=\"http://gohugo.io\">Hugo</a>",
-      #"Theme based <a href=\"https://github.com/rhazdon\">Djordje Atlialp</a>"
+      #"Theme by <a href=\"https://github.com/rhazdon\">Djordje Atlialp</a>"
     ]
 
   # Colors for favicons
@@ -160,7 +160,7 @@ disableHugoGeneratorInject = false
   # Social icons
   [[params.social]]
     name = "email"
-    url  = "mailto:j.a.[email protected]"
+    url  = "mailto:[email protected]"
 
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@@ -170,11 +170,11 @@ disableHugoGeneratorInject = false
     name = "googlescholar"
     url  = "https://scholar.google.com/citations?user=4GMr_qsAAAAJ&hl=en/"
 
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-    weight    = 1
-    copyright = '<a href="https://creativecommons.org/licenses/by-nc/4.0/" target="_blank" rel="noopener">CC BY-NC 4.0</a>'
+#[languages]
+#  [languages.en]
+#    subtitle  = "PhD Student  and Researcher"
+#    weight    = 1
+#    copyright = '<a href="https://creativecommons.org/licenses/by-nc/4.0/" target="_blank" rel="noopener">CC BY-NC 4.0</a>'
 
 #  [languages.fr]
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content/about/index.md

@@ -9,6 +9,10 @@ I'm John Charlton, a Postdoctoral Research Fellow at the [University of Sheffiel
 
 My work is in the field of Computational Pathology, which seeks to utilise modern hardware advancements, developments in algorithms, and connect between different disciplines, to forward healthcare. I am specifically examining detections of head and neck cancers, with the aim of improving the detection and prognosis.
 
+## Neopath
+
+
+
 ## PhD
 
 I completed my PhD, as well as carried out 3 years of Research Associate work in the [Department of Computer Science](https://www.sheffield.ac.uk/dcs), in the [Visual Computing Group](https://www.sheffield.ac.uk/dcs/research/groups/visual-computing/home). Where my focus was of GPU computing, and simulating pedestrian crowds.
@@ -29,8 +33,51 @@ I have examined the use of the ORCA model on GPUs, originally created by [van de
 
 ## RateSetter
 
-As a research associate I am examining the Platform-Train Interface (PTI) within train stations. This has been particularly interesting during COVID times as social distancing  greatly changes the boarding and alighting behaviour of people. 
+As a research associate I examined the Platform-Train Interface (PTI) within train stations. This is the region of the platform and train where people move to board and alight. It is of particular interest because this is the cause of largest variation in train services, and understanding it more fully can lead to further insights for everyone involved in travelling on trains.
+
+I worked on RateSetter over three years, and during that time I worked on various projects regarding simulating the PTI process. The three projects were (and the year they commenced): 
+
+- Predicting a new fleet of trains at Liverpool stations (2019)
+- How the PTI process is affected by COVID (2020)
+- Changes to the platform to help people move around (2021)
+
+It has been really interesting to bring together two departments, computer science and mechanical engineering, to work on a joint topic. The exertise in the two areas come together to create complex, accurate models which can validate and predict future behaviour.
+
+The best place to find more about how RateSetter works is from the initial paper ["Ratesetter: Roadmap for faster, safer, and better platform train interface design and operation using evolutionary optimisation"](https://dl.acm.org/doi/pdf/10.1145/3205455.3205605) and [my PhD thesis]({{< ref "/publications/phd-thesis" >}}), particularly chapter 4, on simulation model accuracy.
+
+The following sections detail these RateSetter projects in more detail.
+
+### Liverpool
+RateSetter had already been tested on previous projects before I joined, and my first task was understanding how it worked, and what I could bring to enhance it.
+
+The project was designed in three steps. First was to measure the PTI process at various stations in Liverpool using the current fleet of trains. Then to simulate and make predictions about how this should change with the new fleet of trains. Finally to measure the PTI process with the new trains, and examine how well the predictions lined up.
+
+However, delays in rolling out the new trains by Merseyrail meant that much of the final parts of the project could not be carried out during the project timeline. RateSetter still had work to do, however, as the COVID-19 pandemic started up at this time.
+
+### COVID
+Studying the PTI has been particularly interesting during COVID times as social distancing greatly changed the boarding and alighting behaviour of people. New variable and parameters arose, such as the idea of different amounts of social distancing, as well as the existance of people who have their own rules for how they want to socially distance.
+
+![Alt text](6506326_247776b9_original.jpg)
+A sign close to Manchester Picadilly reminding people to stay apart
+Copyright [David Dixon](https://www.geograph.org.uk/profile/43729) and licensed for [reuse](https://www.geograph.org.uk/reuse.php?id=6506326) under this [Creative Commons Licence](http://creativecommons.org/licenses/by-sa/2.0/)
+
+This project was with [RSSB](https://www.rssb.co.uk/) and [Network Rail](https://www.networkrail.co.uk/) to provide guidance to Britain's railway authorities about how they should approach the PTI with the pandemic. Key factors of this work were: the rapid turn around of results; continual feedback and changes of the governing authorities; and people's changing behaviours throughout the pandemic.
+
+My work involved studying CCTV footage of people at train station platforms and reasoning what sort of simplified rules could be written. These rules can then be translated to mathematical representation, in order to create virtual simulations that represent what people were really doing at the platform.
+
+This work took place around the country from Manchester Picadilly to London's Blackfriars. Platform layout, train configuration, time of day, and many other factors were all considered when developing the simulation model.
+
+The result was a powerful predicting simulation which could estimate how much longer a train needed to wait for people to board and alight due to COVID. This information was given to RSSB and Network Rail who then incorporated it into their nationwide information to station managers.
+
+### Peckham Rye
+[Peckahm Rye](https://osm.org/go/euuvD2Shr) is a London Tube station that suffers from high pedestrian congestion on its platform. This is in part due to the old Victorian engineering which has been difficult to modernise. The RateSetter team and I were tasked with figuring out what changes to the station layout would be best.
+
+The initial process involved validating the simulation model against the particulars of Peckham Rye, including train layout, platform layout, as well as the statistical behaviours of the passengers (such as how fast they walk).
+
+![Google Maps view of Peckham Rye Station](pr-gm.png)
+![Visually simple computer simulation of the same station](pr-sim.png)
+These two images show a satellite view Peckham Rye station, and its associated computer simulation. A lot of the details on the platform are covered by the platform roof.
 
-My work has involved creating a computer model of the PTI boarding-alighting process, validating it against CCTV from train stations, and then using the model to make predictions on how different parameters (e.g. platform layout, stock type) will affect this PTI process.
+This validated simulation of Peckham Rye then meant we could make predictions with high confidence. The results of different platform changes were explored, and the results were given to the station owners. The results of the different platform changes found in the simulation were weighed up against cost and practial constraints by the station owners. From my own perspective it felt like our findings were mostly discarded. I think because many of the layouts we found most promising were not all that practical to implement. 
 
-It has been really interesting to bring together two departments, computer science and mechanical engineering, to work on a joint topic. The exertise in the two areas come together to create complex, accurate models which can validate and predict future behaviour.
+In the end, I'm not entirely sure which route Peckham Rye will go. I hope one day, in a few years time once they have completed the construction works, to visit the station and see what changes they have made, and whether the insights I provided were taken into account, or just used to justify the idea already suggested before the start of the project.

content/contact/index.md

@@ -3,12 +3,13 @@ title: "Contact"
 date: 2022-07-14T11:35:02+01:00
 ---
 
-The School of Clinical Dentistry,
-University of Sheffield,
-19 Claremont Crescent,
-Sheffield,
-S10 2TA,
-UK
+<!-- Note the extra spaces at the end of the line for line breaks -->
+The School of Clinical Dentistry,  
+University of Sheffield,  
+19 Claremont Crescent,  
+Sheffield,  
+S10 2TA,  
+UK  
 
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content/publications/phd-thesis.md

@@ -0,0 +1,19 @@
+---
+title: "Ph.D Thesis"
+date: 2023-11-08T12:44:04Z #Date paper was published, or rought date of relevance
+draft: false
+summary: My PhD thesis
+submission: "Published" #or "Published"
+journal: #Submitted journal name
+doi: https://etheses.whiterose.ac.uk/33512/
+manuscript: "../manuscripts/_John_Charlton____Thesis.pdf" #add the pdf to the content/publications/manuscript folder and insert filename here
+---
+
+The culmination of many years of hard work, struggle, procrastination, anxiety and effort.
+
+### The Ph. D Viva
+Many thanks to [Peter Lawrence](https://www.gre.ac.uk/people/rep/faculty-of-engineering-and-science/peter-lawrence) at the University of Greenwich for reading through this, and providing many questions to me during my viva.
+And thanks to [Dawn Walker](https://www.sheffield.ac.uk/dcs/people/academic/dawn-walker) at Sheffield University for also grilling me in the viva. It was a memory and lasting experience, and I'm glad it's over!
+
+### Abstract:
+Central to simulating pedestrian crowds is their motion and behaviour. It is required to understand how pedestrians move to simulate and predict scenarios with crowds of people. Pedestrian behaviours enhance the range of motions people can demonstrate, resulting in greater variety, believability, and accuracy. Models with complex computations and motion have difficulty in being extended with additional behaviours. This is because the structure of these models are not designed in a way that is generally compatible with collision avoidance behaviours. To address this issue, this thesis will research a possible pedestrian model that can simulate collision response with a wide range of additional behaviours. The model will do so by using constraints, a limit on the velocity of a person's movement. The proposed model will use constraints as the core computation. By describing behaviours in terms of constraints, these behaviours can be combined with the proposed model. Pedestrian simulations strike a balance between model complexity and runtime speed. Some models focus entirely on the complexity and accuracy of people, while other models focus on creating believable yet lightweight and performant simulations. Believable crowds look realistic to human observation, but do not match up to numerical analysis under scrutiny. The larger the population, and the more complex the motion of people, the slower the simulation will run. One route for improving performance of software is by using Graphical Processing Units (GPUs). GPUs are devices with theoretical performance that far outperforms equivalent multi-core CPUs. Research literature tends to focus on either the accuracy, or the performance optimisations of pedestrian crowd simulations. This suggests that there is opportunity to create more accurate models that run relatively quickly. Real time is a useful measure of model runtime. A simulation that runs in real time can be interactive and respond live to user input. By increasing the performance of the model, larger and more complex models can be simulated. This in turn increases the range of applications the model can represent. This thesis will develop a performant pedestrian simulation that runs in real time. It will explore how suitable the model is for GPU acceleration, and what performance gains can be obtained by implementing the model on the GPU.

readme.md

@@ -1,6 +1,13 @@
 # Personal Site
 
-Code for my personal site
+Code for my personal site. Built using [Hugo](https://gohugo.io)
+
+## Getting this repo
+This repo contains a submodule. When cloning, ensure submodules are also incorporated, either with `git clone --recurse-submodules #this-repo.git`, or for already clones repos, 
+```
+git submodule init 
+git submodule update
+```
 
 ### To Create a published paper