Please contact me if you are interested in selecting
any of these projects.
NOTE: FOR PROJECTS DW-UG-6 - DW-UG-9 (as
advertised on MOLE) please see this
page
DW-UG-1 Implementation of a Multiscale Cellular-Automata/ODE model of the human colon.
Supervisors Dr Dawn Walker and Dr Bernard Corfe
Biological tissue is a multiscale system
where subcellular level events influence cell behaviours,
which in turn affect tissue structure and modify disease risk.
The human colon is a particular example of this, where the
tissue is composed of a large number of flask-like structures
called crypts, which all contain individual biological cells,
which divide, migrate and die. We have previously published an
ODE (Ordinary Differential Equation) model of the colon crypt
(Smallbone, K., & Corfe, B. M. (2014). A mathematical
model of the colon crypt capturing compositional dynamic
interactions between cell types. International Journal of
Experimental Pathology, 95(1), 1-7). The model is available in
xml: BIOMD0000000517.
Cellular Automata is a computational paradigm that has been applied to the simulation of many real world systems. The system to be modelled is divided is represented as a lattice, with the properties of each lattice site (or geometric cell) at the next time step influenced by its current state and that of its neighbours.
The student will
develop a model of the colon, wherein each crypt is
represented as a single geometric cell in a cellular automata
model. The number of cells in this crypt will be informed by
solving an ODE model . Rules
for interactions between crypts within the CA will be
developed in collaboration with the supervisory team. The overarching goal of
the research team is to develop a CA on the scale of an
entire colon or population. Over time and with iterative
fitting to public health data the model will allow us to
understand better the mechanisms of disease incidence. The project that
will be undertaken by the student successfully joining our
team will be to undertake critical components of the
computational development.
The aim of this project will be to:
i) write a cellular automata-based solver with Matlab or Python, representing multiple crypts in the colon.
ii) expand the functionality to allow an ODE to be solved in each geometric cell of the CA (crypt) at each time point.
iii) Carry out full testing of this model from both a software (unit testing) and modelling (sensitivity analysis) perspective.
Prerequisites - successful
completion of COM2005 Bioinspred computing is advised for COM
students.
COM students are recommended to take the L3 optional module COM3001 Modelling and Simulation in Natural Systems.
Programming in Matlab or Python.
Suitable for Bioengineering Students with excellent programming skills.
DW-UG-2 Implementation of a Tree-based algorithm for contact detection.
Supervisors Dr Dawn Walker and Tim Ingham-Dempster
It is possible to simulate a population of growing biological cells by representing each as a circle (or sphere in 3D) which has the ability to move, grow and interact with its neighbours. A non trivial problem that arises from this implementation is how to detect and correct for the physical overlap that inevitably arises between these virtual growing, dividing objects, which does not occur in real biological cell populations.
Overlapping circles representing cells in an agent-based simulation
Previously, this issue has been dealt with by implementing a simple algorithm which compares the position and radius of every cell with every other cell in the model. This algorithm is effective, but computationally intensive (scaling as n-squared), so adds significant overhead to what would otherwise be a lightweight simulation.
The objective of this project is to develop an alternative tree-based search approach to detect contact or overlap between circles and compare the results and efficiency of this approach with the results of the existing simple implementation for a set of test cases. Specifically, the tasks are:
1. Develop a algorithm to randomly generate a set of overlapping spheres and a tree-based search to detect contact and overlap.
2. Allow specific test cases of circle locations and radii can be read from an existing file.
3. Develop a process to compare the execution time with the existing executable file which has been developed based on a sequential n-squared approach.
4. If successful, extend the algorithm to a sub-cellular element models, where each individual cell/circle is in turn divided into a further set of internal circular elements.
Further possible extensions include consideration of the 3D (spherical cell) case.
Ideally, these algorithms will be developed
in C#, C++ or C, but Python, Java or Matlab-based approaches
will be permitted for students without the background
programming language skills.
DW-UG-3
Development of a Cellular Automata-based Teaching Tool in
Python
Cellular Automata based simulation is a bio-inspired approach where dynamic real-world phenomena can be modelled by a grid of communicating cells which change state according to simple transition rules, based on their current condition and that of their neighbours. The approach is also used as a tool in exploring complexity and concepts of artificial life and intelligence.
The objective of this project is to develop a user-friendly, robust computational tool in Python that can be deployed on university machines or elsewhere and used as the basis for teaching the above concepts in an undergraduate computer laboratory class environment. Specifically, the tasks are:
· Develop a tool to allow the execution of 1D cellular automata, in particular, Wolfram’s 256 simple automata rules.
· Develop a tool to allow the execution of 2D cellular automata, in particular, Conway’s Game of Life.
In both cases, users should be able to interact with the code to change initial conditions, boundary conditions and neighbourhood rules in a simple, intuitive way.
Good software engineering development practices should be used throughout the project and ideally, the student would user test any software developed both informally and in a classroom environment.
Possible extensions include optimisation of the software for computational efficiency, or using the tool as the basis for a computational simulation experiment of the student’s choice.
Prerequisites – successful completion of COM2005, preferably with a good mark in the CA project component.
DW-UG-4 Development
of an agent-based model of cellular interactions in
multiple myeloma
Supervisors Dr Dawn Walker, Dr Paul Richmond and Dr Andrew Chantry (Department of Oncology)
Myeloma is a bone marrow cancer. Tumour progression depends on an interplay between malignant myeloma cells and key components of the bone marrow micro-environment. Part of this process is the destruction of bone, due to an alteration in the numbers of bone producing cells (osteoblasts) and bone destroying cells (osteoclasts). This is known as osteolytic bone disease.
In order to identify potential drug therapies in order to target this process and improve patient outcomes, we first need to be able to understand the fine balance of cellular interactions and their influence on the bone microenvironment. Computational models can be a useful tool for encapsulating knowledge about systems and also for testing hypotheses and running virtual experiments.
The aim of this project is to develop a computational model consisting of different interacting cell types (e.g. myeloma cells, osteoclasts, osteoblasts) where each individual cell can be represented as a “software agent”. These virtual cells will reside in and interact with a three dimensional environment representing the bone marrow. The knowledge required to set up this model will be extracted from the literature.
Specifically, the tasks involved in this project will be:
· Survey of the literature to understand the nature and behaviour of the individual cell types involved in the development of osteolytic bone disease and their key interactions.
· Design and programme and three dimensional agent-based model representing a simplified version of this system.
· Design and implement virtual experiments representing the effect of possible drug intraventions (treatment).
Prerequisites The student should have good programming skills. Preferred programming languages are C/C++, Python or Matlab, though Java will be considered.
The student is recommended to take the optional module COM3001 Modelling and Simulation in Natural Systems.
Prior knowledge of biology is not a
requirement.
DW-UG-5
Development of a Unified Authorisation Framework for a Web
Interface
As part of INSIGNEO’s MultiSim project
there is the requirement to create a web interface for the
Hypermodelling framework. This web interface in turn will
require a security and user access framework that will allow
Users’ levels of access to be defined not only on an
individual level but also by attributes that define the role
they play within the organisation.
This framework should also be configurable to allow for the
easy addition of Menus and Menu Items so that, given the right
privileges, a User can quickly configure the layout (and
possibly style) of the web application.
The main deliverables for this project will be; a simple web
gui with a configurable menu structure, supporting complicated
User and Attribute access privileges; and a database to
support this.
Prerequisites
HTML5, Python, Javascript (desirable), Database Administration
(desirable), Django (desirable)
If interested in this project, please
contact Garry Thompson (g.thompson "@" sheffield.ac.uk) for
further details with myself in cc.
DW-UG-10 Modelling and Conflict
Detection of RBAC Policies based on Petri Nets
Role-Based Access Control (RBAC) policy is broadly applied in
computer (HPC) security and scheduling systems as well as
workflow management. The design of the policy is always a
challenge. It can be associated with constraints on users,
roles, time, session, Separation of Duty (SoD) as well as
Binding of Duty (BoD). With the increase in policy complexity
and specific use cases, there will be more conflicts appearing
in the policy design.
This projects aims to model and analyse the RBAC policy and detect the conflicts, and will be verified based on case studies, such as HPC access control policy, business workflow policy or medical management policy.
Petri-nets are a mathematical modelling language for the modelling of concurrent, asynchronous and non-deterministic systems. There are also tools, such as CPN-tools based on Petri-net, that can be used for such modelling and verification purposes.
The deliverable
for this project will be a Petri-net model based on CPN-tools
that can analyse, verify the system based on the RBAC policies
as well as detect the conflicts.
Prerequisites
Basic knowledge on statistical analysis.
Knowledge of a functional programming language.
Students
selecting this project would be recommended to take the
optional third year module: COM3190
Reading List
1. Kahloul, L., Djouani, K., Tfaili, W.,
Chaoui, A., & Amirat, Y. (2010). Modeling and Verification
of RBAC Security Policies Using Colored Petri Nets and
CPN-Tool. In Networked Digital Technologies (pp. 604-618).
Springer Berlin Heidelberg.
2. He, L., Huang, C., Duan, K., Li, K.,
Chen, H., Sun, J., & Jarvis, S. A. (2012). Modeling and
analyzing the impact of authorization on workflow
executions.Future Generation Computer Systems, 28(8),
1177-1193.
3. He, L., Duan, K., Chen, X., Zou, D., Han,
Z., Fadavinia, A., & Jarvis, S. A. (2011, July). Modelling
workflow executions under role-based authorisation control. In
Services Computing (SCC), 2011 IEEE International Conference
on(pp. 200-208). IEEE.
If interested
in this project, please contact Kewei Duan (k.duan "@"
sheffield.ac.uk) for further details with myself in cc.
DW-UG-11 Development of a web
interface for scientific visualisation
The MultiSim project aims to
create a new generation of predictive models capable of
handling complex multi-scale and multiphysics problems,
focussing on the human musculoskeletal system http://insigneo.org/multisim_
This computer science project will focus in the construction of the web application. This web application will be build using django (python web framework) and will be focused specifically on the clinicians as end-users.
Prerequistes:
* Python, HTML, javascript
(desirable)
* Knowledge and experience
of Web Design
* Knowledge of Graphical
User Interface Design
Contacts
* Dr Dawn Walker
(internal)
* Dr Nicolas Gruel
(external)
For further information, see:
http://insigneo.org/multisim_If interested
in this project, please contact Nicolas Gruel (n.gruel "@"
sheffield.ac.uk) for further details with myself in cc.
DW-UG-12 Development of a
MAF-like framework using ParaViewWeb
Multimod Application Framework (MAF - openmaf.org) is an open source freely available framework for the rapid development of applications based on the Visualisation Tookit (VTK) and other specialized libraries. It provides high level components that can be easily combined to develop a vertical application in different areas of scientific visualization. Up to now, it is developed based on desktop OS.
Nowadays, the concept of Web 2.0 dominates the design pattern of web applications together with the growing influence of the concept of Cloud computing. A trend can be observed that a considerable amount of applications are developed based on highly interactive, web page interfaces. In the area of scientific visualization, ParaViewWeb has stepped forward as a pioneer to provide a collection of web-services that make it possible for web-clients to show interactive visualization components in web pages. There are some engineering simulation tools being developed based on ParaViewWeb, such as SimScale.
The deliverable for this project will be a browser-based framework/application that is developed based on ParaViewWeb. It should be able to execute the basic functions of MAF framework.
Prerequisites
Knowledge on C++ (for understanding the existing version of MAF), and Python programming languages.
Knowledge on Web design and GUI design
Knowledge on scientific visualisation (desirable)
Reading List
- Viceconti, M., Zannoni, C., Testi, D., Petrone, M., Perticoni, S., Quadrani, P., ... & Clapworthy, G. (2007). The multimod application framework: a rapid application development tool for computer aided medicine. Computer methods and programs in biomedicine, 85(2), 138-151.
- http://www.paraview.org/Wiki/ParaViewWeb
- https://simscale.com
- openmaf.org
If interested in this project, please contact Kewei Duan (k.duan "@" sheffield.ac.uk) for further details with myself in cc.