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MSc student project

A project suitable for an MSc project of three months.

Detection and elimination of personal data contained in medical images

5 January 2010 - 4:13pm — Jano.van.Hemert
Student: 
Yassar Almutairi

Principal goal: evaluating and implementing different techniques for detecting, recognising and eliminating text containing personal data in medical images.

Project status: 
Finished
Degree level: 
MSc
Background: 
Good programming skills; experience with image processing desirable
Supervisors @ NeSC: 
David.Rodriguez
Fan.Zhu
Student project type: 
MSc student project
References: 
- James Z. Wang, Michel Bilello and Gio Wiederhold, A Textual Information Detection and Elimination System for Secure Medical Image Distribution Journal of the American Medical Informatics Association, Proceedings of the AMIA Annual Symposium, vol. 1997 symposium suppl., pp. 896, Nashville, TN, October 1997. - Datong Chen, Jean-Marc Odobez, Hervé Bourlard, Text detection, recognition in images and video frames. Pattern Recognition 37(3): 595-608 (2004) - I. Neamatullah et al. “Automated de-identification of free-text medical records” BMC Medical Informatics and Decision Making 2008, 8:32

Rapid portals for cloud computing

27 November 2009 - 3:50pm — Jano.van.Hemert
Student: 
Gareth Francis
Grade: 
first

Principle goal: to extend Rapid, which is existing technology, so that it can run compute jobs on several cloud infrastructures seamlessly, whilst ensuring additional drawbacks of cloud computing technology are overcome.

Project status: 
Finished
Degree level: 
MSc
Supervisors @ NeSC: 
Jano.van.Hemert
Jos.Koetsier
Subject areas: 
e-Science
Other
WWW Tools and Programming
Student project type: 
MSc student project

Rapid development of a web portal for cosmology data analysis

27 November 2009 - 2:53pm — Jano.van.Hemert

Principle goal: to design and implement a web portal using Rapid (http://research.nesc.ac.uk/rapid/) that allows advanced users to create new analyses and that allows all users to pick up and use these analyses on data from astronomy data archives.

Project status: 
Finished
Degree level: 
MSc
Supervisors @ NeSC: 
Jano.van.Hemert
Jos.Koetsier
Other supervisors: 
Thomas Kitching, Institute for Astronomy, University of Edinburgh
Subject areas: 
e-Science
Other
WWW Tools and Programming
Student project type: 
MSc student project

Create Parallel Data Mining Algorithms for Cloud Computing

13 January 2009 - 9:22am — Jano.van.Hemert
Student: 
Tantana Saengngam
Grade: 
first

Principle goal: to take an existing algorithm and to make it parallel in a cloud computing environment following the Map and Reduce approach of Google.

Project status: 
Finished
Degree level: 
MSc
Supervisors @ NeSC: 
Jano.van.Hemert
Liangxiu.Han
Subject areas: 
Algorithm Design
Computer Architecture
Distributed Systems
Machine Learning/Neural Networks/Connectionist Computing
Student project type: 
MSc student project
References: 
[1] C.-T. Chu, S. K. Kim, Y.-A. Lin, Y. Yu, G. R. Bradski, A. Y. Ng, and K. Olukotun. Map-reduce for machine learning on multicore. In B. Schölkopf, J. C. Platt, and T. Hoffman, editors, NIPS, pages 281–288. MIT Press, 2006. [2] http://eucalyptus.cs.ucsb.edu/

Mining Andean-to-Amazon ecosystem data to understand the underlying environmental factors

6 January 2009 - 4:32pm — Jano.van.Hemert
Student: 
Makrymallis Antonios
Grade: 
second1

Principle goals: to use data mining techniques to understand how variables drive ecosystem functioning and a qualitative study to determine which of a variety of data mining techniques best replicates observed ecosystem processes.

Project status: 
Finished
Degree level: 
MSc
Background: 
Courses on Data Mining and Exploration; Genetic Algorithms and Genetic Programming; Introductory Applied Machine Learning courses are desirable but not critical for this project.
Supervisors @ NeSC: 
Jano.van.Hemert
Liangxiu.Han
Other supervisors: 
Dr Rachel Walcott (School of Geosciences) and Dr Patrick Meir (School of Geosciences)
Subject areas: 
Genetic Algorithms/Evolutionary Computing
Machine Learning/Neural Networks/Connectionist Computing
Student project type: 
MSc student project
References: 
[1] Re: the SOM Algorithm: http://www.cis.hut.fi/research/som_lvq_pak.shtml [2] Publication analysing Martian landscape data: http://www.lpi.usra.edu/science/stepinskiWebPage/pdfFiles/compGeo32y2006.pdf [3] The Andean project: http://darwin.winston.wfu.edu/andes/index.php?n=Main.HomePage

Grid-enable A Biomedical Database

28 November 2008 - 11:03am — Jano.van.Hemert
Student: 
Mark MacGillivray
Grade: 
first

The number of databases that contain biomedical data is increasing rapidly. Many of these databases are stand-alone and this makes it difficult for researchers to perform queries and analyses over data that spans multiple databases.

Project status: 
Finished
Degree level: 
MSc
Background: 
Practical experience with web services and databases essential. Knowledge of workflow concepts desirable.
Supervisors @ NeSC: 
Jano.van.Hemert
Other supervisors: 
Marco Roos, Bioinformatician, Institute for Informatics, University of Amsterdam Wendy Bickmore, Group leader, Human Genetics Unit, Medical Research Council
Subject areas: 
e-Science
Databases
Other
Student project type: 
MSc student project

Generate A Portal for Brain Imaging

26 November 2008 - 9:24am — Jano.van.Hemert
Student: 
Albert Heyrovsky
Grade: 
first

Although some scientists, such as many physicists, may prefer a command line approach to submitting computational jobs, a majority of scientists want to be shielded from the innards of a computer. A popular approach is to build portals; user community web sites that allow job submissions from the convenience of a web browser.

Project status: 
Finished
Degree level: 
MSc
Background: 
Proficient in XML
Supervisors @ NeSC: 
Jano.van.Hemert
Jos.Koetsier
David.Rodriguez
Other supervisors: 
Trevor Carpenter, SFC Brain Imaging Research Centre, University of Edinburgh.
Subject areas: 
e-Science
Other
Projects: 
Rapid
Student project type: 
MSc student project

Parallelising CocaPhase

18 June 2008 - 9:45am — Jano.van.Hemert
Student: 
Omer Jilani

The purpose of the project is to improve the efficiency of an existing application (CocaPhase) used to analyze a subset of chromosomes within a large genotype data. The project will take the program CocaPhase as an input and will reduce its run time by applying parallel programming techniques in the first phase. The second phase will enable the program to be run in a distributed environment over a Grid network (NGS and/or ECDF).

Project status: 
Finished
Degree level: 
MSc
Supervisors @ NeSC: 
v1jweiss
Other supervisors: 
Murray Cole, School of Informatics
Subject areas: 
e-Science
Distributed Systems
Parallel Programming
Student project type: 
MSc student project

Mobile Code Execution in a Workflow Environment

6 February 2008 - 1:12pm — Jano.van.Hemert
Student: 
Adarsh Hiremangalur Ramsesh

The OGSA-DAI system provides an extensive suite of activities that can extract, transform, deliver and store data held in a variety of distributed data resources. While it is easy to add new activities to provide new functionality it would be of great interest to be able to add new behaviour to OGSA-DAI workflows dynamically.

Project status: 
Finished
Degree level: 
MSc
Background: 
The student should be comfortable with the Java programming language and willing to do some investigation on the potential interfaces between OGSA-DAI's activities and the external code.
Supervisors @ NeSC: 
Malcolm.Atkinson
kkarasav
Subject areas: 
e-Science
Student project type: 
MSc student project
References: 
OGSA-DAI: http://www.ogsadai.org.uk Mobile Code: Internal OGSA-DAI report (can send on request) Java's Scripting framework: https://scripting.dev.java.net/ and http://www.mozilla.org/rhino/ScriptingJava.html

Refine OGSA-DAI installation for rapid deployment of distributed data servers

29 January 2008 - 5:10pm — Jano.van.Hemert
Student: 
David Macrandal

Goal: To refining OGSA-DAI installation for rapid deployment of distributed data servers supporting Gene Therapy clinical trials in Cystic Fibrosis.

Description

Project status: 
Finished
Degree level: 
MSc
Supervisors @ NeSC: 
Jano.van.Hemert
Rob.Kitchen
Subject areas: 
e-Science
Student project type: 
MSc student project
References: 
What is cystic fibrosis? http://en.wikipedia.org/wiki/Cystic_fibrosis OGSA-DAI documentation: http://www.ogsadai.org.uk/documentation/ogsadai3.0

A generic metadata management tool for large-scale data-intensive applications

7 January 2008 - 4:40pm — Jano.van.Hemert
Student: 
Pei Pei
Grade: 
first

Principal goal: to build a generic metadata management tool for supporting large-scale scientific data intensive applications in e-Science research projects.

Project status: 
Finished
Degree level: 
MSc
Background: 
Knowledge of programming in Java; knowledge of Databases and Web Services
Supervisors @ NeSC: 
Liangxiu.Han
Subject areas: 
e-Science
Databases
Distributed Systems
Student project type: 
MSc student project
References: 
[1] Meta-data standards http://metadata-standards.org [2] Adrienne Tannenbaum, Metadata Solutions: Using Metamodels, Repositories, XML, and Enterprise Portals to Generate Information on Demand, Addison-Wesley, 2002. ISBN 0-201-71976-2 [3] David Marco, Building and Managing the Meta Data Repository: A Full Lifecycle Guide, Wiley, 2000. ISBN 0-471-35523-2 [4] David C. Hay, Data Model Patterns: A Metadata Map, Morgan Kaufman, 2006. ISBN 0-12-088798-3

Hybrid architectures for Web service Orchestration

7 January 2008 - 4:31pm — Jano.van.Hemert
Student: 
Nikos Kyprianou
Grade: 
first

Note: Nikos' thesis received the highest average mark for an MSc dissertation in 2008

Principal goal: building/extending a Java-based framework for decentralised Web services orchestration.

Project status: 
Finished
Degree level: 
MSc
Background: 
Excellent working knowledge of Java, Knowledge and interest in highly Distributed systems, Good written skills, there is scope for publication.
Supervisors @ NeSC: 
abarker1
Jano.van.Hemert
Other supervisors: 
Jon Weissman
Subject areas: 
e-Science
Computer Architecture
Computer Communication/Networking
Distributed Systems
Software Engineering
Student project type: 
MSc student project

Database Replication in a Service-Oriented Architecture

7 January 2008 - 4:27pm — Jano.van.Hemert
Student: 
Kemian Dang

Principal goal: to implement, evaluate and refine a database replication mechanism for heterogeneous database systems.

Project status: 
Finished
Degree level: 
MSc
Background: 
Good programming skills, some familiarity with distributed systems
Supervisors @ NeSC: 
ychen3
Subject areas: 
Computer Architecture
Databases
Other
System Level Integration
Student project type: 
MSc student project
References: 
[1] Transaction-Based Grid Database Replication http://www.allhands.org.uk/2007/proceedings/papers/842.pdf

A Job Submission Portal for Computational Chemistry

6 December 2007 - 10:52am — Jano.van.Hemert
Student: 
Jessie Li

Although some scientists, such as many physicists, may prefer a commandline approach to submitting computational jobs, a majority of scientists want to be shielded from the commandline. A popular approach is to build portals; user community web sites that allow job submissions from the convenience of a web browser.

Project status: 
Finished
Degree level: 
MSc
Background: 
Experience with job submissions on the Grid. Knowledge of how to handle grid certificates. Not afraid of XML.
Supervisors @ NeSC: 
Jano.van.Hemert
spramman
Other supervisors: 
Andrew Turner, http://homepages.ed.ac.uk/dwhr10/
Subject areas: 
e-Science
Software Engineering
Student project type: 
MSc student project

The Effects of Distribution and Parallelisation on the Performance of OGSA-DAI Enactments

27 August 2007 - 2:53pm — Jano.van.Hemert
Student: 
Amin Khan

Grid computing provides technologies for building high performance scientific and business applications. Grid applications need access to distributed and heterogeneous data sources and OGSA-DAI midd leware provides data services to access and integrate data sources. Paral lelism has been used extensively for designing efficient data and computation intensive applications. This project aims to explore paral lelism in OGSA-DAI services to achieve performance improvements for data applications designed using OGSA-DAI services.

Project status: 
Finished
Degree level: 
MSc
Supervisors @ NeSC: 
Malcolm.Atkinson
kkarasav
Other supervisors: 
Dr. Maurizio Marchese (Università degli Studi di Trento)
Subject areas: 
Computer Architecture
Databases
Distributed Systems
Other
Software Engineering
Student project type: 
MSc student project
References: 
OGSA-DAI (www.ogsa-dai.org.uk)

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