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Finished student projects

The list of student projects below are all finished.

Improving quality and reliability of results in gene expression studies by accounting for systematic artefacts

14 August 2009 - 4:39pm — Jano.van.Hemert
Student: 
Rob Kitchen

With the growing complexity and procurement costs of these high-throughput platforms, it is becoming increasingly common for the experiments to be deployed in central ‘core facilities’. This service-oriented paradigm is a recent development and one that is generally welcomed by lab-researchers and data-analysts as it encourages the standardisation of experimental protocols and reduces costs of hardware maintenance.

Project status: 
Finished
Degree level: 
PhD
Supervisors @ NeSC: 
Jano.van.Hemert
Other supervisors: 
Prof Peter Clarke (School of Physics); Dr Varrie Ogilvie (Molecular Medicine Centre, University of Edinburgh)
Subject areas: 
e-Science
Bioinformatics
Student project type: 
PhD student project

Google Summer of Code 2009: Generating User Interfaces to the Cloud

21 March 2009 - 9:21pm — Jano.van.Hemert
Student: 
Raviteja Dodda

Rapid is a unique way of quickly designing and delivering web portal interfaces to applications that require computational resources, such as utility computing infrastructures or high-performance computing facilities. It focuses on the requirements of the end-user by designing customised user interfaces for domain-specific applications that allow users to achieve particular tasks.

Project status: 
Finished
Degree level: 
NR
Background: 
Knowledge of Java is required. A bit of experience with XML is useful.
Supervisors @ NeSC: 
Jano.van.Hemert
Jos.Koetsier
Subject areas: 
e-Science
WWW Tools and Programming
Projects: 
Rapid
Student project type: 
Internship student project
References: 
Rapid: http://research.nesc.ac.uk/rapid/ Google Summer of Code 2009: http://socghop.appspot.com/ OMII-UK: http://www.omii-uk.ac.uk/ EUCALYPTUS: http://eucalyptus.cs.ucsb.edu/ Hadoop: http://hadoop.apache.org/

Improving knowledge curation in structured wiki-like collaborative environments

10 February 2009 - 3:22pm — Jano.van.Hemert
Student: 
Luna De Ferrari

This work aims at defining, modelling and evaluating the integrated use of collaborative software and machine learning for building high quality knowledge resources. A possible scenario is Molecular Biology, where high-throughput data production is overwhelming the traditional centralised data annotation by paid experts. Many biological resources have moved to collaborative software platforms, predominantly wikis, in an effort to involve the wider community and replicate the success story of Wikipedia.

Project status: 
Finished
Degree level: 
PhD
Supervisors @ NeSC: 
Jano.van.Hemert
Other supervisors: 
Igor Goryanin, School of Informatics; Stuart Aitken, AIAI
Student project type: 
PhD student project
References: 
[1] William A Baumgartner, K. Bretonnel Cohen, Lynne M Fox, George Acquaah-Mensah, and Lawrence Hunter. Manual curation is not suffcient for annotation of genomic databases. Bioinformatics, 23(13):i41–i48, Jul 2007.

Planning Emergency Movement for the Built Environment

10 February 2009 - 3:17pm — Jano.van.Hemert
Student: 
Thomas French

The goal of this project is to investigate methods for finding emergency movement plans in dynamic and uncertain environments, specifically buildings. Current techniques used to solve these problems, like (Opasanon, 2004), make unrealistic assumptions about human behaviour during emergency movement. For example, they assume that occupants travelling through a building do not directly interact, and, therefore, provide instructions that presume people who arrive at a decision point at the same time will split up if told to do so.

Project status: 
Finished
Degree level: 
PhD
Supervisors @ NeSC: 
Jano.van.Hemert
Other supervisors: 
Austin Tate, AIAI; Stephen Potter, AIAI; Gerhard Wickler, AIAI; Jose Torero, School of Engineering
Subject areas: 
e-Science
Algorithm Design
Genetic Algorithms/Evolutionary Computing
Projects: 
FireGrid
Student project type: 
PhD student project
References: 
(Opasanon, 2004) S. Opasanon. On Finding Paths and Flows in Multicriteria, Stochastic and Time-Varying Networks. PhD thesis, University of Maryland, 2004. (SFPE, 2002) SFPE. SFPE Handbook for Fire Protection Engineering. National Fire Pro- tection Association, 3rd edition, January 2002.

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/

Predicting earthquake impact with laptop motion sensors

7 January 2009 - 9:24pm — Jano.van.Hemert
Student: 
Gary Mcgilvary
Grade: 
first

Principle goal: to make clever use of the sudden motion sensor of Apple notebooks to map the impact of earthquakes in densely populated areas.

Project status: 
Finished
Degree level: 
UG4
Supervisors @ NeSC: 
Jano.van.Hemert
Other supervisors: 
Rémy Bossu, European-Mediterranean Seismological Centre, France; Fabrice Cotton, Grenoble University, France
Subject areas: 
e-Science
Distributed Systems
Mobile Computation
WWW Tools and Programming
Student project type: 
UG4 student project
References: 
[1] http://en.wikipedia.org/wiki/Seismic_wave [2] http://en.wikipedia.org/wiki/Sudden_Motion_Sensor [3] http://www.agu.org/pubs/crossref/2008/2008EO250001.shtml [4] http://www.suitable.com/tools/seismac.html [5] http://www.emsc-csem.org/

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

Mining and visualising family tree networks from online genealogy information

6 January 2009 - 4:29pm — Jano.van.Hemert

Principle goal: to construct a data harvesting system with an associated semantic web-enabled store for genealogical data with a method for querying the data which you test using at least one query.

Project status: 
Finished
Degree level: 
UG4
Background: 
Applied Databases; Data Integration and Exchange; Querying and Storing XML; Knowledge Modelling and Management courses are desirable but not critical for this project.
Supervisors @ NeSC: 
Jano.van.Hemert
Other supervisors: 
Rachel Walcott (School of GeoSciences)
Subject areas: 
e-Science
Databases
WWW Tools and Programming
Student project type: 
UG4 student project
References: 
[1] http://www.familysearch.org [2] http://en.wikipedia.org/wiki/GEDCOM [3] http://www.backspace.com/mapapp/

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

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