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Finished student projects
The list of student projects below are all finished.
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.
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.
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.
[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.
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.
(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.
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.
[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/
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.
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.
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.
Marco Roos, Bioinformatician, Institute for Informatics, University of Amsterdam
Wendy Bickmore, Group leader, Human Genetics Unit, Medical Research Council
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.
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.
