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ICHEC Summer Scholarships 2011


The ICHEC Summer Scholarships provides funding for a select number of talented senior undergraduate students to undertake 10-week summer projects located in Galway or Dublin. It provides exciting opportunities for students worldwide to undertake projects related to HPC/computational science, all in the environment of a national HPC centre under the supervision of ICHEC's computational scientists and systems staff.

Important Dates

Application deadline: 13th March 2011 (Sunday)
Project start date: 13th June 2011 (Monday)
Project end date: 19th August 2011 (Friday)


Successful candidates will be given a stipend of EUR 3000 for the duration of the project to cover living expenses (paid fortnightly over 10 weeks). Appropriate accommodation is provided at no extra cost (may or may not include utility bills). ICHEC also subsidises travel expenses up to a capped amount based on the location of the candidate (EU countries: EUR 400; Rest of the world: EUR 1000).


Each applicant must specify at least one preferred project (chosen from the list below). Up to 4 projects can be specified in order of preference. Please note that applicants will be asked to comment briefly on their motivation in selecting a particular project. Projects that were on offer in previous years can be viewed at Past Projects


  1. 3-D visualisation techniques to study the output of the Met Éireann forecast model, Harmonie

    3-D scientific visualisation is well-suited for assessing the results from many types of simulations, including models of climate and weather systems. This can be used to investigate potential model errors and model quality, particularly in the case of extreme storms. The student will work with visualisation toolkits such as Visit, Vapour, Paraview, etc. ICHEC will provide expertise and supervision in the fields of environmental science and visualisation; the project also provides the opportunity to collaborate with Met Éireann, the Irish national weather forecasting agency. Furthermore, the scope of the project will encompass the production of climate-related outreach material.

  2. Cloud computing and applications

    Cloud computing is increasingly getting popular among the HPC community for capacity planning and to offer flexibility to potential HPC users. But very little has been done so far on benchmarking data parallel applications against MPI applications (especially for large datasets). The aim of this project is to explore this further. Specific goals of the project include the following:

    • Installation/configuration of open-source packages (e.g. Hadoop suite) and testing of sample MapReduce applications
    • Set-up of cloud-enabled bioinformatics applications (i.e. CloudBurst) and testing it using sample datasets
    • Benchmarking CloudBurst and parallelised bioinformatics applications

  3. Automated job analysis on HPC systems

    As HPC systems such as those run by ICHEC become larger and their userbase more diverse, monitoring and spotting jobs which are not performing correctly becomes increasingly challenging to do without elements of automation.

    When a job is submitted, queued and executed a significant amount of data about it is available. The intention of this project is to analyse aspects of the submission of jobs and their execution with a view to reporting individual jobs or patterns of jobs which are potentially sub-optimal. Appropriate action can then be taken by ICHEC staff to correct problems or work with the users concerned to investigate the problem further. It is envisaged that a number of tools would be written to address different problems with differing presentation requirements though all would use the same data sources.

    Important skills for this project include data analysis techniques as well as experience with scripting languages such as Perl or Python, SQL, and working in a Linux environment in order to be able to implement these techniques.

  4. Bioinformatics on the GPU

    Many bioinformatics software tools follow the single instruction, multiple data (SIMD) paradigm. Hence GPGPU has the potential to provide relatively inexpensive, scalable solutions to increasingly data-intensive problems in biology. There are already a number of algorithms which has been implemented on the GPU (e.g. Smith-Waterman, BLASTP), most of which report significant speed-ups over CPU implementations.

    The goal of this project is to implement some of the existing bioinformatics GPGPU codes on ICHEC hardware and to assess their behaviour, applicability and useability. There are opportunities to carry out real scientific analyses in collaboration with ICHEC users and to enable previously-infeasible computations. The codes will cover a range of areas including biological sequence comparisons, molecular phylogenetics and high-throughput DNA sequencing.

    ICHEC has been awarded by NVIDIA the status of CUDA Research Center, see our GPGPU Section for more information.

  5. OpenBabel: optimisation of the MMFF94 routines using OpenMP and OpenCL

    At the heart of many computational chemistry modeling suites are the forcefields and their associated energy and gradient functions. One such forcefield, MMFF94 (Merck Molecular Force Field 94), was developed by Thomas A. Halgren at Merck and has become one of the most widely used in the drug design domain.

    OpenBabel is an open source cheminformatics project and MMFF94 is one of many forcefields it provides. OpenBabel has been downloaded over 164,000 times and is used by over 40 related projects.

    This project will involve the optimisation and parallelisation of the MMFF94 functions within OpenBabel and will be conducted in collaboration with Dr. Noel O'Boyle at University College Cork.

  6. Web services and workflows for automated protein-protein interaction discovery

    Protein-protein interactions are responsible for controlling many of the cell's functions, but how they are regulated is still poorly understood. Large high-throughput methods have enabled us to catalogue these interactions in the cell in a systematic manner. What is missing currently is the ability to analyse such datasets more intuitively and help biologists understand the data more clearly.

    The aim of this project is to create bioinformatics workflows that will allow the automated discovery of protein domains and their partner ligands. The specificity of such domain-ligand recognition is often contained in short linear motifs. This project will involve the creation of web services based on applications that search for novel instances of motifs, as well as related analyses, and integration of these web services into workflows. This work will then be applied to phosphorylation motifs in yeast, where they play key roles in signal transduction and are central to our understanding of cellular communication.



Undergraduate students from third-level institutions worldwide are eligible to apply. Candidates are expected to be proficient in English for every-day communication and completion of a written report at the end of the project (with perhaps a short presentation). Since the projects require a computational background and proficiency at programming, preferences will be given to senior undergraduates (those in the final 2 years of their degrees).

How do I apply?

Before you begin the application process, please ensure the following:

  • You have your CV in electronic format (preferably in PDF format)
  • From the list of projects above, you have identified at least one preferred project; up to 4 preferred projects in order of preference. You are also expected to state briefly your motivation for each selection.
  • You are available to work on the project for the entire 10-week duration (see above for start and end dates) in Ireland. Small deviations may be possible to suit your schedule but please state this clearly in your application (in the Additional Info section).

--> Proceed to ICHEC Summer Scholarship application form.


Further Information

For further information regarding the Summer Scholarships, please contact our Education & Training Coordinator.