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New and Emerging Areas


Research is in the Clouds for CIT's Bioinformatics Group

November 2012

The Marie Curie Industry-Academia Partnerships and Pathways (IAPP) programme grant has been awarded to CIT's bioinformatics research group. The grant,  worth over €1.3 million and will run over 4 years, is focused on the development of advanced cloud computing techniques for large-scale bacterial genome sequencing and medical diagnostics/prognostics. read more ...

 


Bioinformatics

Bioinformatics Group Science Progress  2010

 

This new interdisciplinary team consists of Roy Sleator (Department of Biological Sciences), Paul Walsh and Paul Rothwell (Department of Computer Science) and MSc candidate John Carroll. While Biotechnology and ICT were perhaps the hottest buzzwords of recent times; ‘the new kid on the block’ - Bioinformatics - combines ICT and biotechnology within a new biology based information science; one in which high end computing is applied to identify new genes, predict new protein structures and even to design new and improved drugs.

The group which was formalised this year with the support of Michael Loftus head of the Faculty of Engineering and Science and Hugh McGlynn and Jim O’Dwyer (heads of Biological sciences and computer science respectively), has already had its first joint paper published in the March issue of the scientific journal Archives of Microbiology. In this paper Sleator and Walsh provide a comprehensive overview of the power of combining skills in biology and computing to predict the function of newly identified proteins, simply by analysing the DNA and protein sequence data. Furthermore, an article by Sleator on how bioinformatics can be used to predict evolutionary trends recently made the cover of the journal Science Progress with a computer predicted image of myglobin (pictured above).

Another significant focus of the group, and the subject of John Carroll’s MSc project, is the development new algorithms to help researchers to identify important gene sequences from the huge amounts of data being generated by large scale sequencing projects; such as the human microbiome project – which aims to identify all the genes of all the microbes in the body (which, believe it or not, outnumber our own human cells by a factor of 10!).

The group is also at the prototyping stage for a new software tool that allows researchers to manage bioinformatics research in a secure and auditable computing environment that is compliant to FDA standards. This research stems from requirements gathering from over 100 bioinformatics active researchers. With this software biotechnology professionals will be able to construct workflows and research outputs for genomic research on any computer or mobile device that is connected to the Internet.

In addition to being an active research team, the CIT bioinformatics group is also actively involved in progressing the teaching of this new discipline within the Institute – one of the major movements in this direction is the establishment of a new taught masters (MSc) in computational biology; an interdisciplinary field in which students will be exposed to the most up-to-date training in computing and biology.

 

News October 2011

(L to R) Professor Victor Jongeel, Dr Roy Sleator and Dr Paul Walsh at the Genomics Institute of University of Illinois at Champagne Urbana. The green, yellow and red sculptures represent the resolved three dimensional structures of the ribosomes representing the three domains of life: Eukaryota, Bacteria and Achaea (a new kingdom of life defined by Carl Woose in 1977 – Woose is currently professor of microbiology at the University of Illinois at Urbana-Champaign).Research Success for CIT’s Bioinformatics’ Group

(L to R) Professor Victor Jongeel, Dr Roy Sleator and Dr Paul Walsh at the Genomics Institute of University of Illinois at Champagne Urbana. The green, yellow and red sculptures represent the resolved three dimensional structures of the ribosomes representing the three domains of life: Eukaryota, Bacteria and Achaea (a new kingdom of life defined by Carl Woose in 1977 – Woose is currently professor of microbiology at the University of Illinois at Urbana-Champaign).

 

 

 

CIT’s Bioinformatics research group has achieved funding success with the award of a €90,000 Enterprise Ireland (EI) Commercialisation Fund grant to Dr Roy Sleator of Biological Sciences and Dr Paul Walsh from Computing. The award is to further commercialisation of their BioMapper software research tool. This adds to significant resent achievements, including:

  • An agreement with Microsoft to provide state-of-the-art cloud hosting and storage to enable BioMapper to be even more responsive.
  • An evaluation agreement from University of Chicago.
  • An agreement with Notre Dame’s Comparative Bioinformatics Group to provide T-Coffee services for multiple sequence alignment.

This adds to the strengthening of interdisciplinary research between the Departments of Computing and Biological Sciences at CIT, along with the recruitment of lecturer and researcher Aisling O’Driscoll as well as the launch of a taught MSc in Computational Biology, which had its first intake this semester.


BIO-EXPLORE

To download BIO-EXPLORE newsletter: BIO-Explore Issue 1

The BIO-EXPLORE research group is a team of inter-disciplinary scientists from the Departments of Biological Sciences Chemistry and Maths & Computing. They are committed to developing and implementing platform technologies to underpin their core research areas of diagnostics, bio-analysis, antimicrobial screening, bio-informatics and peptide engineering.

The group is made up of 6 principal investigators and 26 postgraduate students many of which are engaged in interdisciplinary projects.


MEDIC

Medical Technologies is a new and emerging area of research within CIT. The Medical Engineering Design and Innovation Centre (MEDIC) is an industry-led applied research centre that specialises in Medical Technologies from proof of concept through to commercialisation. The centre draws expertise from a number of areas within the Institute including the Departments of Mechanical, Biomedical, Manufacturing and Electronics Engineering, as well as Applied Physics and Instrumentation. The centre boasts a state-of-the-art ‘gait’ analysis system and a fully equipped Biomaterials laboratory and is working with many of the top Biomedical Engineering companies in Cork.

For more information please click on the following link: http://www.medic.ie/

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Flooding Prescience


Researchers from the Computing Department had some prescience recently after they created computer models of flooding in Cork city. William Lynn, a computer graphics researcher based in the NMCI under the supervision of computing lecturers Dr Paul Walsh and Helen Fagan, has created computer graphics software that allows planning decision makers to visualise the effect of potential climate change on coastal regions.

Climate change represents one of the greatest environmental, social and economic threats facing the planet. The European Union is committed to working constructively for a global agreement to control climate change, and is leading the way by taking ambitious action of its own. The CIT team is working towards this goal by supporting the IMCORE project, which is the Innovative Management for Europe’s Changing Coastal Resource. The CIT team is currently developing a methodology and software to aid Coastal Managers across NW Europe to visualise flooding scenarios and preventative measures. As part of its work the team produced the flooding scenario mock-up, shown below, 6 weeks before the flooding events of November 2009, using software developed for the project by William Lynn.

The team also exhibited its technical findings at the EuroGraphics Conference in Trinity College Dublin in December.

One of the main requirements of the project was to be able to quickly visualise any city in different flooding scenarios. The flooding visualisations were developed using video game technology. The team created RainBath; software designed for climate change flooding visualisations. The flooding water is based on games such as Gear of War, Half-Life2 and Unreal Engine. The 3D model of Cork city was created using the popular tool Google Sketch-Up, the city is then viewed in the RainBath engine using the flooding water. RainBath can also take in any 3D models created for Google Earth. Large cities can have thousands of buildings, the team created extra software for Google Sketch-Up that allows the semi-automatic creation of different cities based on city plans. The user or player has complete freedom to explore Cork city during flood, which can be at any level from a few inches to hundreds of metres. The CIT team’s flooding visualisation tools can be used to visualise the flooding of nearly any area in full 3D, this has prompted interests from a number of flooding and climate change projects.

The CIT team is currently creating a virtual tour of Spike Island using the RainBath Engine and plan to place videos on the Internet in the near future.