Real Virtuality: A Step Change from Virtual Reality

Location: D'Arcy Thompson Room, School of Computing Sciences, UEA
Date: 13:00-14:00 8 Jun 2012
Speaker: Prof. Alan Chalmers
Organiser: Dr. Katharina Huber
Institution: Warwick Digital Laboratory. University of Warwick
Abstract: Real Virtuality is defined as a true high-fidelity multi-sensory virtual environment that evokes the same perceptual response from a viewer as if he/she was actually present, or "there", in the real scene being depicted. Such environments are interactive and simulate actual physics. Five senses (visuals, audio, smell, feel and taste) are concurrently stimulated to deliver real world modalities naturally and in real time. This talk discusses how Real Virtuality is able to compute and deliver authentic real-world stimuli and thus exploit cross-modal effects which are a key feature of how humans perceive the real world and in doing so significantly reduce the amount of computation actually needed for any environment. This, coupled with the processing power of modern computer hardware, including parallel processing, allows Real Virtuality to achieve ‘realism in real time', despite the high computational demands of high-fidelity, physically-based rendering.

Spring Phylogenetics at UEA 2012
Location: D'Arcy Thomson Room, School of Computing Sciences, UEA
Date: 13:00-17:00 17 Apr 2012
Organiser: Dr. Katharina Huber and Miss Sarah Bastkowski
Institution: School of Computing Sciences, UEA

Structure and enumeration of level-k phylogenetic networks
Location: D'Arcy Thompson Room, School of Computing Sciences, UEA
Date: 13:00-17:00 17 Apr 2012
Speaker: Philippe Gambette
Organiser: Dr. Katharina Huber
Institution: Université Paris-Est Marne-la-Vallée. Paris. France
Abstract: Phylogenetic networks generalize the tree concept to model Evolution. In rooted phylogenetic networks, some vertices have two parents: they correspond to species resulting from hybridization between two ancestral species, or having received a gene from another species through horizontal gene transfer. The "level" of a phylogenetic network measure how much its structure differs from a tree structure. Considering phylogenetic networks with bounded level allows to obtain efficient reconstruction or comparison algorithms. I will present some properties of phylogenetic networks with bounded level, showing how they can be obtained from a finite set of generators, and present some results about the enumeration of level-1 and 2 networks.

Minimizing Hybridizations
Location: D'Arcy Thompson room, School of Computing Sciences, UEA
Date: 13:00-17:00 17 Apr 2012
Speaker: Leo van Iersel
Organiser: Dr. Katharina Huber
Institution: Centrum Wiskunde & Informatica, Amsterdam, The Netherlands.
Abstract: Given a collection of trees describing the evolution of different genes, a well-studied problem is to compute the minimum number of hybridizations necessary to explain the conflicts among the trees. A constructive variant of this problem is to construct a rooted binary network that contains each of the given trees and has a minimum number of vertices with indegree 2. I will review this problem and present several recent results.

Transcriptome sequencing and associative transcriptomics
Location: D' Arcy Thompson Room, School of Computing Sciences, UEA
Date: 14:00-15:00 30 Mar 2012
Speaker: Dr. Martin Trick
Organiser: Dr. Katharina Huber
Institution: Computational and Systems Biology, John Innes Centre
Abstract: So called Next Generation DNA sequencing technologies are revolutionising genomics. Transcriptome sequencing in important crop plants with complex genomes will be discussed, together with some of the bioinformatics challenges it presents, and some applications for crop improvement will be illustrated.

Copying with Modification: Analysis of Textual Variation by Latent Tree
Location: D'Arcy Thompson Room, School of Computing Sciences, UEA
Date: 13:00-14:00 23 Mar 2012
Speaker: Dr. Teemu Roos
Organiser: Dr. Katharina Huber
Institution: Helsinki Institute for Information Technology HIIT
Abstract: It has long been known that textual traditions that are produced by repeated copying with modification, as well as many other cultural objects, evolve in ways that can be likened to biological evolution. Hence, it is not surprising that many techniques initially developed for building evolutionary trees (phylogenetics) can be applied to the analysis of such cultural objects. I will discuss recent advances obtained by tailoring several phylogenetic tools for the study of textual traditions. In particular, I will describe a new method based on Bayesian networks and the so called structural expectation-maximization (structural EM) algorithm. In experiments with artificially created textual traditions, the new method outperforms current state-of-the-art in the specific task of reconstructing copying histories both in terms of a numerical score as well as interpretability.

EBI Roadshow
Location: Bio 0.12, UEA
Date: 09.30-17.00 1 Mar 2012
Organiser: Dr. Katharina Huber, Dr. Richard Bowater
Institution: UEA
Materials: EBI Programme (pdf 34 KB), Ensembl presentation (pdf 6 MB), Ensembl course book (pdf 6 MB), IntEnz Presentation (pdf 607 KB), IntEnz Tutorial (pdf 26 KB), Rhea Presentation (pdf 94 KB), Rhea Tutorial (pdf 38 KB), Enzyme Portal Presentation (pdf 2.3 MB), Enzyme Portal Tutorial (pdf 27 KB)

Evolutionary origins and physical constraints of terpene chemical diversity
Location: D'Arcy Thompson Room, School of Computing Sciences, UEA
Date: 14:00-15:00 24 Feb 2012
Speaker: Dr Paul ÓMáille
Organiser: Dr Katharina Huber
Institution: Department of Metabolic Biology, John Innes Centre
Abstract: Terpenes are the largest and most structurally complex group of plant natural products, numbering well over 30,000 known compounds. These metabolites are essential for plant ecological viability while providing numerous important bioactives for human uses. Remarkably, the stereochemical complexity of terpene hydrocarbon skeletons largely derives from a single enzyme-catalyzed reaction by terpene synthases. This lecture will describe recent work on sesquiterpene synthases, a class of terpene synthase, capable of producing one of 300 stereochemically distinct hydrocarbon skeletons from a universal substrate farnesyl diphosphate. How do sesquiterpene synthases create such tremendous chemical diversity? To what extent does terpene chemical diversity reflect the intrinsic reactivity of the substrate? I will discuss results of a multidisciplinary approach involving physical organic chemistry, X-ray crystallography, enzymology, analytical chemistry and protein engineering towards addressing these questions and introduce graph theoretic approaches to understanding enzyme function.

Research at the Wellcome Trust Sanger Institute and the Pfam protein family database
Location: D'Arcy Thompson Room (School of Computing Sciences)
Date: 14:00-15:00 10 Feb 2012
Speaker: Dr. Marco Punta
Organiser: Dr. Katharina Huber
Institution: Wellcome Trust Sanger Institute, Hinxton UK
Abstract: In this talk I will first give a brief overview of research at the Sanger Institute. Then I will introduce the Pfam database that groups protein regions into families via sequence similarity. I will describe the way Pfam can be used, in combination with other existing tools, to gain insight into protein structure and function. In this context I will discuss the tricks and treats of annotation-transfer by homology. Finally, I will talk about future Pfam developments and the challenges that lie ahead.

Modelling Microtubule Dynamics
Location: D'Arcy Thompson Room (School of Computing Sciences)
Date: 14:00-15:00 27 Jan 2012
Speaker: Dr. Scott Grandison
Organiser: Dr. Katharina Huber
Institution: School of Computing Sciences, UEA
Abstract: Microtubules are subcellular filaments that are associated with many functions including cell division, nuclear positioning and growth.
They interact with each other in simple ways, yet from those simple interactions they are able to form complex structures. It's this combination of complex behaviour arising from simple interactions that makes them an attractive system for theoretical study. In this talk I'll present some of our recent modelling work.