With the wealth of high-throughput sequencing data generated by recent large-scale consortia, predictive gene expression modelling has become an important tool for integrative analysis of transcriptomic and epigenetic data. However, sequencing data-s
ets are characteristically large, and previously modelling frameworks are typically inefficient and unable to leverage multi-core or distributed processing architectures. In this study, we detail an efficient and parallelised MapReduce implementation of gene expression modelling. We leverage the computational efficiency of this framework to provide an integrative analysis of over fifty histone modification data-sets across a variety of cancerous and non-cancerous cell-lines. Our results demonstrate that the genome-wide relationships between histone modifications and mRNA transcription are lineage, tissue and karyotype-invariant, and that models trained on matched epigenetic/transcriptomic data from non-cancerous cell-lines are able to predict cancerous expression with equivalent genome-wide fidelity.
The NUbots are an interdisciplinary RoboCup team from The University of Newcastle, Australia. The team has a history of strong contributions in the areas of machine learning and computer vision. The NUbots have participated in RoboCup leagues since 2
002, placing first several times in the past. In 2014 the NUbots also partnered with the University of Newcastle Mechatronics Laboratory to participate in the RobotX Marine Robotics Challenge, which resulted in several new ideas and improvements to the NUbots vision system for RoboCup. This paper summarizes the history of the NUbots team, describes the roles and research of the team members, gives an overview of the NUbots robots, their software system, and several associated research projects.
Motivation: Predictive modelling of gene expression is a powerful framework for the in silico exploration of transcriptional regulatory interactions through the integration of high-throughput -omics data. A major limitation of previous approaches is
their inability to handle conditional and synergistic interactions that emerge when collectively analysing genes subject to different regulatory mechanisms. This limitation reduces overall predictive power and thus the reliability of downstream biological inference. Results: We introduce an analytical modelling framework (TREEOME: tree of models of expression) that integrates epigenetic and transcriptomic data by separating genes into putative regulatory classes. Current predictive modelling approaches have found both DNA methylation and histone modification epigenetic data to provide little or no improvement in accuracy of prediction of transcript abundance despite, for example, distinct anti-correlation between mRNA levels and promoter-localised DNA methylation. To improve on this, in TREEOME we evaluate four possible methods of formulating gene-level DNA methylation metrics, which provide a foundation for identifying gene-level methylation events and subsequent differential analysis, whereas most previous techniques operate at the level of individual CpG dinucleotides. We demonstrate TREEOME by integrating gene-level DNA methylation (bisulfite-seq) and histone modification (ChIP-seq) data to accurately predict genome-wide mRNA transcript abundance (RNA-seq) for H1-hESC and GM12878 cell lines. Availability: TREEOME is implemented using open-source software and made available as a pre-configured bootable reference environment. All scripts and data presented in this study are available online at http://sourceforge.net/projects/budden2015treeome/.
Performing massive data mining experiments with multiple datasets and methods is a common task faced by most bioinformatics and computational biology laboratories. WEKA is a machine learning package designed to facilitate this task by providing tools
that allow researchers to select from several classification methods and specific test strategies. Despite its popularity, the current WEKA environment for batch experiments, namely Experimenter, has four limitations that impact its usability: the selection of value ranges for methods options lacks flexibility and is not intuitive; there is no support for parallelisation when running large-scale data mining tasks; the XML schema is difficult to read, necessitating the use of the Experimenters graphical user interface for generation and modification; and robustness is limited by the fact that results are not saved until the last test has concluded. FlexDM implements an interface to WEKA to run batch processing tasks in a simple and intuitive way. In a short and easy-to-understand XML file, one can define hundreds of tests to be performed on several datasets. FlexDM also allows those tests to be executed asynchronously in parallel to take advantage of multi-core processors, significantly increasing usability and productivity. Results are saved incrementally for better robustness and reliability. FlexDM is implemented in Java and runs on Windows, Linux and OSX. As we encourage other researchers to explore and adopt our software, FlexDM is made available as a pre-configured bootable reference environment. All code, supporting documentation and usage examples are also available for download at http://sourceforge.net/projects/flexdm.
Physically-realistic simulated environments are powerful platforms for enabling measurable, replicable and statistically-robust investigation of complex robotic systems. Such environments are epitomised by the RoboCup simulation leagues, which have b
een successfully utilised to conduct massively-parallel experiments in topics including: optimisation of bipedal locomotion, self-localisation from noisy perception data and planning complex multi-agent strategies without direct agent-to-agent communication. Many of these systems are later transferred to physical robots, making the simulation leagues invaluable well-beyond the scope of simulated soccer matches. In this study, we provide an overview of the RoboCup simulation leagues and describe their properties as they pertain to replicable and robust robotics research. To demonstrate their utility directly, we leverage the ability to run parallelised experiments to evaluate different competition formats (e.g. round robin) for the RoboCup 2D simulation league. Our results demonstrate that a previously-proposed hybrid format minimises fluctuations from true (statistically-significant) team performance rankings within the time constraints of the RoboCup world finals. Our experimental analysis would be impossible with physical robots alone, and we encourage other researchers to explore the potential for enriching their experimental pipelines with simulated components, both to minimise experimental costsand enable others to replicate and expand upon their results in a hardware-independent manner.
Computer vision plays a major role in the robotics industry, where vision data is frequently used for navigation and high-level decision making. Although there is significant research in algorithms and functional requirements, there is a comparative
lack of emphasis on how best to map these abstract concepts onto an appropriate software architecture. In this study, we distinguish between the functional and non-functional requirements of a computer vision system. Using a RoboCup humanoid robot system as a case study, we propose and develop a software architecture that fulfills the latter criteria. The modifiability of the proposed architecture is demonstrated by detailing a number of feature detection algorithms and emphasizing which aspects of the underlying framework were modified to support their integration. To demonstrate portability, we port our vision system (designed for an application-specific DARwIn-OP humanoid robot) to a general-purpose, Raspberry Pi computer. We evaluate performance on both platforms and compare them to a vision system optimised for functional requirements only. The architecture and implementation presented in this study provide a highly generalisable framework for computer vision system design that is of particular benefit in research and development, competition and other environments in which rapid system evolution is necessary.
The NUbots team, from The University of Newcastle, Australia, has had a strong record of success in the RoboCup Standard Platform League since first entering in 2002. The team has also competed within the RoboCup Humanoid Kid-Size League since 2012.
The 2014 team brings a renewed focus on software architecture, modularity, and the ability to easily share code. This paper summarizes the history of the NUbots team, describes the roles and research of the team members, gives an overview of the NUbots robots and software system, and addresses relevant research projects within the the Newcastle Robotics Laboratory.
The selection of an appropriate competition format is critical for both the success and credibility of any competition, both real and simulated. In this paper, the automated parallelism offered by the RoboCupSoccer 2D simulation league is leveraged t
o conduct a 28,000 game round-robin between the top 8 teams from RoboCup 2012 and 2013. A proposed new competition format is found to reduce variation from the resultant statistically significant team performance rankings by 75% and 67%, when compared to the actual competition results from RoboCup 2012 and 2013 respectively. These results are statistically validated by generating 10,000 random tournaments for each of the three considered formats and comparing the respective distributions of ranking discrepancy.
