e-Research

November

• Life Science Computation Seminar - 12-1pm Friday November 6, Level 1 Seminar Room, Borchardt Library
  
  'Systems Biology for Drug Discovery'
  Professor Liam O'Connor, Professor of Systems Biology & Bioinformatics, Bioscience Research Centre, La Trobe University
  
  Post-genomic era drug discovery takes place in the context of an exponentially growing amount of genomic, transcriptomic, proteomic and chemical data. Making sense of all this information often requires going beyond reductionist models of biology and pharmacology. Dr O'Connor's research involves using multiple diverse data types to extend our knowledge of the developmental and molecular signaling pathways dysregulated in disease.
  
  Professor O'Connor has recently joined the Biosciences Research Centre as the Chair of Systems Biology and Bioinformatics. Immediatley prior to this appointment, Liam was the Director of Quantitative Biology at the Novartis Institutes for BioMedical Research (NIBR), where he had global responsibility for computational and systems biology for the Novartis research community. Liam began his career in computer science and mathematics before switching to biology. After his PhD at the Walter and Eliza Hall Institute in Melbourne, Australia and postdoctoral work at the MIT Center for Cancer Research, he joined Incyte Genomics, then MDS Proteomics, then Novartis Pharmaceuticals.
  
  http://www.versi.edu.au/versi/lsc-oconnor.html
  

October

• Bioinformatics Australia 2009
   
  The Bioinformatics Australia 2009 conference will be the fourth national meeting held by the Bioinformatics Australia Society. This annual meeting will showcase Australia’s scientific activity in the key areas of bioinformatics and computational biology.
   
  In addition to the scientific content, this meeting will provide networking opportunities with bioinformatics and biotechnology stakeholders in Australia for students, users and developers of bioinformatics resources as well as ICT and life scientists interested in bioinformatics.
   
  The Bioinformatics Australia 2009 conference will be held concurrently with the AusBiotech 2009 National Conference and sharing events, exhibition and networking space. The conference will include scientific sessions, panel sessions and discussion forum.
  
  

• Life Science Computation Seminar - Friday 30th October, 12-1pm - Level 1 Seminar Room, Borchardt Library

  ‘Bacterial turbulence’
  Dr Prabhakar Ranganathan, Lecturer, Department of Mechanical Engineering, Monash University
  
  Dramatic patterns of synchronized motion are often observed in large flocks of birds or shoals of fish, and have fascinated scientists for a long time. Such displays throw up two basic questions. Firstly, how do flocks manage to co-ordinate themselves over very large distances with no apparent means of long-range communication? And secondly, do the self-organized patterns serve some purpose at all for the individuals involved, and for the overall flock? Although there have been several recent breakthroughs in understanding such behaviour, there are at present no firm answers to these questions, mostly due to the lack of controlled experiments on large mobile populations.
  
  Complex patterns - reminiscent of turbulent flows in fluids - are also observed in colonies of mobile bacterial cells moving on surfaces, or in fluid environments. We can now perform controlled experiments on bacterial systems to gain insight into the larger problem of self-organization in mobile populations. Moreover, understanding the physical mechanisms behind the ability of pathogens like Pseudomonas aeruginosa to rapidly colonize surfaces may prove useful in controlling biofilm formation, often implicated in diseases like cystic fibrosis.
  
  This talk will broadly review how biophysics, fluid mechanics and high-performance computing are being used to understand this phenomenon of "bacterial turbulence".
  
  

• Life Science Computation Seminar - Friday 23rd October, 12-1pm - Level 1 Seminar Room, Borchardt Library
  
  'Gas phase chemistry of some biologically relevant molecules'
  Dr George N Khairallah, School of Chemistry, Bio21 Institute, Melbourne University
  
  Mass spectrometers offer an ideal 'chemical laboratory' for the study of the intrinsic ionic reactions in the gas-phase. They provide a milieu where reactions can be studied without the interference of solvents and counterions usually present in solution. In the recent years, mass spectrometry (MS), in particular electrospray ionisation mass spectrometry (ESI/MS), was shown to be a powerful tool in the study of biomolecules and their non-covalent interactions. More recently, with the advancement in computing, theoretical chemistry calculations are playing a bigger role in studying the structures, energetic and mechanisms of reactions studied in the gas phase. These calculations are essential to help interpret and understand the observations made during mass spectrometry studies.
  
  Further information: http://www.versi.edu.au/versi/lsc-khairallah.html

• Life Science Computation Seminar - Friday 16th October, 12-1pm - Level 1 Seminar Room, Borchardt Library
  
  ‘Algorithmic Challenges of High Throughput Sequencing’
  Professor Justin Zobel, Program leader and Principal Research Fellow, NICTA, Professor School of Computer Science and Software Engineering, the University of Melbourne
  
  New sequencing technologies are creating vast quantities of DNA data, and presenting biomedical scientists with new approaches to their research questions.  The data and these questions are posing dramatic challenges for computational researchers, where breakthroughs are required to keep pace with the rate of change of biomedical technologies.  Using two of NICTA's current algorithmic research projects as examples - in DNA storage and sequence assembly - this talk is an examination of bioinformatic computational challenges and some of the roles that algorithmic research can have in biomedical science.
  A more detailed abstract for this talk: http://www.versi.edu.au/versi/lsc-zobel.html
  
  
• Life Science Computation Seminar – Friday 9th October, 12-1pm - Level 1 Seminar Room, Borchardt Library
  
  ‘High Throughput Computing for Biological Sciences: Tools and Techniques’
  Professor David Abramson, Faculty of Information Technology, Monash University
  
  High Throughput Computing (HTC) provides rapid execution of large computational experiments that can be broken into a number of smaller components. This usually arises in experiments that involve parameter estimation and exploration, but also occurs in algorithms that scatter and gather computationally bound applications. HTC has had an increasing impact on science, medicine and engineering over the years, and is currently used in a number of research projects at Monash.
  
  Over the years we have developed a family of software tools (called Nimrod) that makes it easy to specify large parametric experiments of this type. Nimrod provides seamless access to a range of computational resources, from local workstations to distributed clusters. Here we will discuss the application of this technology to problems in life sciences, ranging from drug design, cardiac modelling, clinical radiotherapy and protein structure determination.
  http://www.versi.edu.au/versi/lsc-abramson.html
  
  
  
• Life Science Computation Seminar – Friday 2nd October, 12-1pm - Level 1 Seminar Room, Borchardt Library
  
  'The Virtual Physiological Human/Physiome Project'
  Professor Peter J Hunter, Director, Auckland Bioengineering Institute
  
  The Physiome Project, an internationally collaborative effort to provide an integrative multi-scale modeling framework for computational physiology, has recently been boosted by a European initiative called the ‘Virtual Physiological Human’ (VPH) .  The combined VPH/Physiome Project aims to link biochemical network systems biology models and biophysically and anatomically based bioengineering models to medical imaging and biomedical signal analysis. The primary achievements so far are the development of markup languages (CellML, FieldML), freely accessible model repositories based on the markup languages, and open source computational tools for authoring, visualizing, executing and analyzing these models.  
  In addition to describing these standards and illustrating their applications, particularly for cardiac modelling, the talk will discuss current efforts to develop metadata standards for annotating model components (parameters and variables) with terms from existing ontologies such as GO , FMA  and OPB  that describe the biological, anatomical and biophysical meaning of these components. This development is benefitting from a collaboration with the systems biology SBML community . A new standard for encoding time-varying biomedical signals and associated metadata, called BiosignalML and being developed by the EMBS Technical Committee on ‘Computational Biology and the Physiome’, will also be described.  
  
  Peter is speaking as part of the Monash University Cardiac Modelling workshop: http://www.messagelab.monash.edu.au/cardiacmodellingworkshop09
  http://www.versi.edu.au/versi/lsc-hunter.html
  
  
  

September

• Nature News special - Data sharing
  Sharing knowledge is essential for the progress of science, but researchers do not always release data and research materials, even after publication of work. Earlier this year, two research communities held meetings with a broad range of stakeholders to discuss this issue, and they report their proposals to promote data sharing in biology in two Opinion articles in this week’s Nature.
  
  The agendas of these meetings are intended to spark community discussion and authors from both agendas will respond to reader comments in two free Nature Network forums surrounding prepublication data sharing and postpublication data sharing. Be sure to have your say.
  In addition, a News Feature examines the technical and cultural hurdles that can keep scientists from sharing data. Exploring issues from antiquated technology to a lack of trust in other scientists, the article highlights a range of potential solutions.
  
  Access the Nature News special free online.
  
  
• eVolution - adventures in eResearch & eLearning - conducted by CSHE and the Director, eResearch on 29 and 30 September at The Barbara Falk Room, Level 1, 715 Swanston St, Carlton
  
  The Centre for the Study of Higher Education, in partnership with Professor Leon Sterling, Director, eResearch at The University of Melbourne is running two interactive seminars on eResearch and eLearning. All university staff interested in learning about the latest developments in these two areas are invited to attend.
  
  The seminars will feature speakers including:
  • Professor John O’Callaghan, Director, Victorian Life Sciences Computation Initiative (VLSCI)
  • Representatives from the Australian Research Collaboration Service (ARCS)
  • Professor John Furness, Department of Anatomy and Cell Biology
  • Dr Nathan Faggian, Centre for Neuroscience
  • Ms Helen Hayes, Director, Knowledge Transfer
  • Ms Diane Squires, Manager, Media & Public Relations, The Melbourne Newsroom
  • Professor David Williams, Department of Physiology
  • Associate Professor Peter Tregloan, School of Chemistry
  
  Professor Phil Long, founding Director, Centre for Educational Innovation and Technology, the University of Queensland, will deliver a keynote speech on Wednesday September 30.
  
  Interested staff are encouraged to register early, as there is a cap of 50 places. Morning tea and lunch will be provided. Further program details will be available shortly. Check www.cshe.unimelb.edu.au/academic_dev/eseminars09.html for details
  
  
• Life Science Computation Seminar - Friday 25th September, 12-1pm, Level 1 Seminar Room, Borchardt Library
  
  'Genomic Data Analysis of Ovarian Cancer' - Professor David Bowtell, Group Leader, Cancer Genomics & Biochemistry Laboratory, Peter MacCallum Cancer Centre
  
  Cancer can be considered to be a genetic 'software' problem. The cellular complement of DNA (genome) represents an embedded code that allows the cell to perform autonomous and cell-environment interactive functions. The DNA code is disrupted in a cancer cell, due to inherited and/or acquired defects, allowing the cell to inappropriately divide, spread (metastasize) and survive. Cancer research of the last two decades has focused finding genes that are defective in cancer, with several hundred identified to date. Recent research has allowed whole genome scans for inherited risk factors and somatic mutational events. These surveys are at a particularly intense stage at present, with many genome wide associations studies reported in the last year and whole genome sequencing of cancer genomes now underway. It is anticipated that in the future there will be an increasing focus on modeling the interaction between these mutational events. The VLSCI should be of substantial value in allowing analysis of cancer genomes and in particular, helping understand how mutations cooperate to allow the major phenotypes of malignancy. The presentation will overview these concepts and developments.
  http://www.versi.edu.au/versi/lsc-bowtell.html
  
  
• Life Science Computation Seminar – Friday 18th September, 12-1pm - Level 1 Seminar Room, Borchardt Library
  
  'Quantum Chemistry: from atoms to proteins and beyond. How accurate can we get?' - Dr David Wilson, Department of Chemistry, La Trobe University
  
  In this presentation, the state-of-the-art in quantum chemistry research and applications will be outlined, with the aim of highlighting the impressive accuracy that can be obtained for small molecules (and the significant computational resources required). Applications to larger molecules (of both materials science and biological interest) will be outlined, along with recent work on modeling protein-ligand interactions using molecular dynamics.
  http://www.versi.edu.au/versi/lsc-wilson.html

• Life Science Computation Seminar - Friday 11th September, 12-1pm - Level 1 Seminar Room, Borchardt Library
  ‘Computational methods in drug design and development’ - Dr David Chalmers, Medicinal Chemistry and Drug Action, Faculty of Pharmacy and Pharmaceutical Sciences, Monash University
  
  Drug development is a multidisciplinary process involving a large number of processes, including; identification of a drug target, bioassays, structural biology, synthetic medicinal chemistry, drug design and evaluation of the drug behaviour in the body.  Each of these processes, in itself, is a complex task and there is a significant risk of failure at any step on the development path.
  Accordingly, there is wide interest in computational methods which can enhance or speed up any of these processes.  This talk will provide an overview of computational methods in drug development and give examples of the application molecular docking and molecular dynamics to problems in drug development including fragment-based drug design, modelling of G-protein coupled receptors and using molecular dynamics to model drug formulations.
  
  
• Life Science Computation Seminar - Friday 4th September -
  ‘Development of Pharmacogenomic Classifier Models for Epilepsy Treatment Outcomes’ - Professor Terence J. O'Brien, The Department of Medicine, The Royal Melbourne and Western Hospital, The University of Melbourne and Dr Melanie Bahlo, Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research.
  
  Approximately 30% of patients treated for epilepsy, the most common chronic neurological disease, will not achieve seizure control. The identification of genetic markers that provide accurate prediction in an individual patient of their biological chance of seizure control with AED treatment would have significant clinical and scientific value. However, it is unlikely in complex diseases such as epilepsy, affecting heterogeneous populations, that a single SNP will adequately explain treatment outcomes. Our group has developed and published an approach to developing multigenic models to classify treatment outcomes - utilizing dimension reduction, machine learning (kNN) and cross-validation approaches.
  As a VLSCI Stage 0 project we are applying this approach in an attempt to develop a multigenic classifier for patients in a group of epilepsies, the idiopathic generalised epilepsies (IGE), which have a strong genetic contribution to their pathogenesis.
  Dr. Bahlo will outline our approaches that her group have used on a pharmacogenomics Hepatitis C study. These are mainly based on standard statistical approaches such as data reduction and logistic model building. Professor O'Brien will discuss current problems with this approach and specific issues that plague genetics data.

August

• Life Science Computation Seminar - Friday 28th August, ‘Simulating cardiovascular disease - the role of Computational Fluid Dynamics’ - Dr Kris Ryan, Department of Mechanical and Aerospace Engineering, Monash University
  
  Cardiovascular diseases are the number one cause of death world-wide as calculated by the World Health Organization. The role of fluid dynamic forces on the health of the vascular system is of significant interest for a wide range of these diseases. For example, the ability of a platelet to adhere to a surface is directly related to the history of fluid forces which affect it, having particular implications for the progression of thrombosis; while aneurysm growth is accentuated by the weakening of arterial walls enhanced by the pressure and shear forces exerted by the circulation system.
  
  This presentation will consider the role of highly accurate numerical simulations of fluid flow in developing our understanding of cardiovascular disease. Two investigations will be considered; the first simulates the flow past an in-vitro thrombus. This investigation provides researchers with an accurate evaluation of the shear stress history of platelets encountering a thrombus in an in-vitro environment and represents the first step in our ability to completely simulate the growth of thrombi. Experimental measurement of the shear history on a platelet is currently impossible - and our investigations represent a breakthrough in this field. The second investigation considers fluid forces acting on non-axisymmetric abdominal aortic aneurysm profiles, and in particular the effect of eccentricity of the aneurysm profile on the fluid forces acting on the vessel walls. This effect has not been considered in the past, even though non-axisymmetric profiles are more representative of clinical cases. Both investigations require significant computational resources, relying heavily on a highly efficient algorithm and highly parallelized computational architecture for success.
  
  Dr Kris Ryan is a specialist in applying highly accurate numerical techniques to fluid flow problems in a wide variety of applications as diverse as aircraft wake analysis to biological flows. Dr Ryan is a key member of the FLAIR research group, specializing in experimental and computational fluid mechanics research. The FLAIR group focuses on fundamental investigation of fluids problems which impact the automotive, aeronautical, industrial and bio-medical fields. Findings from Dr Ryan’s research are published in leading journals worldwide.
  
  
• AuScope Web Services Roadshow 2009- Melbourne (2 June), Hobart (3 June), Darwin (12 June), Canberra (19 June), Perth (11 August), Brisbane (21 August), Maitland (24 August) and Adelaide (26 August)
  
  The AuScope Web Services Roadshow is a workshop designed to showcase how the Geoscience Community, through the NCRIS funded AuScope Community Earth Model, is establishing an Australian Geoscience Network to provide “transparent access” to data and knowledge about the Australian landscape. The Network also supports online access to open source processing tools.  The one-day event includes an Executive Briefing and a Technology Briefing. 
  
  
• Monday 24 August 12.30 - 2.00pm; BioGrid Australia Seminar -"Efficient Health Research; Improving research outcomes using technology", Lovell Theatre, RMH Main Block

  This talk profiled health research in epidemiology and health from leading researchers from The Karolinska Institutet in Sweden. The data from clinical to biobank data is enabling research which is improving our knowledge of disease processes and treatment. The talk also highlighted the technologies used including both innovative data collection as well as technologies to connect distributed health data in a privacy protected manner.

• Life Science Computation Seminar - Friday August 14 -The Future Bioeconomy and Human Health - Level 1 Seminar Room, Borchardt Library
  Professor Ben Cocks, Research Director, Biosciences Platform and Professor, Animal Genetics and Genomics, Department of Primary Industries.
  Biotechnology continues to provide new solutions for human disease and improved agricultural production. Integrated biosciences research applied to understanding the complete systems underpinning mammalian health, and a revolution in the ability to design organisms, will support new approaches to address global challenges such as limited food supply, human disease, and greenhouse emissions. Further information including Professor Cocks' biography: http://www.versi.edu.au/versi/lsc-cocks.html

• Employment Opportunity in the field of e-Research: Learning and Development Specialist - Intersect is looking for an expert in education to establish and drive their Learning and Development strategy. This Specialist will be responsible for designing and facilitating professional development programs for Intersect’s internal and external stakeholder groups. If you are interested in learning more about this role contact hrmanager@intersect.org.au

July

• eResearch SA is hiring
  An opportunity exists for an eResearch Data Consultant with eResearch SA and the Australian National Data Service (ANDS). Operating as a member of the eResearch SA team, located at the University of Adelaide, you will work with research clients to develop requirements specifications to achieve the goals of ANDS and eResearch SA. You will assist in delivering advice on the management of research data and the implementation of software, policy, work flows and other change management processes required to expand the accessibility, usability and capabilities of research data.
  Applications close: Friday, 17 July 2009
  
  

June

• Remote interaction strengthens relationships
  Undergraduate physics students recently enjoyed a real-life experience of using the PX1 beamline – without leaving their classroom.
  10 students and staff were connected to the PX1 (high-throughput protein crystallography) beamline at the Australian Synchrotron via the Virtual BeamLine project's video-conferencing links, work area overview cameras, storage gateway, metadata viewer and PX1's NoMachine remote desktop software. In collaboration with three other La Trobe students at the beamline, powder samples were loaded for identification and analysis with the students at the La Trobe end remotely controlling the beamline operations via Blu-Ice on NoMachine. The outputs from the beamline were duly interpreted by the students, who inferred the nature of the various materials by assessing the powder diffraction patterns and conferring remotely with one another on the physical nature of the materials.
  The class activities introduced some of tomorrow’s scientists to the remote and onsite capabilities of the synchrotron in general and the PX1 beamline in particular, as well as forming part of the students’ assessed coursework.
  The collaboration was the brainchild of Paul Pigram and Peter Kappen (La Trobe University) and Anton Tadich (Australian Synchrotron soft x-ray spectroscopy team), together with Rachel Williamson (Australian Synchrotron protein crystallography team) and Chris Myers from the Victorian eResearch Strategic Initiative (VeRSI). Everyone involved in the class was delighted with the experience.
  The Australian Synchrotron and La Trobe University look forward to further educational collaborations.
  
  
• spatial@gov Conference 2009 - June 15-16, Canberra
  The Conference will address the rapidly increasing demand for information on how spatial capabilities can improve the ability of governments at all levels to inform their policy development, enhance service delivery and gain efficiencies in internal business processes. Experts will present on topical themes including water, social inclusion, indigenous culture and local government. Australian presenters will describe how spatial tools have supported the response to the Victorian bushfires through tactical and operational mapping, and how national water concerns are being addressed through the application of world leading spatial capabilities. International presenters will describe relevant activities in other countries.
  
  
• Half-day visualisation workshop organised by The Monash e-Research Centre - June 17, 9.00am to lunchtime, Clayton campus.
  A number of esteemed speakers have been scheduled to present including two researchers from the US who will be speaking via high definition from UC San Diego as part of the MURPA seminar series.
  
  Professor Chris Johnson, Director of the Scientific Computing and Imaging Institute at the University of Utah and a world leading researcher in scientific visualisation, will be discussing biomedical imaging and modelling in neurology and cardiology. Jurgen Schulze, project scientist at Calit2, will present an overview of immersive visualisation at Calit2. Professor Gary Egan from the Howard Florey Institute will discuss brain imaging and its application as a research tool in the neurosciences. Dr Rob Bryson-Richardson will present the application of optical projection tomography (OPT) to create 3D models of embryonic development. Dr Kieran Short will discuss the development of imaging, visualisation and quantification approaches for the analysis of organogenesis.
  
  
• Job Vacancy - Collections Australia Network - Outreach Officer

  In conjunction with the National Project Manager the Outreach Officer is responsible for delivering the CAN outreach programme which is targeted to meet the needs of the collecting sector in Australia.  The CAN Outreach Officer will be responsible for promoting public and professional interest in the Collections Australia Network and for fostering increased awareness of and usage of its online capabilities and resources - Clerk Grade 5/6, Ultimo, Temporary Full-Time.
  Applications Close: Friday, 26 June 2009

May

• Educause Australasia 2009 - May 3-6, Perth Convention Exhibition Centre
  Summary: This is the premier event for professionals working in higher education who manage technologies to advance scholarship, learning and teaching.
  Theme: "Innovate, Collaborate, Sustain". The conference will explore IT, Learning & Teaching and Library challenges in the areas of: Innovation, Emerging Technologies and Trends, Leadership, Management and Planning, Collaboration, Learning and Teaching, Information Management and Access, Sustainability, Information Technology