Great story about how the CVL is driving R@CMon (the Monash NeCTAR Node)
The CVL on R@CMon blog entry on the R@CMon (Research @ Cloud Monash) blog.
Atom Probe Workbench v1.0 released
An Atom Probe Microscope (APM) is used to characterise the chemistry and 3D structure of materials (such as metals, alloys, semiconductors, superconductors, ceramics) at the atomic scale. The Atom Probe Workbench (APW) contains the computational tools that are necessary to analyse data from an APM, and runs on Linux (CentOS version 6.4) Virtual Machines within the NeCTAR cloud. The Atom Probe Workbench was developed as one of four application drivers of the NeCTAR Characterisation Virtual Laboratory (CVL) project: Energy Materials - Atom Probe.
Introducing the CVL Energy Materials - X-ray Project
The "NeCTAR CVL Energy Materials - X-Ray" (CVL EM X-Ray) sub-project is well underway towards making the Mango software suite more widely available and accessible to the Australian research community, and provide AMMRT CT researchers with access to a sophisticated, scalable 3D image processing toolkit. The sub-project builds on the expertise and reputation of the ANU's Department of Applied Mathematics in the Research School of Physics and Engineering. The Department has an experienced blend of theoreticians and experimentalists working together to develop micro-CT (micro-computed tomography) instruments and software for quantitative analysis of large 3D data sets.
Workflows in the CVL Neuroimaging Workbench
The NeCTAR CVL Neuroimaging sub-project will soon begin work on a neuroimaging workflow. The initial target is a workflow that allows users to perform the complex task of generating a morphometric minimum deformation average of a group of images. This process requires a large amount of pre-processing, checking of input data and is generally only feasible on large datasets via the use of a small compute cluster. For example it takes on the order of a week to generate an average model of a mouse brain using a fairly conservative approach on a small 20 core linux cluster. More advanced versions of this workflow involve permuting the model generation thus extending the processing time.
Introducing the CVL Neuroimaging sub-project
The NeCTAR CVL Neuroimaging sub-project is underway with multiple tools integrated so far. The team working on this integration are based at the Centre for Advanced Imaging (CAI) at the University of Queensland (UQ). It comprises, Harald Waxenegger, Dr Adam Lin, Prof Graham Galloway and Dr Andrew Janke the sub-project manager. So far this neuroimaging workbench has integrated the most popular analysis packages and added these to the CVL repository allowing their installation on any NeCTAR node and some of the HPC systems, most notably MASSIVE. An additional component of the Neuro-CVL is the integration of a databasing and workflow system that will ease the transition of data from multiple Imaging systems around Australia managed by the National imaging Facility (NIF). This work is expected to begin shortly with researchers at the University of Melbourne (Neil Killeen and King Chiu) and the Research Computing Centre in UQ (Minh Huynh).
Instrument integration in the CVL Structural Biology Workbench
The CVL for Structural Biology (CVL-SB) has recently seen success with integrating a key instrument at Monash Micro Imaging. The result of the work is that researchers who are using the Hitachi H7500 TEM now have a ready workflow for data capture and management, and then processing and visualization using the CVL Desktop. Since February 2013, 18 researchers have used this functionality to manage 140 data sets and 2,531 individual images.
May 2013 Milestone for CVL EMAP
Our previous milestone in May 2013 saw a pre-production system of the CVL EMAP workbench as well as the CVL EMAP workflow systems, demonstrated to the atom probe Scientific Advisory Committee (SAC) for the CVL project. These two systems were trialled by a handful of University of Sydney atom probe researchers; with user acceptance tests performed by one of our atom probe PhD students. When used together, the workbench will provide powerful interactive visualisation programs as well as the capacity to develop new tools. The workflow engine will provide pre-set workflows and the power to easily create new ones.
Introducing the CVL EMAP sub-project
The "NeCTAR CVL Energy Materials - Atom Probe" (CVL EMAP) sub-project is well underway. The team comprises three groups: AMMRF, ICT at the University of Sydney, and developers at Intersect Australia*. This arrangement has been working quite well, with Intersect looking after the system architecture and system administration of the project, and the University of Sydney teams looking after project management, user requirements, and soon, user acceptance testing.
Atom probe microscopy is an experimental technique that reveals the chemistry and structures of materials at the nanometre (10-9 m) scale. The University of Sydney, via the flagship instruments program of the Australian Microscopy & Microanalysis Research Facility (AMMRF), houses two Local Electrode Atom Probes that are manufactured by Cameca Instruments. These atom probes gather atomic resolution data, which is key to unlocking some of the mysteries of structure-property relationships in materials such as metals and semiconductors. The basic atom probe workflow takes the raw atom probe data, consisting of hundreds of millions of atoms, and transforms it into information that is used to build knowledge of effective material selection, processing and design.
MASSIVE / CVL Launcher drives adoption of the MASSIVE Desktop
A major goal of the developers at the Characterisation Virtual Laboratory (CVL) is to build software infrastructure to make high performance computing more accessible to a wider range of Australian researchers. To achieve this, we’re developing an online desktop environment that can be accessed remotely, providing researchers with a ready-made interactive analysis environment. We expect this will allow scientists to focus on using tools and applying sophisticated analysis techniques, rather than on installing and configuring software or copying data. Users of MASSIVE will know that a version of this environment, the MASSIVE Desktop, is now available and can be accessed easily using a simple Mac, Windows or Linux tool called the MASSIVE Launcher.
One research group that has made good use of the MASSIVE Desktop and Launcher is the Functional Anatomy and Biomechanics Lab (FABLab) at Monash University, who use the desktop to access biomedical segmentation and visualisation software.
A quick introduction to the Characterisation Virtual Laboratory
The “21st century microscope” will not be a single instrument; rather it will be an orchestration of specialised imaging technologies, data storage facilities, and specialised data processing engines. The Characterisation Virtual Laboratory will be a powerful platform essential to the future capability of Australian scientists by integrating Australia’s research imaging facilities with computational and data storage infrastructure and tools.
Australian scientists are increasingly using characterisation technologies that enable: higher spatial resolution and chemical resolution; higher dimensional (>3D) approaches; and examination of rapid dynamic processes. To make effective use of these capabilities, researchers must have easy access to a wide collection of sophisticated processing and analysis tools, packaged and accessible in a recognisable manner, and including research enablers such as standard test data and libraries.