Collaborative working - from HPC, Vis to AG developments in Australia

The large distances that we face in Australia mean that electronically enabled remote collaborations are gaining traction. The Access Grid (AG), for multi-site, room-to-room meetings and collaborative working, is now widely used in the university sector. Decades of R&D and infrastructure building in High Performance Computing (HPC), cyber-infrastructure and now e-infrastructure, have led to a rich fabric of distributed computing, data and user interface technologies in Australia. We will present recent AG developments including shared files systems based on the Storage Resource Broker (SRB), shared software applications (eg molecular viewers, GIS) and High Definition Video capabilities, all integrated within the AG systems. These systems now provide a richer collaborative working environment for accessing e-infrastructure facilities

The Effect of Connectivity, Proximity and Market Structure on R&D Networks

In a seminal paper, Goyal and Moraga-Gonzalez (2001) use an undirected network to characterize knowledge flows between firms engaging in research in an oligopolistic market. In their paper, firms are regarded as inhabiting a research joint venture (RJV), if they share the same edge of the network. These firms are allowed an R&D spillover of 1; the outside firms (firms not sharing an edge in the network) are permitted a constant knowledge spillover that is less than one. We begin our paper by showing that this last assumption has important consequences when dealing with R&D networks of size greater than or equal to six firms. We present examples of topologically non-equivalent networks that have the same degree of connectivity and generate identical outcomes in terms of R&D effort, firm profits and total welfare. We then modify their model so that R&D spillovers decrease as the number of shortest paths increases between any two firms. We show that under product differentiated Cournot and Bertrand competition, we have different outcomes for all economic variables. We also show that R&D effort increases with respect to the number of collaborative links if firms are in a weakly competitive market, whereas it declines if firms are in a more competitive market where products are closer substitutes. We also find that in more competitive markets there is a conflict between the stability and the efficiency of RJVs.

Automatic particle picking algorithms for high resolution single particle analysis

As new genome sequencing initiatives are completed, one of the next great challenges of cell biology is the atomic resolution structure determination of the enormous number of proteins they encode. Single particle analysis is a technique which produces 3D structures by computationally aligning high resolution electron microscope images of individual, randomly oriented molecules. One of the limiting factors in producing a high resolution 3D reconstruction is obtaining a large enough representative dataset (~100,000 particles). Traditionally particles have been picked manually but this is a slow and labour intensive process. This paper describes two automatic particle picking algorithms, based on correlation and edge detection, which have been shown to be capable of quickly selecting a large number of particles in micrographs. Currently circular and rectangular particles are able to be picked

Network Analysis and Visualization of Mouse Retina Connectivity Data

<div><p>The largest available cellular level connectivity map, of a 0.1 mm sample of the mouse retina Inner Plexiform Layer, was analysed using network models and visualized using spectral graph layouts and observed cell coordinates. This allows key nodes in the network to be identified with retinal neurons. Their strongest synaptic links can trace pathways in the network, elucidating possible circuits. Modular decomposition of the network, by sampling signal flows over nodes and links using the InfoMap method, shows discrete modules of cone bipolar cells that form a tiled mosaic in the retinal plane. The highest flow nodes, calculated by InfoMap, proved to be the most useful landmarks for elucidating possible circuits. Their dominant links to high flow amacrine cells reveal possible circuits linking bipolar through to ganglion cells and show an Off-On discrimination between the Left-Right sections of the sample. Circuits suggested by this analysis confirm known roles for some cells and point to roles for others.</p></div

Layout of high signal flow SAC.

<p>3D plot of SAC-Off and SAC-On cells, along with their highest weight (>10) links to all other neurons. Cell positions (in x-y plane), were calculated from the centroid of the soma in the EM photos [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158626#pone.0158626.ref002" target="_blank">2</a>]. Layers in the EM plane are schematic, estimated from the EM photos and standard texts [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158626#pone.0158626.ref013" target="_blank">13</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158626#pone.0158626.ref014" target="_blank">14</a>]. Scale bar, 10 μm. Module membership is color coded as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158626#pone.0158626.g001" target="_blank">Fig 1</a>.</p

High resolution tiled display walls

Scalable high-resolution tiled display walls are becoming increasingly important to decision makers and researchers because high pixel counts in combination with large screen areas facilitate content rich, simultaneous display of computer-generated visualization information and high-definition video data from multiple sources. This tutorial is designed to cater for new users as well as researchers who are currently operating tiled display walls or 'OptiPortals'. We will discuss the current and future applications of display wall technology and explore opportunities for participants to collaborate and contribute in a growing community. Multiple tutorial streams will cover both hands-on practical development, as well as policy and method design for embedding these technologies into the research process. Attendees will be able to gain an understanding of how to get started with developing similar systems themselves, in addition to becoming familiar with typical applications and large-scale visualisation techniques. Presentations in this tutorial will describe current implementations of tiled display walls that highlight the effective usage of screen real-estate with various visualization datasets, including collaborative applications such as visualcasting, classroom learning and video conferencing. A feature presentation for this tutorial will be given by Jurgen Schulze from Calit2 at the University of California, San Diego. Jurgen is an expert in scientific visualization in virtual environments, human-computer interaction, real-time volume rendering, and graphics algorithms on programmable graphics hardware

Layout of high signal flow amacrine cells.

<p>3D plot of the top 10 amacrine cells, along with their highest weight (>10) links to all other neurons. Cell position (in y, z axes), were calculated from the centroid of the soma as revealed in EM photos [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158626#pone.0158626.ref002" target="_blank">2</a>]. Layers estimated as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158626#pone.0158626.g002" target="_blank">Fig 2</a>. Scale bar, 10 μm. Modules colored as in Figs <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158626#pone.0158626.g001" target="_blank">1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158626#pone.0158626.g002" target="_blank">2</a>.</p

2D layout of cone BC modules in the mouse retina sample.

<p>EM coordinates in the 2D retinal plane of key cone BCs coloured by their module membership, along with the convex hull enscribing members of each module. The centroid location of each module is marked (+).</p