Alfredo Tirado-Ramos

From molecule to man: Decision support in individualized E-health

Computer science provides the language needed to study and understand complex multiscale, multiscience systems. ViroLab, a grid-based decision-support system, demonstrates how researchers can now study diseases from the DNA level all the way up to medical responses to treatment

Grid Services for HLA-Based Distributed Simulation Frameworks

Problem Solving Environments offer an integrating approach for constructing and running complex systems and components, such as distributed simulation and decision support systems. New distributed infrastructures like the Grid support the access to a large variety of core services and resources in a secure environment. In this paper we propose an approach to Grid access for interactive Problem Solving Environments built on top of the High Level Architecture (HLA), a mature distributed simulation framework. This approach is based on a set of Grid Services which allow the setup and interactive steering of complex Grid applications consisting of modules for simulation and visualization. We discuss a three-level approach to the problem. In the first step we focus on discovery of HLA Runtime Infrastructure (RTI) processes that coordinate distributed components of an interactive application. Next we investigate efficient Grid-based data transfer protocols as a promising alternative for current RTI communication. Finally, we will completely replace RTI by Grid technology mechanisms. As a proof-of-concept example, we use the CrossGrid biomedical simulation application, which requires near real time steering of simulation parameters during runtime of the simulation running on the Grid.

Virtual Laboratory for Development and Execution of Biomedical Collaborative Applications

The ViroLab Virtual Laboratory is a collaborative platform for scientists representing multiple fields of expertise while working together on common scientific goals. This environment makes it possible to combine efforts of computer scientists, virology and epidemiology experts and experienced physicians to support future advances in HIV-related research and treatment. The paper explains the challenges involved in building a modern, inter-organizational platform to support science and gives an overview of solutions to these challenges. Examples of real-world problems applied in the presented environment are also described to prove the feasibility of the solution.

Performance analysis of direct N-body algorithms for astrophysical simulations on distributed systems

We discuss the performance of direct summation codes used in the simulation of astrophysical stellar systems on highly distributed architectures. These codes compute the gravitational interaction among stars in an exact way and have an O(N^2) scaling with the number of particles. They can be applied to a variety of astrophysical problems, like the evolution of star clusters, the dynamics of black holes, the formation of planetary systems, and cosmological simulations. The simulation of realistic star clusters with sufficiently high accuracy cannot be performed on a single workstation but may be possible on parallel computers or grids. We have implemented two parallel schemes for a direct N-body code and we study their performance on general purpose parallel computers and large computational grids. We present the results of timing analyzes conducted on the different architectures and compare them with the predictions from theoretical models. We conclude that the simulation of star clusters with up to a million particles will be possible on large distributed computers in the next decade. Simulating entire galaxies however will in addition require new hybrid methods to speedup the calculation.

Automatic composition and selection of semantic web services

Interactive applications like Problem Solving Environments require on demand access to Web Services, where the services are autonomously discovered, composed, selected and invocated based on a description of requested capabilities. Semantic Web Services aim at providing semantically interpretable capabilities through the use of shared ontologies. We demonstrate how Grid Services for an interactive biomedical application are annotated with a domain ontology, and propose algorithms for automated composition and selection of workflows, where workflows are created by semantically matching service capabilities, and where workflow selection is based on a trade-off between the types of semantic matches in the workflow and the number of services. The algorithms are demonstrated on semantically annotated Grid Services in the biomedical application.

Information object definition-based unified modeling language representation of DICOM structured reporting: a case study of transcoding DICOM to XML.

Supplement 23 to DICOM (Digital Imaging and Communications for Medicine), Structured Reporting, is a specification that supports a semantically rich representation of image and waveform content, enabling experts to share image and related patient information. DICOM SR supports the representation of textual and coded data linked to images and waveforms. Nevertheless, the medical information technology community needs models that work as bridges between the DICOM relational model and open object-oriented technologies. The authors assert that representations of the DICOM Structured Reporting standard, using object-oriented modeling languages such as the Unified Modeling Language, can provide a high-level reference view of the semantically rich framework of DICOM and its complex structures. They have produced an object-oriented model to represent the DICOM SR standard and have derived XML-exchangeable representations of this model using World Wide Web Consortium specifications. They expect the model to benefit developers and system architects who are interested in developing applications that are compliant with the DICOM SR specification.

An integrative approach to high-performance biomedical problem solving environments on the Grid

We conduct computer simulation experiments in pre-operative planning of vascular reconstruction with a physician in the experimental loop. We constructed a problem solving environment, which offers an integrative approach for constructing and running complex interactive systems. Grid resources are used for access to medical image repositories, segmentation services, simulation of blood flow, and visualization in virtual environments of the simulated results together with medical data obtained from MRI/CT scanners. This case study in vascular reconstruction planning has been validated via contextual analysis in a number of hospitals, resulting in a set of new requirements gathered for future versions of the system.

Multiplexed highly-accurate DNA sequencing of closely-related HIV-1 variants using continuous long reads from single molecule, real-time sequencing

Single Molecule, Real-Time (SMRT®) Sequencing (Pacific Biosciences, Menlo Park, CA, USA) provides the longest continuous DNA sequencing reads currently available. However, the relatively high error rate in the raw read data requires novel analysis methods to deconvolute sequences derived from complex samples. Here, we present a workflow of novel computer algorithms able to reconstruct viral variant genomes present in mixtures with an accuracy of >QV50. This approach relies exclusively on Continuous Long Reads (CLR), which are the raw reads generated during SMRT Sequencing. We successfully implement this workflow for simultaneous sequencing of mixtures containing up to forty different >9 kb HIV-1 full genomes. This was achieved using a single SMRT Cell for each mixture and desktop computing power. This novel approach opens the possibility of solving complex sequencing tasks that currently lack a solution.

Grid Resource Allocation by Means of Option Contracts

In Grid environments, where virtual organization resources are allocated to users using mechanisms analogue to market economies, strong price fluctuations can have an impact on the nontrivial quality-of-service expected by end users. In this paper, we investigate the effects of the use of option contracts on the quality of service offered by a broker-based Grid resource allocation model. Option contracts offer users the possibility to buy or sell Grid resources in the future for a strike price specified in a contract. By buying, borrowing and selling option contracts using a hedge strategy users can benefit from expected price changes. In this paper, we consider three hedge strategies: the butterfly spread which profits from small changes, the straddle which benefits from large price changes, and the call strategy which benefits from soaring prices. Using our model based on an abstract Grid architecture, we find that the use of hedge strategies augment the ratio of successfully finished jobs to failed jobs. We show that the degree of successfulness from hedge strategies changes when the number of contributed resources changes. By means of a model, we also show that the effects of the butterfly spread is mainly explained by the amount of contributed resources. The dynamics of the two other hedge strategies are best explained by observing the price behavior. We also find that by using hedge strategies the users can increase the probability that a job will finish before the deadline. We conclude that hedging using options is a promising approach to improve resource allocation in environments where resources are allocated by using a commodity market mechanism.

Integration of Blood Flow Visualization on the Grid: The FlowFish/GVK Approach

We have developed the FlowFish package for blood flow visualization of vascular disorder simulations, such as aneurysms and stenosis. We use a Lattice-Boltzmann solver for flow process simulation to test the efficiency of the visualization classes, and experiment with the combination of grid applications and corresponding visualization clients on the European Crossgrid testbed, to assess grid accessability and visualization data transfer performance.