Code interoperability and standard data formats in quantum chemistry and quantum dynamics: The Q5/D5Cost data model.

Code interoperability and the search for domain-specific standard data formats represent critical issues in many areas of computational science. The advent of novel computing infrastructures such as computational grids and clouds make these issues even more urgent. The design and implementation of a common data format for quantum chemistry (QC) and quantum dynamics (QD) computer programs is discussed with reference to the research performed in the course of two Collaboration in Science and Technology Actions. The specific data models adopted, Q5Cost and D5Cost, are shown to work for a number of interoperating codes, regardless of the type and amount of information (small or large datasets) to be exchanged. The codes are either interfaced directly, or transfer data by means of wrappers; both types of data exchange are supported by the Q5/D5Cost library. Further, the exchange of data between QC and QD codes is addressed. As a proof of concept, the H + H2 reaction is discussed. The proposed scheme is shown to provide an excellent basis for cooperative code development, even across domain boundaries. Moreover, the scheme presented is found to be useful also as a production tool in the grid distributed computing environment.

Cooperative modelling and design on the computing grid: data, flux and knowledge interoperability.

The fast interconnections of the presently available distributed platforms allow scientists to target highly complex problems by chaining software developed and maintained by experts of the relevant fields. A pillar of such cooperative endeavor in molecular and materials science and technologies is the so-called grid empowered molecular simulator that combines the expertise of molecular science theorists (electronic structure and nuclei dynamics) and experimentalists in order to build and validate ab initio models. This line has prompted an unprecedented level of data format standardization procedures, the bridging of high throughput and high performance platforms, the assemblage of ad hoc designed virtual experiments. In addition this approach has prompted the design and development of tools allowing the evaluation of the quality of the cooperative effort produced by the members of a given research community as well as its rewards to such effort through a credit economy is reported.

ImmunoGrid: towards agent-based simulations of the human immune system at a natural scale.

The ultimate aim of the EU-funded ImmunoGrid project is to develop a natural-scale model of the human immune system-that is, one that reflects both the diversity and the relative proportions of the molecules and cells that comprise it-together with the grid infrastructure necessary to apply this model to specific applications in the field of immunology. These objectives present the ImmunoGrid Consortium with formidable challenges in terms of complexity of the immune system, our partial understanding about how the immune system works, the lack of reliable data and the scale of computational resources required. In this paper, we explain the key challenges and the approaches adopted to overcome them. We also consider wider implications for the present ambitious plans to develop natural-scale, integrated models of the human body that can make contributions to personalized health care, such as the European Virtual Physiological Human initiative. Finally, we ask a key question: How long will it take us to resolve these challenges and when can we expect to have fully functional models that will deliver health-care benefits in the form of personalized care solutions and improved disease prevention?

Identification of microRNA activity by Targets' Reverse EXpression.

MOTIVATION: Non-coding microRNAs (miRNAs) act as regulators of global protein output. While their major effect is on protein levels of target genes, it has been proven that they also specifically impact on the messenger RNA level of targets. Prominent interest in miRNAs strongly motivates the need for increasing the options available to detect their cellular activity. RESULTS: We used the effect of miRNAs over their targets for the detection of miRNA activity using mRNAs expression profiles. Here we describe the method, called T-REX (from Targets' Reverse EXpression), compare it to other similar applications, show its effectiveness and apply it to build activity maps. We used six different target predictions from each of four algorithms: TargetScan, PicTar, DIANA-microT and DIANA Union. First, we proved the sensitivity and specificity of our technique in miRNA over-expression and knock-out animal models. Then, we used whole transcriptome data from acute myeloid leukemia to show that we could identify critical miRNAs in a real life, complex, clinically relevant dataset. Finally, we studied 66 different cellular conditions to confirm and extend the current knowledge on the role of miRNAs in cellular physiology and in cancer. AVAILABILITY: Software is available at http://aqua.unife.it and is free for all users with no login requirement.

ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization.

Vaccine research is a combinatorial science requiring computational analysis of vaccine components, formulations and optimization. We have developed a framework that combines computational tools for the study of immune function and vaccine development. This framework, named ImmunoGrid combines conceptual models of the immune system, models of antigen processing and presentation, system-level models of the immune system, Grid computing, and database technology to facilitate discovery, formulation and optimization of vaccines. ImmunoGrid modules share common conceptual models and ontologies. The ImmunoGrid portal offers access to educational simulators where previously defined cases can be displayed, and to research simulators that allow the development of new, or tuning of existing, computational models. The portal is accessible at .

ImmunoGrid - the virtual human immune system project.

ImmunoGrid is a 3 year project funded by the European Union which began in February 2006 and establishes an infrastructure for the simulation of the immune system that integrates processes at molecular, cellular and organ levels. It is designed for applications that support clinical outcomes such as the design of vaccines, immunotherapies and optimization of immunization protocols. The first phase of the project concentrated on improving and extending current models of the immune system. We are now entering the second phase which will design and implement a human immune system simulator. Since the new models are orders of magnitude more complex than the previous ones, grid technologies will be essential in providing the necessary computer infrastructure. The final phase of the project will validate the simulator with pre-clinical trials using mouse models.

The Effect of the Basis-Set Superposition Error on the Calculation of Dispersion Interactions: A Test Study on the Neon Dimer.

The dispersion interactions of the Ne2 dimer were studied using both the long-range perturbative and supramolecular approaches: for the long-range approach, full CI or string-truncated CI methods were used, while for the supramolecular treatments, the energy curves were computed by using configuration interaction with single and double excitation (CISD), coupled cluster with single and double excitation, and coupled-cluster with single and double (and perturbative) triple excitations. From the interatomic potential-energy curves obtained by the supramolecular approach, the C6 and C8 dispersion coefficients were computed via an interpolation scheme, and they were compared with the corresponding values obtained within the long-range perturbative treatment. We found that the lack of size consistency of the CISD approach makes this method completely useless to compute dispersion coefficients even when the effect of the basis-set superposition error on the dimer curves is considered. The largest full-CI space we were able to use contains more than 1 billion symmetry-adapted Slater determinants, and it is, to our knowledge, the largest calculation of second-order properties ever done at the full-CI level so far. Finally, a new data format and libraries (Q5Cost) have been used in order to interface different codes used in the present study.