Reactive Programming of Simulations in Physics

We consider the Reactive Programming (RP) approach to simulate physical systems. The choice of RP is motivated by the fact that RP genuinely offers logical parallelism, instantaneously broadcast events, and dynamic creation/destruction of parallel components and events. To illustrate our approach, we consider the implementation of a system of Molecular Dynamics, in the context of Java with the Java3D library for 3D visualisation

Agents for educational games and simulations

This book consists mainly of revised papers that were presented at the Agents for Educational Games and Simulation (AEGS) workshop held on May 2, 2011, as part of the Autonomous Agents and MultiAgent Systems (AAMAS) conference in Taipei, Taiwan. The 12 full papers presented were carefully reviewed and selected from various submissions. The papers are organized topical sections on middleware applications, dialogues and learning, adaption and convergence, and agent applications

Chemical Informatics Functionality in R

The flexibility and scope of the R programming environment has made it a popular choice for statistical modeling and scientific prototyping in a number of fields. In the field of chemistry, R provides several tools for a variety of problems related to statistical modeling of chemical information. However, one aspect common to these tools is that they do not have direct access to the information that is available from chemical structures, such as contained in molecular descriptors. We describe the rcdk package that provides the R user with access to the CDK, a Java framework for cheminformatics. As a result, it is possible to read in a variety of molecular formats, calculate molecular descriptors and evaluate fingerprints. In addition, we describe the rpubchem that will allow access to the data in PubChem, a public repository of molecular structures and associated assay data for approximately 8 million compounds. Currently, the package allows access to structural information as well as some simple molecular properties from PubChem. In addition the package allows access to bio-assay data from the PubChem FTP servers.

CREOLE: a Universal Language for Creating, Requesting, Updating and Deleting Resources

In the context of Service-Oriented Computing, applications can be developed following the REST (Representation State Transfer) architectural style. This style corresponds to a resource-oriented model, where resources are manipulated via CRUD (Create, Request, Update, Delete) interfaces. The diversity of CRUD languages due to the absence of a standard leads to composition problems related to adaptation, integration and coordination of services. To overcome these problems, we propose a pivot architecture built around a universal language to manipulate resources, called CREOLE, a CRUD Language for Resource Edition. In this architecture, scripts written in existing CRUD languages, like SQL, are compiled into Creole and then executed over different CRUD interfaces. After stating the requirements for a universal language for manipulating resources, we formally describe the language and informally motivate its definition with respect to the requirements. We then concretely show how the architecture solves adaptation, integration and coordination problems in the case of photo management in Flickr and Picasa, two well-known service-oriented applications. Finally, we propose a roadmap for future work.Comment: In Proceedings FOCLASA 2010, arXiv:1007.499

Grid service orchestration using the Business Process Execution Language (BPEL)

Modern scientific applications often need to be distributed across grids. Increasingly applications rely on services, such as job submission, data transfer or data portal services. We refer to such services as grid services. While the invocation of grid services could be hard coded in theory, scientific users want to orchestrate service invocations more flexibly. In enterprise applications, the orchestration of web services is achieved using emerging orchestration standards, most notably the Business Process Execution Language (BPEL). We describe our experience in orchestrating scientific workflows using BPEL. We have gained this experience during an extensive case study that orchestrates grid services for the automation of a polymorph prediction application

Evaluating the Relationship Between Running Times and DNA Sequence Sizes using a Generic-Based Filtering Program.

Generic programming depends on the decomposition of programs into simpler components which may be developed separately and combined arbitrarily, subject only to well- defined interfaces. Bioinformatics deals with the application of computational techniques to data present in the Biological sciences. A genetic sequence is a succession of letters which represents the basic structure of a hypothetical DNA molecule, with the capacity to carry information. This research article studied the relationship between the running times of a generic-based filtering program and different samples of genetic sequences in an increasing order of magnitude. A graphical result was obtained to adequately depict this relationship. It was also discovered that the complexity of the generic tree program was O (log2 N). This research article provided one of the systematic approaches of generic programming to Bioinformatics, which could be instrumental in elucidating major discoveries in Bioinformatics, as regards efficient data management and analysis

COEL: A Web-based Chemistry Simulation Framework

The chemical reaction network (CRN) is a widely used formalism to describe macroscopic behavior of chemical systems. Available tools for CRN modelling and simulation require local access, installation, and often involve local file storage, which is susceptible to loss, lacks searchable structure, and does not support concurrency. Furthermore, simulations are often single-threaded, and user interfaces are non-trivial to use. Therefore there are significant hurdles to conducting efficient and collaborative chemical research. In this paper, we introduce a new enterprise chemistry simulation framework, COEL, which addresses these issues. COEL is the first web-based framework of its kind. A visually pleasing and intuitive user interface, simulations that run on a large computational grid, reliable database storage, and transactional services make COEL ideal for collaborative research and education. COEL's most prominent features include ODE-based simulations of chemical reaction networks and multicompartment reaction networks, with rich options for user interactions with those networks. COEL provides DNA-strand displacement transformations and visualization (and is to our knowledge the first CRN framework to do so), GA optimization of rate constants, expression validation, an application-wide plotting engine, and SBML/Octave/Matlab export. We also present an overview of the underlying software and technologies employed and describe the main architectural decisions driving our development. COEL is available at http://coel-sim.org for selected research teams only. We plan to provide a part of COEL's functionality to the general public in the near future.Comment: 23 pages, 12 figures, 1 tabl

chemf : a purely functional chemistry toolkit

Background: Although programming in a type-safe and referentially transparent style offers several advantages over working with mutable data structures and side effects, this style of programming has not seen much use in chemistry-related software. Since functional programming languages were designed with referential transparency in mind, these languages offer a lot of support when writing immutable data structures and side-effects free code. We therefore started implementing our own toolkit based on the above programming paradigms in a modern, versatile programming language. Results: We present our initial results with functional programming in chemistry by first describing an immutable data structure for molecular graphs together with a couple of simple algorithms to calculate basic molecular properties before writing a complete SMILES parser in accordance with the OpenSMILES specification. Along the way we show how to deal with input validation, error handling, bulk operations, and parallelization in a purely functional way. At the end we also analyze and improve our algorithms and data structures in terms of performance and compare it to existing toolkits both object-oriented and purely functional. All code was written in Scala, a modern multi-paradigm programming language with a strong support for functional programming and a highly sophisticated type system. Conclusions: We have successfully made the first important steps towards a purely functional chemistry toolkit. The data structures and algorithms presented in this article perform well while at the same time they can be safely used in parallelized applications, such as computer aided drug design experiments, without further adjustments. This stands in contrast to existing object-oriented toolkits where thread safety of data structures and algorithms is a deliberate design decision that can be hard to implement. Finally, the level of type-safety achieved by Scala highly increased the reliability of our code as well as the productivity of the programmers involved in this project