JIDT: An information-theoretic toolkit for studying the dynamics of complex systems

Complex systems are increasingly being viewed as distributed information processing systems, particularly in the domains of computational neuroscience, bioinformatics and Artificial Life. This trend has resulted in a strong uptake in the use of (Shannon) information-theoretic measures to analyse the dynamics of complex systems in these fields. We introduce the Java Information Dynamics Toolkit (JIDT): a Google code project which provides a standalone, (GNU GPL v3 licensed) open-source code implementation for empirical estimation of information-theoretic measures from time-series data. While the toolkit provides classic information-theoretic measures (e.g. entropy, mutual information, conditional mutual information), it ultimately focusses on implementing higher-level measures for information dynamics. That is, JIDT focusses on quantifying information storage, transfer and modification, and the dynamics of these operations in space and time. For this purpose, it includes implementations of the transfer entropy and active information storage, their multivariate extensions and local or pointwise variants. JIDT provides implementations for both discrete and continuous-valued data for each measure, including various types of estimator for continuous data (e.g. Gaussian, box-kernel and Kraskov-Stoegbauer-Grassberger) which can be swapped at run-time due to Java's object-oriented polymorphism. Furthermore, while written in Java, the toolkit can be used directly in MATLAB, GNU Octave, Python and other environments. We present the principles behind the code design, and provide several examples to guide users.Comment: 37 pages, 4 figure

Let's Annotate to Let Our Code Run in Parallel

This paper presents an approach that exploits Java annotations to provide meta information needed to automatically transform plain Java programs into parallel code that can be run on multicore workstation. Programmers just need to decorate the methods that will eventually be executed in parallel with standard Java annotations. Annotations are automatically processed at launch-time and parallel byte code is derived. Once in execution the program automatically retrieves the information about the executing platform and evaluates the information specified inside the annotations to transform the byte-code into a semantically equivalent multithreaded version, depending on the target architecture features. The results returned by the annotated methods, when invoked, are futures with a wait-by-necessity semantics.Comment: 4 pages, 1 figur

Implementing the Gaia Astrometric Global Iterative Solution (AGIS) in Java

This paper provides a description of the Java software framework which has been constructed to run the Astrometric Global Iterative Solution for the Gaia mission. This is the mathematical framework to provide the rigid reference frame for Gaia observations from the Gaia data itself. This process makes Gaia a self calibrated, and input catalogue independent, mission. The framework is highly distributed typically running on a cluster of machines with a database back end. All code is written in the Java language. We describe the overall architecture and some of the details of the implementation.Comment: Accepted for Experimental Astronom

The Java system dependence graph

The Program Dependence Graph was introduced by Ottenstein and Ottenstein in 1984 [14]. It was suggested to be a suitable internal program representation for monolithic programs, for the purpose of carrying out certain software engineering operations such as slicing and the computation of program metrics. Since then, Horwitz et al. have introduced the multi-procedural equivalent System Dependence Graph [9]. Many authors have proposed object-oriented dependence graph construction approaches [11, 10, 20, 12]. Every approach provides its own benefits, some of which are language specific. This paper is based on Java and combines the most important benefits from a range of approaches. The result is a Java System Dependence Graph, which summarises the key benefits offered by different approaches and adapts them (if necessary) to the Java language

Towards an aspect weaving BPEL engine

This position paper proposes the use of dynamic aspects and the visitor design pattern to obtain a highly configurable and extensible BPEL engine. Using these two techniques, the core of this infrastructural software can be customised to meet new requirements and add features such as debugging, execution monitoring, or changing to another Web Service selection policy. Additionally, it can easily be extended to cope with customer-specific BPEL extensions. We propose the use of dynamic aspects not only on the engine itself but also on the workflow in order to tackle the problems of Web Service hot deployment and hot fixes to long running processes. In this way, composing aWeb Service "on-the-fly" means weaving its choreography interface into the workflow

Transparent Replication Using Metaprogramming in Cyan

Replication can be used to increase the availability of a service by creating many operational copies of its data called replicas. Active replication is a form of replication that has strong consistency semantics, easier to reason about and program. However, creating replicated services using active replication still demands from the programmer the knowledge of subtleties of the replication mechanism. In this paper we show how to use the metaprogramming infrastructure of the Cyan language to shield the application programmer from these details, allowing easier creation of fault-tolerant replicated applications through simple annotations.Comment: 8 page

Using Java for distributed computing in the Gaia satellite data processing

In recent years Java has matured to a stable easy-to-use language with the flexibility of an interpreter (for reflection etc.) but the performance and type checking of a compiled language. When we started using Java for astronomical applications around 1999 they were the first of their kind in astronomy. Now a great deal of astronomy software is written in Java as are many business applications. We discuss the current environment and trends concerning the language and present an actual example of scientific use of Java for high-performance distributed computing: ESA's mission Gaia. The Gaia scanning satellite will perform a galactic census of about 1000 million objects in our galaxy. The Gaia community has chosen to write its processing software in Java. We explore the manifold reasons for choosing Java for this large science collaboration. Gaia processing is numerically complex but highly distributable, some parts being embarrassingly parallel. We describe the Gaia processing architecture and its realisation in Java. We delve into the astrometric solution which is the most advanced and most complex part of the processing. The Gaia simulator is also written in Java and is the most mature code in the system. This has been successfully running since about 2005 on the supercomputer "Marenostrum" in Barcelona. We relate experiences of using Java on a large shared machine. Finally we discuss Java, including some of its problems, for scientific computing.Comment: Experimental Astronomy, August 201