Using linear programming for weights identification of generalized bonferroni means in R

The generalized Bonferroni mean is able to capture some interaction effects between variables and model mandatory requirements. We present a number of weights identification algorithms we have developed in the R programming language in order to model data using the generalized Bonferroni mean subject to various preferences. We then compare its accuracy when fitting to the journal ranks dataset.

J-Circos: an interactive Circos plotter

Circos plots are graphical outputs that display three dimensional chromosomal interactions and fusion transcripts. However, the Circos plot tool is not an interactive visualization tool, but rather a figure generator. For example, it does not enable data to be added dynamically nor does it provide information for specific data points interactively. Recently, an R-based Circos tool (RCircos) has been developed to integrate Circos to R, but similarly, Rcircos can only be used to generate plots. Thus, we have developed a Circos plot tool (J-Circos) that is an interactive visualization tool that can plot Circos figures, as well as being able to dynamically add data to the figure, and providing information for specific data points using mouse hover display and zoom in/out functions. J-Circos uses the Java computer language to enable, it to be used on most operating systems (Windows, MacOS, Linux). Users can input data into J-Circos using flat data formats, as well as from the Graphical user interface (GUI). J-Circos will enable biologists to better study more complex chromosomal interactions and fusion transcripts that are otherwise difficult to visualize from next-generation sequencing data. Availability and implementation: J-circos and its manual are freely available at http://www.australianprostatecentre.org/research/software/jcircos CONTACT: j.an@qut.edu.au Supplementary information: Supplementary data are available at Bioinformatics online.

An improved TIGER2 implementation for NAMD suitable for the Blue Gene architecture

Here we present an improved implementation of the TIGER2 Replica Exchange Molecular Dynamics (REMD) method, using the replica exchange Application Programming Interface (API) found in contemporary versions of the NAMD Molecular Dynamics Package. The implementation takes the form of a TCL script which is used in conjunction with the standard configuration file. This implementation is validated against a previous TIGER2 implementation, as well as data reported for the original TIGER2 simulations. Our implementation is compatible with a range of architectures; crucially it enables the use of this wrapper with the BlueGene/Q architecture, in addition to the x86 architecture. Program summary: Program title: TIGER2-NAMD. Catalogue identifier: AEWC_v1_0. Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEWC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland. Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 34151. No. of bytes in distributed program, including test data, etc.: 424217. Distribution format: tar.gz. Programming language: Tcl 8.5. Computer: x86 Clusters, BlueGene/Q, Workstations. Operating system: Linux, IBM Compute Node Kernel. Has the code been vectorised or parallelised?: Yes. MPI Parallelism. Classification: 3. External routines: NAMD 2.9 (http://www.ks.uiuc.edu/Research/namd/). Nature of problem: Replica Exchange Molecular Dynamics. Solution method: Each replica runs through multiple cycles of heating and cooling with exchanges between them being attempted. Running time: Typically 30 mins, up to an hour.

An experimental study on the failure tolerant control of a redundant planar serial manipulator via pseudo-inverse approach

In this paper, fault-tolerant control of redundant planar serial manipulators has been investigated experimentally via an offline method called psuedo-inverse reconfiguration method. Minimizing the end-effector's velocity jump via an optimal mapping of joint failures into healthy joints velocity space can be regarded as the main contribution of this reconfiguration approach. This algorithm has been simulated and implemented on a four-link serial manipulator named as TaArm. It should be mentioned that for simulation and practical tests, C++ programming language in QtCreator environment has been used which provided high computational speed. Two scenarios has been selected for simulation and implementation studies and results shows that the algorithm considerably removes the velocity jump of the end-effector in both simulation and experimetal studies.

Opportunities and challenges with J2SE 5 for introductory programming teaching

The recent release of the Java version 5.0 "Tiger" introduces some significant language changes. For educators, some of these changes provide opportunities to improve teaching, while others pose additional problems that require awareness to avoid them. The authors have recently completed the inclusion of support for all new language features into a wellknown educational IDE for Java – BlueJ – and in the course of doing so evaluated each of them for usefulness in education, and developed pedagogic strategies to handle the inherent opportunities and challenges. This has formed the basis of the design of the features in BlueJ which support the language changes. In this paper, we describe the results of our evaluation, provide recommendations on treatment of the new features in introductory courses and discuss how BlueJ may be used to illustrate important aspects.

Introductory computer programming as a means for extending spatial and temporal understanding

Should computer programming be taught within schools of architecture?

Incorporating even low-level computer programming within architectural education curricula is a matter of debate but we have found it useful to do so for two reasons: as an introduction or at least a consolidation of the realm of descriptive geometry and in providing an environment for experimenting in morphological time-based change.

Mathematics and descriptive geometry formed a significant proportion of architectural education until the end of the 19th century. This proportion has declined in contemporary curricula, possibly at some cost for despite major advances in automated manufacture, Cartesian measurement is still the principal ‘language’ with which to describe building for construction purposes. When computer programming is used as a platform for instruction in logic and spatial representation, the waning interest in mathematics as a basis for spatial description can be readdressed using a left-field approach. Students gain insights into topology, Cartesian space and morphology through programmatic form finding, as opposed to through direct manipulation.

In this context, it matters to the architect-programmer how the program operates more than what it does. This paper describes an assignment where students are given a figurative conceptual space comprising the three Cartesian axes with a cube at its centre. Six Phileban solids mark the Cartesian axial limits to the space. Any point in this space represents a hybrid of one, two or three transformations from the central cube towards the various Phileban solids. Students are asked to predict the topological and morphological outcomes of the operations. Through programming, they become aware of morphogenesis and hybridisation. Here we articulate the hypothesis above and report on the outcome from a student group, whose work reveals wider learning opportunities for architecture students in computer programming than conventionally assumed.

Experiences in porting a virtual reality system to Java

Practical experience in porting a large virtual reality system from C/C++ to Java indicates that porting this type of real-time application is both feasible, and has several merits. The ability to transfer objects in space and time allows useful facilities such as distributed agent support and persistence to be added. Reflection and type comparisons allow flexible manipulations of objects of different types at run-time. Native calls and native code compilation reduce or remove the overhead of interpreting code.Problems encountered include difficulty in achieving cross-platform code portability, limitations of the networking libraries in Java, and clumsy coding practices forced by the language.