Software

About: Software is a research topic. Over the lifetime, 130577 publications have been published within this topic receiving 2028987 citations. The topic is also known as: computer software & computational tool.

A high-level 3D visualization API for Java and ImageJ

Abstract: Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set. Here we present a platform-independent framework based on Java and Java 3D for accelerated rendering of biological images. Our framework is seamlessly integrated into ImageJ, a free image processing package with a vast collection of community-developed biological image analysis tools. Our framework enriches the ImageJ software libraries with methods that greatly reduce the complexity of developing image analysis tools in an interactive 3D visualization environment. In particular, we provide high-level access to volume rendering, volume editing, surface extraction, and image annotation. The ability to rely on a library that removes the low-level details enables concentrating software development efforts on the algorithm implementation parts. Our framework enables biomedical image software development to be built with 3D visualization capabilities with very little effort. We offer the source code and convenient binary packages along with extensive documentation at http://3dviewer.neurofly.de .

The Analysis of Gene Expression Data: Methods and Software

Abstract: This book presents practical approaches for the analysis of data from gene expression micro-arrays. It describes the conceptual and methodological underpinning for a statistical tool and its implementation in software. The book includes coverage of various packages that are part of the Bioconductor project and several related R tools. The materials presented cover a range of software tools designed for varied audiences.

The ALPS project release 2.0: open source software for strongly correlated systems

Abstract: We present release 2.0 of the ALPS (Algorithms and Libraries for Physics Simulations) project, an open source software project to develop libraries and application programs for the simulation of strongly correlated quantum lattice models such as quantum magnets, lattice bosons, and strongly correlated fermion systems. The code development is centered on common XML and HDF5 data formats, libraries to simplify and speed up code development, common evaluation and plotting tools, and simulation programs. The programs enable non-experts to start carrying out serial or parallel numerical simulations by providing basic implementations of the important algorithms for quantum lattice models: classical and quantum Monte Carlo (QMC) using non-local updates, extended ensemble simulations, exact and full diagonalization (ED), the density matrix renormalization group (DMRG) both in a static version and a dynamic time-evolving block decimation (TEBD) code, and quantum Monte Carlo solvers for dynamical mean field theory (DMFT). The ALPS libraries provide a powerful framework for programmers to develop their own applications, which, for instance, greatly simplify the steps of porting a serial code onto a parallel, distributed memory machine. Major changes in release 2.0 include the use of HDF5 for binary data, evaluation tools in Python, support for the Windows operating system, the use of CMake as build system and binary installation packages for Mac OS X and Windows, and integration with the VisTrails workflow provenance tool. The software is available from our web server at http://alps.comp-phys.org/.

On the automatic modularization of software systems using the Bunch tool

Abstract: Since modern software systems are large and complex, appropriate abstractions of their structure are needed to make them more understandable and, thus, easier to maintain. Software clustering techniques are useful to support the creation of these abstractions by producing architectural-level views of a system's structure directly from its source code. This paper examines the Bunch clustering system which, unlike other software clustering tools, uses search techniques to perform clustering. Bunch produces a subsystem decomposition by partitioning a graph of the entities (e.g., classes) and relations (e.g., function calls) in the source code. Bunch uses a fitness function to evaluate the quality of graph partitions and uses search algorithms to find a satisfactory solution. This paper presents a case study to demonstrate how Bunch can be used to create views of the structure of significant software systems. This paper also outlines research to evaluate the software clustering results produced by Bunch.

An information retrieval approach for automatically constructing software libraries

Abstract: A technology for automatically assembling large software libraries which promote software reuse by helping the user locate the components closest to her/his needs is described. Software libraries are automatically assembled from a set of unorganized components by using information retrieval techniques. The construction of the library is done in two steps. First, attributes are automatically extracted from natural language documentation by using an indexing scheme based on the notions of lexical affinities and quantity of information. Then a hierarchy for browsing is automatically generated using a clustering technique which draws only on the information provided by the attributes. Due to the free-text indexing scheme, tools following this approach can accept free-style natural language queries. >