Showing papers on "Software published in 2012"

Fiji: an open-source platform for biological-image analysis

Abstract: Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

WinGX and ORTEP for Windows: an update

Abstract: The WinGX suite provides a complete set of programs for the treatment of small-molecule single-crystal diffraction data, from data reduction and processing, structure solution, model refinement and visualization, and metric analysis of molecular geometry and crystal packing, to final report preparation in the form of a CIF. It includes several well known pieces of software and provides a repository for programs when the original authors no longer wish to, or are unable to, maintain them. It also provides menu items to execute external software, such as the SIR and SHELX suites of programs. The program ORTEP for Windows provides a graphical user interface (GUI) for the classic ORTEP program, which is the original software for the illustration of anisotropic displacement ellipsoids. The GUI code provides input capabilities for a wide variety of file formats, and extra functionality such as geometry calculations and ray-traced outputs. The programs WinGX and ORTEP for Windows have been distributed over the internet for about 15 years, and this article describes some of the more modern features of the programs.

Gwyddion: an open-source software for SPM data analysis

Abstract: In this article, we review special features of Gwyddion—a modular, multiplatform, open-source software for scanning probe microscopy data processing, which is available at http://gwyddion.net/. We describe its architecture with emphasis on modularity and easy integration of the provided algorithms into other software. Special functionalities, such as data processing from non-rectangular areas, grain and particle analysis, and metrology support are discussed as well. It is shown that on the basis of open-source software development, a fully functional software package can be created that covers the needs of a large part of the scanning probe microscopy user community.

New development in freefem

Abstract: This is a short presentation of the freefem++ software. In Section 1, we recall most of the characteristics of the software, In Section 2, we recall how to to build the weak form of a partial differential equation (PDE) from the strong form. In the 3 last sections, we present different examples and tools to illustrated the power of the software. First we deal with mesh adaptation for problems in two and three dimension, second, we solve numerically a problem with phase change and natural convection, and the finally to show the possibilities for HPC we solve a Laplace equation by a Schwarz domain decomposition problem on parallel computer.

SciMAT : A new science mapping analysis software tool

Abstract: This article presents a new open-source software tool, SciMAT, which performs science mapping analysis within a longitudinal framework. It provides different modules that help the analyst to carry out all the steps of the science mapping workflow. In addition, SciMAT presents three key features that are remarkable in respect to other science mapping software tools: (a) a powerful preprocessing module to clean the raw bibliographical data, (b) the use of bibliometric measures to study the impact of each studied element, and (c) a wizard to configure the analysis. © 2012 Wiley Periodicals, Inc.

Meta-analyses and Forest plots using a microsoft excel spreadsheet: step-by-step guide focusing on descriptive data analysis

Abstract: Meta-analyses are necessary to synthesize data obtained from primary research, and in many situations reviews of observational studies are the only available alternative. General purpose statistical packages can meta-analyze data, but usually require external macros or coding. Commercial specialist software is available, but may be expensive and focused in a particular type of primary data. Most available softwares have limitations in dealing with descriptive data, and the graphical display of summary statistics such as incidence and prevalence is unsatisfactory. Analyses can be conducted using Microsoft Excel, but there was no previous guide available. We constructed a step-by-step guide to perform a meta-analysis in a Microsoft Excel spreadsheet, using either fixed-effect or random-effects models. We have also developed a second spreadsheet capable of producing customized forest plots. It is possible to conduct a meta-analysis using only Microsoft Excel. More important, to our knowledge this is the first description of a method for producing a statistically adequate but graphically appealing forest plot summarizing descriptive data, using widely available software.

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

Abstract: Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software.

PDFgetX3: A rapid and highly automatable program for processing powder diffraction data into total scattering pair distribution functions

Abstract: PDFgetX3 is a new software application for converting X-ray powder diffraction data to atomic pair distribution function (PDF). PDFgetX3 has been designed for ease of use, speed and automated operation. The software can readily process hundreds of X-ray patterns within few seconds and is thus useful for high-throughput PDF studies, that measure numerous datasets as a function of time, temperature or other environment parameters. In comparison to the preceding programs, PDFgetX3 requires fewer inputs, less user experience and can be readily adopted by novice users. The live-plotting interactive feature allows to assess the effects of calculation parameters and select their optimum values. PDFgetX3 uses an ad-hoc data correction method, where the slowly-changing structure independent signal is filtered out to obtain coherent X-ray intensities that contain structure information. The outputs from PDFgetX3 have been verified by processing experimental PDFs from inorganic, organic and nanosized samples and comparing them to their counterparts from previous established software. In spite of different algorithm, the obtained PDFs were nearly identical and yielded highly similar results when used in structure refinement. PDFgetX3 is written in Python language and features well documented, reusable codebase. The software can be used either as standalone application or as a library of PDF-processing functions that can be called on from other Python scripts. The software is free for open academic research, but requires paid license for commercial use.

System and method for a cloud computing abstraction layer with security zone facilities

Abstract: In embodiments of the present invention improved capabilities are described for a virtualization environment adapted for development and deployment of at least one software workload, the virtualization environment having a metamodel framework that allows the association of a policy to the software workload upon development of the workload that is applied upon deployment of the software workload. This allows a developer to define a security zone and to apply at least one type of security policy with respect to the security zone including the type of security zone policy in the metamodel framework such that the type of security zone policy can be associated with the software workload upon development of the software workload, and if the type of security zone policy is associated with the software workload, automatically applying the security policy to the software workload when the software workload is deployed within the security zone.

FLEXBAR—Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms

Abstract: Quantitative and systems biology approaches benefit from the unprecedented depth of next-generation sequencing. A typical experiment yields millions of short reads, which oftentimes carry particular sequence tags. These tags may be: (a) specific to the sequencing platform and library construction method (e.g., adapter sequences); (b) have been introduced by experimental design (e.g., sample barcodes); or (c) constitute some biological signal (e.g., splice leader sequences in nematodes). Our software FLEXBAR enables accurate recognition, sorting and trimming of sequence tags with maximal flexibility, based on exact overlap sequence alignment. The software supports data formats from all current sequencing platforms, including color-space reads. FLEXBAR maintains read pairings and processes separate barcode reads on demand. Our software facilitates the fine-grained adjustment of sequence tag detection parameters and search regions. FLEXBAR is a multi-threaded software and combines speed with precision. Even complex read processing scenarios might be executed with a single command line call. We demonstrate the utility of the software in terms of read mapping applications, library demultiplexing and splice leader detection. FLEXBAR and additional information is available for academic use from the website: http://sourceforge.net/projects/flexbar/.

Building Research Equipment with Free, Open-Source Hardware

Abstract: Most experimental research projects are executed with a combination of purchased hardware equipment, which may be modified in the laboratory and custom single-built equipment fabricated inhouse. However, the computer software that helps design and execute experiments and analyze data has an additional source: It can also be free and open-source software (FOSS) ( 1 ). FOSS has the advantage that the code is openly available for modification and is also often free of charge. In the past, customizing software has been much easier than custom-building equipment, which often can be quite costly because fabrication requires the skills of machinists, glassblowers, technicians, or outside suppliers. However, the open-source paradigm is now enabling creation of open-source scientific hardware by combining three-dimensional (3D) printing with open-source microcontrollers running on FOSS. These developments are illustrated below by several examples of equipment fabrication that can better meet particular specifications at substantially lower overall costs.

CrystFEL: a software suite for snapshot serial crystallography

Abstract: In order to address the specific needs of the emerging technique of `serial femtosecond crystallography', in which structural information is obtained from small crystals illuminated by an X-ray free-electron laser, a new software suite has been created. The constituent programs deal with viewing, indexing, integrating, merging and evaluating the quality of the data, and also simulating patterns. The specific challenges addressed chiefly concern the indexing and integration of large numbers of diffraction patterns in an automated manner, and so the software is designed to be fast and to make use of multi-core hardware. Other constituent programs deal with the merging and scaling of large numbers of intensities from randomly oriented snapshot diffraction patterns. The suite uses a generalized representation of a detector to ease the use of more complicated geometries than those familiar in conventional crystallography. The suite is written in C with supporting Perl and shell scripts, and is available as source code under version 3 or later of the GNU General Public License.

Teaching hydrological modeling with a user-friendly catchment-runoff-model software package

Abstract: Computer models, especially conceptual models, are frequently used for catchment hydrology studies. Teaching hydrological modeling, however, is challenging, since students have to both understand general model concepts and be able to use particular computer programs when learning to apply computer models. Here we present a new version of the HBV ( Hydrologiska Byrans Vattenavdelning ) model. This software provides a user-friendly version that is especially useful for education. Different functionalities, such as an automatic calibration using a genetic algorithm or a Monte Carlo approach, as well as the possibility to perform batch runs with predefined model parameters make the software interesting especially for teaching in more advanced classes and research projects. Different teaching goals related to hydrological modeling are discussed and a series of exercises is suggested to reach these goals.

rapidSTORM: accurate, fast open-source software for localization microscopy.

Abstract: Besides being versatile and fast, rapidSTORM is easy to use, deploy, inspect and extend. It is open source and based on widespread, mature, portable and open technologies such as C++, the GNU tool chain and wxWidgets. A graphical user interface and user manual allow quick acquaintance. Automated prerelease validation and wide use on a range of biological targets ensure reliable results. rapidSTORM is regularly updated, and both source code and compiled packages are available from our website at http://www.superresolution.biozentrum.uni-wuerzburg.de/.

EASE-Grid 2.0: Incremental but Significant Improvements for Earth-Gridded Data Sets

Abstract: Defined in the early 1990s for use with gridded satellite passive microwave data, the Equal-Area Scalable Earth Grid (EASE-Grid) was quickly adopted and used for distribution of a variety of satellite and in situ data sets. Conceptually easy to understand, EASE-Grid suffers from limitations that make it impossible to format in the widely popular GeoTIFF convention without reprojection. Importing EASE-Grid data into standard mapping software packages is nontrivial and error-prone. This article defines a standard for an improved EASE-Grid 2.0 definition, addressing how the changes rectify issues with the original grid definition. Data distributed using the EASE-Grid 2.0 standard will be easier for users to import into standard software packages and will minimize common reprojection errors that users had encountered with the original EASE-Grid definition.

Arduino: a low-cost multipurpose lab equipment.

Abstract: Typical experiments in psychological and neurophysiological settings often require the accurate control of multiple input and output signals. These signals are often generated or recorded via computer software and/or external dedicated hardware. Dedicated hardware is usually very expensive and requires additional software to control its behavior. In the present article, I present some accuracy tests on a low-cost and open-source I/O board (Arduino family) that may be useful in many lab environments. One of the strengths of Arduinos is the possibility they afford to load the experimental script on the board’s memory and let it run without interfacing with computers or external software, thus granting complete independence, portability, and accuracy. Furthermore, a large community has arisen around the Arduino idea and offers many hardware add-ons and hundreds of free scripts for different projects. Accuracy tests show that Arduino boards may be an inexpensive tool for many psychological and neurophysiological labs.

Frama-C: a software analysis perspective

Abstract: Frama-C is a source code analysis platform that aims at conducting verification of industrial-size C programs. It provides its users with a collection of plug-ins that perform static analysis, deductive verification, and testing, for safety- and security-critical software. Collaborative verification across cooperating plug-ins is enabled by their integration on top of a shared kernel and datastructures, and their compliance to a common specification language. This foundational article presents a consolidated view of the platform, its main and composite analyses, and some of its industrial achievements.

Apero, an open source bundle adjusment software for automatic calibration and orientation of set of images

Abstract: . IGN has developed a set of photogrammetric tools, APERO and MICMAC, for computing 3D models from set of images. This software, developed initially for its internal needs are now delivered as open source code. This paper focuses on the presentation of APERO the orientation software. Compared to some other free software initiatives, it is probably more complex but also more complete, its targeted user is rather professionals (architects, archaeologist, geomophologist) than people. APERO uses both computer vision approach for estimation of initial solution and photogrammetry for a rigorous compensation of the total error; it has a large library of parametric model of distortion allowing a precise modelization of all the kind of pinhole camera we know, including several model of fish-eye; there is also several tools for geo-referencing the result. The results are illustrated on various application, including the data-set of 3D-Arch workshop.

Hierarchical Linear Modeling: Guide and Applications

Abstract: This book provides a brief, easy-to-read guide to implementing hierarchical linear modeling using three leading software platforms, followed by a set of original how-to applications articles following a standardard instructional format The "guide" portion consists of five chapters by the editor, providing an overview of HLM, discussion of methodological assumptions, and parallel worked model examples in SPSS, SAS, and HLM software The "applications" portion consists of ten contributions in which authors provide step by step presentations of how HLM is implemented and reported for introductory to intermediate applications

Self-adaptive software needs quantitative verification at runtime

Abstract: Continually verify self-adaptation decisions taken by critical software in response to changes in the operating environment.

Hardware/Software Codesign: The Past, the Present, and Predicting the Future

Abstract: Hardware/software codesign investigates the concurrent design of hardware and software components of complex electronic systems. It tries to exploit the synergy of hardware and software with the goal to optimize and/or satisfy design constraints such as cost, performance, and power of the final product. At the same time, it targets to reduce the time-to-market frame considerably. This paper presents major achievements of two decades of research on methods and tools for hardware/software codesign by starting with a historical survey of its roots, by highlighting its major research directions and achievements until today, and finally, by predicting in which direction research in codesign might evolve in the decades to come.

libdft: practical dynamic data flow tracking for commodity systems

Abstract: Dynamic data flow tracking (DFT) deals with tagging and tracking data of interest as they propagate during program execution. DFT has been repeatedly implemented by a variety of tools for numerous purposes, including protection from zero-day and cross-site scripting attacks, detection and prevention of information leaks, and for the analysis of legitimate and malicious software. We present libdft, a dynamic DFT framework that unlike previous work is at once fast, reusable, and works with commodity software and hardware. libdft provides an API for building DFT-enabled tools that work on unmodified binaries, running on common operating systems and hardware, thus facilitating research and rapid prototyping. We explore different approaches for implementing the low-level aspects of instruction-level data tracking, introduce a more efficient and 64-bit capable shadow memory, and identify (and avoid) the common pitfalls responsible for the excessive performance overhead of previous studies. We evaluate libdft using real applications with large codebases like the Apache and MySQL servers, and the Firefox web browser. We also use a series of benchmarks and utilities to compare libdft with similar systems. Our results indicate that it performs at least as fast, if not faster, than previous solutions, and to the best of our knowledge, we are the first to evaluate the performance overhead of a fast dynamic DFT implementation in such depth. Finally, libdft is freely available as open source software.

PyElph - a software tool for gel images analysis and phylogenetics

Abstract: This paper presents PyElph, a software tool which automatically extracts data from gel images, computes the molecular weights of the analyzed molecules or fragments, compares DNA patterns which result from experiments with molecular genetic markers and, also, generates phylogenetic trees computed by five clustering methods, using the information extracted from the analyzed gel image. The software can be successfully used for population genetics, phylogenetics, taxonomic studies and other applications which require gel image analysis. Researchers and students working in molecular biology and genetics would benefit greatly from the proposed software because it is free, open source, easy to use, has a friendly Graphical User Interface and does not depend on specific image acquisition devices like other commercial programs with similar functionalities do. PyElph software tool is entirely implemented in Python which is a very popular programming language among the bioinformatics community. It provides a very friendly Graphical User Interface which was designed in six steps that gradually lead to the results. The user is guided through the following steps: image loading and preparation, lane detection, band detection, molecular weights computation based on a molecular weight marker, band matching and finally, the computation and visualization of phylogenetic trees. A strong point of the software is the visualization component for the processed data. The Graphical User Interface provides operations for image manipulation and highlights lanes, bands and band matching in the analyzed gel image. All the data and images generated in each step can be saved. The software has been tested on several DNA patterns obtained from experiments with different genetic markers. Examples of genetic markers which can be analyzed using PyElph are RFLP (Restriction Fragment Length Polymorphism), AFLP (Amplified Fragment Length Polymorphism), RAPD (Random Amplification of Polymorphic DNA) and STR (Short Tandem Repeat). The similarity between the DNA sequences is computed and used to generate phylogenetic trees which are very useful for population genetics studies and taxonomic classification. PyElph decreases the effort and time spent processing data from gel images by providing an automatic step-by-step gel image analysis system with a friendly Graphical User Interface. The proposed free software tool is suitable for researchers and students which do not have access to expensive commercial software and image acquisition devices.

System and method for speaker recognition on mobile devices

Abstract: A speaker recognition system for authenticating a mobile device user includes an enrollment and learning software module, a voice biometric authentication software module, and a secure software application. Upon request by a user of the mobile device, the enrollment and learning software module displays text prompts to the user, receives speech utterances from the user, and produces a voice biometric print. The enrollment and training software module determines when a voice biometric print has met at least a quality threshold before storing it on the mobile device. The secure software application prompts a user requiring authentication to repeat an utterance based at least on an attribute of a selected voice biometric print, receives a corresponding utterance, requests the voice biometric authentication software module to verify the identity of the second user using the utterance, and, if the user is authenticated, imports the voice biometric print.

Acquisition of high resolution three-dimensional models using free, open-source, photogrammetric software

Abstract: The 3D digitisation of palaeontological resources is of tremendous use to the field, providing the means to archive, analyse, and visualise specimens that would otherwise be too large to handle, too valuable to destructively sample, or simply in a different geographic location. Digitisation of a specimen to produce a 3D digital model often requires the use of expensive laser scanning equipment or proprietary digital reconstruction software, making the technique inaccessible to many workers. Presented here is a guide for producing high resolution 3D models from photographs, using freely available open-source software. To demonstrate the accuracy and flexibility of the approach, a number of examples are given, including a small trilobite (~0.04 m), a large mounted elephant skeleton (~3 m), and a very large fossil tree root system (~6 m), illustrating that the method is equally applicable to specimens or even outcrops of all sizes. The digital files of the models produced in this paper are included. The results demonstrate that production of digital models from specimens for research or archival purposes is available to anyone, and it is hoped that an increased use of digitisation techniques will facilitate research and encourage collaboration and dissemination of digital data. Peter L. Falkingham. School of Earth, Atmospheric and Environmental Science, University of Manchester, Williamson Building, Oxford Road, Manchester, M13 9PL, UK. peter.falkingham@manchester.ac.uk

Introducing an R package for luminescence dating analysis

Abstract: For routine luminescence dating applications the commonly used Riso readers are bundled with analysis software, such as Viewer or Analyst. These software solutions are appropriate for most of the regular dating and publication jobs, and enable assessment of luminescence characteristics and provide basic statistical data treatment. However, for further statistical analysis and data treatments, this software may reach its limits. In such cases, open programming languages are a more appropriate approach. Here, we present the R package ‘Luminescence’ for a more flexible handling of luminescence data and related plotting purposes, using the statistical programming language R. The R language as well as the package and the source code are provided under the General Public License (GPL) conditions and are available for free. The basic functionality of the package is described along with three application examples. This package is not an alternative to the existing software (Analyst, Viewer) but may provide a collection of additional tools to analyse luminescence data and serve as a platform for further contributions.

SeqTrace: a graphical tool for rapidly processing DNA sequencing chromatograms.

Abstract: Modern applications of Sanger DNA sequencing often require converting a large number of chromatogram trace files into high-quality DNA sequences for downstream analyses. Relatively few nonproprietary software tools are available to assist with this process. SeqTrace is a new, free, and open-source software application that is designed to automate the entire workflow by facilitating easy batch processing of large numbers of trace files. SeqTrace can identify, align, and compute consensus sequences from matching forward and reverse traces, filter low-quality base calls, and end-trim finished sequences. The software features a graphical interface that includes a full-featured chromatogram viewer and sequence editor. SeqTrace runs on most popular operating systems and is freely available, along with supporting documentation, at http://seqtrace.googlecode.com/.

Algorithms and data structures for massively parallel generic adaptive finite element codes

Abstract: Today's largest supercomputers have 100,000s of processor cores and offer the potential to solve partial differential equations discretized by billions of unknowns. However, the complexity of scaling to such large machines and problem sizes has so far prevented the emergence of generic software libraries that support such computations, although these would lower the threshold of entry and enable many more applications to benefit from large-scale computing.We are concerned with providing this functionality for mesh-adaptive finite element computations. We assume the existence of an “oracle” that implements the generation and modification of an adaptive mesh distributed across many processors, and that responds to queries about its structure. Based on querying the oracle, we develop scalable algorithms and data structures for generic finite element methods. Specifically, we consider the parallel distribution of mesh data, global enumeration of degrees of freedom, constraints, and postprocessing. Our algorithms remove the bottlenecks that typically limit large-scale adaptive finite element analyses.We demonstrate scalability of complete finite element workflows on up to 16,384 processors. An implementation of the proposed algorithms, based on the open source software p4est as mesh oracle, is provided under an open source license through the widely used deal.II finite element software library.