Free Software Tools Research Articles

HisTOOLogy: an open-source tool for quantitative analysis of histological sections.

HisTOOLogy is an open-source software for the quantification of digital colour images of histological sections. The simple graphical user interface enables both expert and non-expert users to rapidly extract useful information from stained tissue sections. The software's main feature is a generalizable colour separation algorithm based on k-means clustering which accurately and reproducibly returns the amount of colour per unit area for any stain, thus allowing the quantification of tissue components. Here we describe HisTOOLogy's algorithms and graphical user interface structure, showing how it can be used to separate different dye colours in several classical stains. In addition, to demonstrate how the tool can be employed to obtain quantitative information on biological tissues, the effect of different hepatic tissue decellularization protocols on cell removal and matrix preservation was assessed through image analysis using HisTOOLogy and compared with conventional DNA and total protein content assays. HisTOOLogy's performance was also compared with ImageJ's colour deconvolution plug-in, demonstrating its advantages in terms of ease of use and speed of colour separation.

Methodology and calculator for high precision regression fits of pyranometer angular responsivities and the associated uncertainties

An easy to implement method for accurately utilizing pyranometer incidence angle dependent calibration factors, or responsivities (μV/W/m2), along with the associated uncertainties has been developed. This method uses algorithms for creating single polynomial functions dependent on the incidence angle to characterize both the pyranometer responsivity and the upper prediction interval of the associated standard uncertainties. Single polynomial functions are easier to implement in spreadsheet software and programming environments than the simpler to formulate piecewise polynomials and splines. The polynomials are of high degree, extrapolated to 0° and 90°, and solved using robust techniques to avoid oscillations and overshoots, which can occur when using other interpolation methods. A free software tool was created that calculates the functions using the algorithms presented in this paper, and it was tested on the calibrated responsivities and uncertainties of 40 pyranometers representing six (6) different models. All of the obtained fits closely represent the data with R2 values greater than 0.98.

Obfuscating Live Computer Forensic Investigative Process on a Windows 7 Operating System: A Criminal's Perspective

forensic investigation is conducted when the computer system is turned on whilst the data is gathered in a forensically sound manner, from the physical memory, in the form of evidence. As time progressed, criminals have been developing methodologies by which live analysis could be defeated. One such method implemented by the criminals is that of a rookit being installed on the victim's machine. A rookit can be dangerous, and very risky to deal with from an investigator's point of view, because it has the power to subvert the kernel of an operating system. This paper presents, how easy it is for a criminal to thwart the process of live forensic investigation by downloading and installing free software tools; needing, no prior knowledge of the windows 7 operating system's kernel, and how frustrating it would be for the investigator to examine the computer system and make a valid forensic report. Thus, making live analysis a daunting task for the forensic investigator on field. Finally, a mathematical formula is derived for detecting the presence of hidden processes in the memory.

FREEWAT - FREE and open source software tools for WATer resource management: an Horizon 2020 for promoting innovative ICT tools in water management

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Análisis Comparativo de Ajuste en Entrenamiento de Redes Neuronales artificiales a partir de las Librerías Open NN y ALGLIB

<p>En las últimas décadas son muchos los avances que han tenido lugar en el desarrollo de aplicaciones y alcances de las redes neuronales artificiales, y de igual modo el desarrollo tecnológico en el área de la computación. Este tipo de avances han incidido directamente en el número de publicaciones de aplicaciones, en diversas áreas del conocimiento, basadas en este método de inteligencia artificial.</p><p>Ahora bien, hasta el presente sigue siendo tema de discusión la idoneidad y aplicabilidad de herramientas de software libre para facilitar la implementación y la calidad de resultados. En este contexto, este trabajo representa un análisis comparativo de aplicaciones usando las librerías ALGLIB y Open NN (Open Source Neural Networks C++ Library), orientadas al entrenamiento y reproducción de redes neuronales artificiales. De igual modo, se establece una evaluación de los resultados obtenidos a partir de los niveles de correlación entre la salida de valores para redes entrenadas y un conjunto de datos de entrenamiento simulados.</p>

Building a virtual ligand screening pipeline using free software: a survey.

Virtual screening, the search for bioactive compounds via computational methods, provides a wide range of opportunities to speed up drug development and reduce the associated risks and costs. While virtual screening is already a standard practice in pharmaceutical companies, its applications in preclinical academic research still remain under-exploited, in spite of an increasing availability of dedicated free databases and software tools. In this survey, an overview of recent developments in this field is presented, focusing on free software and data repositories for screening as alternatives to their commercial counterparts, and outlining how available resources can be interlinked into a comprehensive virtual screening pipeline using typical academic computing facilities. Finally, to facilitate the set-up of corresponding pipelines, a downloadable software system is provided, using platform virtualization to integrate pre-installed screening tools and scripts for reproducible application across different operating systems.

MANTIS: an R package that simulates multilocus models of pathogen evolution.

BackgroundIn host-pathogen systems the development of immunity by the host places pressure on pathogens, by setting up competition between genetic variants due to the establishment of cross-protective responses. These pressures can lead to pathogen-specific, ubiquitous dynamic behaviours. Understanding the evolutionary forces that shape these patterns is one of the key goals of computationally simulated epidemiological models. Despite the contribution of such research methods in recent years to our current understanding of pathogen evolution, the availability of free software tools for the general public remains scarce.ResultsWe developed the Multilocus ANTIgenic Simulator (MANTIS) software package for the R statistical environment. MANTIS can simulate and analyse epidemiological time-series generated under the biological assumptions of the strain theory of host-pathogen systems by Gupta et al.ConclusionsMANTIS wraps a C/C++ ordinary-differential equations system and Runge-Kutta solver into a set of user-friendly R functions. These include routines to numerically simulate the system and others to analyse, visualize and export results. For this, the package offers its own set of time-series plotting and exportation functions. MANTIS’s main goal is to serve as a free, ready-to-use academic software tool. Its open source nature further provides an opportunity for users with advanced programming skills to expand its capabilities. Here, we describe the background theory, implementation, basic functionality and usage of this package. MANTIS is freely available from http://www.eeid.ox.ac.uk/mantisunder the GPL license.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0598-9) contains supplementary material, which is available to authorized users.

FREEWAT: FREE and open source software tools for WATer resource management

FREEWAT is an HORIZON 2020 project financed by the EU Commission under the call WATER INNOVATION: BOOSTING ITS VALUE FOR EUROPE. FREEWAT main result will be an open source and public domain GIS integrated modelling environment for the simulation of water quantity and quality in surface water and groundwater with an integrated water management and planning module. FREEWAT aims at promoting water resource management by simplifying the application of the Water Framework Directive and other EU water related Directives. Specific objectives of the FREEWAT project are: to coordinate previous EU and national funded research to integrate existing software modules for water management in a single environment into the GIS based FREEWAT; to support the FREEWAT application in an innovative participatory approach gathering technical staff and relevant stakeholders (in primis policy and decision makers) in designing scenarios for the proper application of water policies.The open source characteristics of the platform allow to consider this an initiative ad includendum (looking for inclusion of other entities), as further research institutions, private developers etc. may contribute to the platform development.Through creating a common environment among water research/professionals, policy makers and implementers, FREEWAT main impact will be on enhancing science- and participatory approach and evidence-based decision making in water resource management, hence producing relevant and appropriate outcomes for policy implementation. The Consortium is constituted by partners from various water sectors from 10 EU countries, plus Turkey and Ukraine. Synergies with the UNESCO HOPE initiative on free and open source software in water management greatly boost the value of the project. Large stakeholders involvement is thought to guarantee results dissemination and exploitation.

ProSight Lite: graphical software to analyze top-down mass spectrometry data.

Many top-down proteomics experiments focus on identifying and localizing PTMs and other potential sources of “mass shift” on a known protein sequence. A simple application to match ion masses and facilitate the iterative hypothesis testing of PTM presence and location would assist with the data analysis in these experiments. ProSight Lite is a free software tool for matching a single candidate sequence against a set of mass spectrometric observations. Fixed or variable modifications, including both PTMs and a select number of glycosylations, can be applied to the amino acid sequence. The application reports multiple scores and a matching fragment list. Fragmentation maps can be exported for publication in either portable network graphic (PNG) or scalable vector graphic (SVG) format. ProSight Lite can be freely downloaded from http://prosightlite.northwestern.edu, installs and updates from the web, and requires Windows 7 or a higher version.

ProSight Lite: Graphical software to analyze top-down mass spectrometry data

Many top-down proteomics experiments focus on identifying and localizing PTMs and other potential sources of “mass shift” on a known protein sequence. A simple application to match ion masses and facilitate the iterative hypothesis testing of PTM presence and location would assist with the data analysis in these experiments. ProSight Lite is a free software tool for matching a single candidate sequence against a set of mass spectrometric observations. Fixed or variable modifications, including both PTMs and a select number of glycosylations, can be applied to the amino acid sequence. The application reports multiple scores and a matching fragment list. Fragmentation maps can be exported for publication in either portable network graphic (PNG) or scalable vector graphic (SVG) format. ProSight Lite can be freely downloaded from http://prosightlite.northwestern.edu, installs and updates from the web, and requires Windows 7 or a higher version.

Mathematical modeling of growth of Salmonella spp. and spoilage microorganisms in raw oysters

The main objective of this study was to develop the primary and secondary models to describe the growth kinetics of Salmonella as well as background microorganisms in raw, shucked oysters. Samples, inoculated with a cocktail of two Salmonella serotypes, S. Typhimurium (CICC22956) and S. Enteritidis (CICC21482), were incubated at 4, 8, 12, 16, 20, 25, 30, 33, 37, 40, and 43 °C. Growth of Salmonella was observed at all temperatures, except at 4 °C. The background microorganisms grew at all temperatures. All growth curves clearly exhibited lag, exponential and stationary phases, and were analyzed using the Huang growth model. Three secondary models (Ratkowsky square-root, Huang square-root, and Cardinal parameter models) were compared for evaluating the effect of temperature on bacterial growth rates. Data analysis was performed using IPMP 2013, a free predictive microbiology software tool developed by the USDA ARS.The Cardinal parameters model underestimated the specific rates of the microorganisms at low temperatures. The Huang square-root model was more suitable than the Ratkowsky square-root model for describing the effect of temperature on growth of Salmonella, while the Ratkowsky square-root model, on the other hand, was more suitable for background microorganisms. For both Salmonella and background microorganisms, the logarithms of the lag phase were expressed as linear functions of the logarithms of specific growth rates. The results of this study can be used by the food retailers and regulatory agencies to estimate the microbial shelf-life of raw, shucked oysters.

Review of free software tools for image analysis of fluorescence cell micrographs.

An increasing number of free software tools have been made available for the evaluation of fluorescence cell micrographs. The main users are biologists and related life scientists with no or little knowledge of image processing. In this review, we give an overview of available tools and guidelines about which tools the users should use to segment fluorescence micrographs. We selected 15 free tools and divided them into stand-alone, Matlab-based, ImageJ-based, free demo versions of commercial tools and data sharing tools. The review consists of two parts: First, we developed a criteria catalogue and rated the tools regarding structural requirements, functionality (flexibility, segmentation and image processing filters) and usability (documentation, data management, usability and visualization). Second, we performed an image processing case study with four representative fluorescence micrograph segmentation tasks with figure-ground and cell separation. The tools display a wide range of functionality and usability. In the image processing case study, we were able to perform figure-ground separation in all micrographs using mainly thresholding. Cell separation was not possible with most of the tools, because cell separation methods are provided only by a subset of the tools and are difficult to parametrize and to use. Most important is that the usability matches the functionality of a tool. To be usable, specialized tools with less functionality need to fulfill less usability criteria, whereas multipurpose tools need a well-structured menu and intuitive graphical user interface.

Finite Element Simulation by Free Software Tools

This paper presents a finite element based environment for the simulation of two dimensional electromagnetic field problems, especially electric motors. The graphical user interface, the finite element mesh generator and the computational functions are free software tools that have been developed by scientific teams from all over the world. The aim of this work is to realize a new software environment that can be used in the simulation of two dimensional problems as well as in education.

Propuesta metodológica para el estudio volumétrico de cerámica arqueológica a través de programas free-software de edición 3D: el caso de las necrópolis celtibéricas del área meseteña

Nowadays the free-software programs have been converted into the ideal tools for the archaeological researches, reaching the same level as other commercial programs. For that reason, the 3D modeling tool Blender has reached in the last years a great popularity offering similar characteristics like other commercial 3D editing programs such as 3D Studio Max or AutoCAD. Recently, it has been developed the necessary script for the volumetric calculations of three-dimnesional objects, offering great possibilities to calculate the volume of the archaeological ceramics. In this paper, we present a methodological approach for the volumetric studies with Blender and a study case of funerary urns from several celtiberians cemeteries of the Spanish Meseta. The goal is to demonstrate the great possibilities that the 3D editing free-software tools have in the volumetric studies at the present time.

Transaction network analysis for studying Local Exchange Trading Systems (LETS): Research potentials and limitations

The numerous studies of Local Exchange Trading Systems (LETS) have so far been based mostly on qualitative approaches. The aim of this paper is to introduce the method of transaction network analysis as an important complement to these studies, enabling one to quantitatively describe functioning of LETS in terms of the actual flows of currency, materialized transactions and topology of the exchange network, the types of information markedly missing in most of the existing LETS studies. We demonstrate the potentials of the method on the case of the LETS initiative “RozLEŤSe” based in Brno, Czech Republic. Looking at the transaction flows using the network analysis approach, we identify the key members of the group, network characteristics of the exchange system and its development over time. This allows us not only to provide a complex description of the system, but also to simulate certain scenarios (e.g. removal of a key person from the network). Within the discussion of potentials and limitations of applying transaction network analysis for studying LETS and other community currency initiatives (e.g. time banks) on a larger scale, we also provide a free accessible software tool for doing so and invite other researchers to cooperate on the task.

Multidimensional modeling and analysis of large and complex watercourse data: an OLAP-based solution

This paper presents the application of Data Warehouse (DW) and On-Line Analytical Processing (OLAP) technologies to the field of water quality assessment. The European Water Framework Directive (DCE, 2000) underlined the necessity of having operational tools to help in the interpretation of the complex and abundant information regarding running waters and their functioning. Several studies have exemplified the interest in DWs for integrating large volumes of data and in OLAP tools for data exploration and analysis.Based on free software tools, we propose an extensible relational OLAP system for the analysis of physicochemical and hydrobiological watercourse data. This system includes: (i) two data cubes; (ii) an Extract, Transform and Load (ETL) tool for data integration; and (iii) tools for OLAP exploration. Many examples of OLAP analysis (thematic, temporal, spatiotemporal, and multiscale) are provided. We have extended an existing framework with complex aggregate functions that are used to define complex analysis indicators. Additional analysis dimensions are also introduced to allow their calculation and also for purposes of rendering information. Finally, we propose two strategies to address the problem of summarizing heterogeneous measurement units by: (i) transforming source data at the ETL tier, and (ii) introducing an additional analysis dimension at the OLAP server tier.

Numerical study of unsteady cavitation on 2D NACA0015 hydrofoil using free/open source software

The free/open source software as OpenFOAM, Salome meshing and python language under Debian Linux system are evaluated to model unsteady cavitating turbulent flow around a NACA0015 hydrofoil. Based on the cavitation model proposed by Kunz and large eddy simulation (LES) method, we denote the benefits of free software and open source tools as an alternative to proprietary software of computational fluid mechanics, and provided a modified cavitation model to improve numerical accuracy. The simulation results of typical break-off cycle for cavitation shedding are compared to available experimental data, and validated using image processing to find percentage of similarities. The sheet cavity frequency of 7.752 Hz was obtained based on cavitation evolution and pressure fluctuations. The study gives relevant information for CFD software development in the future.

Semi‐supervised classification of vegetation: preserving the good old units and searching for new ones

AbstractAimThe unsupervised nature of traditional numerical methods used to classify vegetation hinders the development of comprehensive vegetation classification systems. Each new unsupervised classification yields partitions that are partly inconsistent with previous classifications and change group membership for some sites. In contrast, supervised methods account for previously established vegetation units, but cannot define new ones. Therefore, we introduce the concept of semi‐supervised classification to community ecology and vegetation science. Semi‐supervised classification formally reproduces the existing units in a supervised mode and simultaneously identifies new units among unassigned sites in an unsupervised mode. We discuss the concept of semi‐supervised clustering, introduce semi‐supervised variants of two clustering algorithms that produce groups with crisp boundaries, k‐means and partitioning around medoids (PAM), provide a free software tool to perform these classifications and demonstrate the advantages using example data sets of vegetation plots.MethodsSemi‐supervised methods use a priori information about group membership for some sites to define centroids (k‐means) or medoids (PAM) of site groups that represent previously established vegetation units. They identify these groups in a species hyperspace and assign new sites to them. At the same time, they search for a user‐defined number of new groups. We compared the unsupervised, supervised and semi‐supervised methods using an example of a forest vegetation data set that was previously classified using expert knowledge, and assessed how well these methods reproduced vegetation units defined by experts. Then we compared supervised and semi‐supervised methods in a task when a grassland vegetation classification established in one country was extended to two neighbouring countries.Results and conclusionsExample analyses of vegetation plot data sets demonstrated that semi‐supervised variants of k‐means and PAM are extremely valuable tools for extending existing vegetation classifications while preserving previously defined vegetation units. They can be used both for identifying so far unrecognized vegetation types in the regions where a vegetation classification already exists and for extending a vegetation classification from a particular region to neighbouring regions with partly identical but partly different vegetation types. Both k‐means and PAM provide site groups with crisp boundaries, which makes them a simpler alternative to fuzzy clustering methods.

Quantifying Urban Sprawl with Spatial Autocorrelation Techniques using Multi-Temporal Satellite Data

This study deals with the use of satellite TM multi-temporal data coupled with statistical analyses to quantitatively estimate urban expansion and soil consumption for small towns in southern Italy. The investigated area is close to Bari and was selected because highly representative for Italian urban areas. To cope with the fact that small changes have to be captured and extracted from TM multi-temporal data sets, we adopted the use of spectral indices to emphasize occurring changes, and geospatial data analysis to reveal spatial patterns. Analyses have been carried out using global and local spatial autocorrelation, applied to multi-date NASA Landsat images acquired in 1999 and 2009 and available free of charge. Moreover, in this paper each step of data processing has been carried out using free or open source software tools, such as, operating system (Linux Ubuntu), GIS software (GRASS GIS and Quantum GIS) and software for statistical analysis of data (R). This aspect is very important, since it puts no limits and allows everybody to carry out spatial analyses on remote sensing data. This approach can be very useful to assess and map land cover change and soil degradation, even for small urbanized areas, as in the case of Italy, where recently an increasing number of devastating flash floods have been recorded. These events have been mainly linked to urban expansion and soil consumption and have caused loss of human lives along with enormous damages to urban settlements, bridges, roads, agricultural activities, etc. In these cases, remote sensing can provide reliable operational low cost tools to assess, quantify and map risk areas.

Towards a Holistic Framework for the Evaluation of Emergency Plans in Indoor Environments

One of the most promising fields for ambient intelligence is the implementation of intelligent emergency plans. Because the use of drills and living labs cannot reproduce social behaviors, such as panic attacks, that strongly affect these plans, the use of agent-based social simulation provides an approach to evaluate these plans more thoroughly. (1) The hypothesis presented in this paper is that there has been little interest in describing the key modules that these simulators must include, such as formally represented knowledge and a realistic simulated sensor model, and especially in providing researchers with tools to reuse, extend and interconnect modules from different works. This lack of interest hinders researchers from achieving a holistic framework for evaluating emergency plans and forces them to reconsider and to implement the same components from scratch over and over. In addition to supporting this hypothesis by considering over 150 simulators, this paper: (2) defines the main modules identified and proposes the use of semantic web technologies as a cornerstone for the aforementioned holistic framework; (3) provides a basic methodology to achieve the framework; (4) identifies the main challenges; and (5) presents an open and free software tool to hint at the potential of such a holistic view of emergency plan evaluation in indoor environments.