Alternative Software Research Articles

A computational evaluation of some free mathematical software for scientific computing

The purpose of this paper is to present a computational comparison of some well-known free mathematical programs. Specifically, these programs are FreeMat, Mathnium, Octave, R and Scilab. All these programs are designed in order to be used either in the scientific community or the industry. Moreover, an additional aim of this paper is to propose open source alternative software which can replace commercial mathematical software. Several issues concerning available operating system platforms, data structures, languages’ structure, matrix operations, program modularization, libraries, packages, profiling tools and online help facilities are addressed in this paper. Discussions on their weaknesses and strengths characteristics are presented. Finally, a speed comparison of some frequently used algorithms, procedures and operations within software is also presented.

Formal reasoning about lazy-STM programs

Transactional memory (TM) is an easy-using parallel programming model that avoids common problems associated with conventional locking techniques. Several researchers have proposed a large amount of alternative hardware and software TM implementations. However, few ones focus on formal reasoning about these TM programs. In this paper, we propose a framework at assembly level for reasoning about lazy software transactional memory (STM) programs. First, we give a software TM implementation based on lightweight locks. These locks are also one part of the shared memory. Then we define the semantics of the model operationally, and the lightweight locks in transaction are non-blocking, avoiding deadlocks among transactions. Finally we design a logic -- a combination of permission accounting in separation logic and concurrent separation logic -- to verify various properties of concurrent programs based on this machine model. The whole framework is formalized using a proof-carrying-code (PCC) framework.

How The Electronic Health Record Did Not Measure Up To The Demands Of Our Medical Home Practice

The American Recovery and Reinvestment Act (ARRA) of 2009 will soon provide billions of dollars to small physician practices nationwide to encourage adoption of electronic health records. Although shifting from paper to computers should lead to better and cheaper care, the transition is complex. In this paper we describe our struggles to adapt a commercial electronic health record to an innovative practice serving high-cost patients with chronic diseases. Limitations in the technology gave rise to medication errors, interruptions in work flow, and other problems common to paper systems. Our experience should encourage providers and policy makers to consider alternative software and informatics models before investing in currently available systems.

COMBINATORIAL RECONSTRUCTION OF HALF-SIBLING GROUPS FROM MICROSATELLITE DATA

While full-sibling group reconstruction from microsatellite data is a well-studied problem, reconstruction of half-sibling groups is much less studied, theoretically challenging, and computationally demanding. In this paper, we present a formulation of the half-sibling reconstruction problem and prove its APX-hardness. We also present exact solutions for this formulation and develop heuristics. Using biological and synthetic datasets we present experimental results and compare them with the leading alternative software COLONY. We show that our results are competitive and allow half-sibling group reconstruction in the presence of polygamy, which is prevalent in nature.

The Space Package: Tight Integration between Space and Semantics

Interpretation of spatial features often requires combined reasoning over geometry and semantics. We introduce the Space package, an open source SWI-Prolog extension that provides spatial indexing capabilities. Together with the existing semantic web reasoning capabilities of SWI-Prolog, this allows efficient integration of spatial and semantic queries and provides an infrastructure for declarative programming with space and semantics. There are few systems that provide indexing and reasoning facilities for both spatial and semantic data. A common solution is to combine separate semantic reasoning and geospatial services. Such loose coupling has the disadvantage that each service cannot make use of the statistics of the other. This makes optimization of such a service-oriented architecture hard. The SWI-Prolog Space and Semantic web packages provide a native Prolog interface to both spatial and semantic indexing and reasoning, which makes it easy to write combined query optimizers. Another advantage of the Space package is that it allows declarative logic programming, which means in practice that you say what you want to compute instead of how to compute it. The actual indexing machinery is encapsulated inside Prolog predicates. In this article we describe the interface of the Space package, compare its functionality to alternative software libraries, and show how to work with it using three example applications. These example illustrations include reasoning over movement patterns, dynamically loading geospatial linked data off the semantic web, and setting up a simple KML server.

Software as Risk: Introduction of Open Standards in the Danish Public Sector

In June 2006, the Danish parliament passed a resolution introducing open standards for software in the public sector. Open standards ensure interoperability in software. The introduction of open standards facilitates the spread of alternative software solutions, such as open source software, into environments (e.g., the public sector) that have hitherto been dominated by software produced by the proprietary software industry. In this article, the authors analyze the political process that led to the passing of the resolution, arguing that the concepts of risk and governmentality associated with Ulrich Beck (1992b) and Mitchell Dean (1999) allows one to theorize about this process. In so doing, they draw attention to the significance of the notion of risk in the context of public-sector software.

Geo-Genealogy of Irish Surnames

Please click here to download the map associated with this article. This paper outlines the design and production of the Geo-genealogy of Irish Surnames map. The largeformat A0 print document uses classic Irish symbology and themes to create a visually striking representation of historic and numeric data relating to Irish surnames from the 1890 Irish census. Created using Esri ArcGIS, the map was designed to illustrate the flexibility and quality afforded by modern GIS for high quality cartographic design and production without recourse to alternative software.

Comparing NOMINATE and IDEAL: Points of Difference and Monte Carlo Tests

Empirical models of spatial voting allow us to infer legislators' locations in an abstract policy or ideological space using their roll‐call votes. Over the past 25 years, these models have provided new insights about the U.S. Congress, and legislative behavior more generally. There are now a number of alternative models, estimators, and software packages that researchers can use to recover latent issue or ideological spaces from voting data. These different tools usually produce substantively similar estimates, but important differences also arise. We investigated the sources of observed differences between two leading methods, NOMINATE and IDEAL. Using data from the 1994 to 1997 Supreme Court and the 109th Senate, we determined that while some observed differences in the estimates produced by each model stem from fundamental differences in the models' underlying behavioral assumptions, others arise from arbitrary differences in implementation. Our Monte Carlo experiments revealed that neither model has a clear advantage over the other in the recovery of legislator locations or roll‐call midpoints in either large or small legislatures.

233-P: DQB1 sequence based typing preferential amplification problem: Evaluation of alternative sequencing chemistry and software

233-P: DQB1 sequence based typing preferential amplification problem: Evaluation of alternative sequencing chemistry and software

Using search theory to determine an applications selection strategy

The literature on software selection focuses mainly on identifying and ensuring the evaluation of those attributes of alternative commercial software products relevant to meeting the functional and non-functional requirements of the acquiring organisation. Once these attributes are determined, however, the firm acquiring the product must still decide on its selection strategy: which products should be evaluated, in what order, and at what point is it no longer beneficial to continue to evaluate additional products. We applied search theory to solve this problem of determining the selection strategy. This resulted in an optimal strategy but changes the way we view and manage software acquisition. In particular, the approach suggested that software acquisition may be better managed as an ongoing process instead of as a project with a distinct start and end. The approach formally incorporated the strategic importance of the application to the firm in determining the optimal strategy, a consideration that does not appear in the normal requirements-based approach to software selection.

Python Environment for Bayesian Learning: Inferring the Structure of Bayesian Networks from Knowledge and Data

In this paper, we introduce PEBL, a Python library and application for learning Bayesian network structure from data and prior knowledge that provides features unmatched by alternative software pac...

Measuring ocular aberrations and image quality in peripheral vision with a clinical wavefront aberrometer

Background: Clinical aberrometers are accurate, robust instruments for measuring wavefront aberrations for foveal vision but several practical concerns arise when performing aberrometry of the peripheral field. The purpose of this study was to evaluate these concerns experimentally using a physical eye model.Methods: A physical model eye was constructed to provide a stable test case that resembled a human eye. Aberrations were measured with a commercial Shack‐Hartmann aberrometer along lines‐of‐sight ranging from zero to 45° of eccentricity. Commercial software for wavefront reconstruction and Zernike analysis was adapted for use with elliptical entrance pupils encountered off‐axis.Results: Pupil dimensions estimated from the array of Shack‐Hartmann spots captured by the wavefront sensor followed geometrical optics predictions up to 30° eccentricity. With careful attention to detail, aberration analysis over an elliptical pupil was verified with alternative software. Retinal image quality declined slowly as eccentricity increased due to the eye model's spherical aberration. The total RMS computed from Zernike coefficients overestimated the total RMS computed based on the wavefront error of the elliptical pupil.Conclusion: Measurement of off‐axis wavefront aberrations of a model eye over a restricted range of eccentricities is possible with the COAS clinical wavefront aberrometer and auxiliary lenses to correct astigmatism. When central image quality is good, the off‐axis aberrations will have a powerful effect on peripheral image quality. When central image quality is poor, the additional effect of off‐axis aberrations will be minor.

Are two heads better than one for software development? the productivity paradox of pair programming

Extreme programming is currently gaining popularity as an alternate software development methodology. Pair programming, a core practice of this methodology, involves two programmers working collaboratively to develop software. This study examined the efficacy of pair programming by comparing the performance effectiveness and affective responses of collaborating pairs with those of individual programmers treated as nominal pairs. In a controlled laboratory experiment involving student subjects, proxies for entry level programmers working on entry level tasks, two factors were manipulated: programming setting (collaborative pair versus individuals) and programming task complexity (high versus low). Participants who worked in the individual condition were randomly combined into nominal pairs. The performance and affective responses of the collaborating pairs were then compared with those of the best performers and the second best performers of each nominal pair. Results indicated that programming pairs performed at the level above the second best performers and at the level of the best performers in each nominal pair. This relationship was found to be consistent across both levels of task complexity. Consequently, there was no evidence of an assembly bonus effect, where the performance of a collaborating pair exceeds the performance of its best member working alone. While this finding may appear counterintuitive due to the general perception of two heads being better than one, it is consistent with the findings in small group research. When affective responses were considered, programming pairs reported higher levels of satisfaction than those of the best and second-best performing members in nominal pairs. They also showed higher levels of confidence in their performance compared to those of the second-best members. But the confidence levels of pairs were no different from those of the best performing members in nominal pairs. Theoretical and practical implications of these findings are presented.

Modelling of cubic Bézier curves by electronic circuits

In this paper, analog techniques have been utilized to translate the mathematical formulation of arbitrary functions into electronic circuits which embody instantaneous DC relationships between sets of voltages having a limited dynamic range of variation. Suitable building blocks and electronic circuits have been designed to implement some of the basic functional operations. These functional operations were used to embody an analog modelling technique for the generation of free-form curves based on Bezier curve generation method. To draw a specified curve, the control parameters represented by a group of variable resistors are set at specified positions. These positions correspond to values of the control polygon vertices coordinates that uniquely define the curve shape. To change curve shape, the only requirement is to vary the control parameters represented by the variable resistors, and therefore, the user can use this electronic generation method as a shape designer. Using this analog modelling technique, one can generate curves at speed much more comparable to the alternative software modelling on a digital computer.

Are Two Heads Better than One for Software Development? The Productivity Paradox of Pair Programming

Extreme programming is currently gaining popularity as an alternate software development methodology. Pair programming, a core practice of this methodology, involves two programmers working collaboratively to develop software. This study examined the efficacy of pair programming by comparing the performance effectiveness and affective responses of collaborating pairs with those of individual programmers treated as nominal pairs. In a controlled laboratory experiment involving student subjects, proxies for entry level programmers working on entry level tasks, two factors were manipulated: programming setting (collaborative pair versus individuals) and programming task complexity (high versus low). Participants who worked in the individual condition were randomly combined into nominal pairs. The performance and affective responses of the collaborating pairs were then compared with those of the best performers and the second best performers of each nominal pair. Results indicated that programming pairs performed at the level above the second best performers and at the level of the best performers in each nominal pair. This relationship was found to be consistent across both levels of task complexity. Consequently, there was no evidence of an "assembly bonus effect," where the performance of a collaborating pair exceeds the performance of its best member working alone. While this finding may appear counterintuitive due to the general perception of two heads being better than one, it is consistent with the findings in small group research. When affective responses were considered, programming pairs reported higher levels of satisfaction than those of the best and second-best performing members in nominal pairs. They also showed higher levels of confidence in their performance compared to those of the second-best members. But the confidence levels of pairs were no different from those of the best performing members in nominal pairs. Theoretical and practical implications of these findings are presented.

Methods for Assessing Uncertainty in Fundamental Assumptions and Associated Models for Cancer Risk Assessment

The distributional approach for uncertainty analysis in cancer risk assessment is reviewed and extended. The method considers a combination of bioassay study results, targeted experiments, and expert judgment regarding biological mechanisms to predict a probability distribution for uncertain cancer risks. Probabilities are assigned to alternative model components, including the determination of human carcinogenicity, mode of action, the dosimetry measure for exposure, the mathematical form of the dose-response relationship, the experimental data set(s) used to fit the relationship, and the formula used for interspecies extrapolation. Alternative software platforms for implementing the method are considered, including Bayesian belief networks (BBNs) that facilitate assignment of prior probabilities, specification of relationships among model components, and identification of all output nodes on the probability tree. The method is demonstrated using the application of Evans, Sielken, and co-workers for predicting cancer risk from formaldehyde inhalation exposure. Uncertainty distributions are derived for maximum likelihood estimate (MLE) and 95th percentile upper confidence limit (UCL) unit cancer risk estimates, and the effects of resolving selected model uncertainties on these distributions are demonstrated, considering both perfect and partial information for these model components. A method for synthesizing the results of multiple mechanistic studies is introduced, considering the assessed sensitivities and selectivities of the studies for their targeted effects. A highly simplified example is presented illustrating assessment of genotoxicity based on studies of DNA damage response caused by naphthalene and its metabolites. The approach can provide a formal mechanism for synthesizing multiple sources of information using a transparent and replicable weight-of-evidence procedure.

Basin‐Scale Transmissivity and Storativity Estimation Using Hydraulic Tomography

While tomographic inversion has been successfully applied to laboratory- and field-scale tests, here we address the new issue of scale that arises when extending the method to a basin. Specifically, we apply the hydraulic tomography (HT) concept to jointly interpret four multiwell aquifer tests in a synthetic basin to illustrate the superiority of this approach to a more traditional Theis analysis of the same tests. Transmissivity and storativity are estimated for each element of a regional numerical model using the geostatistically based sequential successive linear estimator (SSLE) inverse solution method. We find that HT inversion is an effective strategy for incorporating data from potentially disparate aquifer tests into a basin-wide aquifer property estimate. The robustness of the SSLE algorithm is investigated by considering the effects of noisy observations, changing the variance of the true aquifer parameters, and supplying incorrect initial and boundary conditions to the inverse model. Ground water flow velocities and total confined storage are used as metrics to compare true and estimated parameter fields; they quantify the effectiveness of HT and SSLE compared to a Theis solution methodology. We discuss alternative software that can be used for implementing tomography inversion.

Geamm v.1.4: a versatile program for mixed model analysis of gene expression data

The research contract of J. Casellas was partially financed by Spain s Ministerio de Educacion y Ciencia (programa Juan de la Cierva). The authors are indebted to J. L. Noguera, R. Quintanilla, R. N. Pena and A. Canovas for their helpful comments. This software has been developed within the frame of research projects AGL2004-08368-C03/GAN, AGL2002-04271-C03 and GEN2003-20658-C05-05. GEAMM v.1.4 has been extensively tested on several data sets and results were checked for consistency with alternative software when possible.7 The authors would appreciate to be informed of any detected bug.

Comparing Nominate and Ideal: Points of Difference and Monte Carlo Tests

Empirical models of spatial voting allow legislators' locations in an abstract policy or ideological space to be inferred from their roll call votes. Over the past 25 years, these models have provided new insights about the US Congress and legislative behavior more generally (see, for example, Poole and Rosenthal, 1997). There are now a number of alternative models, estimators, and software that researchers can use to recover latent issue or ideological spaces from voting data. While these different estimators usually produce substantively similar estimates, important differences also arise. In this paper, we investigate the sources of observed differences between two leading methods, NOMINATE and IDEAL. Considering data from the 1994 to 1997 Supreme Court and the 109th Senate, we demonstrate that while some observed differences in the estimates produced by each model stem from fundamental differences in their underlying behavioral assumptions, others arise from arbitrary differences in implementation. Using Monte Carlo experiments, we find that neither model has a clear advantage over the other in the recovery of legislator locations or roll call midpoints in either large or small legislatures.

Portable telepathology: methods and tools

Telepathology is becoming easier to implement in most pathology departments. In fact e-mail image transmit can be done from almost any pathologist as a simplistic telepathology system. We tried to develop a way to improve capabilities of communication among pathologists with the idea that the system should be affordable for everybody. We took the premise that any pathology department would have microscopes and computers with Internet connection, and selected a few elements to convert them into a telepathology station. Needs were reduced to a camera to collect images, a universal microscope adapter for the camera, a device to connect the camera to the computer, and a software for the remote image transmit. We found out a microscope adapter (MaxView Plus) that allowed us connect almost any domestic digital camera to any microscope. The video out signal from the camera was sent to the computer through an Aver Media USB connector. At last, we selected a group of portable applications that were assembled into a USB memory device.Portable applications are computer programs that can be carried generally on USB flash drives, but also in any other portable device, and used on any (Windows) computer without installation. Besides when unplugging the device, none of personal data is left behind. We selected open-source applications, and based the pathology image transmission to VLC Media Player due to its functionality as streaming server, portability and ease of use and configuration. Audio transmission was usually done through normal phone lines. We also employed alternative videoconferencing software, SightSpeed for bi-directional image transmission from microscopes, and conventional cameras allowing visual communication and also image transmit from gross pathology specimens.All these elements allowed us to install and use a telepathology system in a few minutes, fully prepared for real time image broadcast.