Transportation disadvantage impedance indexing: A methodological approach to reduce policy shortcomings

Access to transport systems and the connection to such systems provided to essential economic and social activities are critical to determine households' transportation disadvantage levels. In spite of the developments in better identifying transportation disadvantaged groups, the lack of effective policies resulted in the continuum of the issue as a significant problem. This paper undertakes a pilot case investigation as test bed for a new approach developed to reduce transportation policy shortcomings. The approach, ‘disadvantage-impedance index’, aims to ease transportation disadvantages by employing representative parameters to measure the differences between policy alternatives run in a simulation environment. Implemented in the Japanese town of Arao, the index uses trip-making behaviour and resident stated preference data. The results of the index reveal that even a slight improvement in accessibility and travel quality indicators makes a significant difference in easing disadvantages. The index, integrated into a four-step model, proves to be highly robust and useful in terms of quick diagnosis in capturing effective actions, and developing potentially efficient policies.

VIP Barcoding: Composition vector-based software for rapid species identification based on DNA barcoding

Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time-consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user-friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two-stage algorithm. First, an alignment-free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment-based K2P distance nearest-neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment-free methods and (ii) higher scalability than alignment-based distance methods and character-based methods. These results suggest that this platform is able to deal with both large-scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/.

Leveraging of software as a service by small and medium enterprises: Information systems capabilities and organisational complementarities

This research explored how small and medium enterprises can achieve success with software as a service (SaaS) applications from cloud. Based upon an empirical investigation of six growth oriented and early technology adopting small and medium enterprises, this study proposes a SaaS for small and medium enterprise success model with two approaches: one for basic and one for advanced benefits. The basic model explains the effective use of SaaS for achieving informational and transactional benefits. The advanced model explains the enhanced use of software as a service for achieving strategic and transformational benefits. Both models explicate the information systems capabilities and organizational complementarities needed for achieving success with SaaS.

On the sensitivity of elastic waves due to structural damages:Time-frequency based indexing method

Time-frequency analysis of various simulated and experimental signals due to elastic wave scattering from damage are performed using wavelet transform (WT) and Hilbert-Huang transform (HHT) and their performances are compared in context of quantifying the damages. Spectral finite element method is employed for numerical simulation of wave scattering. An analytical study is carried out to study the effects of higher-order damage parameters on the reflected wave from a damage. Based on this study, error bounds are computed for the signals in the spectral and also on the time-frequency domains. It is shown how such an error bound can provide all estimate of error in the modelling of wave propagation in structure with damage. Measures of damage based on WT and HHT is derived to quantify the damage information hidden in the signal. The aim of this study is to obtain detailed insights into the problem of (1) identifying localised damages (2) dispersion of multifrequency non-stationary signals after they interact with various types of damage and (3) quantifying the damages. Sensitivity analysis of the signal due to scattered wave based on time-frequency representation helps to correlate the variation of damage index measures with respect to the damage parameters like damage size and material degradation factors.

Understanding the use of a bug tracking system in a global software development setup

Bug fixing is a highly cooperative work activity where developers, testers, product managers and other stake-holders collaborate using a bug tracking system. In the context of Global Software Development (GSD), where software development is distributed across different geographical locations, we focus on understanding the role of bug trackers in supporting software bug fixing activities. We carried out a small-scale ethnographic fieldwork in a software product team distributed between Finland and India at a multinational engineering company. Using semi-structured interviews and in-situ observations of 16 bug cases, we show that the bug tracker 1) supported information needs of different stake holder, 2) established common-ground, and 3) reinforced issues related to ownership, performance and power. Consequently, we provide implications for design around these findings.

A Survey Of Software Dependability

This paper presents on overview of the issues in precisely defining, specifying and evaluating the dependability of software, particularly in the context of computer controlled process systems. Dependability is intended to be a generic term embodying various quality factors and is useful for both software and hardware. While the developments in quality assurance and reliability theories have proceeded mostly in independent directions for hardware and software systems, we present here the case for developing a unified framework of dependability—a facet of operational effectiveness of modern technological systems, and develop a hierarchical systems model helpful in clarifying this view. In the second half of the paper, we survey the models and methods available for measuring and improving software reliability. The nature of software “bugs”, the failure history of the software system in the various phases of its lifecycle, the reliability growth in the development phase, estimation of the number of errors remaining in the operational phase, and the complexity of the debugging process have all been considered to varying degrees of detail. We also discuss the notion of software fault-tolerance, methods of achieving the same, and the status of other measures of software dependability such as maintainability, availability and safety.

Software simulation of the EEG

The literature contains many examples of digital procedures for the analytical treatment of electroencephalograms, but there is as yet no standard by which those techniques may be judged or compared. This paper proposes one method of generating an EEG, based on a computer program for Zetterberg's simulation. It is assumed that the statistical properties of an EEG may be represented by stationary processes having rational transfer functions and achieved by a system of software fillers and random number generators.The model represents neither the neurological mechanism response for generating the EEG, nor any particular type of EEG record; transient phenomena such as spikes, sharp waves and alpha bursts also are excluded. The basis of the program is a valid ‘partial’ statistical description of the EEG; that description is then used to produce a digital representation of a signal which if plotted sequentially, might or might not by chance resemble an EEG, that is unimportant. What is important is that the statistical properties of the series remain those of a real EEG; it is in this sense that the output is a simulation of the EEG. There is considerable flexibility in the form of the output, i.e. its alpha, beta and delta content, which may be selected by the user, the same selected parameters always producing the same statistical output. The filtered outputs from the random number sequences may be scaled to provide realistic power distributions in the accepted EEG frequency bands and then summed to create a digital output signal, the ‘stationary EEG’. It is suggested that the simulator might act as a test input to digital analytical techniques for the EEG, a simulator which would enable at least a substantial part of those techniques to be compared and assessed in an objective manner. The equations necessary to implement the model are given. The program has been run on a DEC1090 computer but is suitable for any microcomputer having more than 32 kBytes of memory; the execution time required to generate a 25 s simulated EEG is in the region of 15 s.

Effects of the digital subtitling software on the subtitling process : A survey among Finnish professional television subtitlers

Tutkielma käsittelee suomalaisten televisiotekstittäjien ammatillisuutta, käännösprosessia ja digitaalisten tekstitysohjelmien vaikutuksia tekstitysprosessiin ammattitekstittäjien näkökulmasta. Suomen television digitalisoituminen on aiheuttanut mullistuksia myös tekstitysalalla kun tekstitettävä kuvamateriaali on ryhdytty toimittamaan käännöstoimistoille ja tekstittäjille digitaalisena. Teoriaosuudessa käsitellään käännös- ja tekstitystutkimusta sekä koulutusta Suomessa, ammattitaitoa ja ammatillisuutta sekä kääntämisen apukeinoja. Tekstittäminen esitellään erikoistuneena kääntämisen muotona. On kuitenkin myös huomioitava, että kääntäminen on yksi vaihe tekstitysprosessissa. Teoriaosuus päättyy suomalaisten televisiotekstittäjien arjen ja työkentän nykytilanteen käsittelyyn – tekstittäjät työskentelevät monenlaisilla työehdoilla ja laadun kriteerit saatetaan joutua arvioimaan uudelleen. Empiirisen osan alussa esitetään, että suomalaisia televisiotekstittäjiä on haastateltu yllättävän vähän, ja Jääskeläisen ajatuksiin nojaten mainitaan, että tekstittämisen alalla on vielä paljon tutkimatta – etenkin suomalaisesta tekstitysprosessista löytyy tutkittavaa. Tutkimuskohde on ammatikseen televisioon tekstityksiä tekevät kääntäjät. Suomalaiselle tekstitykseen erikoistuneelle käännöstoimistolle työskenteleville tekstittäjille lähetettiin alkutalvesta 2008 kyselylomake, jolla kartoitettiin sekä monivalintakysymyksillä että avoimilla kysymyksillä heidän ammatillisuuttaan, työmenetelmiään, käännös- ja tekstitysprosessiaan, ammattiylpeyttään ja -identiteettiään, ajanhallintaansa, sekä heidän käyttämäänsä digitaalista tekstitysohjelmaa. Tutkimuksessa kävi ilmi, että lähes kolmanneksella vastaajista on ammatistaan neutraali tai jopa negatiivinen käsitys. Näitä tekstittäjiä yhdistää se seikka, että kaikilla on alle 5 vuotta kokemusta alalta. Valtaosa vastanneista on kuitenkin ylpeitä siitä, että toimivat suomen kielen ammattilaisina. Tekstitysprosessi oli lomakkeessa jaettu esikatseluvaiheeseen, käännösvaiheeseen, ajastamisvaiheeseen ja korjauskatseluvaiheeseen. Tekstittäjät pyydettiin mm. arvioimaan tekstitysprosessinsa kokonaiskestoa. Kestoissa ilmeni suuria eroavaisuuksia, joista ainakin osa korreloi kokemuksen kanssa. Runsas puolet vastaajista on hankkinut digitaalisen tekstitysohjelmiston käyttöönsä ja osa ajastaa edelleen käännöstoimistossa muun muassa ohjelmiston kalleuden vuoksi. Digitaalisen ohjelmiston myötä tekstitysprosessiin ja työkäytänteisiin on tullut muutoksia, kun videonauhureista ja televisioista on siirrytty pelkän tietokoneen käyttöön. On mahdollista tehdä etätyötä kaukomailta käsin, kääntää ja ajastaa lomittain tai tehdä esiajastus ja kääntää sitten. Digitaalinen tekniikka on siis mahdollistanut tekstitysprosessin muuttumisen ja vaihtoehtoiset työmenetelmät, mutta kaikista menetelmistä ei välttämättä ole tekstittäjälle hyötyä. Perinteinen tekstitysprosessi (esikatselu, repliikkijakojen merkitseminen käsikirjoitukseen, kääntäminen ja repliikkien laadinta, korjaukset ja tarkastuskatselu) vaikuttaa edelleen tehokkaimmalta. Vaikka työkäytänteet eroavat toisistaan, kokonaiskäsitys on se, että digitalisoitumisen alkukangertelujen jälkeen tekstittäjien työskentely on tehostunut.

Laboratory information management software for genotyping workflows: Applications in high throughput crop genotyping

Background: With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow Results: A laboratory information management system (LIMS) has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat) genotyping data from the legume (chickpea, groundnut and pigeonpea) and cereal (sorghum and millets) crops of importance in the semi-arid tropics. Conclusions: A laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping laboratory. The application with source code is freely available for academic users and can be downloaded from http://www.icrisat.org/bt-software-d-lims.htm

Simple software processes and tests improve the reliability and usefulness of a model.

Models are abstractions of reality that have predetermined limits (often not consciously thought through) on what problem domains the models can be used to explore. These limits are determined by the range of observed data used to construct and validate the model. However, it is important to remember that operating the model beyond these limits, one of the reasons for building the model in the first place, potentially brings unwanted behaviour and thus reduces the usefulness of the model. Our experience with the Agricultural Production Systems Simulator (APSIM), a farming systems model, has led us to adapt techniques from the disciplines of modelling and software development to create a model development process. This process is simple, easy to follow, and brings a much higher level of stability to the development effort, which then delivers a much more useful model. A major part of the process relies on having a range of detailed model tests (unit, simulation, sensibility, validation) that exercise a model at various levels (sub-model, model and simulation). To underline the usefulness of testing, we examine several case studies where simulated output can be compared with simple relationships. For example, output is compared with crop water use efficiency relationships gleaned from the literature to check that the model reproduces the expected function. Similarly, another case study attempts to reproduce generalised hydrological relationships found in the literature. This paper then describes a simple model development process (using version control, automated testing and differencing tools), that will enhance the reliability and usefulness of a model.

Breedcow and Dynama software redevelopment

The project renewed the Breedcow and Dynama software making it compatible with modern computer operating systems and platforms. Enhancements were also made to the linkages between the individual programs and their operation. The suite of programs is a critical component of the skill set required to make soundly based plans and production choices in the north Australian beef industry.

Automatic Lameness Detection in a Milking Robot : Instrumentation, measurement software, algorithms for data analysis and a neural network model

The aim of this thesis is to develop a fully automatic lameness detection system that operates in a milking robot. The instrumentation, measurement software, algorithms for data analysis and a neural network model for lameness detection were developed. Automatic milking has become a common practice in dairy husbandry, and in the year 2006 about 4000 farms worldwide used over 6000 milking robots. There is a worldwide movement with the objective of fully automating every process from feeding to milking. Increase in automation is a consequence of increasing farm sizes, the demand for more efficient production and the growth of labour costs. As the level of automation increases, the time that the cattle keeper uses for monitoring animals often decreases. This has created a need for systems for automatically monitoring the health of farm animals. The popularity of milking robots also offers a new and unique possibility to monitor animals in a single confined space up to four times daily. Lameness is a crucial welfare issue in the modern dairy industry. Limb disorders cause serious welfare, health and economic problems especially in loose housing of cattle. Lameness causes losses in milk production and leads to early culling of animals. These costs could be reduced with early identification and treatment. At present, only a few methods for automatically detecting lameness have been developed, and the most common methods used for lameness detection and assessment are various visual locomotion scoring systems. The problem with locomotion scoring is that it needs experience to be conducted properly, it is labour intensive as an on-farm method and the results are subjective. A four balance system for measuring the leg load distribution of dairy cows during milking in order to detect lameness was developed and set up in the University of Helsinki Research farm Suitia. The leg weights of 73 cows were successfully recorded during almost 10,000 robotic milkings over a period of 5 months. The cows were locomotion scored weekly, and the lame cows were inspected clinically for hoof lesions. Unsuccessful measurements, caused by cows standing outside the balances, were removed from the data with a special algorithm, and the mean leg loads and the number of kicks during milking was calculated. In order to develop an expert system to automatically detect lameness cases, a model was needed. A probabilistic neural network (PNN) classifier model was chosen for the task. The data was divided in two parts and 5,074 measurements from 37 cows were used to train the model. The operation of the model was evaluated for its ability to detect lameness in the validating dataset, which had 4,868 measurements from 36 cows. The model was able to classify 96% of the measurements correctly as sound or lame cows, and 100% of the lameness cases in the validation data were identified. The number of measurements causing false alarms was 1.1%. The developed model has the potential to be used for on-farm decision support and can be used in a real-time lameness monitoring system.

NEESTIMATOR v2: re-implementation of software for the estimation of contemporary effective population size (N-e) from genetic data

NeEstimator v2 is a completely revised and updated implementation of software that produces estimates of contemporary effective population size, using several different methods and a single input file. NeEstimator v2 includes three single-sample estimators (updated versions of the linkage disequilibrium and heterozygote-excess methods, and a new method based on molecular coancestry), as well as the two-sample (moment-based temporal) method. New features include the following: (i) an improved method for accounting for missing data; (ii) options for screening out rare alleles; (iii) confidence intervals for all methods; (iv) the ability to analyse data sets with large numbers of genetic markers (10000 or more); (v) options for batch processing large numbers of different data sets, which will facilitate cross-method comparisons using simulated data; and (vi) correction for temporal estimates when individuals sampled are not removed from the population (Plan I sampling). The user is given considerable control over input data and composition, and format of output files. The freely available software has a new JAVA interface and runs under MacOS, Linux and Windows.

Information sharing in distance collaboration: A software engineering perspective

Information sharing in distance collaboration: A software engineering perspective, QueenslandFactors in software engineering workgroups such as geographical dispersion and background discipline can be conceptually characterized as "distances", and they are obstructive to team collaboration and information sharing. This thesis focuses on information sharing across multidimensional distances and develops an information sharing distance model, with six core dimensions: geography, time zone, organization, multi-discipline, heterogeneous roles, and varying project tenure. The research suggests that the effectiveness of workgroups may be improved through mindful conducts of information sharing, especially proactive consideration of, and explicit adjustment for, the distances of the recipient when sharing information.