Decision - Support Software Tool Handbook

The road and transport industry in Australia and overseas has come a long way to understanding the impact of road traffic noise on the urban environment. Most road authorities now have guidelines to help assess and manage the impact of road traffic noise on noise-sensitive areas and development. While several economic studies across Australia and overseas have tried to value the impact of noise on property prices, decision-makers investing in road traffic noise management strategies have relatively limited historic data and case studies to go on. The perceived success of a noise management strategy currently relies largely on community expectations at a given time, and is not necessarily based on the analysis of the costs and benefits, or the long-term viability and value to the community of the proposed treatment options. With changing trends in urban design, it is essential that the 'whole-of-life' costs and benefits of noise ameliorative treatment options and strategies be identified and made available for decisionmakers in future investment considerations. For this reason, CRC for Construction Innovation Australia funded a research project, Noise Management in Urban Environments to help decision-makers with future road traffic noise management investment decisions. RMIT University and the Queensland Department of Main Roads (QDMR) have conducted the research work, in collaboration with the Queensland Department of Public Works, ARUP Pty Ltd, and the Queensland University of Technology. The research has formed the basis for the development of a decision-support software tool, and helped collate technical and costing data for known noise amelioration treatment options. We intend that the decision support software tool (DST) should help an investment decision-maker to be better informed of suitable noise ameliorative treatment options on a project-by-project basis and identify likely costs and benefits associated with each of those options. This handbook has been prepared as a procedural guide for conducting a comparative assessment of noise ameliorative options. The handbook outlines the methodology and assumptions adopted in the decision-support framework for the investment decision-maker and user of the DST. The DST has been developed to provide an integrated user-friendly interface between road traffic noise modelling software, the relevant assessment criteria and the options analysis process. A user guide for the DST is incorporated in this handbook.

A software tool for simulating spatial separation and kinetics in biological membranes

Self-segregation and compartimentalisation are observed experimentally to occur spontaneously on live membranes as well as reconstructed model membranes. It is believed that many of these processes are caused or supported by anomalous diffusive behaviours of biomolecules on membranes due to the complex and heterogeneous nature of these environments. These phenomena are on the one hand of great interest in biology, since they may be an important way for biological systems to selectively localize receptors, regulate signaling or modulate kinetics; and on the other, they provide an inspiration for engineering designs that mimick natural systems. We present an interactive software package we are developing for the purpose of simulating such processes numerically using a fundamental Monte Carlo approach. This program includes the ability to simulate kinetics and mass transport in the presence of either mobile or immobile obstacles and other relevant structures such as liquid-ordered lipid microdomains. We also present preliminary simulation results regarding the selective spatial localization and chemical kinetics modulating power of immobile obstacles on the membrane, obtained using the program.

PAnalyzer: A software tool for protein inference in shotgun proteomics

Background Protein inference from peptide identifications in shotgun proteomics must deal with ambiguities that arise due to the presence of peptides shared between different proteins, which is common in higher eukaryotes. Recently data independent acquisition (DIA) approaches have emerged as an alternative to the traditional data dependent acquisition (DDA) in shotgun proteomics experiments. MSE is the term used to name one of the DIA approaches used in QTOF instruments. MSE data require specialized software to process acquired spectra and to perform peptide and protein identifications. However the software available at the moment does not group the identified proteins in a transparent way by taking into account peptide evidence categories. Furthermore the inspection, comparison and report of the obtained results require tedious manual intervention. Here we report a software tool to address these limitations for MSE data. Results In this paper we present PAnalyzer, a software tool focused on the protein inference process of shotgun proteomics. Our approach considers all the identified proteins and groups them when necessary indicating their confidence using different evidence categories. PAnalyzer can read protein identification files in the XML output format of the ProteinLynx Global Server (PLGS) software provided by Waters Corporation for their MSE data, and also in the mzIdentML format recently standardized by HUPO-PSI. Multiple files can also be read simultaneously and are considered as technical replicates. Results are saved to CSV, HTML and mzIdentML (in the case of a single mzIdentML input file) files. An MSE analysis of a real sample is presented to compare the results of PAnalyzer and ProteinLynx Global Server. Conclusions We present a software tool to deal with the ambiguities that arise in the protein inference process. Key contributions are support for MSE data analysis by ProteinLynx Global Server and technical replicates integration. PAnalyzer is an easy to use multiplatform and free software tool.

Automatic refinement of user requirements : a case study in software tool evaluation

This paper presents an assessment of system effectiveness in automatic requirements refinement by comparing results obtained from experts and novices with those achieved by the system. As the investigated system was a combination of a tightly inter-connected methods and a tool, the evaluation framework melded together a number of distinct methodological approaches structured into three empirical studies, which aimed at the construction of a case problem domain, calibrating the system using this defined domain elements and finally using the calibrated system to assess its effectiveness. In consequence, it was concluded that the evaluated methods and tools were effective in supporting requirements refinement.

Highlights in Analytical Chemistry in Switzerland: OMA & OPA - A Software Tool for Mass Spectrometric Sequencing of Nucleic Acids

Oligonucleotides comprising unnatural building blocks, which interfere with the translation machinery, have gained increased attention for the treatment of gene-related diseases (e.g. antisense, RNAi). Due to structural modifications, synthetic oligonucleotides exhibit increased biostability and bioavailability upon administration. Consequently, classical enzyme-based sequencing methods are not applicable to their sequence elucidation and verification. Tandem mass spectrometry is the method of choice for performing such tasks, since gas-phase dissociation is not restricted to natural nucleic acids. However, tandem mass spectrometric analysis can generate product ion spectra of tremendous complexity, as the number of possible fragments grows rapidly with increasing sequence length. The fact that structural modifications affect the dissociation pathways greatly increases the variety of analytically valuable fragment ions. The gas-phase dissociation of oligonucleotides is characterized by the cleavage of one of the four bonds along the phosphodiester chain, by the accompanying loss of nucleases, and by the generation of internal fragments due to secondary backbone cleavage. For example, an 18-mer oligonucleotide yields a total number of 272’920 theoretical fragment ions. In contrast to the processing of peptide product ion spectra, which nowadays is highly automated, there is a lack of tools assisting the interpretation of oligonucleotide data. The existing web-based and stand-alone software applications are primarily designed for the sequence analysis of natural nucleic acids, but do not account for chemical modifications and adducts. Consequently, we developed a software to support the interpretation of mass spectrometric data of natural and modified nucleic acids and their adducts with chemotherapeutic agents.