Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

Background: The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. Results: In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. Conclusions: With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined

Beyond Dualisms in Methodology: An Integrative Design Research Medium "MAPS" and some Reflections

Design research is an academic issue and increasingly an essential success factor for industrial, organizational and social innovation. The fierce rejection of 1st generation design methods in the early 1970s resulted in the postmodernist attitude of "no methods", and subsequently, after more than a decade, in the strong adoption of scientific methods, or "the" scientific method, for design research. The current situation regarding methodology is characterized by unproductive dualisms such as scientific methods vs. designerly methods, normative methods vs. descriptive methods, research vs. design. The potential of the early (1st generation) methods is neglected and the practical usefulness of design research is impeded. The suggestion for 2nd generation methods as discussed by Rittel and others has hardly been taken up in design. The development of a methodological tool / medium for research through design – MAPS – (which is the central part of the paper) presents the cause and catalyst for some reflections about the usability / desirability / usefulness of methodical support for the design (research) process. Keywords: Integrative Design Research Medium, Research Through Design, MAPS, Methodology</p

Establishing a Central Archive for Transit Passenger Data

This report describes the rationale, background, establishing organization, and future steps of CATPAD, the Central Archive for Transit Passenger Data. The Central Archive for Transit Passenger Data is a repository that collects, indexes, archives, and makes available online the transit survey instruments, data, and reports collected across the country. This resource is unique in its focus on the disaggregated information of individual transit users – information that is critical for a range of transportation planning analyses. In addition, where available, CATPAD contains aggregated information, such as station boardings and service and fare schedules, to provide key context for the disaggregate person-level data. The Central Archive for Transit Passenger Data seeks to overcome the current impediments to accessing transit survey data by providing a single, searchable, internet archive to store and disseminate this valuable information. The Central Archive for Transit Passenger Data explicitly aims to expand the public return on the considerable investment made to gather transit passenger data. The resource is designed from the start to serve the needs of a range of use cases from transportation planners and policy makers to researchers and community advocates. The goal of CATPAD is to make useful data available to inform transit decision making at all levels and to foster ongoing refinement of the nation’s transit network

An artefact repository to support distributed software engineering

The Open Source Component Artefact Repository (OSCAR) system is a component of the GENESIS platform designed to non-invasively inter-operate with work-flow management systems, development tools and existing repository systems to support a distributed software engineering team working collaboratively. Every artefact possesses a collection of associated meta-data, both standard and domain-specific presented as an XML document. Within OSCAR, artefacts are made aware of changes to related artefacts using notifications, allowing them to modify their own meta-data actively in contrast to other software repositories where users must perform all and any modifications, however trivial. This recording of events, including user interactions provides a complete picture of an artefact's life from creation to (eventual) retirement with the intention of supporting collaboration both amongst the members of the software engineering team and agents acting on their behalf

Characteristics, accuracy and reverification of robotised articulated arm CMMs

VDI article 2617 specifies characteristics to describe the accuracy of articulated arm coordinate measuring machines (AACMMs) and outlines procedures for checking them. However the VDI prescription was written with a former generation of machines in mind: manual arms exploiting traditional touch probe technologies. Recent advances in metrology have given rise to noncontact laser scanning tools and robotic automation of articulated arms – technologies which are not adequately characterised using the VDI specification. In this paper we examine the “guidelines” presented in VDI 2617, finding many of them to be ambiguous and open to interpretation, with some tests appearing even to be optional. The engineer is left significant flexibility in the execution of the test procedures and the manufacturer is free to specify many of the test parameters. Such flexibility renders the VDI tests of limited value and the results can be misleading. We illustrate, with examples using the Nikon RCA, how a liberal interpretation of the VDI guidelines can significantly improve accuracy characterisation and suggest ways in which to mitigate this problem. We propose a series of stringent tests and revised definitions, in the same vein as VDI 2617 and similar US standards, to clarify the accuracy characterisation process. The revised methodology includes modified acceptance and reverification tests which aim to accommodate emerging technologies, laser scanning devices in particular, while maintaining the spirit of the existing and established standards. We seek to supply robust re-definitions for the accepted terms “zero point” and “useful arm length”, pre-supposing nothing about the geometry of the measuring device. We also identify a source of error unique to robotised AACMMs employing laser scanners – the forward-reverse pass error. We show how eliminating this error significantly improves the repeatability of a device and propose a novel approach to the testing of probing error based on statistical uncertainty