MARVIN: a medical research application framework based on open source software

This paper describes the open source framework MARVIN for rapid application development in the field of biomedical and clinical research. MARVIN applications consist of modules that can be plugged together in order to provide the functionality required for a specific experimental scenario. Application modules work on a common patient database that is used to store and organize medical data as well as derived data. MARVIN provides a flexible input/output system with support for many file formats including DICOM, various 2D image formats and surface mesh data. Furthermore, it implements an advanced visualization system and interfaces to a wide range of 3D tracking hardware. Since it uses only highly portable libraries, MARVIN applications run on Unix/Linux, Mac OS X and Microsoft Windows.

A Fully Automatic Calibration Framework for Navigated Ultrasound Imaging

Navigated ultrasound (US) imaging is used for the intra-operative acquisition of 3D image data during imageguided surgery. The presented approach includes the design of a compact and easy to use US calibration device and its integration into a software application for navigated liver surgery. User interaction during the calibration process is minimized through automatic detection of the calibration process followed by automatic image segmentation, calculation of the calibration transform and validation of the obtained result. This leads to a fast, interaction-free and fully automatic calibration procedure enabling intra-operative

Spy: A Flexible Code Profiling Framework

Code profiling is an essential activity to increase software quality. It is commonly employed in a wide variety of tasks, such as supporting program comprehension, determining execution bottlenecks, and assessing code coverage by unit tests. Spy is an innovative framework to easily build profilers and visualize profiling information. The profiling information is obtained by inserting dedicated code before or after method execution. The gathered profiling information is structured in line with the application structure in terms of packages, classes, and methods. Spy has been instantiated on four occasions so far. We created profilers dedicated to test coverage, time execution, type feedback, and profiling evolution across version. We also integrated Spy in the Pharo IDE. Spy has been implemented in the Pharo Smalltalk programming language and is available under the MIT license.

Mondrian: An Agile Visualization Framework

Data visualization is the process of representing data as pictures to support reasoning about the underlying data. For the interpretation to be as easy as possible, we need to be as close as possible to the original data. As most visualization tools have an internal meta-model, which is different from the one for the presented data, they usually need to duplicate the original data to conform to their meta-model. This leads to an increase in the resources needed, increase which is not always justified. In this work we argue for the need of having an engine that is as close as possible to the data and we present our solution of moving the visualization tool to the data, instead of moving the data to the visualization tool. Our solution also emphasizes the necessity of reusing basic blocks to express complex visualizations and allowing the programmer to script the visualization using his preferred tools, rather than a third party format. As a validation of the expressiveness of our framework, we show how we express several already published visualizations and describe the pros and cons of the approach.

VirtualMesh: An Emulation Framework for Wireless Mesh Networks in OMNeT++

Wireless Mesh Networks (WMN) have proven to be a key technology for increased network coverage of Internet infrastructures. The development process for new protocols and architectures in the area of WMN is typically split into evaluation by network simulation and testing of a prototype in a test-bed. Testing a prototype in a real test-bed is time-consuming and expensive. Irrepressible external interferences can occur which makes debugging difficult. Moreover, the test-bed usually supports only a limited number of test topologies. Finally, mobility tests are impractical. Therefore, we propose VirtualMesh as a new testing architecture which can be used before going to a real test-bed. It provides instruments to test the real communication software including the network stack inside a controlled environment. VirtualMesh is implemented by capturing real traffic through a virtual interface at the mesh nodes. The traffic is then redirected to the network simulator OMNeT++. In our experiments, VirtualMesh has proven to be scalable and introduces moderate delays. Therefore, it is suitable for predeployment testing of communication software for WMNs.

Categorizing Developer Information Needs in Software Ecosystems

We present the results of an investigation into the nature of the information needs of software developers who work in projects that are part of larger ecosystems. In an open- question survey we asked framework and library developers about their information needs with respect to both their upstream and downstream projects. We investigated what kind of information is required, why is it necessary, and how the developers obtain this information. The results show that the downstream needs are grouped into three categories roughly corresponding to the different stages in their relation with an upstream: selection, adop- tion, and co-evolution. The less numerous upstream needs are grouped into two categories: project statistics and code usage. The current practices part of the study shows that to sat- isfy many of these needs developers use non-specific tools and ad hoc methods. We believe that this is a largely unexplored area of research.

Assimilation of Compliance Software in Highly Regulated Industries: An Empirical Multitheoretical Investigation

In this paper we follow a theory-based approach to study the assimilation of compliance software in highly regulated multinational enterprises. These relatively new software products support the automation of controls which are associated with mandatory compliance requirements. We use institutional and success factor theories to explain the assimilation of compliance software. A framework for analyzing the assimilation of Access Control Systems (ACS), a special type of compliance software, is developed and used to reflect the experiences obtained in four in-depth case studies. One result is that coercive, mimetic, and normative pressures significantly effect ACS assimilation. On the other hand, quality aspects have only a moderate impact at the beginning of the assimilation process, in later phases the impact may increase if performance and improvement objectives become more relevant. In addition, it turns out that position of the enterprises and compatibility heavily influence the assimilation process.

Explaining Variations in Client Extra Costs between Software Projects Offshored to India

Gaining economic benefits from substantially lower labor costs has been reported as a major reason for offshoring labor-intensive information systems services to low-wage countries. However, if wage differences are so high, why is there such a high level of variation in the economic success between offshored IS projects? This study argues that offshore outsourcing involves a number of extra costs for the ^his paper was recommended for acceptance by Associate Guest Editor Erran Carmel. client organization that account for the economic failure of offshore projects. The objective is to disaggregate these extra costs into their constituent parts and to explain why they differ between offshored software projects. The focus is on software development and maintenance projects that are offshored to Indian vendors. A theoretical framework is developed a priori based on transaction cost economics (TCE) and the knowledge-based view of the firm, comple mented by factors that acknowledge the specific offshore context The framework is empirically explored using a multiple case study design including six offshored software projects in a large German financial service institution. The results of our analysis indicate that the client incurs post contractual extra costs for four types of activities: (1) re quirements specification and design, (2) knowledge transfer, (3) control, and (4) coordination. In projects that require a high level of client-specific knowledge about idiosyncratic business processes and software systems, these extra costs were found to be substantially higher than in projects where more general knowledge was needed. Notably, these costs most often arose independently from the threat of oppor tunistic behavior, challenging the predominant TCE logic of market failure. Rather, the client extra costs were parti cularly high in client-specific projects because the effort for managing the consequences of the knowledge asymmetries between client and vendor was particularly high in these projects. Prior experiences of the vendor with related client projects were found to reduce the level of extra costs but could not fully offset the increase in extra costs in highly client-specific projects. Moreover, cultural and geographic distance between client and vendor as well as personnel turnover were found to increase client extra costs. Slight evidence was found, however, that the cost-increasing impact of these factors was also leveraged in projects with a high level of required client-specific knowledge (moderator effect).

Managing Knowledge Transfer in Software-Maintenance Outsourcing Transitions: A System-Dynamics Perspective

The existing literature suggests that transitions in software-maintenance offshore outsourcing projects are prone to knowledge transfer blockades, i.e. situations in which the activities that would yield effective knowledge transfer do not occur, and that client management involvement is central to overcome them. However, the theoretical understanding of the knowledge transfer blockade is limited, and the reactive management behavior reported in case studies suggests that practitioners may frequently be astonished by the dynamics that may give rise to the blockade. Drawing on recent research from offshore sourcing and reference theories, this study proposes a system dynamics framework that may explain why knowledge transfer blockades emerge and how and why client management can overcome the blockade. The results suggest that blockades may emerge from a vicious circle of weak learning due to cognitive overload of vendor staff and resulting negative ability attributions that result in reduced helping behavior and thus aggravate cognitive load. Client management may avoid these vicious circles by selecting vendor staff with strong prior related experience. Longer phases of coexistence of vendor staff and subject matter experts and high formal and clan controls may also mitigate vicious circles.

The Moldable Debugger: A Framework for Developing Domain-Specific Debuggers

Debuggers are crucial tools for developing object-oriented software systems as they give developers direct access to the running systems. Nevertheless, traditional debuggers rely on generic mechanisms to explore and exhibit the execution stack and system state, while developers reason about and formulate domain-specific questions using concepts and abstractions from their application domains. This creates an abstraction gap between the debugging needs and the debugging support leading to an inefficient and error-prone debugging effort. To reduce this gap, we propose a framework for developing domain-specific debuggers called the Moldable Debugger. The Moldable Debugger is adapted to a domain by creating and combining domain-specific debugging operations with domain-specific debugging views, and adapts itself to a domain by selecting, at run time, appropriate debugging operations and views. We motivate the need for domain-specific debugging, identify a set of key requirements and show how our approach improves debugging by adapting the debugger to several domains.

Practical domain-specific debuggers using the Moldable Debugger framework

Understanding the run-time behavior of software systems can be a challenging activity. Debuggers are an essential category of tools used for this purpose as they give developers direct access to the running systems. Nevertheless, traditional debuggers rely on generic mechanisms to introspect and interact with the running systems, while developers reason about and formulate domain-specific questions using concepts and abstractions from their application domains. This mismatch creates an abstraction gap between the debugging needs and the debugging support leading to an inefficient and error-prone debugging effort, as developers need to recover concrete domain concepts using generic mechanisms. To reduce this gap, and increase the efficiency of the debugging process, we propose a framework for developing domain-specific debuggers, called the Moldable Debugger, that enables debugging at the level of the application domain. The Moldable Debugger is adapted to a domain by creating and combining domain-specific debugging operations with domain-specific debugging views, and adapts itself to a domain by selecting, at run time, appropriate debugging operations and views. To ensure the proposed model has practical applicability (i.e., can be used in practice to build real debuggers), we discuss, from both a performance and usability point of view, three implementation strategies. We further motivate the need for domain-specific debugging, identify a set of key requirements and show how our approach improves debugging by adapting the debugger to several domains.