UNLABELLED The analysis of gene regulatory networks (GRNs) is a central goal of bioinformatics highly accelerated by the advent of new experimental techniques, such as RNA interference. A battery of reverse engineering methods has been developed in recent years to reconstruct the underlying GRNs from these and other experimental data. However, the performance of the individual methods is poorly...

The International Workshops on Meta-Models and Schemas for Reverse Engineering aim at utilizing metatechnology for the development and use of reverse engineering toolsets. The focus of ateM 2004 is the integration of meta-technology of model driven engineering into reverse engineering. 1. Model Driven Engineering Model Driven Engineering (MDE) approaches are becoming increasingly popular. The M...

Genetic regulatory networks (GRNs) are complex, large-scale, and spatially and temporally distributed. These characteristics impose challenging demands on software tools for building GRN models, and so there is a need for custom tools. In this paper, we report on our ongoing development of BioTapestry, an open source, freely available computational tool designed specifically for building GRN mo...

Software reverse engineering involves analyzing computer program executables to understand their structure, functionality, and behavior. In this paper, common reverse engineering functions are decomposed to isolate the information-processing and sensemaking subtasks involved. This paper reviews the applicable literature on eliciting mental models of software reverse engineers. Based on the lite...

Reverse Engineering is focused on the challenging task of understanding legacy program code without having suitable documentation. Using a transformational forward engineering perspective, we gain the insight that much of this difficulty is caused by design decisions made during system development. Such decisions “hide” the program functionality and performance requirements in the final system ...

An important open problem in Reverse Mathematics ([16, 25]) is the reduction of the first-order strength of the base theory from IΣ1 to I∆0 + exp. The system ERNA, a version of Nonstandard Analysis based on the system I∆0 + exp, provides a partial solution to this problem. Indeed, Weak König’s lemma and many of its equivalent formulations from Reverse Mathematics can be ‘pushed down’ into ERNA,...

The International Workshop on Meta-Models and Schemas for Reverse Engineering aims at utilizing meta-technology for the development of reverse engineering toolsets. The workshop objective is to determine and specify areas in reverse engineering which will benefit from meta-technology and to discover and discuss meta-technologies which will provide significant additional support for developing a...

Research in systems biology focuses on the prediction and control of the behavior of biochemical networks through the use of mathematical models that accurately capture the responses of the network to certain types of perturbations. The construction of models based on the observations of these responses, referred to as reverse engineering, is an important step in discovering the structure and d...

Tools built in an ad hoc way and without proper models often display problems for both tool users and designers. Firstly, without systematic analysis and good understanding of the underlying software process model, we have little chance to design a tool that will adequately address user’s needs. Next, because one tool is often used in many different situations and by people who have different w...

Reverse engineering a program constructs a high-level representation suitable for various software development purposes such as documentation or reengineering. Unfortunately however, there are no established guidelines to assess the adequacy of such a representation. We propose two such criteria, completeness and accuracy, and show how they can be determined during the course of reversing the r...