Showing papers on "Interaction network published in 1997"

A Knowledge Base for D. melanogaster Gene Interactions Involved in Pattern Formation

Abstract: The understanding of pattern formation in Drosophila requires the handling of the many genetic and molecular interactions which occur between developmental genes. For that purpose, a knowledge base (KNIFE) has been developed in order to structure and manipulate the interaction data. KNIFE contains data about interactions published in the literature and gathered from various databases. These data are structured in an object knowledge representation system into various interrelated entities. KNIFE can be browsed through a WWW interface in order to select, classify and examine the objects and their references in other bases. It also provides specialised biological tools such as interaction network manipulation and diagnosis of missing interactions.

The use of SHIFT in system design

Abstract: SHIFT is a programming language for describing dynamic networks of hybrid automata. Such systems consist of components which can be created, interconnected and destroyed and the system evolves. Components exhibit hybrid behavior, consisting of continuous-time phases separated by discrete-event transitions. Components may evolve independently, or they may interact through their inputs, outputs and exported events. The interaction network itself may evolve. This paper illustrates how SHIFT was used to analyze multiple merge junction automated highways for safety and efficiency by several design teams comprising graduate students, research engineers and faculty.

Using interaction networks for visualisation of message passing

Abstract: Understanding software structured as separate programs that communicate via message passing requires understanding how the various programs interact with each other, as well as understanding the individual programs in isolation An interaction network display shows in a visual way message passing within and between programs We have implemented an interaction network monitor for the MINIX operating system, for use in showing students how the system programs and processes of MINIX interact to provide operating system services We give three examples to demonstrate the insights into message-based systems that can be gained from studying interaction network displays

The Use of S IFT in System Design

Abstract: Shift is a programming language for describing dynamic networks of hybrid automata. Such systems consist of components which can be created, interconnected and destroyed as the system evolves. Components exhibit hybrid behavior, consisting of continuous-time phases separated by discreteevent transitions. Components may evolve independently, or they may interact through their inputs, outputs and exported events. The interaction network itself may evolve. This paper illustrates how SHIFT was used to analyze multiple merge junction automated highways for safety and efficiency by several design teams comprising graduate students, research engineers and faculty.

A knowledge base for D. melanogaster gene interactions involved in pattern formation

Abstract: The understanding of pattern formation in Drosophila requires the handling of the many genetic and molecular interactions which occur between developmental genes. For that purpose, a knowledge base (KNIFE) has been developed in order to structure and manipulate the interaction data. KNIFE contains data about interactions published in the literature and gathered from various databases. These data are structured in an object knowledge representation system into various interrelated entities. KNIFE can be browsed through a WWW interface in order to select, classify and examine the objects and their references in other bases. It also provides specialised biological tools such as interaction network manipulation and diagnosis of missing interactions. We are interested in the biological process of pattern formation in Drosophila and in understanding the basis of specific identity acquisition by the different body parts [Fasano et al. 1991; Rrder, Vola and Kerridge 1992; Alexandre et al. 1996]. In Drosophila, different classes of genes involved in the segmentation processes (maternal, gap, pair-rule and segment polarity genes) divide the embryo along the antero-posterior axis into repeated homologous units [Niisslein-Volhard and Wieschaus 1980; Gaul and J~ickle 1990] which will develop specific identities and morphogenetic features under the control of homeotic genes [Lewis 1978]. Specific interactions within and between these gene families are essential for the establishment of a correct body pattern. Being able to access, query and manipulate the data on these developmental genes and their functional interactions within specific regulatory networks is now an important requirement for developmental and molecular biologists studying gene regulation. Gene molecular interactions, i.e. direct molecular interactions involving DNA,RNA and proteins, play an essential role in all known biological processes. Although different databases exist for each of these three types of