Consistency in Multi-Viewpoint Architectural Design of Enterprise Information Systems

Different stakeholders in the design of an enterprise information system have their own view on that design. To help produce a coherent design this paper presents a framework that aids in specifying relations between such views. To help produce a consistent design the framework also aids in specifying consistency rules that apply to the view relations and in checking the consistency according to those rules. The framework focuses on the higher levels of abstraction in a design, we refer to design at those levels of abstraction as architectural design. The highest level of abstraction that we consider is that of business process design and the lowest level is that of software component design. The contribution of our framework is that it provides a collection of basic concepts that is common to viewpoints in the area of enterprise information systems. These basic concepts aid in relating viewpoints by providing: (i) a common terminology that helps stakeholders to understand each others concepts; and (ii) a basis for defining re-usable consistency rules. In particular we define re-usable rules to check consistency between behavioural views that overlap or are a refinement of each other. We also present an architecture for a tool suite that supports our framework. We show that our framework can be applied, by performing a case study in which we specify the relations and consistency rules between the RM-ODP enterprise, computational and information viewpoints

Intrinsically Disordered C-Terminal Tails of \u3cem\u3eE. coli\u3c/em\u3e Single-Stranded DNA Binding Protein Regulate Cooperative Binding to Single-Stranded DNA

The homotetrameric Escherichia coli single-stranded DNA binding protein (SSB) plays a central role in DNA replication, repair and recombination. E. coli SSB can bind to long single-stranded DNA (ssDNA) in multiple binding modes using all four subunits [(SSB)65 mode] or only two subunits [(SSB)35 binding mode], with the binding mode preference regulated by salt concentration and SSB binding density. These binding modes display very different ssDNA binding properties with the (SSB)35 mode displaying highly cooperative binding to ssDNA. SSB tetramers also bind an array of partner proteins, recruiting them to their sites of action. This is achieved through interactions with the last 9 amino acids (acidic tip) of the intrinsically disordered linkers (IDLs) within the four C-terminal tails connected to the ssDNA binding domains. Here, we show that the amino acid composition and length of the IDL affects the ssDNA binding mode preferences of SSB protein. Surprisingly, the number of IDLs and the lengths of individual IDLs together with the acidic tip contribute to highly cooperative binding in the (SSB)35 binding mode. Hydrodynamic studies and atomistic simulations suggest that the E. coli SSB IDLs show a preference for forming an ensemble of globular conformations, whereas the IDL from Plasmodium falciparum SSB forms an ensemble of more extended random coils. The more globular conformations correlate with cooperative binding

Formal executable descriptions of biological systems

The similarities between systems of living entities and systems of concurrent processes may support biological experiments in silico. Process calculi offer a formal framework to describe biological systems, as well as to analyse their behaviour, both from a qualitative and a quantitative point of view. A couple of little examples help us in showing how this can be done. We mainly focus our attention on the qualitative and quantitative aspects of the considered biological systems, and briefly illustrate which kinds of analysis are possible. We use a known stochastic calculus for the first example. We then present some statistics collected by repeatedly running the specification, that turn out to agree with those obtained by experiments in vivo. Our second example motivates a richer calculus. Its stochastic extension requires a non trivial machinery to faithfully reflect the real dynamic behaviour of biological systems