Dag Björklund

BODIL: a molecular modeling environment for structure-function analysis and drug design.

BODIL is a molecular modeling environment geared to help the user to quickly identify key features of proteins critical to molecular recognition, especially (1) in drug discovery applications, and (2) to understand the structural basis for function. The program incorporates state-of-the-art graphics, sequence and structural alignment methods, among other capabilities needed in modern structure–function–drug target research. BODIL has a flexible design that allows on-the-fly incorporation of new modules, has intelligent memory management, and fast multi-view graphics. A beta version of BODIL and an accompanying tutorial are available at http://www.abo.fi/fak/mnf/bkf/research/johnson/bodil.html

A language for multiple models of computation

We introduce a new kernel language for modeling hardware/software systems, adopting multiple heterogenous models of computation. The language has formal operational semantics, and is well suited for model checking, code synthesis etc. For different blocks of code, different scheduling policies can be applied, to reflect the different interpretations of, for example, parallelism in different models of computation. The user can add his own scheduling policies, to use or explore different models of computation.

A unified approach to code generation from behavioral diagrams

In this article we show how to use the Rialto intermediate language, to capture the semantics of UML behavioral diagrams. The Rialto language has a formal semantics given as structural operational rules and it supports semantic variations. It can be used to uniformly describe thc behavior of a combination of several diagrams and as a bridge from UML models to animation and production code.

Efficient code synthesis from synchronous dataflow graphs

We present a novel approach for efficient code synthesis from synchronous dataflow specifications. The method avoids duplication of code blocks when compiling SDF graphs regardless of whether a single appearance schedule can be found for the graph or not. This also means that we can use schedules that require minimal buffer memory but are not single appearance schedules. The method has been developed within the compiler for the Rialto language, which we have developed for use as an intermediate language for code synthesis from heterogeneous models of computation. The optimization technique presented in the paper can, however, very well also be used without the Rialto language.

A Workbench to Experiment on New Model Engineering Applications

There are many di.erent tools that support, in one way or another, the Uni.ed Modeling Language (UML), but most of these tools are targeted to software developers. The System Modeling Workbench (SMW) [8] is a collection of tools targeted to those interested in doing research on new modeling languages and constructing tools to transform and derive new artifacts from models in those languages.

Rialto to B: an exercise in formal development of a language for multiple models of computation

Rialto is a textual language for modeling heterogeneous systems, where different computational models are represented by scheduling policies that manage concurrent activities in the system. Rialto has a formal semantics defined using structured operational rules, which allows for the application of formal verification techniques to programs in the language. We show that the B method is suitable for this purpose. We present an approach for translating the language into B, where we have specified the actual Rialto semantics as a program interpreter in B. Rialto programs can automatically be translated into B specifications and we can use this interpreter to animate and validate them.

Towards a Kernel Language for Heterogeneous Computing

What is characteristic of modern embedded systems like mobile phones, multimedia terminals, etc. is that their design requires several different description techniques: The radio-frequency part of a mobile phone is designed using analog techniques, the signal processing part can be described using synchronous data-flow, while the protocol stack uses an extended finite state machine based description model. This heterogeneity poses a challenge to embedded system design methodologies, and has resulted in a search for a System Level Design Language (SLDL) for describing both software and hardware. We believe that to obtain a good SLDL one needs to first understand what the combination of models of computation means. To this end we are developing a kernel language in which it is possible to use different models of computation. The main contributions of this work are: (1) a common set of concepts that form the basis of the kernel language, (2) a formally defined operational semantics, which also makes it possible to verify designs using e.g. model-checking, (3) the explicit use of atomicity and, (4) the introduction of the notion of execution policy.

Rialto profile in the SMW toolkit

We present an extension to the System Modeling Workbench to transform UML behavioral diagrams into specifications in Rialto. Rialto is a behavioral description language with formally defined semantics that supports multiple models of computation and can be compiled into compact code in different target languages.