An automated wrapper-based approach to the design of dependable software

The design of dependable software systems invariably comprises two main activities: (i) the design of dependability mechanisms, and (ii) the location of dependability mechanisms. It has been shown that these activities are intrinsically difficult. In this paper we propose an automated wrapper-based methodology to circumvent the problems associated with the design and location of dependability mechanisms. To achieve this we replicate important variables so that they can be used as part of standard, efficient dependability mechanisms. These well-understood mechanisms are then deployed in all relevant locations. To validate the proposed methodology we apply it to three complex software systems, evaluating the dependability enhancement and execution overhead in each case. The results generated demonstrate that the system failure rate of a wrapped software system can be several orders of magnitude lower than that of an unwrapped equivalent

Soft tissue structure modelling for use in orthopaedic applications and musculoskeletal biomechanics

We present our methodology for the three-dimensional anatomical and geometrical description of soft tissues, relevant for orthopaedic surgical applications and musculoskeletal biomechanics. The technique involves the segmentation and geometrical description of muscles and neurovascular structures from high-resolution computer tomography scanning for the reconstruction of generic anatomical models. These models can be used for quantitative interpretation of anatomical and biomechanical aspects of different soft tissue structures. This approach should allow the use of these data in other application fields, such as musculoskeletal modelling, simulations for radiation therapy, and databases for use in minimally invasive, navigated and robotic surgery

Automatic C library wrapping Ctypes from the trenches

At some point of time many Python developers at least in computational science will face the situation that they want to interface some natively compiled library from Python. For binding native code to Python by now a larger variety of tools and technologies are available. This paper focuses on wrapping shared C libraries, using Python's default Ctypes. Particularly tools to ease the process (by using code generation) and some best practises will be stressed. The paper will try to tell a step by step story of the wrapping and development process, that should be transferable to similar problems

Integrating Deep-Web Information Sources

Deep-web information sources are difficult to integrate into automated business processes if they only provide a search form. A wrapping agent is a piece of software that allows a developer to query such information sources without worrying about the details of interacting with such forms. Our goal is to help soft ware engineers construct wrapping agents that interpret queries written in high-level structured languages. We think that this shall definitely help reduce integration costs because this shall relieve developers from the burden of transforming their queries into low-level interactions in an ad-hoc manner. In this paper, we report on our reference framework, delve into the related work, and highlight current research challenges. This is intended to help guide future research efforts in this area.Ministerio de Educación y Ciencia TIN2007-64119Junta de Andalucía P07-TIC-2602Junta de Andalucía P08-TIC-4100Ministerio de Ciencia e Innovación TIN2008-04718-

Construction and Software Design for a Microcomputer Controlled pH/Ion Titrator

The construction of an automated titration device is described. The major components include an Apple II+ Microcomputer and 8-bit parallel interface. Fisher Accumet, Model 520 Digital pH/lon Meter, Gilmont Micrometer Buret of 2.5 mL capacity, Sigma stepper motor, power supply and driver to operate the buret, and a constant temperature bath of ± 0.005 °C stability. The limitations of the system are 0.001 pH/0.1 mv for the pH/ion sensing system, and 0.125 μL per step for the buret. The system as described is designed to determine equilibrium constants for metal ion-amino acid complexes. By changing the software a variety of different pH and redox titration experiments may be performed. A computer program used to operate the stepper motor driven syringe buret and record the pH from a digital pH meter is described. The program uses both Apple BASIC and assembly language. This is a closed loop operation in which the data from the pH meter is used to control the amount of reagent delivered by the buret. The results are displayed graphically as the titration proceeds. The variance of the pH readings are calculated using an assembly language subroutine and the calculations are done with zero round-off error

Towards automated support for extraction of reusable components

A cost effective introduction of software reuse techniques requires the reuse of existing software developed in many cases without aiming at reusability. This paper discusses the problems related to the analysis and reengineering of existing software in order to reuse it. We introduce a process model for component extraction and focus on the problem of analyzing and qualifying software components which are candidates for reuse. A prototype tool for supporting the extraction of reusable components is presented. One of the components of this tool aids in understanding programs and is based on the functional model of correctness. It can assist software engineers in the process of finding correct formal specifications for programs. A detailed description of this component and an example to demonstrate a possible operational scenario are given

Ancient properties of spider silks revealed by the complete gene sequence of the prey-wrapping silk protein (AcSp1).

Spider silk fibers have impressive mechanical properties and are primarily composed of highly repetitive structural proteins (termed spidroins) encoded by a single gene family. Most characterized spidroin genes are incompletely known because of their extreme size (typically >9 kb) and repetitiveness, limiting understanding of the evolutionary processes that gave rise to their unusual gene architectures. The only complete spidroin genes characterized thus far form the dragline in the Western black widow, Latrodectus hesperus. Here, we describe the first complete gene sequence encoding the aciniform spidroin AcSp1, the primary component of spider prey-wrapping fibers. L. hesperus AcSp1 contains a single enormous (∼19 kb) exon. The AcSp1 repeat sequence is exceptionally conserved between two widow species (∼94% identity) and between widows and distantly related orb-weavers (∼30% identity), consistent with a history of strong purifying selection on its amino acid sequence. Furthermore, the 16 repeats (each 371-375 amino acids long) found in black widow AcSp1 are, on average, >99% identical at the nucleotide level. A combination of stabilizing selection on amino acid sequence, selection on silent sites, and intragenic recombination likely explains the extreme homogenization of AcSp1 repeats. In addition, phylogenetic analyses of spidroin paralogs support a gene duplication event occurring concomitantly with specialization of the aciniform glands and the tubuliform glands, which synthesize egg-case silk. With repeats that are dramatically different in length and amino acid composition from dragline spidroins, our L. hesperus AcSp1 expands the knowledge base for developing silk-based biomimetic technologies

50 years of isolation

The traditional means for isolating applications from each other is via the use of operating system provided “process” abstraction facilities. However, as applications now consist of multiple fine-grained components, the traditional process abstraction model is proving to be insufficient in ensuring this isolation. Statistics indicate that a high percentage of software failure occurs due to propagation of component failures. These observations are further bolstered by the attempts by modern Internet browser application developers, for example, to adopt multi-process architectures in order to increase robustness. Therefore, a fresh look at the available options for isolating program components is necessary and this paper provides an overview of previous and current research on the area

DOLFIN: Automated Finite Element Computing

We describe here a library aimed at automating the solution of partial differential equations using the finite element method. By employing novel techniques for automated code generation, the library combines a high level of expressiveness with efficient computation. Finite element variational forms may be expressed in near mathematical notation, from which low-level code is automatically generated, compiled and seamlessly integrated with efficient implementations of computational meshes and high-performance linear algebra. Easy-to-use object-oriented interfaces to the library are provided in the form of a C++ library and a Python module. This paper discusses the mathematical abstractions and methods used in the design of the library and its implementation. A number of examples are presented to demonstrate the use of the library in application code