Metacomputing in practice: a distributed compute server for pharmaceutical industry

We describe a distributed high-performance compute server that has been implemented for running compute-intensive applications on a mixture of HPC systems interconnected by Inter-and Intranet. With a practical industrial background, our work focusses on high availability, efficient job load balancing, security, and the easy integration of HPC computing into the daily work-flow at pharmaceutical companies.

The work was done in the course of the ESPRIT project P A Distributed Pharmaceutical Application Server The client software is implemented in Java. All results are displayed in a web browser and can be forwarded to the next stage of applications used in the drug design cycle. The server software handles the job load balancing between the participating HPC nodes and is capable of managing multi-site applications.

Our environment currently supports four key applications that are used in rational drug design and drug target identification. They range from the automatic functional annotation of protein sequences to three-dimensional protein structure prediction tools and protein comparison applications.     

Note on the interpretation of electroluminescence images using their spectral information

We show how to use the reciprocity between electroluminescence and solar cell quantum efficiency for the simulation and interpretation of electroluminescence images. The analysis of the spectral properties of the electroluminescence images obtained by using different short- and long-pass filters yields information about surface recombination velocity, bulk diffusion length and reflection of the back side in flat and textured solar cells.     

Potent Inhibition of Acid Sphingomyelinase by Phosphoinositide Analogues

The different mammalian sphingomyelinases are involved in cell regulation, apoptosis and inflammatory events. Recent reports suggest pharmacological potential especially for inhibitors of the acid sphingomyelinase. Phosphatidyl inositol‐3,5bisphosphate (PtdIns3,5P₂) is the most potent selective acid sphingomyelinase inhibitor known to date. In the present study, we synthesized analogues of PtdIns3,5P₂ for initial structure–activity‐relationship (SAR) studies. We identified an inhibitor that is easy to synthesize, that has superior chemical and biophysical properties when compared to PtdIns3,5P₂ and that should be stable against virtually all phospholipases. Last but not least, the new inhibitor partially protected cells from dexamethasone‐induced cell death.     

Aluminium in wild mushrooms and cultivated Agaricus bisporus

 The aluminium content in wild mushrooms (n = 271, 19 species) and in cultivated Agaricus bisporus (n = 15) was determined by graphite furnace atomic absorption spectroscopy. With an aluminium content of 30 – 50 μ/g dry matter (DM) Boletus and Xerocomus species, the most well-known and most popular mushrooms, proved to be poor in aluminium. Several species of the genus Suillus, Macrolepiota rhacodes, Hypholoma capnoides as well as individual samples of Russula ochroleuca and Amanita rubescens contained high aluminium concentrations of about 100 μg/g DM and more. Cultivated Agaricus bisporus had the lowest aluminium content, i. e. 14 μg/g DM. The site, its geological origin as well as the mushroom species influenced the aluminium content in the fruitbodies: these factors require further investigation. Mushrooms do not contribute significantly to aluminium intake by humans. Received: 23 January 1997     

Efficient Sequence Alignment with Side-Constraints by Cluster Tree Elimination

Aligning DNA and protein sequences is a core technique in molecular biology. Often, it is desirable to include partial prior knowledge and conditions in an alignment. Going beyond prior work, we aim at the integration of such side constraints in free combination into alignment algorithms. The most common and successful technique for efficient alignment algorithms is dynamic programming (DP). However, a weakness of DP is that one cannot include additional constraints without specifically tailoring a new DP algorithm. Here, we discuss a declarative approach that is based on constraint techniques and show how it can be extended by formulating additional knowledge as constraints. We take special care to obtain the efficiency of DP for sequence alignment. This is achieved by careful modeling and applying proper solving strategies. Finally, we apply our method to the scanning for RNA motifs in large sequences. This case study demonstrates how the new approach can be used in real biological problems. A prototypic implementation of the method is available at .     

An optimality criteria based method for discrete design optimization taking into account buildability constraints

This paper presents a heuristic design optimization method specifically developed for practicing structural engineers. Practical design optimization problems are often governed by buildability constraints. The majority of optimization methods that have recently been proposed for design optimization under buildability constraints are based on evolutionary computing. While these methods are generally easy to implement, they require a large number of function evaluations (finite element analyses), and they involve algorithmic parameters that require careful tuning. As a consequence, both the computation time and the engineering time are high. The discrete design optimization algorithm presented in this paper is based on the optimality criteria method for continuous optimization. It is faster than an evolutionary algorithm and it is free of tuning parameters. The algorithm is successfully applied to two classical benchmark problems (the design of a ten-bar truss and an eight-story frame) and to a practical truss design optimization problem.     

Imaging-sonar observations of salmonid interactions with a vertical axis instream turbine

Anthropogenic activities and their influences on aquatic systems is an important topic, especially considering the growing interest in using the earth's resources in a sustainable way. One of those anthropogenic activities is the introduction of renewable technologies into the aquatic environment such as instream turbines. Environmental studies around those technologies are often still ongoing due to their novelty. During the spring of 2018, juvenile individuals of two salmonid species, Atlantic salmon and brown trout were released upstream a vertical axis instream turbine in the river Dal (Dalälven) in eastern Sweden. The aim of this study was to investigate the swimming behavior of the salmonids around a small-scale prototype vertical axis instream turbine. The swimming pattern and the possible response of avoiding the vertical axis instream turbine were documented with a multi beam sonar. A control area, next to the turbine, was used as reference. No consistent results were shown for trout as they were passing the control area with a statistically high variation, and specimens were rarely observed in proximity of the turbine, neither if the turbine was operating nor at stand still. Salmon clearly avoided the operating turbine, but did not avoid the turbine when it was at stand still, and was often observed swimming straight through the turbine area. These findings indicate that operating this type of instream turbine in a river affects the swimming behavior of Atlantic salmon but is unlikely to affect its migration paths. For brown trout, the statistical results are inconclusive, although data indicate a response of avoiding the turbine. The species are in little risk to suffer physical harm as no fish entered the rotating turbine, despite very turbid water conditions.