PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology

PARALIGN is a rapid and sensitive similarity search tool for the identification of distantly related sequences in both nucleotide and amino acid sequence databases. Two algorithms are implemented, accelerated Smith–Waterman and ParAlign. The ParAlign algorithm is similar to Smith–Waterman in sensitivity, while as quick as BLAST for protein searches. A form of parallel computing technology known as multimedia technology that is available in modern processors, but rarely used by other bioinformatics software, has been exploited to achieve the high speed. The software is also designed to run efficiently on computer clusters using the message-passing interface standard. A public search service powered by a large computer cluster has been set-up and is freely available at , where the major public databases can be searched. The software can also be downloaded free of charge for academic use

Seasonal and interannual variability in abundance and population development of Calanus finmarchicus at the western entrance to the Barents Sea, 1995–2019

Data on copepodid abundance and stage composition of Calanus finmarchicus was collected with seasonal resolution (5–6 times a year) from four stations along an oceanographic transect across the western Barents Sea Opening over 25 years (1995–2019). The stations were located in the Norwegian Coastal Current (NCC), inflowing Atlantic water (two stations), and near the Arctic polar front south of Bear Island. Mean copepodite abundance in the water column for the four stations increased from a level around 1000–10,000 individuals m−2 in winter to 30,000–100,000 individuals m−2 in summer (maximum 670,000 m−2). The overwintering (G0) population was dominated by copepodite stage 5 (CV) (40–70%) but with a relatively high fraction also of stage CIV (25–35%) in January. During winter, there was a progressive development of CVs into adult males and females, with mean abundances from 1500 to 4000 adult females m−2 in April and May for the stations in the NCC and Atlantic water. Young copepodids of the new spring generation (G1) appeared with relatively high abundances in April at the NCC station and in May at the Atlantic water stations. The data showed a gradient of later development from south to north, reflected both in the maturation of the overwintering generation and in the development of the spring generation. Back-calculations based on temperature-dependent development time suggested peak spawning around late April to mid-May for the Atlantic water stations, and a month or so earlier (in March) for the NCC station, during an early phase of the spring phytoplankton growth. The spring generation developed as a distinct cohort but with large interannual variability in numbers. In Atlantic water, the composition of the copepodid developmental stages in August resembled the situation in June, although it was slightly more advanced. This is interpreted to reflect development of a second generation (G2) spawned upstream sometime in June or early July. The June data suggests that only a small fraction of the G1 cohort develops into adults that spawn and form the G2. There was a tendency of increased summer abundance of C. finmarchicus in the inflow region of the southwestern Barents Sea after about 2005. This may be related to the wind regime with more eastward wind-stress at the Barents Sea opening in recent ‘high Calanus’ years compared to ‘low Calanus’ years in the early 2000s.publishedVersio

MOSIS : Modelling Semantically Interoperable Web Service Compositions

The use of information from different, often distributed, sources is part of many applications today, and in many cases these are heterogeneous sources developed independently without the intention of serving one specific application. This introduces the problem of semantic heterogeneity. Different sources are usually based on different vocabularies even in cases where they operate within the same domain. Data items defined in one source may have different definitions in another source although they really are the same (synonyms), and items that are different in reality may have similar definitions in two different sources (homonyms). There is a need for using these sources with regards to the meaning of the items in question not how they are defined in the sources, thus achieving what is called semantic interoperability. The distributed sources that will be treated in this thesis are Web Services. Web Services provide a programmatic access point through the web to a set of related functionalities, and these can be combined to create a new Web Service with added value. The combination of Web Services is called a Web Service composition. Web Service composition impose several semantic interoperability issues. First of all Web Services need to be discovered, you can use it if you don't know it exists, and this requires a semantical match between the descriptions of a requested service and the descriptions of existing services. Secondly, when you compose service, you need to make sure that information from one service that will be used as input to another service is semantically related to the input. In order to deal with semantic interoperability issues concerning Web Service compositions we propose MOSIS (MOdelling Semantically Interoperable web Service compositions). MOSIS makes use of UML models and principles from Model Driven Architecture (MDA) to model the discovery, the composition and the ontologies used to define semantically the concepts involved. As an effect of using UML modelling we claim that both the process of using ontologies and defining them will become easier for developers unfamiliar with ontology description and developing. MOSIS facilitates functionality based Web Service discovery which makes it possible to match descriptions of a Web Service with descriptions of existing Web Services. In addition to this MOSIS provides measures of dealing with mappings that have to be developed in order to make sure that output from one service can be used as input to another

A feasibility study in model based prediction of impact of changes on system quality

We propose a method, called PREDIQT, for model based prediction of impact of architecture design changes on system quality attributes. PREDIQT supports simultaneous analysis of several quality attributes and their trade-offs. This paper argues for the feasibility of the PREDIQT method based on a comprehensive industrial case study targeting a system for managing validation of electronic certificates and signatures worldwide. We first give an overview of the PREDIQT method, and then present an evaluation of the method in terms of a feasibility study and a thought experiment. The evaluation focuses on security and its trade-offs with the overall quality attributes of the target system Oppdragsgiver: Research Council of Norwa

A feasibility study in model based prediction of impact of changes on system quality

-We propose a method, called PREDIQT, for model based prediction of impact of architecture design changes on system quality attributes. PREDIQT supports simultaneous analysis of several quality attributes and their trade-offs. This paper argues for the feasibility of the PREDIQT method based on a comprehensive industrial case study targeting a system for managing validation of electronic certificates and signatures worldwide. We first give an overview of the PREDIQT method, and then present an evaluation of the method in terms of a feasibility study and a thought experiment. The evaluation focuses on security and its trade-offs with the overall quality attributes of the target system Oppdragsgiver: Research Council of Norwa

A feasibility study in model based prediction of impact of changes on system quality

-We propose a method, called PREDIQT, for model based prediction of impact of architecture design changes on system quality attributes. PREDIQT supports simultaneous analysis of several quality attributes and their trade-offs. This paper argues for the feasibility of the PREDIQT method based on a comprehensive industrial case study targeting a system for managing validation of electronic certificates and signatures worldwide. We first give an overview of the PREDIQT method, and then present an evaluation of the method in terms of a feasibility study and a thought experiment. The evaluation focuses on security and its trade-offs with the overall quality attributes of the target system Oppdragsgiver: Research Council of Norwa