| 1. |
- Hardisty, Alex R., et al.
(författare)
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BioVeL: A virtual laboratory for data analysis and modelling in biodiversity science and ecology
- 2016
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Ingår i: BMC Ecology. - : Springer Science and Business Media LLC. - 1472-6785. ; 16
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Tidskriftsartikel (refereegranskat)abstract
- © 2016 The Author(s).Background: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as "Web services") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust "in silico" science. However, use of this approach in biodiversity science and ecology has thus far been quite limited. Results: BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on-line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible 'virtual laboratory', free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity. Conclusions: Our work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.
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| 2. |
- Falkman, Göran, 1968-, et al.
(författare)
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SOMWeb - Towards an Infrastructure for Knowledge Sharing in Oral Medicine
- 2005
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Ingår i: Connecting Medical Informatics and Bio-Informatics: Proceedings of MIE2005 - The XIXth International Congress of the European Federation for Medical Informatics. - Amsterdam : IOS Press. - 1586035495 ; 116, s. 527-32, s. 527-532
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Konferensbidrag (refereegranskat)abstract
- In a net-based society, clinicians can come together for cooperative work and distance learning around a common medical material. This requires suitable techniques for cooperative knowledge management and user interfaces that are adapted to both the group as a whole and to individuals. To support distributed management and sharing of clinical knowledge, we propose the development of an intelligent web community for clinicians within oral medicine. This virtual meeting place will support the ongoing work on developing a digital knowledge base, providing a foundation for a more evidence-based oral medicine. The presented system is founded on the use and development of web services and standards for knowledge modelling and knowledge-based systems. The work is conducted within the frame of a well-established cooperation between oral medicine and computer science.
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| 3. |
- Futo, M., et al.
(författare)
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Embryo-Like Features in Developing Bacillus subtilis Biofilms
- 2021
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Ingår i: Molecular Biology and Evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 38:1, s. 31-47
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Tidskriftsartikel (refereegranskat)abstract
- Correspondence between evolution and development has been discussed for more than two centuries. Recent work reveals that phylogeny-ontogeny correlations are indeed present in developmental transcriptomes of eukaryotic clades with complex multicellularity. Nevertheless, it has been largely ignored that the pervasive presence of phylogeny-ontogeny correlations is a hallmark of development in eukaryotes. This perspective opens a possibility to look for similar parallelisms in biological settings where developmental logic and multicellular complexity are more obscure. For instance, it has been increasingly recognized that multicellular behavior underlies biofilm formation in bacteria. However, it remains unclear whether bacterial biofilm growth shares some basic principles with development in complex eukaryotes. Here we show that the ontogeny of growing Bacillus subtilis biofilms recapitulates phylogeny at the expression level. Using time-resolved transcriptome and proteome profiles, we found that biofilm ontogeny correlates with the evolutionary measures, in a way that evolutionary younger and more diverged genes were increasingly expressed toward later timepoints of biofilm growth. Molecular and morphological signatures also revealed that biofilm growth is highly regulated and organized into discrete ontogenetic stages, analogous to those of eukaryotic embryos. Together, this suggests that biofilm formation in Bacillus is a bona fide developmental process comparable to organismal development in animals, plants, and fungi. Given that most cells on Earth reside in the form of biofilms and that biofilms represent the oldest known fossils, we anticipate that the widely adopted vision of the first life as a single-cell and free-living organism needs rethinking.
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| 4. |
- Panova, Marina, 1973, et al.
(författare)
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A molecular phylogeny of the north-east Atlantic species of the genus Idotea (Isopoda) with focus on the Baltic Sea
- 2017
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Ingår i: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409. ; 46:2
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Tidskriftsartikel (refereegranskat)abstract
- Today, the marine isopods of the genus Idotea Fabricius, 1798 consist of 26 accepted species. Most species can be found in the Northern Hemisphere. While some species have a cosmopolitan distribution, others are endemic to a few coastlines. In the Baltic Sea, Idotea species have a key role as important meso-grazers. Only three species can be found in this brackish environment, I. balthica, I. chelipes and I. granulosa, while nine species are described from the whole European coast. The goal of the present study was to reconstruct the phylogeny of the genus Idotea and to test whether the Baltic low-salinity tolerant species represent a single lineage within the genus. The phylogeny of north-east Atlantic Idotea species was investigated based on a fragment of the nuclear gene 28S and the mitochondrial gene COI for eight Idotea species. The phylogenetic reconstructions showed that the genus Idotea might not be monophyletic. Neither I. linearis nor I. urotoma did belong to the separated and well-supported Idotea clade of I. balthica, I. chelipes, I. emarginata, I. granulosa, I. metallica and I. pelagica. The three Idotea species found in the Baltic belonged to different lineages, with estimated COI-based divergence time older than 7 Myr. This suggests that the tolerance to low salinity has likely evolved in the genus Idotea more than once.
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| 5. |
- Al Mamun, Md Abdullah, 1982, et al.
(författare)
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Effects of measurements on correlations of software code metrics
- 2019
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Ingår i: Empirical Software Engineering. - : Springer Science and Business Media LLC. - 1382-3256 .- 1573-7616. ; 24:4, s. 2764-2818
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Tidskriftsartikel (refereegranskat)abstract
- ContextSoftware metrics play a significant role in many areas in the life-cycle of software including forecasting defects and foretelling stories regarding maintenance, cost, etc. through predictive analysis. Many studies have found code metrics correlated to each other at such a high level that such correlated code metrics are considered redundant, which implies it is enough to keep track of a single metric from a list of highly correlated metrics.ObjectiveSoftware is developed incrementally over a period. Traditionally, code metrics are measured cumulatively as cumulative sum or running sum. When a code metric is measured based on the values from individual revisions or commits without consolidating values from past revisions, indicating the natural development of software, this study identifies such a type of measure as organic. Density and average are two other ways of measuring metrics. This empirical study focuses on whether measurement types influence correlations of code metrics.MethodTo investigate the objective, this empirical study has collected 24 code metrics classified into four categories, according to the measurement types of the metrics, from 11,874 software revisions (i.e., commits) of 21 open source projects from eight well-known organizations. Kendall's tau-B is used for computing correlations. To determine whether there is a significant difference between cumulative and organic metrics, Mann-Whitney U test, Wilcoxon signed rank test, and paired-samples sign test are performed.ResultsThe cumulative metrics are found to be highly correlated to each other with an average coefficient of 0.79. For corresponding organic metrics, it is 0.49. When individual correlation coefficients between these two measure types are compared, correlations between organic metrics are found to be significantly lower (with p <0.01) than cumulative metrics. Our results indicate that the cumulative nature of metrics makes them highly correlated, implying cumulative measurement is a major source of collinearity between cumulative metrics. Another interesting observation is that correlations between metrics from different categories are weak.ConclusionsResults of this study reveal that measurement types may have a significant impact on the correlations of code metrics and that transforming metrics into a different type can give us metrics with low collinearity. These findings provide us a simple understanding how feature transformation to a different measurement type can produce new non-collinear input features for predictive models.
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| 6. |
- Antinyan, Vard, 1984, et al.
(författare)
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A Complexity Measure for Textual Requirements
- 2016
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Ingår i: Proceedings of 2016 Joint Conference of the International Workshop on Software Measurement and the International Conference on Software Process and Product Measurement (Iwsm-Mensura). - : IEEE. - 9781509041473 - 9781509041480
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Konferensbidrag (refereegranskat)abstract
- Unequivocally understandable requirements are vital for software design process. However, in practice it is hard to achieve the desired level of understandability, because in large software products a substantial amount of requirements tend to have ambiguous or complex descriptions. Over time such requirements decelerate the development speed and increase the risk of late design modifications, therefore finding and improving them is an urgent task for software designers. Manual reviewing is one way of addressing the problem, but it is effort-intensive and critically slow for large products. Another way is using measurement, in which case one needs to design effective measures. In recent years there have been great endeavors in creating and validating measures for requirements understandability: most of the measures focused on ambiguous patterns. While ambiguity is one property that has major effect on understandability, there is also another important property, complexity, which also has major effect on understandability, but is relatively less investigated. In this paper we define a complexity measure for textual requirements through an action research project in a large software development organization. We also present its evaluation results in three large companies. The evaluation shows that there is a significant correlation between the measurement values and the manual assessment values of practitioners. We recommend this measure to be used with earlier created ambiguity measures as means for automated identification of complex specifications.
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| 7. |
- Antinyan, Vard, 1984, et al.
(författare)
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Identifying Complex Functions : By Investigating Various Aspects of Code Complexity
- 2015
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Ingår i: Proceedings of 2015 Science and Information Conference (SAI). - : IEEE Press. - 9781479985470 - 9781479985487 - 9781479985463 ; , s. 879-888
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Konferensbidrag (refereegranskat)abstract
- The complexity management of software code has become one of the major problems in software development industry. With growing complexity the maintenance effort of code increases. Moreover, various aspects of complexity create difficulties for complexity assessment. The objective of this paper is to investigate the relationships of various aspects of code complexity and propose a method for identifying the most complex functions. We have conducted an action research project in two software development companies and complemented it with a study of three open source products. Four complexity metrics are measured, and their nature and mutual influence are investigated. The results and possible explanations are discussed with software engineers in industry. The results show that there are two distinguishable aspects of complexity of source code functions: Internal and outbound complexities. Those have an inverse relationship. Moreover, the product of them does not seem to be greater than a certain limit, regardless of software size. We present a method that permits identification of most complex functions considering the two aspects of complexities. The evaluation shows that the use of the method is effective in industry: It enables identification of 0.5% most complex functions out of thousands of functions for reengineering.
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| 8. |
- Falkman, Göran, 1968-, et al.
(författare)
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Collaboration Patterns in an Online Community of Practice in Oral Medicine
- 2008
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Ingår i: eHealth Beyond the Horizon – Get IT There. - Amsterdam : IOS Press. - 9781586038649 ; 136, s. 175-80
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Konferensbidrag (refereegranskat)abstract
- SOMWeb is an online collaboration system based on Semantic Web technologies, which is used for knowledge sharing and dissemination within an oral medicine community in Sweden. Based on a previous study of the use of SOMWeb, general patterns of interaction and communicative activities involved in community collaboration have been identified. The patterns for one such activity, distance consultation, are described and modeled using techniques from the Pragmatic Web. It is also shown how patterns could inform system design
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| 9. |
- Horkoff, Jennifer, 1980, et al.
(författare)
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Enterprise Modeling for Business Agility
- 2018
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Ingår i: Business & Information Systems Engineering. - : Springer Gabler. - 2363-7005 .- 1867-0202. ; 60:1, s. 1-2
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Tidskriftsartikel (refereegranskat)
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| 10. |
- Karim, Sazzad, et al.
(författare)
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Improved drought tolerance without undesired side effects in transgenic plants producing trehalose
- 2007
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Ingår i: Plant Molecular Biology. - : Springer Science and Business Media LLC. - 0167-4412 .- 1573-5028. ; 64:4, s. 371-386
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Tidskriftsartikel (refereegranskat)abstract
- Most organisms naturally accumulating trehalose upon stress produce the sugar in a two-step process by the action of the enzymes trehalose-6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP). Transgenic plants overexpressing TPS have shown enhanced drought tolerance in spite of minute accumulation of trehalose, amounts believed to be too small to provide a protective function. However, overproduction of TPS in plants has also been found combined with pleiotropic growth aberrations. This paper describes three successful strategies to circumvent such growth defects without loosing the improved stress tolerance. First, we introduced into tobacco a double construct carrying the genes TPS1 and TPS2 (encoding TPP) from Saccharomyces cerevisiae. Both genes are regulated by an Arabidopsis RuBisCO promoter from gene AtRbcS1A giving constitutive production of both enzymes. The second strategy involved stress-induced expression by fusing the coding region of ScTPS1 downstream of the drought-inducible Arabidopsis AtRAB18 promoter. In transgenic tobacco plants harbouring genetic constructs with either ScTPS1 alone, or with ScTPS1 and ScTPS2 combined, trehalose biosynthesis was turned on only when the plants experienced stress. The third strategy involved the use of AtRbcS]A promoter together with a transit peptide in front of the coding sequence of ScTPS1, which directed the enzyme to the chloroplasts. This paper confirms that the enhanced drought tolerance depends on unknown ameliorated water retention as the initial water status is the same in control and transgenic plants and demonstrates the influence of expression of heterologous trehalose biosynthesis genes on Arabidopsis root development.
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