| 1. |
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- 2019
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Journal article (peer-reviewed)
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| 2. |
- Bengtsson-Palme, Johan, 1985, et al.
(author)
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Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data
- 2013
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In: Methods in Ecology and Evolution. - 2041-210X. ; 4:10, s. 914-919
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Journal article (peer-reviewed)abstract
- The nuclear ribosomal internal transcribed spacer (ITS) region is the primary choice for molecular identification of fungi. Its two highly variable spacers (ITS1 and ITS2) are usually species specific, whereas the intercalary 5.8S gene is highly conserved. For sequence clustering and blast searches, it is often advantageous to rely on either one of the variable spacers but not the conserved 5.8S gene. To identify and extract ITS1 and ITS2 from large taxonomic and environmental data sets is, however, often difficult, and many ITS sequences are incorrectly delimited in the public sequence databases. We introduce ITSx, a Perl-based software tool to extract ITS1, 5.8S and ITS2 – as well as full-length ITS sequences – from both Sanger and high-throughput sequencing data sets. ITSx uses hidden Markov models computed from large alignments of a total of 20 groups of eukaryotes, including fungi, metazoans and plants, and the sequence extraction is based on the predicted positions of the ribosomal genes in the sequences. ITSx has a very high proportion of true-positive extractions and a low proportion of false-positive extractions. Additionally, process parallelization permits expedient analyses of very large data sets, such as a one million sequence amplicon pyrosequencing data set. ITSx is rich in features and written to be easily incorporated into automated sequence analysis pipelines. ITSx paves the way for more sensitive blast searches and sequence clustering operations for the ITS region in eukaryotes. The software also permits elimination of non-ITS sequences from any data set. This is particularly useful for amplicon-based next-generation sequencing data sets, where insidious non-target sequences are often found among the target sequences. Such non-target sequences are difficult to find by other means and would contribute noise to diversity estimates if left in the data set.
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| 3. |
- Barredo, José I., et al.
(author)
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Mapping and assessment of forest ecosystems and their services : Applications and guidance for decision making in the framework of MAES
- 2015
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Reports (other academic/artistic)abstract
- The aim of this report is to illustrate by means of a series of case studies the implementation of mapping and assessment of forest ecosystem services in different contexts and geographical levels. Methodological aspects, data issues, approaches, limitations, gaps and further steps for improvement are analysed for providing good practices and decision making guidance. The EU initiative on Mappingand Assessment of Ecosystems and their Services (MAES), with the support of all Member States, contributes to improve the knowledge on ecosystem services. MAES is one of the building-block initiatives supporting the EU Biodiversity Strategy to 2020.
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| 4. |
- Bengtsson-Palme, Johan, 1985, et al.
(author)
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Megraft: A software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes
- 2012
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In: Research in Microbiology. - : Elsevier BV. - 0923-2508. ; 163:6-7, s. 407-412
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Journal article (peer-reviewed)abstract
- Metagenomic libraries represent subsamples of the total DNA found at a study site and offer unprecedented opportunities to study ecological and functional aspects of microbial communities. To examine the depth of a community sequencing effort, rarefaction analysis of the ribosomal small subunit (SSU/16S/18S) gene in the metagenome is usually performed. The fragmentary, non-overlapping nature of SSU sequences in metagenomic libraries poses a problem for this analysis, however. We introduce a software package – Megraft – that grafts SSU fragments onto full-length SSU sequences, accounting for observed and unobserved variability, for accurate assessment of species richness and sequencing depth in metagenomics endeavors.
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| 5. |
- Bonagas, Nadilly, et al.
(author)
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Pharmacological targeting of MTHFD2 suppresses acute myeloid leukemia by inducing thymidine depletion and replication stress
- 2022
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In: NATURE CANCER. - : Springer Science and Business Media LLC. - 2662-1347. ; 3:2, s. 156-
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Journal article (peer-reviewed)abstract
- The folate metabolism enzyme MTHFD2 (methylenetetrahydrofolate dehydrogenase/cyclohydrolase) is consistently overexpressed in cancer but its roles are not fully characterized, and current candidate inhibitors have limited potency for clinical development. In the present study, we demonstrate a role for MTHFD2 in DNA replication and genomic stability in cancer cells, and perform a drug screen to identify potent and selective nanomolar MTHFD2 inhibitors; protein cocrystal structures demonstrated binding to the active site of MTHFD2 and target engagement. MTHFD2 inhibitors reduced replication fork speed and induced replication stress followed by S-phase arrest and apoptosis of acute myeloid leukemia cells in vitro and in vivo, with a therapeutic window spanning four orders of magnitude compared with nontumorigenic cells. Mechanistically, MTHFD2 inhibitors prevented thymidine production leading to misincorporation of uracil into DNA and replication stress. Overall, these results demonstrate a functional link between MTHFD2-dependent cancer metabolism and replication stress that can be exploited therapeutically with this new class of inhibitors. Helleday and colleagues describe a nanomolar MTHFD2 inhibitor that causes replication stress and DNA damage accumulation in cancer cells via thymidine depletion, demonstrating a potential therapeutic strategy in AML tumors in vivo.
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| 6. |
- Dengler, Juergen, et al.
(author)
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GrassPlot - a database of multi-scale plant diversity in Palaearctic grasslands
- 2018
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In: Phytocoenologia. - : Schweizerbart. - 0340-269X. ; 48:3, s. 331-347
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Journal article (peer-reviewed)abstract
- GrassPlot is a collaborative vegetation-plot database organised by the Eurasian Dry Grassland Group (EDGG) and listed in the Global Index of Vegetation-Plot Databases (GIVD ID EU-00-003). GrassPlot collects plot records (releves) from grasslands and other open habitats of the Palaearctic biogeographic realm. It focuses on precisely delimited plots of eight standard grain sizes (0.0001; 0.001;... 1,000 m(2)) and on nested-plot series with at least four different grain sizes. The usage of GrassPlot is regulated through Bylaws that intend to balance the interests of data contributors and data users. The current version (v. 1.00) contains data for approximately 170,000 plots of different sizes and 2,800 nested-plot series. The key components are richness data and metadata. However, most included datasets also encompass compositional data. About 14,000 plots have near-complete records of terricolous bryophytes and lichens in addition to vascular plants. At present, GrassPlot contains data from 36 countries throughout the Palaearctic, spread across elevational gradients and major grassland types. GrassPlot with its multi-scale and multi-taxon focus complements the larger international vegetationplot databases, such as the European Vegetation Archive (EVA) and the global database " sPlot". Its main aim is to facilitate studies on the scale-and taxon-dependency of biodiversity patterns and drivers along macroecological gradients. GrassPlot is a dynamic database and will expand through new data collection coordinated by the elected Governing Board. We invite researchers with suitable data to join GrassPlot. Researchers with project ideas addressable with GrassPlot data are welcome to submit proposals to the Governing Board.
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| 7. |
- Nilsson, R. Henrik, 1976, et al.
(author)
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A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts
- 2015
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In: Microbes and Environments. - 1342-6311 .- 1347-4405. ; 30:2, s. 145-150
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Journal article (peer-reviewed)abstract
- The nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen genetic marker for the molecular identification of fungi in environmental sequencing and molecular ecology studies. Several analytical issues complicate such efforts, one of which is the formation of chimeric—artificially joined—DNA sequences during PCR amplification or sequence assembly. Several software tools are currently available for chimera detection, but rely to various degrees on the presence of a chimera-free reference dataset for optimal performance. However, no such dataset is available for use with the fungal ITS region. This study introduces a comprehensive, automatically updated reference dataset for fungal ITS sequences based on the UNITE database for the molecular identification of fungi. This dataset supports chimera detection throughout the fungal kingdom and for full-length ITS sequences as well as partial (ITS1 or ITS2 only) datasets. The performance of the dataset on a large set of artificial chimeras was above 99.5%, and we subsequently used the dataset to remove nearly 1,000 compromised fungal ITS sequences from public circulation. The dataset is available at http://unite.ut.ee/repository.php and is subject to web-based third-party curation.
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| 8. |
- Nilsson, R. Henrik, 1976, et al.
(author)
-
A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts
- 2015
-
In: Microbes and Environments. - 1342-6311 .- 1347-4405. ; 30:2, s. 145-150
-
Journal article (peer-reviewed)abstract
- The nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen genetic marker for the molecular identification of fungi in environmental sequencing and molecular ecology studies. Several analytical issues complicate such efforts, one of which is the formation of chimeric—artificially joined—DNA sequences during PCR amplification or sequence assembly. Several software tools are currently available for chimera detection, but rely to various degrees on the presence of a chimera-free reference dataset for optimal performance. However, no such dataset is available for use with the fungal ITS region. This study introduces a comprehensive, automatically updated reference dataset for fungal ITS sequences based on the UNITE database for the molecular identification of fungi. This dataset supports chimera detection throughout the fungal kingdom and for full-length ITS sequences as well as partial (ITS1 or ITS2 only) datasets. The performance of the dataset on a large set of artificial chimeras was above 99.5%, and we subsequently used the dataset to remove nearly 1,000 compromised fungal ITS sequences from public circulation. The dataset is available at http://unite.ut.ee/repository.php and is subject to web-based third-party curation.
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| 9. |
- Nilsson, R. Henrik, 1976, et al.
(author)
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Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences
- 2012
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In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 4, s. 37-63
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Journal article (peer-reviewed)abstract
- Molecular data form an important research tool in most branches of mycology. A non-trivial proportion of the public fungal DNA sequences are, however, compromised in terms of quality and reliability, contributing noise and bias to sequence-borne inferences such as phylogenetic analysis, diversity assessment, and barcoding. In this paper we discuss various aspects and pitfalls of sequence quality assessment. Based on our observations, we provide a set of guidelines to assist in manual quality management of newly generated, near-full-length (Sanger-derived) fungal ITS sequences and to some extent also sequences of shorter read lengths, other genes or markers, and groups of organisms. The guidelines are intentionally non-technical and do not require substantial bioinformatics skills or significant computational power. Despite their simple nature, we feel they would have caught the vast majority of the severely compromised ITS sequences in the public corpus. Our guidelines are nevertheless not infallible, and common sense and intuition remain important elements in the pursuit of compromised sequence data. The guidelines focus on basic sequence authenticity and reliability of the newly generated sequences, and the user may want to consider additional resources and steps to accomplish the best possible quality control. A discussion on the technical resources for further sequence quality management is therefore provided in the supplementary material.
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| 10. |
- Nilsson, R. Henrik, 1976, et al.
(author)
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Improving ITS sequence data for identification of plant pathogenic fungi
- 2014
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In: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 67:1, s. 11-19
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Journal article (peer-reviewed)abstract
- Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours. These taxa often have complex and poorly understood life cycles, lack observable, discriminatory morphological characters, and may not be amenable to in vitro culturing. As a result, species identification is frequently difficult. Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. A third objective was to enrich the sequences with geographical and ecological metadata. The results – a total of 31,954 changes – are incorporated in and made available through the UNITE database for molecular identification of fungi (http://unite.ut.ee), including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi, and we invite all researchers with pertinent expertise to join the annotation effort.
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| 11. |
- Abarenkov, Kessy, et al.
(author)
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Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)
- 2016
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In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 16, s. 1-15
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Journal article (peer-reviewed)abstract
- Recent molecular studies have identified substantial fungal diversity in indoor environments. Fungi and fungal particles have been linked to a range of potentially unwanted effects in the built environment, including asthma, decay of building materials, and food spoilage. The study of the built mycobiome is hampered by a number of constraints, one of which is the poor state of the metadata annotation of fungal DNA sequences from the built environment in public databases. In order to enable precise interrogation of such data – for example, “retrieve all fungal sequences recovered from bathrooms” – a workshop was organized at the University of Gothenburg (May 23-24, 2016) to annotate public fungal barcode (ITS) sequences according to the MIxS-Built Environment annotation standard (http://gensc.org/mixs/). The 36 participants assembled a total of 45,488 data points from the published literature, including the addition of 8,430 instances of countries of collection from a total of 83 countries, 5,801 instances of building types, and 3,876 instances of surface-air contaminants. The results were implemented in the UNITE database for molecular identification of fungi (http://unite.ut.ee) and were shared with other online resources. Data obtained from human/animal pathogenic fungi will furthermore be verified on culture based metadata for subsequent inclusion in the ISHAM-ITS database (http://its.mycologylab.org).
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| 12. |
- Bengtsson, Anders K.H., et al.
(author)
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Particles, superparticles and twistors
- 1987
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In: Phys. Rev. D36 (1987) 1766.
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Journal article (peer-reviewed)abstract
- The covariant Green-Schwarz action for a superstring has never been quantized covariantly. The physics behind this is discussed. We then consider the corresponding point-particle action in four dimensions, and write down a master action from which it can be obtained as a gauge choice: the ‘‘space-time gauge.’’ There is also a ‘‘twistor gauge,’’ in which covariant quantization is straightforward (as noted previously by Shirafuji).
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| 13. |
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| 14. |
- Bengtsson, Johan, 1985, et al.
(author)
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Metaxa: Automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts
- 2011
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In: SocBiN Bioinformatics Conference, Helsinki, Finland, 2011.
-
Conference paper (other academic/artistic)abstract
- The ribosomal small subunit (SSU) rRNA gene has emerged as an important genetic marker for taxonomic identification in environmental sequencing datasets. However, the gene is not only present in the nuclear genome of eukaryotes and the core genome of prokaryotes, but also in the mitochondria and chloroplasts of eukaryotes. The SSU genes in the core genome, mitochondria and chloroplast are conceptually paralogous and should in most situations not be aligned and analyzed jointly, e.g. when estimating species diversity. Identifying the origin of SSU sequences in complex sequence datasets is a time-consuming and largely manual undertaking. To ease this situation, we have created Metaxa, an automated software tool to extract full-length and partial SSU sequences from larger sequence datasets and assign them to an archaeal, bacte- rial, nuclear eukaryote, mitochondrial, or chloroplast origin. Metaxa very efficiently detects SSU sequences from fragments as short as 200 base pairs, and correctly classifies 97% of the identified genes at read lengths typically obtained from pyrosequencing. In addition, Metaxa shows a false positive rate of 0.00012% when run on random DNA fragments, showing the robustness of the method. We believe that this tool will be useful in microbial and evolutionary ecology as well as in metagenomics.
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| 15. |
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| 16. |
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| 17. |
- Bengtsson-Palme, Johan, 1985, et al.
(author)
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Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets
- 2011
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In: Antonie van Leeuwenhoek: international journal of general and molecular microbiology. - : Springer Science and Business Media LLC. - 0003-6072 .- 1572-9699. ; 100:3, s. 471-475
-
Journal article (peer-reviewed)abstract
- The ribosomal small subunit (SSU) rRNA gene has emerged as an important genetic marker for taxonomic identification in environmental sequencing datasets. In addition to being present in the nucleus of eukaryotes and the core genome of prokaryotes, the gene is also found in the mitochondria of eukaryotes and in the chloroplasts of photosynthetic eukaryotes. These three sets of genes are conceptually paralogous and should in most situations not be aligned and analyzed jointly. To identify the origin of SSU sequences in complex sequence datasets has hitherto been a time-consuming and largely manual undertaking. However, the present study introduces Metaxa (http://microbiology.se/software/metaxa/), an automated software tool to extract full-length and partial SSU sequences from larger sequence datasets and assign them to an archaeal, bacterial, nuclear eukaryote, mitochondrial, or chloroplast origin. Using data from reference databases and from full-length organelle and organism genomes, we show that Metaxa detects and scores SSU sequences for origin with very low proportions of false positives and negatives. We believe that this tool will be useful in microbial and evolutionary ecology as well as in metagenomics.
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| 18. |
- Bengtsson-Palme, Johan, 1985, et al.
(author)
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Metaxa, overview
- 2013
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In: Encyclopedia of Metagenomics. - Berlin : Springer.
-
Book chapter (peer-reviewed)abstract
- Metaxa is a software tool for extracting full-length and partial ribosomal small subunit (SSU; 16S/18S/12S) sequences from metagenomic datasets, and for classifying the extracted sequences to taxonomic domains and organelle of origin. Metaxa is freely available from http://microbiology.se/software/metaxa
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| 19. |
- Bengtsson-Palme, Johan, 1985, et al.
(author)
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Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker
- 2018
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In: Bioinformatics (Oxford, England). - : Oxford University Press (OUP). - 1367-4811 .- 1367-4803. ; 34:23, s. 4027-4033
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Journal article (peer-reviewed)abstract
- Correct taxonomic identification of DNA sequences is central to studies of biodiversity using both shotgun metagenomic and metabarcoding approaches. However, no genetic marker gives sufficient performance across all the biological kingdoms, hampering studies of taxonomic diversity in many groups of organisms. This has led to the adoption of a range of genetic markers for DNA metabarcoding. While many taxonomic classification software tools can be re-trained on these genetic markers, they are often designed with assumptions that impair their utility on genes other than the SSU and LSU rRNA. Here, we present an update to Metaxa2 that enables the use of any genetic marker for taxonomic classification of metagenome and amplicon sequence data.We evaluated the Metaxa2 Database Builder on eleven commonly used barcoding regions and found that while there are wide differences in performance between different genetic markers, our software performs satisfactorily provided that the input taxonomy and sequence data are of high quality.Freely available on the web as part of the Metaxa2 package at http://microbiology.se/software/metaxa2/.Supplementary data are available at Bioinformatics online.
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| 20. |
- Bengtsson-Palme, Johan, 1985, et al.
(author)
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Metaxa2: Improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data
- 2015
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In: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 15:6, s. 1403-1414
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Journal article (peer-reviewed)abstract
- The ribosomal rRNA genes are widely used as genetic markers for taxonomic identification of microbes. Particularly the small subunit (SSU; 16S/18S) rRNA gene is frequently used for species- or genus-level identification, but also the large subunit (LSU; 23S/28S) rRNA gene is employed in taxonomic assignment. The metaxa software tool is a popular utility for extracting partial rRNA sequences from large sequencing data sets and assigning them to an archaeal, bacterial, nuclear eukaryote, mitochondrial or chloroplast origin. This study describes a comprehensive update to metaxa – metaxa2 – that extends the capabilities of the tool, introducing support for the LSU rRNA gene, a greatly improved classifier allowing classification down to genus or species level, as well as enhanced support for short-read (100 bp) and paired-end sequences, among other changes. The performance of metaxa2 was compared to other commonly used taxonomic classifiers, showing that metaxa2 often outperforms previous methods in terms of making correct predictions while maintaining a low misclassification rate. metaxa2 is freely available from http://microbiology.se/software/metaxa2/
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| 21. |
- Bengtsson, Tommy, et al.
(author)
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The Late Emergence of the Socioeconomic Gradient in Adult Mortality: An Urban Phenomenon?
- 2024
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In: Urban Lives. An Industrial City and Its People During the Twentieth Century. - 9780197761090 - 9780197761113 - 9780197761120 ; , s. 281-306
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Book chapter (peer-reviewed)abstract
- Previous research has shown that class differences in adult mortality in the study area emerged only in the mid-twentieth century. Such findings question a universal association between socioeconomic status and mortality. This chapter examines whether these class differences in adult mortality emerged at the same time in urban as in rural areas. The analysis shows that the social class gradient in mortality was more pronounced in the urban than in the rural area, and hence that it was primarily an urban phenomenon. The urban mortality penalty in the study area lasted considerably longer than has been found for Sweden as a whole, but presumably with changing explanations over time. In the early twentieth century, the higher urban mortality was probably connected to poor living conditions in the city, while in the late twentieth century it was likely more related to differences in lifestyle and possibly work-related stress.
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| 22. |
- Birkhofer, Klaus, et al.
(author)
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Relationships between multiple biodiversity components and ecosystem services along a landscape complexity gradient
- 2018
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In: Biological Conservation. - : Elsevier BV. - 0006-3207 .- 1873-2917. ; 218, s. 247-253
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Journal article (peer-reviewed)abstract
- The assessment of effects of anthropogenic disturbance on biodiversity (BD) and ecosystem services (ES) and their relationships are key priorities of the Intergovernmental Panel for Biodiversity and Ecosystem Services. Agricultural landscapes and their associated BD provide multiple ES and it is crucial to understand how relationships between ES and BD components change along gradients of landscape complexity. In this study, we related eight ES potentials to the species richness of five invertebrate, vertebrate and plant taxonomic groups in cereal farming systems. The landscape complexity gradient ranged from areas dominated by annually tilled arable land to areas with high proportions of unfertilized, non-rotational pastures and uncultivated field borders. We show that after accounting for landscape complexity relationships between yield and bird richness or biological control became more positive, but relationships between bird richness and biological control became less positive. The relationship between bird and plant richness turned from positive to negative. Multidiversity (overall biodiversity), was positively related to landscape complexity, whereas multifunctionality (overall ES provision), was not significantly related to either one of these. Our results suggest that multidiversity can be promoted by increasing landscape complexity; however; we found no support for a simultaneous increase of several individual ES, BD components or multifunctionality. These results challenge the assumption that bio-diversity-friendly landscape management will always simultaneously promote multiple ES in agricultural landscapes. Future studies need to verify this pattern by using multi-year data, larger sets of ES and BD components and a study design that is appropriate to address larger spatial scales and relationships in several regions.
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| 23. |
- Dahl, Martin, 1984, et al.
(author)
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Automatic modeling and simulation of robot program behavior in integrated virtual preparation and commissioning
- 2017
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In: Procedia Manufacturing. - : Elsevier BV. - 2351-9789. ; 11, s. 284-291
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Conference paper (peer-reviewed)abstract
- This paper presents a method where the behavior of a robot cell is automatically modeled based on existing robot programs and a simulation model of the cell. Robot programs from the shop floor are uploaded into a virtual manufacturing tool, and a formal model is then generated from the robot programs. Then, control logic is automatically calculated, and the fastest possible execution order is found by using the generated model to formulate an optimization problem. The result is continuously analyzed and validated by simulation in the virtual manufacturing tool.
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| 24. |
- Dahl, Martin, 1984, et al.
(author)
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Control components for Collaborative and Intelligent Automation Systems
- 2019
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In: IEEE International Conference on Emerging Technologies and Factory Automation, ETFA. - 1946-0759 .- 1946-0740. ; 2019-September, s. 378-384
-
Conference paper (peer-reviewed)abstract
- Collaborative and intelligent automation systems need intelligent control systems. Some of this intelligence exist on a per-component basis in the form of vision, sensing, motion, and path planning algorithms. To fully take advantage of this intelligence, also the coordination of subsystems need to exhibit intelligence. While there exist middleware solutions that eases communication, development, and reuse of such subsystems, for example the Robot Operating System (ROS), good coordination also requires knowledge about how control is supposed to be performed, as well as expected behavior of the subsystems. This paper introduces lightweight components that wraps ROS2 nodes into composable control components from which an intelligent control system can be built. The ideas are implemented on a use case involving collaborative robots with on-line path planning, intelligent tools, and human operators.
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| 25. |
- Dahl, Martin, 1984, et al.
(author)
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Guard extraction for modeling and control of a collaborative assembly station
- 2020
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In: IFAC-PapersOnLine. - : Elsevier BV. - 2405-8963. ; 53:4, s. 223-228
-
Conference paper (peer-reviewed)abstract
- A transition system represented by guards and actions can be amended by new guards computed in order to satisfy some specification. If the transition system is the result of composing smaller state machines, guard extraction can be used to put the new guards onto the guards the original state machines. Planning and verification can then be performed directly on the system with additional guards. In this paper we discuss the benefits of applying guard extraction as part of the modeling work in a modular control architecture, where reusable resources are composed using specifications. We show with an example from the development of an industrial demonstrator that even if the specification language is limited to invariant propositions, in practice many common safety specifications can be expressed when combined with a notion of which transitions are allowed to be restricted.
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