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- Grüning, Björn, et al.
(author)
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Bioconda: A sustainable and comprehensive software distribution for the life sciences
- 2017
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Other publication (other academic/artistic)abstract
- We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bioconda improves analysis reproducibility by allowing users to define isolated environments with defined software versions, all of which are easily installed and managed without administrative privileges.
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- Hjalmarson, Emil, et al.
(author)
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Design space exploration and trade-offs in analog amplifier design
- 2003
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In: Integrated Circuit and System Design. Power and Timing Modeling, Optimization and Simulation. - Berlin, Heidelberg : Springer Berlin/Heidelberg. - 3540200746 - 9783540200741 - 9783540397625 ; , s. 338-347
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Conference paper (peer-reviewed)abstract
- In this paper, we discuss an optimization-based approach for design space exploration to find limitations and possible trade-offs between performance metrics in analog circuits. The exploration guides the designer when making design decisions. For the design space exploration, which is expensive in terms of computation time, we use an optimization-based device sizing tool that runs concurrent optimization tasks on a network of workstations. The tool enables efficient and accurate exploration of the available design space. As a design example, we investigate three operational transconductance amplifiers, OTAs, implemented in a standard 0.35-mum CMOS process. This example shows that large savings in terms of chip area and power consumption can be made by selecting the most suitable circuit.
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- Hägglund, Emil
(author)
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Evolution of biological systems linked to complex cell architectures in Planctomycetota
- 2023
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Doctoral thesis (other academic/artistic)abstract
- The eukaryotic cells have a nucleus and membrane-enclosed organelles for functions such as energy production, whereas the prokaryotic cells have a cell wall but no intracellular membrane-bound structures. Species of the Planctomycetota phylum are classified as bacteria but have diverse and complex cell architectures. For example, members of the Gemmataceae have highly invaginated cytoplasmic membranes, the anammox bacteria have a membrane-bound organelle for energy production, and one species, “Candidatus Uabimicrobium amorphum”, can form digestive vacuoles during phagocytotic-like engulfment of other cells.In this thesis, we have performed comparative genomics and evolutionary analyses of bacteria in the Planctomycetota to learn more about the evolution of cellular complexity. The thesis also presents a new workflow to facilitate the assembly of datasets for comparative and evolutionary analysis of prokaryotic species.Comparative analyses of several novel genomes in the Gemmatacea family showed that new protein families have evolved by massive paralogization and fusion of prokaryotic-like domains with eukaryotic-like domains. The analyses showed no strict boundary between prokaryotic and eukaryotic genomes regarding gene lengths, gene paralogy and protein domain composition patterns.Analysis of the “Candidatus Uabimicrobium amorphum” genome revealed an extreme expansion of genes for serine/threonine protein kinases, possibly related to the predatory lifestyle of this species. However, the associated domains differed from those of serine/threonine protein kinases in eukaryotes, suggesting that the expansion and diversification process has occurred independently in eukaryotes and Planctomycetota.Evolutionary studies of the enzymes in the anammox pathway showed that the central enzyme, hydrazine synthase, previously of unknown origin, has homologs in other bacteria, including other members of the Planctomycetota. However, the homologs lacked key residues involved in the formation of hydrazine, suggesting that the anammox reaction has only originated once. Other enzymes in this pathway have been acquired by horizontal gene transfer events followed by duplication and divergence. Further, by studying the evolution of the heme biosynthesis pathway in this phylum, we show that this pathway has been replaced in the anammox bacteria with a strictly anaerobic pathway following horizontal gene transfers from archaea and other bacteria.Thus, although members of the Planctomycetota share many traits with eukaryotes, such as the same types of protein domains and similarities in cellular structures, our analyses show that these features have independent origins and reflect convergent evolution. The results have implications for our understanding of the origin of cellular complexity.
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