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  • 1.
    Abbaszadeh Shahri, Abbas
    KTH, School of Architecture and the Built Environment (ABE), Civil and Architectural Engineering. Islamic Azad University.
    An Optimized Artificial Neural Network Structure to Predict Clay Sensitivity in a High Landslide Prone Area Using Piezocone Penetration Test (CPTu) Data: A Case Study in Southwest of Sweden2016In: Geotechnical and Geological Engineering, ISSN 0960-3182, E-ISSN 1573-1529, p. 1-14Article in journal (Refereed)
    Abstract [en]

    Application of artificial neural networks (ANN) in various aspects of geotechnical engineering problems such as site characterization due to have difficulty to solve or interrupt through conventional approaches has demonstrated some degree of success. In the current paper a developed and optimized five layer feed-forward back-propagation neural network with 4-4-4-3-1 topology, network error of 0.00201 and R2 = 0.941 under the conjugate gradient descent ANN training algorithm was introduce to predict the clay sensitivity parameter in a specified area in southwest of Sweden. The close relation of this parameter to occurred landslides in Sweden was the main reason why this study is focused on. For this purpose, the information of 70 piezocone penetration test (CPTu) points was used to model the variations of clay sensitivity and the influences of direct or indirect related parameters to CPTu has been taken into account and discussed in detail. Applied operation process to find the optimized ANN model using various training algorithms as well as different activation functions was the main advantage of this paper. The performance and feasibility of proposed optimized model has been examined and evaluated using various statistical and analytical criteria as well as regression analyses and then compared to in situ field tests and laboratory investigation results. The sensitivity analysis of this study showed that the depth and pore pressure are the two most and cone tip resistance is the least effective factor on prediction of clay sensitivity.

  • 2.
    Abraham, Mark James
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Murtola, T.
    Schulz, R.
    Páll, Szilárd
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Smith, J. C.
    Hess, Berk
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers2015In: SoftwareX, ISSN 2352-7110, Vol. 1-2, p. 19-25Article in journal (Refereed)
    Abstract [en]

    GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis tools. Several advanced techniques for free-energy calculations are supported. In version 5, it reaches new performance heights, through several new and enhanced parallelization algorithms. These work on every level; SIMD registers inside cores, multithreading, heterogeneous CPU-GPU acceleration, state-of-the-art 3D domain decomposition, and ensemble-level parallelization through built-in replica exchange and the separate Copernicus framework. The latest best-in-class compressed trajectory storage format is supported.

  • 3. Aidas, Kestutis
    et al.
    Angeli, Celestino
    Bak, Keld L.
    Bakken, Vebjorn
    Bast, Radovan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Boman, Linus
    Christiansen, Ove
    Cimiraglia, Renzo
    Coriani, Sonia
    Dahle, Pal
    Dalskov, Erik K.
    Ekstrom, Ulf
    Enevoldsen, Thomas
    Eriksen, Janus J.
    Ettenhuber, Patrick
    Fernandez, Berta
    Ferrighi, Lara
    Fliegl, Heike
    Frediani, Luca
    Hald, Kasper
    Halkier, Asger
    Hattig, Christof
    Heiberg, Hanne
    Helgaker, Trygve
    Hennum, Alf Christian
    Hettema, Hinne
    Hjertenaes, Eirik
    Host, Stinne
    Hoyvik, Ida-Marie
    Iozzi, Maria Francesca
    Jansik, Branislav
    Jensen, Hans Jorgen Aa.
    Jonsson, Dan
    Jorgensen, Poul
    Kauczor, Joanna
    Kirpekar, Sheela
    Kjrgaard, Thomas
    Klopper, Wim
    Knecht, Stefan
    Kobayashi, Rika
    Koch, Henrik
    Kongsted, Jacob
    Krapp, Andreas
    Kristensen, Kasper
    Ligabue, Andrea
    Lutnaes, Ola B.
    Melo, Juan I.
    Mikkelsen, Kurt V.
    Myhre, Rolf H.
    Neiss, Christian
    Nielsen, Christian B.
    Norman, Patrick
    Olsen, Jeppe
    Olsen, Jogvan Magnus H.
    Osted, Anders
    Packer, Martin J.
    Pawlowski, Filip
    Pedersen, Thomas B.
    Provasi, Patricio F.
    Reine, Simen
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Ruden, Torgeir A.
    Ruud, Kenneth
    Rybkin, Vladimir V.
    Salek, Pawel
    Samson, Claire C. M.
    de Meras, Alfredo Sanchez
    Saue, Trond
    Sauer, Stephan P. A.
    Schimmelpfennig, Bernd
    Sneskov, Kristian
    Steindal, Arnfinn H.
    Sylvester-Hvid, Kristian O.
    Taylor, Peter R.
    Teale, Andrew M.
    Tellgren, Erik I.
    Tew, David P.
    Thorvaldsen, Andreas J.
    Thogersen, Lea
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Watson, Mark A.
    Wilson, David J. D.
    Ziolkowski, Marcin
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    The Dalton quantum chemistry program system2014In: Wiley Interdisciplinary Reviews. Computational Molecular Science, ISSN 1759-0876, Vol. 4, no 3, p. 269-284Article in journal (Refereed)
    Abstract [en]

    Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from for a number of UNIX platforms.

  • 4. Alger, Ingela
    et al.
    Weibull, Jörgen W.
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.).
    A generalization of Hamilton's rule-Love others how much?2012In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 299, p. 42-54Article in journal (Refereed)
    Abstract [en]

    According to Hamilton's (1964a, b) rule, a costly action will be undertaken if its fitness cost to the actor falls short of the discounted benefit to the recipient, where the discount factor is Wright's index of relatedness between the two. We propose a generalization of this rule, and show that if evolution operates at the level of behavior rules, rather than directly at the level of actions, evolution will select behavior rules that induce a degree of cooperation that may differ from that predicted by Hamilton's rule as applied to actions. In social dilemmas there will be less (more) cooperation than under Hamilton's rule if the actions are strategic substitutes (complements). Our approach is based on natural selection, defined in terms of personal (direct) fitness, and applies to a wide range of pairwise interactions.

  • 5.
    Ali, Raja Hashim
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    From genomes to post-processing of Bayesian inference of phylogeny2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Life is extremely complex and amazingly diverse; it has taken billions of years of evolution to attain the level of complexity we observe in nature now and ranges from single-celled prokaryotes to multi-cellular human beings. With availability of molecular sequence data, algorithms inferring homology and gene families have emerged and similarity in gene content between two genes has been the major signal utilized for homology inference. Recently there has been a significant rise in number of species with fully sequenced genome, which provides an opportunity to investigate and infer homologs with greater accuracy and in a more informed way. Phylogeny analysis explains the relationship between member genes of a gene family in a simple, graphical and plausible way using a tree representation. Bayesian phylogenetic inference is a probabilistic method used to infer gene phylogenies and posteriors of other evolutionary parameters. Markov chain Monte Carlo (MCMC) algorithm, in particular using Metropolis-Hastings sampling scheme, is the most commonly employed algorithm to determine evolutionary history of genes. There are many softwares available that process results from each MCMC run, and explore the parameter posterior but there is a need for interactive software that can analyse both discrete and real-valued parameters, and which has convergence assessment and burnin estimation diagnostics specifically designed for Bayesian phylogenetic inference.

    In this thesis, a synteny-aware approach for gene homology inference, called GenFamClust (GFC), is proposed that uses gene content and gene order conservation to infer homology. The feature which distinguishes GFC from earlier homology inference methods is that local synteny has been combined with gene similarity to infer homologs, without inferring homologous regions. GFC was validated for accuracy on a simulated dataset. Gene families were computed by applying clustering algorithms on homologs inferred from GFC, and compared for accuracy, dependence and similarity with gene families inferred from other popular gene family inference methods on a eukaryotic dataset. Gene families in fungi obtained from GFC were evaluated against pillars from Yeast Gene Order Browser. Genome-wide gene families for some eukaryotic species are computed using this approach.

    Another topic focused in this thesis is the processing of MCMC traces for Bayesian phylogenetics inference. We introduce a new software VMCMC which simplifies post-processing of MCMC traces. VMCMC can be used both as a GUI-based application and as a convenient command-line tool. VMCMC supports interactive exploration, is suitable for automated pipelines and can handle both real-valued and discrete parameters observed in a MCMC trace. We propose and implement joint burnin estimators that are specifically applicable to Bayesian phylogenetics inference. These methods have been compared for similarity with some other popular convergence diagnostics. We show that Bayesian phylogenetic inference and VMCMC can be applied to infer valuable evolutionary information for a biological case – the evolutionary history of FERM domain.

  • 6.
    Ali, Raja Hashim
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Bark, Mikael
    KTH, School of Information and Communication Technology (ICT).
    Miró, Jorge
    KTH, School of Information and Communication Technology (ICT).
    Muhammad, Sayyed Auwn
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Sjöstrand, J.
    Zubair, Syed M.
    KTH, School of Electrical Engineering (EES), Communication Networks. University of Balochistan, Pakistan.
    Abbas, R. M.
    Arvestad, L.
    VMCMC: A graphical and statistical analysis tool for Markov chain Monte Carlo traces2017In: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 18, no 1, article id 97Article in journal (Refereed)
    Abstract [en]

    Background: MCMC-based methods are important for Bayesian inference of phylogeny and related parameters. Although being computationally expensive, MCMC yields estimates of posterior distributions that are useful for estimating parameter values and are easy to use in subsequent analysis. There are, however, sometimes practical difficulties with MCMC, relating to convergence assessment and determining burn-in, especially in large-scale analyses. Currently, multiple software are required to perform, e.g., convergence, mixing and interactive exploration of both continuous and tree parameters. Results: We have written a software called VMCMC to simplify post-processing of MCMC traces with, for example, automatic burn-in estimation. VMCMC can also be used both as a GUI-based application, supporting interactive exploration, and as a command-line tool suitable for automated pipelines. Conclusions: VMCMC is a free software available under the New BSD License. Executable jar files, tutorial manual and source code can be downloaded from https://bitbucket.org/rhali/visualmcmc/.

  • 7.
    Ali, Raja Hashim
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Muhammad, Sayyed Auwn
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Khan, Mehmodd Alam
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Arvestad, Lars
    Stockholms universitet.
    Quantitative synteny scoring improves homology inference and partitioning of gene families2013In: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 14, p. S12-Article in journal (Refereed)
    Abstract [en]

    Background: Clustering sequences into families has long been an important step in characterization of genes and proteins. There are many algorithms developed for this purpose, most of which are based on either direct similarity between gene pairs or some sort of network structure, where weights on edges of constructed graphs are based on similarity. However, conserved synteny is an important signal that can help distinguish homology and it has not been utilized to its fullest potential. Results: Here, we present GenFamClust, a pipeline that combines the network properties of sequence similarity and synteny to assess homology relationship and merge known homologs into groups of gene families. GenFamClust identifies homologs in a more informed and accurate manner as compared to similarity based approaches. We tested our method against the Neighborhood Correlation method on two diverse datasets consisting of fully sequenced genomes of eukaryotes and synthetic data. Conclusions: The results obtained from both datasets confirm that synteny helps determine homology and GenFamClust improves on Neighborhood Correlation method. The accuracy as well as the definition of synteny scores is the most valuable contribution of GenFamClust.

  • 8.
    Alneberg, Johannes
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Bioinformatic Methods in Metagenomics2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Microbial organisms are a vital part of our global ecosystem. Yet, our knowledge of them is still lacking. Direct sequencing of microbial communities, i.e. metagenomics, have enabled detailed studies of these microscopic organisms by inspection of their DNA sequences without the need to culture them. Furthermore, the development of modern high- throughput sequencing technologies have made this approach more powerful and cost-effective. Taken together, this has shifted the field of microbiology from previously being centered around microscopy and culturing studies, to largely consist of computational analyses of DNA sequences. One such computational analysis which is the main focus of this thesis, aims at reconstruction of the complete DNA sequence of an organism, i.e. its genome, directly from short metagenomic sequences.

    This thesis consists of an introduction to the subject followed by five papers. Paper I describes a large metagenomic data resource spanning the Baltic Sea microbial communities. This dataset is complemented with a web-interface allowing researchers to easily extract and visualize detailed information. Paper II introduces a bioinformatic method which is able to reconstruct genomes from metagenomic data. This method, which is termed CONCOCT, is applied on Baltic Sea metagenomics data in Paper III and Paper V. This enabled the reconstruction of a large number of genomes. Analysis of these genomes in Paper III led to the proposal of, and evidence for, a global brackish microbiome. Paper IV presents a comparison between genomes reconstructed from metagenomes with single-cell sequenced genomes. This further validated the technique presented in Paper II as it was found to produce larger and more complete genomes than single-cell sequencing.

  • 9.
    Alneberg, Johannes
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Sundh, John
    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.
    Bennke, Christin
    Leibniz Institute for Baltic Sea Research, Warnemünde, Germany.
    Beier, Sara
    Leibniz Institute for Baltic Sea Research, Warnemünde, Germany.
    Lundin, Daniel
    Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden.
    Hugerth, Luisa
    KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Stockholm, Sweden.
    Pinhassi, Jarone
    Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden.
    Kisand, Veljo
    University of Tartu, Institute of Technology, Tartu, Estonia.
    Riemann, Lasse
    Section for Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark.
    Jürgens, Klaus
    Leibniz Institute for Baltic Sea Research, Warnemünde, Germany.
    Labrenz, Matthias
    Leibniz Institute for Baltic Sea Research, Warnemünde, Germany.
    Andersson, Anders F.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic SeaManuscript (preprint) (Other academic)
    Abstract [en]

    The Baltic Sea is one of the world’s largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within microbial ecosystems, but are computationally heavy to perform. We here present the BAltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset.

  • 10.
    Andersson, Samuel A.
    et al.
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis and Computer Science, NADA.
    Lagergren, Jens
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis and Computer Science, NADA.
    Motif Yggdrasil: Sampling from a tree mixture model2006In: Research In Computational Molecular Biology, Proceedings / [ed] Apostolico, A; Guerra, C; Istrail, S; Pevzner, P; Waterman, M, 2006, Vol. 3909, p. 458-472Conference paper (Refereed)
    Abstract [en]

    In phylogenetic foot-printing, putative regulatory elements are found in upstream regions of orthologous genes by searching for common motifs. Motifs in different upstream sequences are subject to mutations along the edges of the corresponding phylogenetic tree, consequently taking advantage of the tree in the motif search is an appealing idea. We describe the Motif Yggdrasil sampler; the first Gibbs sampler based on a general tree that uses unaligned sequences. Previous tree-based Gibbs samplers have assumed a star-shaped tree or partially aligned upstream regions. We give a probabilistic model describing upstream sequences with regulatory elements and build a Gibbs sampler with respect to this model. We apply the collapsing technique to eliminate the need to sample nuisance parameters, and give a derivation of the predictive update formula. The use of the tree achieves a substantial increase in nucleotide level correlation coefficient both for synthetic data and 37 bacterial lexA genes.

  • 11.
    Andrade, Jorge
    KTH, School of Biotechnology (BIO), Gene Technology.
    Grid and High-Performance Computing for Applied Bioinformatics2007Doctoral thesis, comprehensive summary (Other scientific)
    Abstract [en]

    The beginning of the twenty-first century has been characterized by an explosion of biological information. The avalanche of data grows daily and arises as a consequence of advances in the fields of molecular biology and genomics and proteomics. The challenge for nowadays biologist lies in the de-codification of this huge and complex data, in order to achieve a better understanding of how our genes shape who we are, how our genome evolved, and how we function.

    Without the annotation and data mining, the information provided by for example high throughput genomic sequencing projects is not very useful. Bioinformatics is the application of computer science and technology to the management and analysis of biological data, in an effort to address biological questions. The work presented in this thesis has focused on the use of Grid and High Performance Computing for solving computationally expensive bioinformatics tasks, where, due to the very large amount of available data and the complexity of the tasks, new solutions are required for efficient data analysis and interpretation.

    Three major research topics are addressed; First, the use of grids for distributing the execution of sequence based proteomic analysis, its application in optimal epitope selection and in a proteome-wide effort to map the linear epitopes in the human proteome. Second, the application of grid technology in genetic association studies, which enabled the analysis of thousand of simulated genotypes, and finally the development and application of a economic based model for grid-job scheduling and resource administration.

    The applications of the grid based technology developed in the present investigation, results in successfully tagging and linking chromosomes regions in Alzheimer disease, proteome-wide mapping of the linear epitopes, and the development of a Market-Based Resource Allocation in Grid for Scientific Applications.

  • 12.
    Andrade, Jorge
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology.
    Andersen, Malin
    KTH, School of Biotechnology (BIO), Gene Technology.
    Berglund, Lisa
    KTH, School of Biotechnology (BIO), Proteomics.
    Odeberg, Jacob
    KTH, School of Biotechnology (BIO), Gene Technology.
    Applications of grid computing in genetics and proteomics2007In: Applied Parallel Computing: State Of The Art In Scientific Computing / [ed] Kagstrom, B; Elmroth, E; Dongarra, J; Wasniewski, J, 2007, Vol. 4699, p. 791-798Conference paper (Refereed)
    Abstract [en]

    The potential for Grid technologies in applied bioinformatics is largely unexplored. We have developed a model for solving computationally demanding bioinformatics tasks in distributed Grid environments, designed to ease the usability for scientists unfamiliar with Grid computing. With a script-based implementation that uses a strategy of temporary installations of databases and existing executables on remote nodes at submission, we propose a generic solution that do not rely on predefined Grid runtime environments and that can easily be adapted to other bioinformatics tasks suitable for parallelization. This implementation has been successfully applied to whole proteome sequence similarity analyses and to genome-wide genotype simulations, where computation time was reduced from years to weeks. We conclude that computational Grid technology is a useful resource for solving high compute tasks in genetics and proteomics using existing algorithms.

  • 13. Ansotegui, Carlos
    et al.
    Luisa Bonet, Maria
    Giraldez-Cru, Jesus
    KTH, School of Computer Science and Communication (CSC), Theoretical Computer Science, TCS. Spanish National Research Council, Spain.
    Levy, Jordi
    Structure features for SAT instances classification2017In: Journal of Applied Logic, ISSN 1570-8683, E-ISSN 1570-8691, Vol. 23, p. 27-39Article in journal (Refereed)
    Abstract [en]

    The success of portfolio approaches in SAT solving relies on the observation that different SAT solvers may dramatically change their performance depending on the class of SAT instances they are trying to solve. In these approaches, a set of features of the problem is used to build a prediction model, which classifies instances into classes, and computes the fastest algorithm to solve each of them. Therefore, the set of features used to build these classifiers plays a crucial role. Traditionally, portfolio SAT solvers include features about the structure of the problem and its hardness. Recently, there have been some attempts to better characterize the structure of industrial SAT instances. In this paper, we use some structure features of industrial SAT instances to build some classifiers of industrial SAT families of instances. Namely, they are the scale-free structure, the community structure and the self similar structure. First, we measure the effectiveness of these classifiers by comparing them to other sets of SAT features commonly used in portfolio SAT solving approaches. Then, we evaluate the performance of this set of structure features when used in a real portfolio SAT solver. Finally, we analyze the relevance of these features on the analyzed classifiers.

  • 14.
    Arvestad, Lars
    KTH, Superseded Departments, Numerical Analysis and Computer Science, NADA.
    Aligning coding DNA in the presence of frame-shift errors1997In: Combinatorial Pattern Matching, 1997, p. 180-190Conference paper (Other academic)
    Abstract [en]

    The problem of aligning two DNA sequences with respect to the fact that they are coding for proteins is discussed. Criteria for a good alignment of coding DNA, together with an algorithm that satisfies them, are presented. The algorithm is robust against frame-shifts and forgiving towards silent substitutions. The important choice of objective function is examined and several variants are proposed.

  • 15.
    Arvestad, Lars
    et al.
    Center for Genomics and Bioinformatics, Karolinska Institutet.
    Berglund, Ann-Charlotte
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Lagergren, Jens
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Sennblad, Bengt
    Center for Genomics and Bioinformatics, Karolinska Institutet.
    Bayesian gene/species tree reconciliation and orthology analysis using MCMC2003In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 19, p. i7-i15Article in journal (Refereed)
    Abstract [en]

    Motivation: Comparative genomics in general and orthology analysis in particular are becoming increasingly important parts of gene function prediction. Previously, orthology analysis and reconciliation has been performed only with respect to the parsimony model. This discards many plausible solutions and sometimes precludes finding the correct one. In many other areas in bioinformatics probabilistic models have proven to be both more realistic and powerful than parsimony models. For instance, they allow for assessing solution reliability and consideration of alternative solutions in a uniform way. There is also an added benefit in making model assumptions explicit and therefore making model comparisons possible. For orthology analysis, uncertainty has recently been addressed using parsimonious reconciliation combined with bootstrap techniques. However, until now no probabilistic methods have been available.

    Results: We introduce a probabilistic gene evolution model based on a birth-death process in which a gene tree evolves ‘inside’ a species tree. Based on this model, we develop a tool with the capacity to perform practical orthology analysis, based on Fitch’s original definition, and more generally for reconciling pairs of gene and species trees. Our gene evolution model is biologically sound (Nei et al., 1997) and intuitively attractive. We develop a Bayesian analysis based on MCMC which facilitates approximation of an a posteriori distribution for reconciliations. That is, we can find the most probable reconciliations and estimate the probability of any reconciliation, given the observed gene tree. This also gives a way to estimate the probability that a pair of genes are orthologs. The main algorithmic contribution presented here consists of an algorithm for computing the likelihood of a given reconciliation. To the best of our knowledge, this is the first successful introduction of this type of probabilistic methods, which flourish in phylogeny analysis, into reconciliation and orthology analysis. The MCMC algorithm has been implemented and, although not yet being in its final form, tests show that it performs very well on synthetic as well as biological data. Using standard correspondences, our results carry over to allele trees as well as biogeography.

  • 16.
    Arvestad, Lars
    et al.
    KTH, Superseded Departments, Numerical Analysis and Computer Science, NADA.
    Bruno, William
    Los Alamos National Laboratory.
    Estimation of Reversible Substitution Matrices from Multiple Pairs of Sequences1997In: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 45, no 6, p. 696-703Article in journal (Refereed)
    Abstract [en]

    We present a method for estimating the most general reversible substitution matrix corresponding to a given collection of pairwise aligned DNA sequences. This matrix can then be used to calculate evolutionary distances between pairs of sequences in the collection. If only two sequences are considered, our method is equivalent to that of Lanave et al. (1984). The main novelty of our approach is in combining data from different sequence pairs. We describe a weighting method for pairs of taxa related by a known tree that results in uniform weights for all branches. Our method for estimating the rate matrix results in fast execution times, even on large data sets, and does not require knowledge of the phylogenetic relationships among sequences. In a test case on a primate pseudogene, the matrix we arrived at resembles one obtained using maximum likelihood, and the resulting distance measure is shown to have better linearity than is obtained in a less general model.

  • 17.
    Auffarth, Benjamin
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Kaplan, Bernhard
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Anders, Lansner
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Map formation in the olfactory bulb by axon guidance of olfactory neurons2011In: Frontiers in Systems Neuroscience, ISSN 1662-5137, E-ISSN 1662-5137, Vol. 5, no 0Article in journal (Refereed)
    Abstract [en]

    The organization of representations in the brain has been observed to locally reflect subspaces of inputs that are relevant to behavioral or perceptual feature combinations, such as in areas receptive to lower and higher-order features in the visual system. The early olfactory system developed highly plastic mechanisms and convergent evidence indicates that projections from primary neurons converge onto the glomerular level of the olfactory bulb (OB) to form a code composed of continuous spatial zones that are differentially active for particular physico?-chemical feature combinations, some of which are known to trigger behavioral responses. In a model study of the early human olfactory system, we derive a glomerular organization based on a set of real-world,biologically-relevant stimuli, a distribution of receptors that respond each to a set of odorants of similar ranges of molecular properties, and a mechanism of axon guidance based on activity. Apart from demonstrating activity-dependent glomeruli formation and reproducing the relationship of glomerular recruitment with concentration, it is shown that glomerular responses reflect similarities of human odor category perceptions and that further, a spatial code provides a better correlation than a distributed population code. These results are consistent with evidence of functional compartmentalization in the OB and could suggest a function for the bulb in encoding of perceptual dimensions.

  • 18.
    Aurell, Erik
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). Aalto University, Finland.
    Innocenti, Nicolas
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). The Hebrew University of Jerusalem, Israel.
    Zhou, Hai-Jun
    State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China.
    The bulk and the tail of minimal absent words in genome sequences2016In: Physical Biology, ISSN 1478-3967, E-ISSN 1478-3975, Vol. 13, no 2, article id 026004Article in journal (Refereed)
    Abstract [en]

    Minimal absent words (MAW) of a genomic sequence are subsequences that are absent themselves but the subwords of which are all present in the sequence. The characteristic distribution of genomic MAWs as a function of their length has been observed to be qualitatively similar for all living organisms, the bulk being rather short, and only relatively few being long. It has been an open issue whether the reason behind this phenomenon is statistical or reflects a biological mechanism, and what biological information is contained in absent words. % In this work we demonstrate that the bulk can be described by a probabilistic model of sampling words from random sequences, while the tail of long MAWs is of biological origin. We introduce the novel concept of a core of a minimal absent word, which are sequences present in the genome and closest to a given MAW. We show that in bacteria and yeast the cores of the longest MAWs, which exist in two or more copies, are located in highly conserved regions the most prominent example being ribosomal RNAs (rRNAs). We also show that while the distribution of the cores of long MAWs is roughly uniform over these genomes on a coarse-grained level, on a more detailed level it is strongly enhanced in 3' untranslated regions (UTRs) and, to a lesser extent, also in 5' UTRs. This indicates that MAWs and associated MAW cores correspond to fine-tuned evolutionary relationships, and suggest that they can be more widely used as markers for genomic complexity.

  • 19. Balbi, P.
    et al.
    Massobrio, P.
    Hellgren Kotaleski, Jeanette
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    A single Markov-type kinetic model accounting for the macroscopic currents of all human voltage-gated sodium channel isoforms2017In: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 13, no 9, article id e1005737Article in journal (Refereed)
    Abstract [en]

    Modelling ionic channels represents a fundamental step towards developing biologically detailed neuron models. Until recently, the voltage-gated ion channels have been mainly modelled according to the formalism introduced by the seminal works of Hodgkin and Huxley (HH). However, following the continuing achievements in the biophysical and molecular comprehension of these pore-forming transmembrane proteins, the HH formalism turned out to carry limitations and inconsistencies in reproducing the ion-channels electrophysiological behaviour. At the same time, Markov-type kinetic models have been increasingly proven to successfully replicate both the electrophysiological and biophysical features of different ion channels. However, in order to model even the finest non-conducting molecular conformational change, they are often equipped with a considerable number of states and related transitions, which make them computationally heavy and less suitable for implementation in conductance-based neurons and large networks of those. In this purely modelling study we develop a Markov-type kinetic model for all human voltage-gated sodium channels (VGSCs). The model framework is detailed, unifying (i.e., it accounts for all ion-channel isoforms) and computationally efficient (i.e. with a minimal set of states and transitions). The electrophysiological data to be modelled are gathered from previously published studies on whole-cell patch-clamp experiments in mammalian cell lines heterologously expressing the human VGSC subtypes (from NaV1.1 to NaV1.9). By adopting a minimum sequence of states, and using the same state diagram for all the distinct isoforms, the model ensures the lightest computational load when used in neuron models and neural networks of increasing complexity. The transitions between the states are described by original ordinary differential equations, which represent the rate of the state transitions as a function of voltage (i.e., membrane potential). The kinetic model, developed in the NEURON simulation environment, appears to be the simplest and most parsimonious way for a detailed phenomenological description of the human VGSCs electrophysiological behaviour.

  • 20.
    Bekkouche, Bo
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). KTH.
    Classification of Neuronal Subtypes in the Striatum and the Effect of Neuronal Heterogeneity on the Activity Dynamics2016Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Clustering of single-cell RNA sequencing data is often used to show what states and subtypes cells have. Using this technique, striatal cells were clustered into subtypes using different clustering algorithms. Previously known subtypes were confirmed and new subtypes were found. One of them is a third medium spiny neuron subtype. Using the observed heterogeneity, as a second task, this project questions whether or not differences in individual neurons have an impact on the network dynamics. By clustering spiking activity from a neural network model, inconclusive results were found. Both algorithms indicating low heterogeneity, but by altering the quantity of a subtype between a low and high number, and clustering the network activity in each case, results indicate that there is an increase in the heterogeneity. This project shows a list of potential striatal subtypes and gives reasons to keep giving attention to biologically observed heterogeneity.

  • 21. Bem, T.
    et al.
    Cabelguen, J. M.
    Ekeberg, Örjan
    KTH, Superseded Departments, Numerical Analysis and Computer Science, NADA.
    Grillner, S.
    From swimming to walking: a single basic network for two different behaviors2003In: Biological Cybernetics, ISSN 0340-1200, E-ISSN 1432-0770, Vol. 88, no 2, p. 79-90Article in journal (Refereed)
    Abstract [en]

    In this paper we consider the hypothesis that the spinal locomotor network controlling trunk movements has remained essentially unchanged during the evolutionary transition from aquatic to terrestrial locomotion. The wider repertoire of axial motor patterns expressed by amphibians would then be explained by the influence from separate limb pattern generators, added during this evolution. This study is based on EMG data recorded in vivo from epaxial musculature in the newt Pleurodeles waltl during unrestrained swimming and walking, and on a simplified model of the lamprey spinal pattern generator for swimming. Using computer simulations, we have examined the output generated by the lamprey model network for different input drives. Two distinct inputs were identified which reproduced the main features of the swimming and walking motor patterns in the newt. The swimming pattern is generated when the network receives tonic excitation with local intensity gradients near the neck and girdle regions. To produce the walking pattern, the network must receive (in addition to a tonic excitation at the girdles) a phasic drive which is out of phase in the neck and tail regions in relation to the middle part of the body. To fit the symmetry of the walking pattern, however, the intersegmental connectivity of the network had to be modified by reversing the direction of the crossed inhibitory pathways in the rostral part of the spinal cord. This study suggests that the 'input drive required for the generation of the distinct walking pattern could, at least partly, be attributed to mechanosensory feedback received by the network directly from the intraspinal stretch-receptor system. Indeed, the input drive required resembles the pattern of activity of stretch receptors sensing the lateral bending of the trunk, as expressed during walking in urodeles. Moreover, our results indicate that a nonuniform distribution of these stretch receptors along the trunk can explain the discontinuities exhibited in the swimming pattern of the newt. Thus, original network controlling axial movements not only through a direct coupling at the central level but also via a mechanical coupling between trunk and limbs, which in turn influences the sensory signals sent back to the network. Taken together, our findings support the hypothesis of a phylogenetic conservatism of the spinal locomotor networks generating axial motor patterns from agnathans to amphibians.

  • 22.
    Benjaminsson, Simon
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Fransson, Peter
    Department of Clinical Neuroscience, Karolinska Institute.
    Lansner, Anders
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    A Novel Model-Free Data Analysis Technique Based on Clustering in a Mutual Information Space: Application to Resting-State fMRI2010In: Frontiers in Systems Neuroscience, ISSN 1662-5137, E-ISSN 1662-5137, Vol. 4, p. 34:1-34:8Article in journal (Refereed)
    Abstract [en]

    Non-parametric data-driven analysis techniques can be used to study datasets with few assumptions about the data and underlying experiment. Variations of independent component analysis (ICA) have been the methods mostly used on fMRI data, e.g., in finding resting-state networks thought to reflect the connectivity of the brain. Here we present a novel data analysis technique and demonstrate it on resting-state fMRI data. It is a generic method with few underlying assumptions about the data. The results are built from the statistical relations between all input voxels, resulting in a whole-brain analysis on a voxel level. It has good scalability properties and the parallel implementation is capable of handling large datasets and databases. From the mutual information between the activities of the voxels over time, a distance matrix is created for all voxels in the input space. Multidimensional scaling is used to put the voxels in a lower-dimensional space reflecting the dependency relations based on the distance matrix. By performing clustering in this space we can find the strong statistical regularities in the data, which for the resting-state data turns out to be the resting-state networks. The decomposition is performed in the last step of the algorithm and is computationally simple. This opens up for rapid analysis and visualization of the data on different spatial levels, as well as automatically finding a suitable number of decomposition components.

  • 23.
    Benjaminsson, Simon
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Herman, Pawel
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Lansner, Anders
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Odour discrimination and mixture segmentation in a holistic model of the mammalian olfactory systemManuscript (preprint) (Other academic)
  • 24.
    Benjaminsson, Simon
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Lansner, Anders
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Nexa: A scalable neural simulator with integrated analysis2012In: Network, ISSN 0954-898X, E-ISSN 1361-6536, Vol. 23, no 4, p. 254-271Article in journal (Refereed)
    Abstract [en]

    Large-scale neural simulations encompass challenges in simulator design, data handling and understanding of simulation output. As the computational power of supercomputers and the size of network models increase, these challenges become even more pronounced. Here we introduce the experimental scalable neural simulator Nexa, for parallel simulation of large-scale neural network models at a high level of biological abstraction and for exploration of the simulation methods involved. It includes firing-rate models and capabilities to build networks using machine learning inspired methods for e. g. self-organization of network architecture and for structural plasticity. We show scalability up to the size of the largest machines currently available for a number of model scenarios. We further demonstrate simulator integration with online analysis and real-time visualization as scalable solutions for the data handling challenges.

  • 25.
    Benjaminsson, Simon
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Lundqvist, Mikael
    A model of categorization, learning of invariant representations and sequence prediction utilizing top-down activityManuscript (preprint) (Other academic)
  • 26.
    Berthet, Pierre
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Hällgren Kotaleski, Jeanette
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Lansner, Anders
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Action selection performance of a reconfigurable Basal Ganglia inspired model with Hebbian-Bayesian Go-NoGo connectivity2012In: Frontiers in Behavioral Neuroscience, ISSN 1662-5153, E-ISSN 1662-5153, Vol. 6, p. 65-Article in journal (Refereed)
    Abstract [en]

    Several studies have shown a strong involvement of the basal ganglia (BG) in action selection and dopamine dependent learning. The dopaminergic signal to striatum, the input stage of the BG, has been commonly described as coding a reward prediction error (RPE), i.e. the difference between the predicted and actual reward. The RPE has been hypothesized to be critical in the modulation of the synaptic plasticity in cortico-striatal synapses in the direct and indirect pathway. We developed an abstract computational model of the BG, with a dual pathway structure functionally corresponding to the direct and indirect pathways, and compared its behaviour to biological data as well as other reinforcement learning models. The computations in our model are inspired by Bayesian inference, and the synaptic plasticity changes depend on a three factor Hebbian-Bayesian learning rule based on co-activation of pre- and post-synaptic units and on the value of the RPE. The model builds on a modified Actor-Critic architecture and implements the direct (Go) and the indirect (NoGo) pathway, as well as the reward prediction (RP) system, acting in a complementary fashion. We investigated the performance of the model system when different configurations of the Go, NoGo and RP system were utilized, e.g. using only the Go, NoGo, or RP system, or combinations of those. Learning performance was investigated in several types of learning paradigms, such as learning-relearning, successive learning, stochastic learning, reversal learning and a two-choice task. The RPE and the activity of the model during learning were similar to monkey electrophysiological and behavioural data. Our results, however, show that there is not a unique best way to configure this BG model to handle well all the learning paradigms tested. We thus suggest that an agent might dynamically configure its action selection mode, possibly depending on task characteristics and also on how much time is available.

  • 27.
    Berthet, Pierre
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Lansner, Anders
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Optogenetic Stimulation in a Computational Model of the Basal Ganglia Biases Action Selection and Reward Prediction Error2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 3, p. e90578-Article in journal (Refereed)
    Abstract [en]

    Optogenetic stimulation of specific types of medium spiny neurons (MSNs) in the striatum has been shown to bias the selection of mice in a two choices task. This shift is dependent on the localisation and on the intensity of the stimulation but also on the recent reward history. We have implemented a way to simulate this increased activity produced by the optical flash in our computational model of the basal ganglia (BG). This abstract model features the direct and indirect pathways commonly described in biology, and a reward prediction pathway (RP). The framework is similar to Actor-Critic methods and to the ventral/ dorsal distinction in the striatum. We thus investigated the impact on the selection caused by an added stimulation in each of the three pathways. We were able to reproduce in our model the bias in action selection observed in mice. Our results also showed that biasing the reward prediction is sufficient to create a modification in the action selection. However, we had to increase the percentage of trials with stimulation relative to that in experiments in order to impact the selection. We found that increasing only the reward prediction had a different effect if the stimulation in RP was action dependent (only for a specific action) or not. We further looked at the evolution of the change in the weights depending on the stage of learning within a block. A bias in RP impacts the plasticity differently depending on that stage but also on the outcome. It remains to experimentally test how the dopaminergic neurons are affected by specific stimulations of neurons in the striatum and to relate data to predictions of our model.

  • 28. Birin, H.
    et al.
    Gal-Or, Z.
    Elias, Isaac
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Tuller, T.
    Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion2008In: Bioinformatics, ISSN 1367-4803, Vol. 24, no 6, p. 826-832Article in journal (Refereed)
    Abstract [en]

    Motivation: The evolution of viruses is very rapid and in addition to local point mutations (insertion, deletion, substitution) it also includes frequent recombinations, genome rearrangements and horizontal transfer of genetic materials (HGTS). Evolutionary analysis of viral sequences is therefore a complicated matter for two main reasons: First, due to HGTs and recombinations, the right model of evolution is a network and not a tree. Second, due to genome rearrangements, an alignment of the input sequences is not guaranteed. These facts encourage developing methods for inferring phylogenetic networks that do not require aligned sequences as input. Results: In this work, we present the first computational approach which deals with both genome rearrangements and horizontal gene transfers and does not require a multiple alignment as input. We formalize a new set of computational problems which involve analyzing such complex models of evolution. We investigate their computational complexity, and devise algorithms for solving them. Moreover, we demonstrate the viability of our methods on several synthetic datasets as well as four biological datasets.

  • 29. Birin, Hadas
    et al.
    Gal-Or, Zohar
    Elias, Isaac
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis and Computer Science, NADA.
    Tuller, Tamir
    Inferring models of rearrangements, recombinations, and horizontal transfers by the minimum evolution criterion2007In: Algorithms in Bioinformatics, Proceedings / [ed] Giancarlo, R; Hannenhalli, S, 2007, Vol. 4645, p. 111-123Conference paper (Refereed)
    Abstract [en]

    The evolution of viruses is very rapid and in addition to local point mutations (insertion, deletion, substitution) it also includes frequent recombinations, genome rearrangements, and horizontal transfer of genetic material. Evolutionary analysis of viral sequences is therefore a complicated matter for two main reasons: First, due to HGTs and recombinations, the right model of evolution is a network and not a tree. Second, due to genome rearrangements, an alignment of the input sequences is not guaranteed. Since contemporary methods for inferring phylogenetic networks require aligned sequences as input, they cannot deal with viral evolution. In this work we present the first computational approach which deals with both genome rearrangements and horizontal gene transfers and does not require a multiple alignment as input. We formalize a new set of computational problems which involve analyzing such complex models of evolution, investigate their computational complexity, and devise algorithms for solving them. Moreover, we demonstrate the viability of our methods on several synthetic datasets as well as biological datasets.

  • 30. Björkman, Eva
    et al.
    Zagal, Juan Cristobal
    Lindeberg, Tony
    KTH, Superseded Departments, Numerical Analysis and Computer Science, NADA.
    Roland, Per E.
    Evaluation of design options for the scale-space primal sketch analysis of brain activation images2000In: : HBM'00, published in Neuroimage, volume 11, number 5, 2000, 2000, Vol. 11, p. 656-656Conference paper (Refereed)
    Abstract [en]

    A key issue in brain imaging concerns how to detect the functionally activated regions from PET and fMRI images. In earlier work, it has been shown that the scale-space primal sketch provides a useful tool for such analysis [1]. The method includes presmoothing with different filter widths and automatic estimation of the spatial extent of the activated regions (blobs).

    The purpose is to present two modifications of the scale-space primal sketch, as well as a quantitative evaluation which shows that these modifications improve the performance, measured as the separation between blob descriptors extracted from PET images and from noise images. This separation is essential for future work of associating a statistical p-value with the scale-space blob descriptors.

  • 31.
    Bresin, Roberto
    KTH, School of Computer Science and Communication (CSC), Speech, Music and Hearing, TMH.
    What is the color of that music performance?2005In: Proceedings of the International Computer Music Conference - ICMC 2005, Barcelona, 2005, p. 367-370Conference paper (Refereed)
    Abstract [en]

    The representation of expressivity in music is still a fairlyunexplored field. Alternative ways of representing musicalinformation are necessary when providing feedback onemotion expression in music such as in real-time tools formusic education, or in the display of large music databases.One possible solution could be a graphical non-verbal representationof expressivity in music performance using coloras index of emotion. To determine which colors aremost suitable for an emotional expression, a test was run.Subjects rated how well each of 8 colors and their 3 nuancescorresponds to each of 12 music performances expressingdifferent emotions. Performances were playedby professional musicians with 3 instruments, saxophone,guitar, and piano. Results show that subjects associateddifferent hues to different emotions. Also, dark colorswere associated to music in minor tonality and light colorsto music in major tonality. Correspondence betweenspectrum energy and color hue are preliminary discussed.

  • 32.
    Bresin, Roberto
    et al.
    KTH, School of Computer Science and Communication (CSC), Speech, Music and Hearing, TMH, Music Acoustics.
    Delle Monache, Stefano
    University of Verona.
    Fontana, Federico
    University of Verona.
    Papetti, Stefano
    University of Verona.
    Polotti, Pietro
    University of Verona.
    Visell, Yon
    McGill University.
    Auditory feedback through continuous control of crumpling sound synthesis2008In: Proceedings of Sonic Interaction Design: Sound, Information and Experience. A CHI 2008 Workshop organized by COST Action IC0601, IUAV University of Venice , 2008, p. 23-28Conference paper (Refereed)
    Abstract [en]

    A realtime model for the synthesis of crumpling sounds ispresented. By capturing the statistics of short sonic transients which give rise to crackling noise, it allows for a consistent description of a broad spectrum of audible physical processes which emerge in several everyday interaction contexts.The model drives a nonlinear impactor that sonifies every transient, and it can be parameterized depending on the physical attributes of the crumpling material. Three different scenarios are described, respectively simulating the foot interaction with aggregate ground materials, augmenting a dining scenario, and affecting the emotional content of a footstep sequence. Taken altogether, they emphasize the potential generalizability of the model to situations in which a precise control of auditory feedback can significantly increase the enactivity and ecological validity of an interface.

  • 33. Cervenka, Simon
    et al.
    Varrone, Andrea
    Fransén, Erik
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Halldin, Christer
    Farde, Lars
    PET Studies of D2-Receptor Binding in Striatal and Extrastriatal Brain Regions: Biochemical Support In Vivo for Separate Dopaminergic Systems in Humans2010In: Synapse, ISSN 0887-4476, E-ISSN 1098-2396, Vol. 64, no 6, p. 478-485Article in journal (Refereed)
    Abstract [en]

    Most molecular imaging studies of the dopamine (DA) system performed to date have focused on the striatum, a region receiving dense dopaminergic innervation. In clinical research on the DA D2-receptor, striatal binding has often been regarded as an index of global DA function, based on the underlying assumption of common regulatory mechanisms for receptor expression across brain regions. Recent data has challenged this view, suggesting differences in genetic regulation between striatal and extrastriatal brain regions. The relationship between binding levels in brain regions has, however, not been directly examined in the same sample. In this study, we searched for interregional correlations between DA D2-receptor availability as determined with Positron Emission Tomography in 16 control subjects. The radioligands [C-11]raclopride and [C-11]FLB 457 were used for measurements of D2-receptor binding in striatal and extrastriatal regions, respectively. No correlation was observed between D2-receptor availability in striatum and any of the extrastriatal regions, as assessed using both region of interest- and voxel-based analyses. Instead, the pattern of correlations was consistent with the model of separate dopaminergic systems as has been originally observed in rodents. These preliminary results encourage approaches searching for individual patterns of receptor binding across the whole brain volume in clinical studies on the dopamine system.

  • 34.
    Chatterjee, Saikat
    et al.
    KTH, School of Electrical Engineering (EES), Communication Theory.
    Koslicki, David
    Dept of Mathematics, Oregon State University, Corvallis, USA.
    Dong, Siyuan
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Innocenti, Nicolas
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Cheng, Lu
    Dept of Mathematics and Statistics, University of Helsinki, Finland.
    Lan, Yueheng
    Dept of Physics, Tsinghua University, Beijing, China.
    Vehkaperä, Mikko
    KTH, School of Electrical Engineering (EES), Communication Theory.
    Skoglund, Mikael
    KTH, School of Electrical Engineering (EES), Centres, ACCESS Linnaeus Centre. KTH, School of Electrical Engineering (EES), Communication Theory.
    K. Rasmussen, Lars
    KTH, School of Electrical Engineering (EES), Communication Theory.
    Aurell, Erik
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Corander, Jukka
    Dept of Signal Processing, Aalto University, Finland.
    SEK: Sparsity exploiting k-mer-based estimation of bacterial community composition2014In: Bioinformatics, ISSN 1460-2059, Vol. 30, no 17, p. 2423-2431Article in journal (Refereed)
    Abstract [en]

    Motivation: Estimation of bacterial community composition from a high-throughput sequenced sample is an important task in metagenomics applications. As the sample sequence data typically harbors reads of variable lengths and different levels of biological and technical noise, accurate statistical analysis of such data is challenging. Currently popular estimation methods are typically time-consuming in a desktop computing environment.

    Results: Using sparsity enforcing methods from the general sparse signal processing field (such as compressed sensing), we derive a solution to the community composition estimation problem by a simultaneous assignment of all sample reads to a pre-processed reference database. A general statistical model based on kernel density estimation techniques is introduced for the assignment task, and the model solution is obtained using convex optimization tools. Further, we design a greedy algorithm solution for a fast solution. Our approach offers a reasonably fast community composition estimation method, which is shown to be more robust to input data variation than a recently introduced related method.

    Availability and implementation: A platform-independent Matlab implementation of the method is freely available at http://www.ee.kth.se/ctsoftware; source code that does not require access to Matlab is currently being tested and will be made available later through the above Web site.

  • 35. Chaudhry, Q. A.
    et al.
    Hanke, Michael
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA.
    Morgenstern, R.
    Dreij, K.
    Surface reactions on the cytoplasmatic membranes - Mathematical modeling of reaction and diffusion systems in a cell2014In: Journal of Computational and Applied Mathematics, ISSN 0377-0427, E-ISSN 1879-1778, Vol. 262, p. 244-260Article in journal (Refereed)
    Abstract [en]

    A human cell consists schematically of an outer cellular membrane, a cytoplasm containing a large number of organelles (mitochondria, endoplasmatic reticulum etc.), a nuclear membrane and finally the cellular nucleus containing DNA. The organelles create a complex and dense system of membranes or sub-domains throughout the cytoplasm. The mathematical description leads to a system of reaction-diffusion equations in a complex geometrical domain, dominated by thin membranous structures with similar physical and chemical properties. In a previous model, we considered only spatially distributed reaction and diffusion processes. However, from experiments it is known that membrane bound proteins play an important role in the metabolism of certain substances. In the present paper we develop a homogenization strategy which includes both volume and surface reactions. The homogenized system is a reaction-diffusion system in the cytoplasm which is coupled to the surrounding cell components by correspondingly modified transfer conditions. The approach is verified by application to a system modeling the cellular uptake and intracellular dynamics of carcinogenic polycyclic aromatic hydrocarbons.

  • 36.
    Cürüklü, Baran
    et al.
    Department of Computer Science and Engineering, Mälardalen University.
    Lansner, Anders
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis and Computer Science, NADA.
    A model of the summation pools within the layer 4 (area 17)2005In: Neurocomputing, ISSN 0925-2312, E-ISSN 1872-8286, Vol. 65, p. 167-172Article in journal (Refereed)
    Abstract [en]

    We propose a developmental model of the summation pools within the layer 4. The model is based on the modular structure of the neocortex and captures some of the known properties of layer 4. Connections between the orientation minicolumns are developed during exposure to visual input. Excitatory local connections are dense and biased towards the iso-orientation domain. Excitatory long-range connections are sparse and target all orientation domains equally. Inhibition is local. The summation pools are elongated along the orientation axis. These summation pools can facilitate weak and poorly tuned LGN input and explain improved visibility as an effect of enlargement of a stimulus.

  • 37.
    Dahl, Sofia
    et al.
    KTH, School of Computer Science and Communication (CSC), Speech, Music and Hearing, TMH, Music Acoustics.
    Bevilacqua, Frédéric
    Bresin, Roberto
    KTH, School of Computer Science and Communication (CSC), Speech, Music and Hearing, TMH, Music Acoustics.
    Clayton, Martin
    Leante, Laura
    Poggi, Isabella
    Rasamimanana, Nicolas
    Gestures in performance2009In: Musical Gestures: Sound, Movement, and Meaning / [ed] Godøy, Rolf Inge; Leman, Marc, New York: Routledge , 2009, p. 36-68Chapter in book (Refereed)
    Abstract [en]

    We experience and understand the world, including music, through body movement–when we hear something, we are able to make sense of it by relating it to our body movements, or form an image in our minds of body movements. Musical Gestures is a collection of essays that explore the relationship between sound and movement. It takes an interdisciplinary approach to the fundamental issues of this subject, drawing on ideas, theories and methods from disciplines such as musicology, music perception, human movement science, cognitive psychology, and computer science.

  • 38. De Schutter, E.
    et al.
    Ekeberg, Örjan
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Hellgren Kotaleski, Jeanette
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Achard, P.
    Lansner, Anders
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Biophysically detailed modelling of microcircuits and beyond2005In: TINS - Trends in Neurosciences, ISSN 0166-2236, E-ISSN 1878-108X, Vol. 28, no 10, p. 562-569Article, review/survey (Refereed)
    Abstract [en]

    Realistic bottom-up modelling has been seminal to understanding which properties of microcircuits control their dynamic behaviour, such as the locomotor rhythms generated by central pattern generators. In this article of the TINS Microcircuits Special Feature, we review recent modelling work on the leech-heartbeat and lamprey-swimming pattern generators as examples. Top-down mathematical modelling also has an important role in analyzing microcircuit properties but it has not always been easy to reconcile results from the two modelling approaches. Most realistic microcircuit models are relatively simple and need to be made more detailed to represent complex processes more accurately. We review methods to add neuromechanical feedback, biochemical pathways or full dendritic morphologies to microcircuit models. Finally, we consider the advantages and challenges of full-scale simulation of networks of microcircuits.

  • 39. Dickson, C. T.
    et al.
    Magistretti, J.
    Shalinsky, M. H.
    Fransén, Erik
    KTH, Superseded Departments, Numerical Analysis and Computer Science, NADA.
    Hasselmo, M. E.
    Alonso, A.
    Properties and role of I-h in the pacing of subthreshold oscillations in entorhinal cortex layer II neurons2000In: Journal of Neurophysiology, ISSN 0022-3077, E-ISSN 1522-1598, Vol. 83, no 5, p. 2562-2579Article, review/survey (Refereed)
    Abstract [en]

    Various subsets of brain neurons express a hyperpolarization-activated inward current (I-h) that has been shown to be instrumental in pacing oscillatory activity at both a single-cell and a network level. A characteristic feature of the stellate cells (SCs) of entorhinal cortex (EC) layer II, those neurons giving rise to the main component of the perforant path input to the hippocampal formation, is their ability to generate persistent, Na+-dependent rhythmic subthreshold membrane potential oscillations, which are thought to be instrumental in implementing theta rhythmicity in the entorhinal-hippocampal network. The SCs also display a robust time-dependent inward rectification in the hyperpolarizing direction that may contribute to the generation of these oscillations. We performed whole cell recordings of SCs in in vitro slices to investigate the specific biophysical and pharmacological properties of the current underlying this inward rectification and to clarify its potential role in the genesis of the subthreshold oscillations. In voltage-clamp conditions, hyperpolarizing voltage steps evoked a slow, noninactivating inward current, which also deactivated slowly on depolarization. This current was identified as I-h because it was resistant to extracellular Ba2+, sensitive to Cs+, completely and selectively abolished by ZD7288, and carried by both Na+ and K+ ions. I-h in the SCs had an activation threshold and reversal potential at approximately -45 and -20 mV, respectively. Its half-activation voltage was -77 mV. Importantly, bath perfusion with ZD7288, but not Ba2+ gradually and completely abolished the subthreshold oscillations, thus directly implicating I-h in their generation. Using experimentally derived biophysical parameters for I-h and the low-threshold persistent Na+ current (I-NaP) present in the SCs, a simplified model of these neurons was constructed and their subthreshold electroresponsiveness simulated. This indicated that the interplay between I-NaP and I-h can sustain persistent subthreshold oscillations in SCs. I-NaP and I-h operate in a push-pull fashion where the delay in the activation/deactivation of I-h gives rise to the oscillatory process.

  • 40.
    Djurfeldt, Mikael
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. nternational Neuroinformatics Coordinating Facility, Stockholm, Sweden .
    Davison, Andrew P.
    Eppler, Jochen M.
    Efficient generation of connectivity in neuronal networks from simulator-independent descriptions2014In: Frontiers in Neuroinformatics, ISSN 1662-5196, E-ISSN 1662-5196, Vol. 8, p. 43-Article in journal (Refereed)
    Abstract [en]

    Simulator-independent descriptions of connectivity in neuronal networks promise greater ease of model sharing, improved reproducibility of simulation results, and reduced programming effort for computational neuroscientists. However, until now, enabling the use of such descriptions in a given simulator in a computationally efficient way has entailed considerable work for simulator developers, which must be repeated for each new connectivity-generating library that is developed. We have developed a generic connection generator interface that provides a standard way to connect a connectivity-generating library to a simulator, such that one library can easily be replaced by another, according to the modeler's needs. We have used the connection generator interface to connect C++ and Python implementations of the previously described connection-set algebra to the NEST simulator. We also demonstrate how the simulator-independent modeling framework PyNN can transparently take advantage of this, passing a connection description through to the simulator layer for rapid processing in C++ where a simulator supports the connection generator interface and falling-back to slower iteration in Python otherwise. A set of benchmarks demonstrates the good performance of the interface.

  • 41.
    Djurfeldt, Mikael
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Hjorth, Johannes
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Eppler, Jochen
    Honda Research Institute.
    Dudani, Niraj
    Helias, Moritz
    University of Freiburg, Germany.
    Potjans, Tobias
    Bhalla, Upinder
    Diesmann, Markus
    Hellgren Kotaleski, Jeanette
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Ekeberg, Örjan
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Run-Time Interoperability Between Neuronal Network Simulators Based on the MUSIC Framework2010In: Neuroinformatics, ISSN 1539-2791, E-ISSN 1559-0089, Vol. 8, no 1, p. 43-60Article in journal (Refereed)
    Abstract [en]

    MUSIC is an API allowing large scale neuron simulators using MPI internally to exchange data during runtime. We provide experiences from the adaptation of two neuronal network simulators of different kinds, NEST and MOOSE, to this API. A multi-simulation of a cortico-striatal network model involving both simulators is performed, demonstrating how MUSIC can promote inter-operability between models written for different simulators and how these can be re-used to build a larger model system. We conclude that MUSIC fulfills the design goals of being portable and simple to adapt to existing simulators. In addition, since the MUSIC API enforces independence between the applications, the multi-simulationcould be built from pluggable component modules without adaptation of the components to each other in terms of simulation time-step or topology of connections between the modules.

  • 42.
    Djurfeldt, Mikael
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Lundqvist, Mikael
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Johansson, Christopher
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Rehn, Martin
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Ekeberg, Örjan
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Lansner, Anders
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Brain-scale simulation of the neocortex on the IBM Blue Gene/L  supercomputer2008In: IBM Journal of Research and Development, ISSN 0018-8646, E-ISSN 2151-8556, Vol. 52, no 1-2, p. 31-41Article in journal (Refereed)
    Abstract [en]

    Biologically detailed large-scale models of the brain can now be simulated thanks to increasingly powerful massively parallel supercomputers. We present an overview, for the general technical reader, of a neuronal network model of layers II/III of the neocortex built with biophysical model neurons. These simulations, carried out on an IBM Blue Gene/Le supercomputer, comprise up to 22 million neurons and 11 billion synapses, which makes them the largest simulations of this type ever performed. Such model sizes correspond to the cortex of a small mammal. The SPLIT library, used for these simulations, runs on single-processor as well as massively parallel machines. Performance measurements show good scaling behavior on the Blue Gene/L supercomputer up to 8,192 processors. Several key phenomena seen in the living brain appear as emergent phenomena in the simulations. We discuss the role of this kind of model in neuroscience and note that full-scale models may be necessary to preserve natural dynamics. We also discuss the need for software tools for the specification of models as well as for analysis and visualization of output data. Combining models that range from abstract connectionist type to biophysically detailed will help us unravel the basic principles underlying neocortical function.

  • 43.
    Djurfeldt, Mikael
    et al.
    KTH, Superseded Departments, Numerical Analysis and Computer Science, NADA.
    Sandberg, Anders
    KTH, Superseded Departments, Numerical Analysis and Computer Science, NADA.
    Ekeberg, Örjan
    KTH, Superseded Departments, Numerical Analysis and Computer Science, NADA.
    Lansner, Anders
    KTH, Superseded Departments, Numerical Analysis and Computer Science, NADA.
    See-A framework for simulation of biologically detailed and artificial neural networks and systems1999In: Neurocomputing, ISSN 0925-2312, E-ISSN 1872-8286, Vol. 26-27, p. 997-1003Article in journal (Refereed)
    Abstract [en]

    See is a software framework for simulation of biologically detailed and artficial neural networks and systems. It includes a general purpose scripting language, based on Scheme,which also can be used interactively, while the basic framework is written in C++. Models can be built on the Scheme level from `simulation objectsa, each representing a population ofneurons, a projection, etc. The simulator provides a flexible and efficient protocol for data transfer between such objects. See contains a user interface to the parallelized, platformindependent, library SPLIT intended for biologically detailed modeling of large-scale networks and is easy to extend with new user code, both on the C++ and Scheme levels.

  • 44.
    DONG, SIYUAN
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB. Aalto University.
    A time dependent adaptive learning process for estimating drug exposure from register data - applied to insulin and its analogues2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 45.
    Dong, Siyuan
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    A time dependent adaptive learning process for estimating drug exposure from register data - applied to insulin and its analogues2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 46. Dunn, Benjamin
    et al.
    Morreaunet, Maria
    Roudi, Yasser
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Correlations and Functional Connections in a Population of Grid Cells2015In: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 11, no 2, article id e1004052Article in journal (Refereed)
    Abstract [en]

    We study the statistics of spike trains of simultaneously recorded grid cells in freely behaving rats. We evaluate pairwise correlations between these cells and, using a maximum entropy kinetic pairwise model (kinetic Ising model), study their functional connectivity. Even when we account for the covariations in firing rates due to overlapping fields, both the pairwise correlations and functional connections decay as a function of the shortest distance between the vertices of the spatial firing pattern of pairs of grid cells, i.e. their phase difference. They take positive values between cells with nearby phases and approach zero or negative values for larger phase differences. We find similar results also when, in addition to correlations due to overlapping fields, we account for correlations due to theta oscillations and head directional inputs. The inferred connections between neurons in the same module and those from different modules can be both negative and positive, with a mean close to zero, but with the strongest inferred connections found between cells of the same module. Taken together, our results suggest that grid cells in the same module do indeed form a local network of interconnected neurons with a functional connectivity that supports a role for attractor dynamics in the generation of grid pattern.

  • 47. Egorov, A. V.
    et al.
    Hamam, B. N.
    Fransén, Erik
    KTH, Superseded Departments, Numerical Analysis and Computer Science, NADA.
    Hasselmo, M. E.
    Alonso, A. A.
    Graded persistent activity in entorhinal cortex neurons2002In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 420, no 6912, p. 173-178Article in journal (Refereed)
    Abstract [en]

    Working memory represents the ability of the brain to hold externally or internally driven information for relatively short periods of time(1,2). Persistent neuronal activity is the elementary process underlying working memory but its cellular basis remains unknown. The most widely accepted hypothesis is that persistent activity is based on synaptic reverberations in recurrent circuits. The entorhinal cortex in the parahippocampal region is crucially involved in the acquisition, consolidation and retrieval of long-term memory traces for which working memory operations are essential(2). Here we show that individual neurons from layer V of the entorhinal cortex-which link the hippocampus to extensive cortical regions(3)-respond to consecutive stimuli with graded changes in firing frequency that remain stable after each stimulus presentation. In addition, the sustained levels of firing frequency can be either increased or decreased in an input-specific manner. This firing behaviour displays robustness to distractors; it is linked to cholinergic muscarinic receptor activation, and relies on activity-dependent changes of a Ca2+-sensitive cationic current. Such an intrinsic neuronal ability to generate graded persistent activity constitutes an elementary mechanism for working memory.

  • 48.
    Ekeberg, Magnus
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Hartonen, Tuomo
    Aurell, Erik
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB. Aalto University, Finland.
    Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences2014In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 276, p. 341-356Article in journal (Refereed)
    Abstract [en]

    Direct-coupling analysis is a group of methods to harvest information about coevolving residues in a protein family by learning a generative model in an exponential family from data. In protein families of realistic size, this learning can only be done approximately, and there is a trade-off between inference precision and computational speed. We here show that an earlier introduced l(2)-regularized pseudolikelihood maximization method called plmDCA can be modified as to be easily parallelizable, as well as inherently faster on a single processor, at negligible difference in accuracy. We test the new incarnation of the method on 143 protein family/structure-pairs from the Protein Families database (PFAM), one of the larger tests of this class of algorithms to date.

  • 49.
    Ekeberg, Örjan
    KTH, Superseded Departments, Numerical Analysis and Computer Science, NADA.
    A combined neuronal and mechanical model of fish swimming1993In: Biological Cybernetics, ISSN 0340-1200, E-ISSN 1432-0770, Vol. 69, no 5-6, p. 363-374Article in journal (Refereed)
    Abstract [en]

    A simulated neural network has been connected to a simulated mechanical environment. The network is based on a model of the spinal central pattern generator producing rhythmic swimming movements in the lamprey and the model is similar to that used in earlier simulations of fictive swimming. Here, the network has been extended with a model of how motoneuron activity is transformed via the muscles to mechanical forces. Further, these forces are used in a two-dimensional mechanical model including interaction with the surrounding water, giving the movements of the different parts of the body. Finally, these movements are fed back through stretch receptors interacting with the central pattern generator. The combined model provides a platform for various simulation experiments relating the currently known neural properties and connectivity to the behavior of the animal in vivo. By varying a small set of parameters, corresponding to brainstem input to the spinal network, a variety of basic locomotor behaviors, like swimming at different speeds and turning can be produced. This paper describes the combined model and its basic properties.

  • 50.
    Ekeberg, Örjan
    et al.
    KTH, Superseded Departments, Numerical Analysis and Computer Science, NADA.
    Blümel, Marcus
    University of Köln.
    Büschges, Ansgar
    University of Köln.
    Dynamic simulation of insect walking2004In: Arthropod structure & development, ISSN 1467-8039, E-ISSN 1873-5495, Vol. 33, no 3, p. 287-300Article in journal (Refereed)
    Abstract [en]

    Insect walking relies on a complex interaction between the environment, body segments, muscles and the nervous system. For the stick insect in particular, previous investigations have highlighted the role of specific sensory signals in the timing of activity of central neural networks driving the individual leg joints. The objective of the current study was to relate specific sensory and neuronal mechanisms, known from experiments on reduced preparations, to the generation of the natural sequence of events forming the step cycle in a single leg. We have done this by simulating a dynamic 3D-biomechanical model of the stick insect coupled to a reduced model of the neural control system, incorporating only the mechanisms under study. The neural system sends muscle activation levels to the biomechanical system, which in turn provides correctly timed propriosensory signals back to the neural model. The first simulations were designed to test if the currently known mechanisms would be sufficient to explain the coordinated activation of the different leg muscles in the middle leg. Two experimental situations were mimicked: restricted stepping where only the coxatrochanteral joint and the femur-tibia joint were free to move, and the unrestricted single leg movements on a friction-free surface. The first of these experimental situations is in fact similar to the preparation used in gathering much of the detailed knowledge on sensory and neuronal mechanisms. The simulations show that the mechanisms included can indeed account for the entire step cycle in both situations. The second aim was to test to what extent the same sensory and neuronal mechanisms would be adequate also for controlling the front and hind legs, despite the large differences in both leg morphology and kinematic patterns. The simulations show that front leg stepping can be generated by basically the same mechanisms while the hind leg control requires some reorganization. The simulations suggest that the influence from the femoral chordotonal organs on the network controlling levation-depression may have a reversed effect in the hind legs as compared to the middle and front legs. This, and other predictions from the model will have to be confirmed by additional experiments.

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