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  • Open Access
    Authors: 
    Saini, Bhupinder Singh; Emmerich, Michael; Mazumdar, Atanu; Afsar, Bekir; Shavazipour, Babooshka; Miettinen, Kaisa;
    Publisher: Zenodo
    Project: AKA | Data-driven Decision Supp... (322221), AKA | Data-driven Decision Supp... (322221)

    This repository contains the implementation of the O-NAUTILUS software as described in the paper "Optimistic NAUTILUS Navigator for Multiobjective Optimization with Costly Function Evaluations". Extract the zip file to obtain the Python files. Install the necessary dependencies in a virtual environment using: poetry install Note that this version of the application only runs on linux systems. Run the app using the following command: python UI/index.py This research was partly funded by the Academy of Finland (grants 322221 and 311877).

  • Open Access English
    Authors: 
    Mohadeseh S. Tahami; Dinc��, Vlad; Lee, Kyung Min; Vila, Roger; Joshi, Mukta; Heikkil��, Maria; Dapporto, Leonardo; Schmid, Sarah; Huemer, Peter; Mutanen, Marko;
    Publisher: Zenodo
    Project: AKA | Advancing the genomic rev... (314702), AKA | Advancing the genomic rev... (314702)

    We studied the evolutionary relationship of two widely distributed parapatric butterfly species, Melitaea athalia and M. celadussa, using the ddRAD sequencing approach, as well as genital morphology and mtDNA data. Melitaea athalia was retrieved as paraphyletic with respect to M. celadussa. Several cases of mito-nuclear discordance and morpho-genetic mismatch were found in the contact zone. Unexpectedly, a strongly diverged and marginally sympatric clade of M. athalia from the Balkans was revealed. An in-depth analysis of genomic structure unravelled high levels of admixture between M. athalia and M. celadussa at the contact zone and deep into the distribution range of M. athalia, though not reaching the Balkan clade. The demographic modelling of populations supported the intermediate nature of M. athalia with regards to M. celadussa and the Balkan clade. However, the dissimilarity matrix of genotype data (PCoA) suggested the Balkan lineage having a genetic component that is unrelated to the athalia-celadussa group. Although narrowly sympatric, almost no signs of gene flow were found between the main M. athalia group and the Balkan clade. We propose two possible scenarios on the historical evolution of our model taxa and the role of the last glacial maximum in shaping their current distribution. Finally, we discuss the complexities regarding the taxonomic delimitation of parapatric taxa.

  • Research software . 2022
    Open Access
    Authors: 
    Schultheis, Erik;
    Publisher: Zenodo
    Project: AKA | High Performance Computin... (347707)

    Implementation of Dismec++ Note that git submodules are not included in this upload, and need to be filled into the `deps` folder manually. Or just clone the git repository recursively from https://github.com/xmc-aalto/dismecpp/tree/v0.1

  • Research software . 2018
    MATLAB
    Authors: 
    Belevich, Ilya;
    Publisher: bio.tools
    Project: AKA | Molecular determinants of... (131650)

    Microscopy image browser (MIB) is a software package for high-performance segmentation and image processing of multidimensional datasets that improves and facilitates the full utilization and quantitative analysis of acquired data.

  • Open Access
    Authors: 
    Häkkinen, Antti;
    Publisher: Zenodo
    Project: AKA | Center of Excellence in C... (284598), EC | HERCULES (667403), AKA | Personalized combination ... (292402), AKA | Center of Excellence in C... (284598), EC | HERCULES (667403), AKA | Personalized combination ... (292402)

    dmml is a tool for identifying differentially methylated sites in tumor samples with varying, unknown tumor cell fraction using a maximum-likelihood method. For the details about the method and validation, please refer to our publication on the matter. Major features: Comparison of up to 31 tumor samples simultaneously Zero, one, or multiple control samples Tumor purity of each sample is automatically estimated; alternatively, prior knowledge about the tumor cell fraction can be injected The estimator models co-methylation of neighboring sites locally in each neighborhood, which properly accounts for correlations within and across CG islands

  • Open Access
    Authors: 
    Tuomo Valkonen;
    Publisher: Zenodo
    Project: AKA | Decoupling preconditioner... (314701), AKA | Decoupling preconditioner... (320022), AKA | Decoupling preconditioner... (314701), AKA | Decoupling preconditioner... (320022)

    This repository contains the codes for the numerical demonstrations in “Regularisation, optimisation, subregularity” (https://arxiv.org/abs/2011.07575). Prerequisites These codes were written for Julia 1.5.2. The package dependencies are from January 2021 when our experiments were run. You may get Julia from julialang.org. Using Navigate your unix shell to the directory containing this README.md and then run: sh $ julia --project=. The first time doing this, to ensure all the dependencies are installed, run julia> ]instantiate Afterwards in the Julia shell, type: julia> using Regtheory This may take a while as Julia precompiles the code. Then, to generate all the experiments in the manuscript, run: julia> batchrun() This will write the data in the manusript to tv-results.txt, and the images to several files of the form data_*.png, reco_*.png, and error_*.png. To alter the computations performed, see src/TV.jl. In particular, the array experiments_tv lists the different the parameters $α$, $δ$, and $N$ while default_params contains the parameters of the algorithm.

  • Research software
    Country: Finland

    The goal of this module is to aggregate building stock data into arbitrary simplified lumped-capacitance thermal models representing the flexible heating/cooling demand of the underlying building stock for large-scale energy system models like Backbone or SpineOpt. Requires building stock data processed by e.g. FinnishBuildingStockData.jl or similar, as well as archetype building definitions according to the template provided in archetype_definitions.json as input. For automatic weather data processing, this module uses the Python sub-module archetypebuildingweather.

  • Open Access
    Authors: 
    Fabritius, Henna;
    Publisher: Zenodo
    Project: AKA | Finnish Centre of Excelle... (129636), AKA | Finnish Centre of Excelle... (250444), AKA | Modern statistical toolbo... (309581), AKA | Finnish Centre of Excelle... (129636), AKA | Finnish Centre of Excelle... (250444), AKA | Modern statistical toolbo... (309581)

    The Zip file contains an R script used for metapopulation simulations in Fabritius et al. (2021): Effects of a mobile disturbance pattern on dynamic patch networks and metapopulation persistence. Ecological Modelling 460: 109738. https://doi.org/10.1016/j.ecolmodel.2021.109738

  • Research software . 2017
    Open Source R
    Authors: 
    Cichonska, Anna;
    Publisher: bio.tools
    Project: EC | ENGAGE (201413), AKA | Multivariate statistical ... (288509), EC | BIOSHARE-EU (261433), AKA | Enhanced learning of hier... (259272), AKA | Predicting risk for coron... (251217), AKA | Finnish centre of excelle... (251170), WT , AKA | Computationally efficient... (257654), AKA | Genetic susceptibility an... (255847)

    Performs multivariate analysis of a single or multiple GWAS based on univariate regression coefficients. It allows multivariate representation of both phenotype and genotype. It extends the statistical technique of canonical correlation analysis to the setting where original individual-level records are not available, and employs a covariance shrinkage algorithm to achieve robustness.

  • Research software . 2022
    Open Access
    Authors: 
    Ondřej Krejčí; , Konrad; Schütt, Ole; , Prokop;
    Publisher: Zenodo
    Project: EC | QMKPFM (845060), EC | QMKPFM (845060)

    Just for GitHub, to get DOI. Otherwise the same, as before: First public release. The version 1.0.0 is still far from being ideal. However tested with FireballTG, FHI-aims and CP2K. GUI should be also working. Still missing: d vs d orbitals understanding problem of lower d orbital ratio for the FePc calculation, after revision of the code automatic rescaling, due to different elements/electrostatics And plenty of more probably.

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