Article
Biochemical Research Methods
Shelvasha Burkes-Patton, Elizabeth A. Cooper, Jessica Schlueter
Summary: RepBox, a suite of Python scripts, improves the efficiency of transposable elements (TEs) identification and categorization in plant genomes compared to existing methods.
BMC BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Lucas S. P. Rudden, Samuel C. Musson, Justin L. P. Benesch, Matteo T. Degiacomi
Summary: Biobox is a Python-based toolbox designed to facilitate the implementation of biomolecular modelling methods.
Article
Computer Science, Interdisciplinary Applications
Alberto Paganini, Florian Wechsung
Summary: Fireshape is an open-source automated shape optimization toolbox designed for the finite element software Firedrake. It utilizes the moving mesh method, allowing users with minimal shape optimization knowledge to easily tackle challenging shape optimization problems constrained by partial differential equations (PDEs).
STRUCTURAL AND MULTIDISCIPLINARY OPTIMIZATION
(2021)
Review
Chemistry, Multidisciplinary
Jackson K. B. Cahn, Jorn Piel
Summary: This review discusses available and emerging techniques for targeted single-cell analysis, with a particular focus on applications to the discovery and study of natural products.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemical Research Methods
Shimon M. Rosenthal, Tvisha Misra, Hala Abdouni, Tess C. Branon, Alice Y. Ting, Ian C. Scott, Anne-Claude Gingras
Summary: Researchers adapted proximity labeling for protein discovery in zebrafish, developing in vivo TurbolD and mini-Turbo labeling techniques. By providing biotin directly in the egg water, they demonstrated successful biotinylation of prey proteins after 12 hours, enabling time-resolved analysis of development.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Article
Robotics
Andrea Testa, Andrea Camisa, Giuseppe Notarstefano
Summary: ChoiRbot is a toolbox for distributed cooperative robotics based on ROS 2, allowing for the execution of complex tasks without a central coordinator. Its modular structure facilitates the implementation of optimization-based distributed control schemes for heterogeneous robot networks.
IEEE ROBOTICS AND AUTOMATION LETTERS
(2021)
Article
Mathematics, Applied
Alex Bespalov, Leonardo Rocchi, David Silvester
Summary: T-IFISS is a finite element software package that focuses on self-adaptive algorithms and rigorous error control for deterministic and parametric elliptic partial differential equations. It provides an open-source MATLAB framework for experimentation and exploration, allowing users to develop new discretizations and test alternative algorithms quickly. Additionally, it serves as a valuable teaching tool for students interested in learning about advanced finite element methodology.
COMPUTERS & MATHEMATICS WITH APPLICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Guignon Valentin, Toure Abdel, Droc Gaetan, Dufayard Jean-Francois, Conte Matthieu, Rouard Mathieu
Summary: Comparative genomics is the analysis of genomic relationships among different species, with GreenPhylDB providing a database for exploring gene families and homologous relationships among plant genomes. By harnessing multiple genome sequences by species, GreenPhylDBv5 introduces the concept of comparative pangenomics to predict homologous relationships and support community curation efforts.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Geosciences, Multidisciplinary
Sebastian Mueller, Lennart Schueler, Alraune Zech, Falk Hesse
Summary: Geostatistics is a subfield of statistics that deals with spatial correlations in applications such as earth sciences. This article introduces GSTools, a user-friendly software suite based on Python that can solve various geostatistical problems, including random field generation, kriging, and variogram estimation. The capabilities of this software suite are demonstrated through example applications.
GEOSCIENTIFIC MODEL DEVELOPMENT
(2022)
Article
Psychology, Mathematical
Mathieu Bernard, Maxime Poli, Julien Karadayi, Emmanuel Dupoux
Summary: Shennong is a Python toolbox and command-line utility for audio speech features extraction, implementing a wide range of well-established state-of-the-art algorithms. It is built on top of the popular Kaldi speech processing library, making it easy to use and integrates with third-party tools from the Python ecosystem.
BEHAVIOR RESEARCH METHODS
(2023)
Article
Geosciences, Multidisciplinary
Stephanie R. James, Nathan Leon Foks, Burke J. Minsley
Summary: The paper proposes a new geophysical standard, GS convention, that utilizes the well-established NetCDF file format and the CF metadata convention. With the accompanying open-source Python package GSPy, methods and workflows for building GS-standardized NetCDF files, importing/exporting data, preparing input files, and visualizing data and models are provided.
FRONTIERS IN EARTH SCIENCE
(2022)
Article
Neurosciences
Hao Guan, Mingxia Liu
Summary: Domain adaptation is an important technique in machine learning-based medical data analysis to reduce distribution differences between different datasets. The Domain Adaptation Toolbox for Medical data analysis (DomainATM) is an open-source software package implemented in MATLAB, offering a collection of popular data adaptation algorithms for medical image analysis. It provides researchers with the capability to perform fast feature-level and image-level adaptation, visualization, and performance evaluation of adaptation methods. Users can also develop and test their own adaptation methods through scripting, enhancing the utility and extensibility of DomainATM. The software, source code, and manual are available online.
Article
Biochemistry & Molecular Biology
Jiankai Wei, Penghui Liu, Fuyun Liu, An Jiang, Jinghan Qiao, Zhongqi Pu, Bingrou Wang, Jin Zhang, Dongning Jia, Yuli Li, Shi Wang, Bo Dong
Summary: Evolutionary developmental biology (evo-devo) is an interdisciplinary field that aims to understand the origin and evolution of developmental processes in different animals. EDomics is a comparative multi-omics database that provides comprehensive genomic, transcriptomic, and single-cell data for 40 representative species. It offers valuable resources and customized datasets for evo-devo research, allowing researchers to decipher the history of developmental evolution across the tree of life.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Zhijian Li, Chao-Chung Kuo, Fabio Ticconi, Mina Shaigan, Julia Gehrmann, Eduardo Gade Gusmao, Manuel Allhoff, Martin Manolov, Martin Zenke, Ivan G. Costa
Summary: This article introduces the Regulatory Genomics Toolbox (RGT), a computational library for the integrative analysis of regulatory genomics data. RGT provides different functionalities to handle genomic signals and regions, and several tools have been developed for distinct downstream analyses. RGT facilitates the customization of computational methods to analyze specific regulatory genomics problems.
BMC BIOINFORMATICS
(2023)
Article
Chemistry, Analytical
Xiaowei Xing, Dong Eui Chang
Summary: The paper introduces the adaptive dynamic programming toolbox (ADPT), a MATLAB-based software package for solving optimal control problems for continuous-time control-affine systems. ADPT generates approximate optimal feedback controls using the adaptive dynamic programming technique and supports two working modes. Multiple setting options are available to accommodate various customized circumstances, with computational precision and time efficiency.
Article
Biotechnology & Applied Microbiology
Miriam Khider, Erik Hjerde, Hilde Hansen, Nils Peder Willassen
Article
Multidisciplinary Sciences
Miriam Khider, Hilde Hansen, Erik Hjerde, Jostein A. Johansen, Nils Peder Willassen
Article
Microbiology
Typhaine Le Doujet, Concetta De Santi, Terje Klemetsen, Erik Hjerde, Nils-Peder Willassen, Peik Haugen
Article
Biology
Steinar Thorvaldsen, Ola Hossjer
JOURNAL OF THEORETICAL BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Jennifer Harrow, John Hancock, Niklas Blomberg
Article
Microbiology
Terje Klemetsen, Christian R. Karlsen, Nils P. Willassen
Summary: Genus Aliivibrio, known for bioluminescence and pathogenic behavior affecting fish farming, has been reclassified and poorly understood phylogenetically since 2007. Through MLSA with 143 bacterial strains, this study identified 12 clades and proposed a new species, Aliivibrio sp. friggae. Marker gene analysis revealed gyrB, pyrH, and recA as superior to 16S rRNA for accurate species classification in Aliivibrio.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Amudha Deepalakshmi Maharajan, Hilde Hansen, Miriam Khider, Nils Peder Willassen
Summary: A. wodanis 06/09/139 utilizes the QS system to regulate various activities that may be important for host colonization or interactions. The production of 3OHC10-HSL by the bacterium is highest at a low temperature of 6 degrees Celsius.
Article
Veterinary Sciences
Amudha Deepalakshmi Maharajan, Erik Hjerde, Hilde Hansen, Nils Peder Willassen
Summary: To survive and compete in a crowded and challenging environment, bacteria like Aliivibrio wodanis 06/09/139 employ different strategies, such as Type VI Secretion Systems (T6SSs) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), to outcompete their competitors. This study analyzed the genome and gene expression profiling of A. wodanis and two QS mutants (Delta ainS and Delta litR) to understand the role of quorum sensing (QS) and these strategies. The findings showed that T6SSs and CRISPR systems are QS-dependent and play a crucial role in the survival of A. wodanis in its natural environment.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Biochemical Research Methods
Fernando Meyer, Adrian Fritz, Zhi-Luo Deng, David Koslicki, Till Robin Lesker, Alexey Gurevich, Gary Robertson, Mohammed Alser, Dmitry Antipov, Francesco Beghini, Denis Bertrand, Jaqueline J. Brito, C. Titus Brown, Jan Buchmann, Aydin Buluc, Bo Chen, Rayan Chikhi, Philip T. L. C. Clausen, Alexandru Cristian, Piotr Wojciech Dabrowski, Aaron E. Darling, Rob Egan, Eleazar Eskin, Evangelos Georganas, Eugene Goltsman, Melissa A. Gray, Lars Hestbjerg Hansen, Steven Hofmeyr, Pingqin Huang, Luiz Irber, Huijue Jia, Tue Sparholt Jorgensen, Silas D. Kieser, Terje Klemetsen, Axel Kola, Mikhail Kolmogorov, Anton Korobeynikov, Jason Kwan, Nathan LaPierre, Claire Lemaitre, Chenhao Li, Antoine Limasset, Fabio Malcher-Miranda, Serghei Mangul, Vanessa R. Marcelino, Camille Marchet, Pierre Marijon, Dmitry Meleshko, Daniel R. Mende, Alessio Milanese, Niranjan Nagarajan, Jakob Nissen, Sergey Nurk, Leonid Oliker, Lucas Paoli, Pierre Peterlongo, Vitor C. Piro, Jacob S. Porter, Simon Rasmussen, Evan R. Rees, Knut Reinert, Bernhard Renard, Espen Mikal Robertsen, Gail L. Rosen, Hans-Joachim Ruscheweyh, Varuni Sarwal, Nicola Segata, Enrico Seiler, Lizhen Shi, Fengzhu Sun, Shinichi Sunagawa, Soren Johannes Sorensen, Ashleigh Thomas, Chengxuan Tong, Mirko Trajkovski, Julien Tremblay, Gherman Uritskiy, Riccardo Vicedomini, Zhengyang Wang, Ziye Wang, Zhong Wang, Andrew Warren, Nils Peder Willassen, Katherine Yelick, Ronghui You, Georg Zeller, Zhengqiao Zhao, Shanfeng Zhu, Jie Zhu, Ruben Garrido-Oter, Petra Gastmeier, Stephane Hacquard, Susanne Haeussler, Ariane Khaledi, Friederike Maechler, Fantin Mesny, Simona Radutoiu, Paul Schulze-Lefert, Nathiana Smit, Till Strowig, Andreas Bremges, Alexander Sczyrba, Alice Carolyn McHardy
Summary: This study presents the results of the second round of the Critical Assessment of Metagenome Interpretation challenges (CAMI II), which is a community-driven effort for comprehensively benchmarking tools for metagenomics data analysis. The results show substantial improvements in assembly, but related strains and assembly quality still pose challenges. Taxon profilers and binners excel at higher bacterial ranks but underperform for viruses and Archaea. The need to improve reproducibility is emphasized by the clinical pathogen detection results.
Article
Multidisciplinary Sciences
June T. Forsberg, Steinar Thorvaldsen
Summary: Children and adolescents have been severely impacted by the COVID-19 pandemic, with increased prevalence of bullying, mental health problems, and reduced quality of life. The study highlights the importance of implementing anti-bullying and psychosocial measures after the pandemic.
SCIENTIFIC REPORTS
(2022)
Article
Education & Educational Research
Siri Sollied Madsen, Jane O'Connor, Aleksander Janes, Andreja Klancar, Rita Brito, Nataliia Demeshkant, Ahmet Sami Konca, Serhii Krasin, Heidi Iren Saure, Beate Gjesdal, Shannon Ludgate, Mustafa Jwaifell, Reham Almuhtadi, Steinar Thorvaldsen
Summary: Researchers and society are divided on the use of digital technology in early childhood education, with some highlighting its benefits and others seeing it as detrimental. However, digital competence is being taught and emphasized globally. The study investigates the perspectives and dynamics of digital competence in early childhood education across multiple countries, finding significant differences and identifying attitudes, skills, and knowledge as predictors of future digital technology use. Further research is needed to understand the contextual differences in educational culture and practice.
EDUCATION SCIENCES
(2023)
Article
Statistics & Probability
Steinar Thorvaldsen, Ola Hossjer
Summary: This article introduces new statistical methods for modeling and analyzing information content in proteins, protein families, and their sequences. It discusses the qualitative and quantitative aspects of genetic information and presents a statistical model that combines genetic function with its probabilistic metric of self-information. The functional information of protein families in the Cath and Pfam databases is estimated using a rejection sampling method. These components of information are considered fundamental aspects of molecular biology.
JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES C-APPLIED STATISTICS
(2023)
Article
Education & Educational Research
Magne Olufsen, Solveig Karlsen, Johannes Saeleset, Steinar Thorvaldsen
Summary: Reforms in teacher education programmes in Nordic countries have sparked a debate on their content, structure, and quality. Norway recently introduced a new Master's-level programme for teaching grades 5-10, where pre-service teachers take specialised content courses and undergo field placements twice a year. This study found that teaching subjects they specialised in had a positive impact on student teaching, with better learning outcomes and use of instructional strategies reported by both pre-service teachers and mentor teachers.
Proceedings Paper
Computer Science, Artificial Intelligence
Peter Ohrstrom, Steinar Thorvaldsen, Ulrik Sandborg-Petersen, Thomas Ploug, David Jakobsen
Summary: This study compares the teaching of a basic logic course in 2020 and 2021, finding that the 2021 course, which utilized e-learning tools during COVID-19 lockdown, achieved better exam results.
INNOVATIVE TECHNOLOGIES AND LEARNING
(2021)
Article
Education & Educational Research
Steinar Thorvaldsen, Siri Sollied Madsen
EDUCATION AND INFORMATION TECHNOLOGIES
(2020)
