Filters








473 Hits in 2.2 sec

PSEUDOMONAS AUREOFACIENS KLUYVER AND PHENAZINE α-CARBOXYLIC ACID, ITS CHARACTERISTIC PIGMENT

William C. Haynes, Frank H. Stodola, Joan M. Locke, Thomas G. Pridham, Howard F. Conway, Virgil E. Sohns, Richard W. Jackson
1956 Journal of Bacteriology  
SUMNIARY A complete description of Pseudonmonas auireofaciens Kluyver based on four strains is given.  ...  By agreement we are presenting (1) Kluyver, we have designated Pseudomonas 1 aureofaciens. One strain was isolated in Dr.  ... 
doi:10.1128/jb.72.3.412-417.1956 fatcat:yl4kbvrswnfb7abua2knqhfh5a

Jupyter in Computational Science

Hans Fangohr, Thomas Kluyver, Massimo DiPierro
2021 Computing in science & engineering (Print)  
THOMAS KLUYVER is currently a software engineer with European XFEL.  ... 
doi:10.1109/mcse.2021.3059494 fatcat:5oxlvj2nvvdvzkyy5icaikimwq

Deliverable: Prototype Remote Desktop and Jupyter Service (4.2)

Lottie Greenwood, Jamie Hall, Hans Fangohr, Thomas Kluyver, Robert Rosca
2020 Zenodo  
This document provides the context of remote data analysis services for the photon and neutron science communities and comments on the status of service provision, user experience and deployment/harmonization aspects across the PaNOSC facilities.
doi:10.5281/zenodo.5905323 fatcat:hkc7ztt3dvdarjqstzh2evi57y

Taxonome: a software package for linking biological species data

Thomas A. Kluyver, Colin P. Osborne
2013 Ecology and Evolution  
Online databases of biological information offer tremendous potential for evolutionary and ecological discoveries, especially if data are combined in novel ways. However, the different names and varied spellings used for many species present major barriers to linking data. Taxonome is a software tool designed to solve this problem by quickly and reproducibly matching biological names to a given reference set. It is available both as a graphical user interface (GUI) for simple interactive use,
more » ... d as a library for more advanced functionality with programs written in Python. Taxonome also includes functions to standardize distribution information to a well-defined set of regions, such as the TDWG World Geographical Scheme for Recording Plant Distributions. In combination, these tools will help biologists to rapidly synthesize disparate datasets, and to investigate large-scale patterns in species traits. 1262
doi:10.1002/ece3.529 pmid:23762512 pmcid:PMC3678480 fatcat:ncaorkpkxffcdldvvgt3ldneka

Deliverable: Report on the current technical elements of data analysis at each partner site (4.1)

Hans Fangohr, Kareem Galal, Jamie Hall, Thomas Kluyver, Carlos Reis, Robert Rosca, William Turner, Thomas Vincent
2019 Zenodo  
This document presents the results of a survey on: scientists and scientific nature of data, tools/services for data analysis and reduction, IT infrastructure and technologies, security aspects and other information at each PaNOSC facility.
doi:10.5281/zenodo.5905386 fatcat:3br2gdxkk5cubh7b4utsi7tf3e

Stable and manipulable Bloch point [article]

Marijan Beg, Ryan A. Pepper, David Cortés-Ortuño, Bilal Atie, Marc-Antonio Bisotti, Gary Downing, Thomas Kluyver, Ondrej Hovorka, Hans Fangohr
2018 arXiv   pre-print
The prediction of magnetic skyrmions being used to change the way we store and process data has led to materials with Dzyaloshinskii-Moriya interaction coming into the focus of intensive research. So far, studies have looked mostly at magnetic systems composed of materials with single chirality. In a search for potential future spintronic devices, combination of materials with different chirality into a single system may represent an important new avenue for research. Using finite element
more » ... agnetic simulations, we study an FeGe disk with two layers of different chirality. We show that for particular thicknesses of layers, a stable Bloch point emerges at the interface between two layers. In addition, we demonstrate that the system undergoes hysteretic behaviour and that two different types of Bloch point exist. These 'head-to-head' and 'tail-to-tail' Bloch point configurations can, with the application of an external magnetic field, be switched between. Finally, by investigating the time evolution of the magnetisation field, we reveal the creation mechanism of the Bloch point. Our results introduce a stable and manipulable Bloch point to the collection of particle-like state candidates for the development of future spintronic devices.
arXiv:1808.10772v1 fatcat:4outlkhu7zb4xlfy5fuzywahim

Stable and manipulable Bloch point

Marijan Beg, Ryan A. Pepper, David Cortés-Ortuño, Bilal Atie, Marc-Antonio Bisotti, Gary Downing, Thomas Kluyver, Ondrej Hovorka, Hans Fangohr
2019 Scientific Reports  
The prediction of magnetic skyrmions being used to change the way we store and process data has led to materials with Dzyaloshinskii-Moriya interaction coming into the focus of intensive research. So far, studies have looked mostly at magnetic systems composed of materials with single chirality. In a search for potential future spintronic devices, combination of materials with different chirality into a single system may represent an important new avenue for research. Using finite element
more » ... agnetic simulations, we study an FeGe disk with two layers of different chirality. We show that for particular thicknesses of layers, a stable Bloch point emerges at the interface between two layers. In addition, we demonstrate that the system undergoes hysteretic behaviour and that two different types of Bloch point exist. These 'head-to-head' and 'tail-to-tail' Bloch point configurations can, with the application of an external magnetic field, be switched between. Finally, by investigating the time evolution of the magnetisation field, we reveal the creation mechanism of the Bloch point. Our results introduce a stable and manipulable Bloch point to the collection of particle-like state candidates for the development of future spintronic devices.
doi:10.1038/s41598-019-44462-2 pmid:31138884 pmcid:PMC6538604 fatcat:t6eqn66srfayhffhd6a4texsgu

Automatic Feedback Provision in Teaching Computational Science [chapter]

Hans Fangohr, Neil O'Brien, Ondrej Hovorka, Thomas Kluyver, Nick Hale, Anil Prabhakar, Arti Kashyap
2020 Lecture Notes in Computer Science  
We describe a method of automatic feedback provision for students learning computational science and data science methods in Python. We have implemented, used and refined this system since 2009 for growing student numbers, and summarise the design and experience of using it. The core idea is to use a unit testing framework: the teacher creates a set of unit tests, and the student code is tested by running these tests. With our implementation, students typically submit work for assessment, and
more » ... ceive feedback by email within a few minutes after submission. The choice of tests and the reporting back to the student is chosen to optimise the educational value for the students. The system very significantly reduces the staff time required to establish whether a student's solution is correct, and shifts the emphasis of computing laboratory student contact time from assessing correctness to providing guidance. The self-paced nature of the automatic feedback provision supports a student-centred learning approach. Students can re-submit their work repeatedly and iteratively improve their solution, and enjoy using the system. We include an evaluation of the system from using it in a class of 425 students.
doi:10.1007/978-3-030-50436-6_45 fatcat:5d6ds3ms5fc4vbxhdf3vv3qnv4

Testing with Jupyter notebooks: NoteBook VALidation (nbval) plug-in for pytest [article]

Hans Fangohr, Vidar Fauske, Thomas Kluyver, Maximilian Albert, Oliver Laslett, David Cortés-Ortuño, Marijan Beg, Min Ragan-Kelly
2020 arXiv   pre-print
The Notebook validation tool nbval allows to load and execute Python code from a Jupyter notebook file. While computing outputs from the cells in the notebook, these outputs are compared with the outputs saved in the notebook file, treating each cell as a test. Deviations are reported as test failures, with various configuration options available to control the behaviour. Application use cases include the validation of notebook-based documentation, tutorials and textbooks, as well as the use of
more » ... notebooks as additional unit, integration and system tests for the libraries that are used in the notebook. Nbval is implemented as a plugin for the pytest testing software.
arXiv:2001.04808v1 fatcat:yzkvgpsz7zgw5imttytqts4r5u

Adaptive Probabilistic Tack Manoeuvre Decision for Sailing Vessels [article]

Sébastien Lemaire and Yu Cao and Thomas Kluyver and Daniel Hausner and Camil Vasilovici and Zhong-yuen Lee and Umberto José Varbaro and Sophia M. Schillai
2019 arXiv   pre-print
To move upwind, sailing vessels have to cross the wind by tacking. During this manoeuvre distance made good may be lost and especially smaller vessels may struggle to complete a tack in averse wind and wave conditions. A decision for the best tack manoeuvre needs to be made based on weather and available tack implementations. This paper develops an adaptive probabilistic tack manoeuvre decision method. The order of attempting different tacking strategies is based on previous success within a
more » ... eout, combined with an exploration component. This method is successfully demonstrated on the 1m long sailing vessel Black Python. Four strategies for crossing the wind were evaluated through adaptive probabilistic choices, and the best was identified without detailed sensory knowledge of the actual weather conditions. Based on the positive results, further improvements for a better selection process are suggested and the potential of using the collected data to recognise the impact of weather conditions on tacking efforts is recognised.
arXiv:1903.06677v1 fatcat:sl7vphsbb5bybgoupjeg4nameq

Unconscious selection drove seed enlargement in vegetable crops

Thomas A. Kluyver, Glynis Jones, Benoît Pujol, Christopher Bennett, Emily J. Mockford, Michael Charles, Mark Rees, Colin P. Osborne
2017 Evolution Letters  
mechanisms have received support from experiments (Hillman and Davies 1990; Milla and Matesanz 2017; Preece et al. 2017 ) and genetic analyses (Clark et al. 2006; Simons et al. 2006 ), but others have not (Kluyver  ... 
doi:10.1002/evl3.6 pmid:30283639 pmcid:PMC6121828 fatcat:vgqhdrozenc2djsvbwcn5fbuga

Did greater burial depth increase the seed size of domesticated legumes?

Thomas A. Kluyver, Michael Charles, Glynis Jones, Mark Rees, Colin P. Osborne
2013 Journal of Experimental Botany  
The independent domestication of crop plants in several regions of the world formed the basis of human civilizations, and attracts considerable interest from archaeologists and biologists. Selection under cultivation led to a suite of domestication traits which distinguish crops from their wild progenitors, including larger seeds in most seed crops. This selection may be classified as 'conscious' or 'unconscious' selection according to whether humans were aware of the changes that they were
more » ... ing. The hypothesis that human cultivation buried seeds deeper than natural dispersal, exerting unconscious selection favouring larger seeds with greater reserves, was tested. Using a comparative approach, accessions of eight grain legumes, originating from independent domestication centres across several continents, were sampled. Seeds were planted at different depths in a controlled environment, and seedling emergence scored for 5 weeks after sowing. Domestication in all species was associated with increased seed mass. In three species, greater mass was not correlated with increased ability to emerge from depth. In five species, emergence depth did correlate with mass, suggesting that selection during domestication may have acted on emergence depth. However, domestication only had a significant effect in two of these species (lentil and mung bean), and the increase in depth was no more than predicted by a cube-root allometric relationship with seed mass. The results do not support the hypothesis that burial under cultivation was a general selection mechanism for increased seed mass during the domestication of grain legumes, but it may have acted in particular species or regions.
doi:10.1093/jxb/ert304 pmid:24058143 fatcat:nl4pw3cxxbccboelojscmncpve

Using Jupyter for reproducible scientific workflows

Marijan Beg, Juliette Belin, Thomas Kluyver, Alexander Konovalov, Min Ragan-Kelley, Nicolas Thiery, Hans Fangohr
2021 Computing in science & engineering (Print)  
Literate computing has emerged as an important tool for computational studies and open science, with growing folklore of best practices. In this work, we report two case studies - one in computational magnetism and another in computational mathematics - where domain-specific software was exposed to the Jupyter environment. This enables high-level control of simulations and computation, interactive exploration of computational results, batch processing on HPC resources, and reproducible workflow
more » ... documentation in Jupyter notebooks. In the first study, Ubermag drives existing computational micromagnetics software through a domain-specific language embedded in Python. In the second study, a dedicated Jupyter kernel interfaces with the GAP system for computational discrete algebra and its dedicated programming language. In light of these case studies, we discuss the benefits of this approach, including progress toward more reproducible and reusable research results and outputs, notably through the use of infrastructure such as JupyterHub and Binder.
doi:10.1109/mcse.2021.3052101 fatcat:qdac3unk75fzdophnssiv7lyha

Fidimag – A Finite Difference Atomistic and Micromagnetic Simulation Package

Marc-Antonio Bisotti, David Cortés-Ortuño, Ryan Pepper, Weiwei Wang, Marijan Beg, Thomas Kluyver, Hans Fangohr
2018 Journal of Open Research Software  
Fidimag is an open-source scientific code for the study of magnetic materials at the nano- or micro-scale using either atomistic or finite difference micromagnetic simulations, which are based on solving the Landau-Lifshitz-Gilbert equation. In addition, it implements simple procedures for calculating energy barriers in the magnetisation through variants of the nudged elastic band method. This computer software has been developed with the aim of creating a simple code structure that can be
more » ... ly installed, tested, and extended. An agile development approach was adopted, with a strong emphasis on automated builds and tests, and reproducibility of results. The main code and interface to specify simulations are written in Python, which allows simple and readable simulation and analysis configuration scripts. Computationally costly calculations are written in C and exposed to the Python interface as Cython extensions. Docker containers are shipped for a convenient setup experience. The code is freely available on GitHub and includes documentation and examples in the form of Jupyter notebooks.
doi:10.5334/jors.223 fatcat:t3snh2qw55d3ffyosu24asks2a

Skyrmion states in thin confined polygonal nanostructures

Ryan Alexander Pepper, Marijan Beg, David Cortés-Ortuño, Thomas Kluyver, Marc-Antonio Bisotti, Rebecca Carey, Mark Vousden, Maximilian Albert, Weiwei Wang, Ondrej Hovorka, Hans Fangohr
2018 Journal of Applied Physics  
Recent studies have demonstrated that skyrmionic states can be the ground state in thin-film FeGe disk nanostructures in the absence of a stabilising applied magnetic field. In this work, we advance this understanding by investigating to what extent this stabilisation of skyrmionic structures through confinement exists in geometries that do not match the cylindrical symmetry of the skyrmion -- such as as squares and triangles. Using simulation, we show that skyrmionic states can form the ground
more » ... state for a range of system sizes in both triangular and square-shaped FeGe nanostructures of 10 nm thickness in the absence of an applied field. We further provide data to assist in the experimental verification of our prediction; to imitate an experiment where the system is saturated with a strong applied field before the field is removed, we compute the time evolution and show the final equilibrium configuration of magnetization fields, starting from a uniform alignment.
doi:10.1063/1.5022567 fatcat:6euwh7tzyvel7m6ssjghrlnjgi
« Previous Showing results 1 — 15 out of 473 results