Discussion of the bacillus funcicularius n.sp., and a few remarks about the gallionella ferruginea ehrenberg

Identification of new bacteria strain, bacillus funicularius n.sp

Teaching photonic integrated circuits with Jupyter notebooks : design, simulation, fabrication

At Ghent University, we have built a course curriculum on integrated photonics, and in particular silicon photonics, based on interactive Jupyter Notebooks. This has been used in short workshops, specialization courses at PhD level, as well as the M.Sc. Photonics Engineering program at Ghent University and the Free University of Brussels. The course material teaches the concepts of on-chip waveguides, basic building blocks, circuits, the design process, fabrication and measurements. The Jupyter notebook environment provides an interface where static didactic content (text, figures, movies, formulas) is mixed with Python code that the user can modify and execute, and interactive plots and widgets to explore the effect of changes in circuits or components. The Python environment supplies a host of scientific and engineering libraries, while the photonic capabilities are based on IPKISS, a commercial design framework for photonic integrated circuits by Luceda Photonics. The IPKISS framework allows scripting of layout and simulation directly from the Jupyter notebooks, so the teaching modules contain live circuit simulation, as well as integration with electromagnetic solvers. Because this is a complete design framework, students can also use it to tape out a small chip design which is fabricated through a rapid prototyping service and then measured, allowing the students to validate the actual performance of their design against the original simulation. The scripting in Jupyter notebooks also provides a self-documenting design flow, and the use of an established design tool guarantees that the acquired skills can be transferred to larger, real-world design projects

Deploying Jupyter Notebooks at scale on XSEDE resources for Science Gateways and workshops

Jupyter Notebooks have become a mainstream tool for interactive computing in every field of science. Jupyter Notebooks are suitable as companion applications for Science Gateways, providing more flexibility and post-processing capability to the users. Moreover they are often used in training events and workshops to provide immediate access to a pre-configured interactive computing environment. The Jupyter team released the JupyterHub web application to provide a platform where multiple users can login and access a Jupyter Notebook environment. When the number of users and memory requirements are low, it is easy to setup JupyterHub on a single server. However, setup becomes more complicated when we need to serve Jupyter Notebooks at scale to tens or hundreds of users. In this paper we will present three strategies for deploying JupyterHub at scale on XSEDE resources. All options share the deployment of JupyterHub on a Virtual Machine on XSEDE Jetstream. In the first scenario, JupyterHub connects to a supercomputer and launches a single node job on behalf of each user and proxies back the Notebook from the computing node back to the user's browser. In the second scenario, implemented in the context of a XSEDE consultation for the IRIS consortium for Seismology, we deploy Docker in Swarm mode to coordinate many XSEDE Jetstream virtual machines to provide Notebooks with persistent storage and quota. In the last scenario we install the Kubernetes containers orchestration framework on Jetstream to provide a fault-tolerant JupyterHub deployment with a distributed filesystem and capability to scale to thousands of users. In the conclusion section we provide a link to step-by-step tutorials complete with all the necessary commands and configuration files to replicate these deployments.Comment: 7 pages, 3 figures, PEARC '18: Practice and Experience in Advanced Research Computing, July 22--26, 2018, Pittsburgh, PA, US

Jupyter in Computational Science

The articles in this special section discusses the applications supported by the Jupyter Notebook. Before notebooks, a scientist working with Python code, for instance, might have used a mixture of script files and code typed into an interactive shell. The shell is good for rapid experimentation, but the code and results are typically transient, and a linear record of everything that was tried would be long and not very clear. The notebook interface combines the convenience of the shell with some of the benefits of saving and editing code in a file, while also incorporating results, including rich output, such as plots, in a document that can be shared with others. The Jupyter Notebook is used through a web browser. Although it is often run locally, on a desktop or a laptop, this design means that it can also be used remotely, so the computation occurs, and the notebook files are saved, on an institutional server, a high-performance computing facility or in the clo

Thermal stability and topological protection of skyrmions in nanotracks

Magnetic skyrmions are hailed as a potential technology for data storage and other data processing devices. However, their stability against thermal fluctuations is an open question that must be answered before skyrmion-based devices can be designed. In this work, we study paths in the energy landscape via which the transition between the skyrmion and the uniform state can occur in interfacial Dzyaloshinskii-Moriya finite-sized systems. We find three mechanisms the system can take in the process of skyrmion nucleation or destruction and identify that the transition facilitated by the boundary has a significantly lower energy barrier than the other energy paths. This clearly demonstrates the lack of the skyrmion topological protection in finite-sized magnetic systems. Overall, the energy barriers of the system under investigation are too small for storage applications at room temperature, but research into device materials, geometry and design may be able to address this

Accelerated Modeling of Near and Far-Field Diffraction for Coronagraphic Optical Systems

Accurately predicting the performance of coronagraphs and tolerancing optical surfaces for high-contrast imaging requires a detailed accounting of diffraction effects. Unlike simple Fraunhofer diffraction modeling, near and far-field diffraction effects, such as the Talbot effect, are captured by plane-to-plane propagation using Fresnel and angular spectrum propagation. This approach requires a sequence of computationally intensive Fourier transforms and quadratic phase functions, which limit the design and aberration sensitivity parameter space which can be explored at high-fidelity in the course of coronagraph design. This study presents the results of optimizing the multi-surface propagation module of the open source Physical Optics Propagation in PYthon (POPPY) package. This optimization was performed by implementing and benchmarking Fourier transforms and array operations on graphics processing units, as well as optimizing multithreaded numerical calculations using the NumExpr python library where appropriate, to speed the end-to-end simulation of observatory and coronagraph optical systems. Using realistic systems, this study demonstrates a greater than five-fold decrease in wall-clock runtime over POPPY's previous implementation and describes opportunities for further improvements in diffraction modeling performance.Comment: Presented at SPIE ASTI 2018, Austin Texas. 11 pages, 6 figure

ClaimChain: Improving the Security and Privacy of In-band Key Distribution for Messaging

The social demand for email end-to-end encryption is barely supported by mainstream service providers. Autocrypt is a new community-driven open specification for e-mail encryption that attempts to respond to this demand. In Autocrypt the encryption keys are attached directly to messages, and thus the encryption can be implemented by email clients without any collaboration of the providers. The decentralized nature of this in-band key distribution, however, makes it prone to man-in-the-middle attacks and can leak the social graph of users. To address this problem we introduce ClaimChain, a cryptographic construction for privacy-preserving authentication of public keys. Users store claims about their identities and keys, as well as their beliefs about others, in ClaimChains. These chains form authenticated decentralized repositories that enable users to prove the authenticity of both their keys and the keys of their contacts. ClaimChains are encrypted, and therefore protect the stored information, such as keys and contact identities, from prying eyes. At the same time, ClaimChain implements mechanisms to provide strong non-equivocation properties, discouraging malicious actors from distributing conflicting or inauthentic claims. We implemented ClaimChain and we show that it offers reasonable performance, low overhead, and authenticity guarantees.Comment: Appears in 2018 Workshop on Privacy in the Electronic Society (WPES'18

Knowledge-base black holes: the next (small) big thing?

Hydraulic EngineeringCivil Engineering and Geoscience