RCX — an R package adapting the Cytoscape Exchange format for biological networks

Motivation The Cytoscape Exchange (CX) format is a JSON-based data structure designed for the transmission of biological networks using standard web technologies. It was developed by the network data exchange, which itself serves as online commons to share and collaborate on biological networks. Furthermore, the Cytoscape software for the analysis and visualization of biological networks contributes structure elements to capture the visual layout within the CX format. However, there is a fundamental difference between data handling in web standards and R. A manual conversion requires detailed knowledge of the CX format to reproduce and work with the networks. Results Here, we present a software package to create, handle, validate, visualize and convert networks in CX format to standard data types and objects within R. Networks in this format can serve as a source for biological knowledge and also capture the results of the analysis of those while preserving the visual layout across all platforms. The RCX package connects the R environment for statistical computing with outside platforms for storage and collaboration, as well as further analysis and visualization of biological networks. Availability RCX is a free and open-source R package, available on Bioconductor from release 3.15 (https://bioconductor.org/packages/RCX) and via GitHub (https://github.com/frankkramer-lab/RCX). Supplementary information Supplementary data are available at Bioinformatics Advances online

Can Distribution Grids Significantly Contribute to Transmission Grids' Voltage Management?

Power generation in Germany is currently transitioning from a system based on large, central, thermal power plants to one that heavily relies on small, decentral, mostly renewable power generators. This development poses the question how transmission grids' reactive power demand for voltage management, covered by central power plants today, can be supplied in the future. In this work, we estimate the future technical potential of such an approach for the whole of Germany. For a 100% renewable electricity scenario we set the possible reactive power supply in comparison with the reactive power requirements that are needed to realize the simulated future transmission grid power flows. Since an exact calculation of distribution grids' reactive power potential is difficult due to the unavailability of detailed grid models on such scale, we optimistically estimate the potential by assuming a scaled, averaged distribution grid model connected to each of the transmission grid nodes. We find that for all except a few transmission grid nodes, the required reactive power can be fully supplied from the modeled distribution grids. This implies that - even if our estimate is overly optimistic - distributed reactive power provisioning will be a technical solution for many future reactive power challenges

Data-dependent visualization of biological networks in the web-browser with NDExEdit

Networks are a common methodology used to capture increasingly complex associations between biological entities. They serve as a resource of biological knowledge for bioinformatics analyses, and also comprise the subsequent results. However, the interpretation of biological networks is challenging and requires suitable visualizations dependent on the contained information. The most prominent software in the field for the visualization of biological networks is Cytoscape, a desktop modeling environment also including many features for analysis. A further challenge when working with networks is their distribution. Within a typical collaborative workflow, even slight changes of the network data force one to repeat the visualization step as well. Also, just minor adjustments to the visual representation not only need the networks to be transferred back and forth. Collaboration on the same resources requires specific infrastructure to avoid redundancies, or worse, the corruption of the data. A well-established solution is provided by the NDEx platform where users can upload a network, share it with selected colleagues or make it publicly available. NDExEdit is a web-based application where simple changes can be made to biological networks within the browser, and which does not require installation. With our tool, plain networks can be enhanced easily for further usage in presentations and publications. Since the network data is only stored locally within the web browser, users can edit their private networks without concerns of unintentional publication. The web tool is designed to conform to the Cytoscape Exchange (CX) format as a data model, which is used for the data transmission by both tools, Cytoscape and NDEx. Therefore the modified network can be directly exported to the NDEx platform or saved as a compatible CX file, additionally to standard image formats like PNG and JPEG

Perspective on code submission and automated evaluation platforms for university teaching

We present a perspective on platforms for code submission and automated evaluation in the context of university teaching. Due to the COVID-19 pandemic, such platforms have become an essential asset for remote courses and a reasonable standard for structured code submission concerning increasing numbers of students in computer sciences. Utilizing automated code evaluation techniques exhibits notable positive impacts for both students and teachers in terms of quality and scalability. We identified relevant technical and non-technical requirements for such platforms in terms of practical applicability and secure code submission environments. Furthermore, a survey among students was conducted to obtain empirical data on general perception. We conclude that submission and automated evaluation involves continuous maintenance yet lowers the required workload for teachers and provides better evaluation transparency for students.Comment: Source code: https://github.com/frankkramer-lab/MISITcms-app. Manuscript accepted for publication in the following Conference - Jorunal: MedInfo 2021, Virtual Conference, October 2-4, 2021 - IOS Pres

From Monolithic Systems to Microservices: An Assessment Framework

Context. Re-architecting monolithic systems with Microservices-based architecture is a common trend. Various companies are migrating to Microservices for different reasons. However, making such an important decision like re-architecting an entire system must be based on real facts and not only on gut feelings. Objective. The goal of this work is to propose an evidence-based decision support framework for companies that need to migrate to Microservices, based on the analysis of a set of characteristics and metrics they should collect before re-architecting their monolithic system. Method. We designed this study with a mixed-methods approach combining a Systematic Mapping Study with a survey done in the form of interviews with professionals to derive the assessment framework based on Grounded Theory. Results. We identified a set consisting of information and metrics that companies can use to decide whether to migrate to Microservices or not. The proposed assessment framework, based on the aforementioned metrics, could be useful for companies if they need to migrate to Microservices and do not want to run the risk of failing to consider some important information