User Friendly

Abstract: Pathway analysis is widely used in omics studies. Pathway-based data integration and visualization is a critical component of the analysis. To address this need, we recently developed a novel R package called Pathview. Pathview maps, integrates and renders a large variety of biological data onto molecular pathway graphs. Here we developed the Pathview Web server, as to make pathway visualization and data integration accessible to all scientists, including those without the special computing skills or resources. Pathview Web features an intuitive graphical web interface and a user centered design. The server not only expands the core functions of Pathview, but also provides many useful features not available in the offline R package. Importantly, the server presents a comprehensive workflow for both regular and integrated pathway analysis of multiple omics data. In addition, the server also provides a RESTful API for programmatic access and conveniently integration in third-party software or workflows. Pathview Web is openly and freely accessible at https://pathview.uncc.edu/.

Abstract: We herein present the graphical user interface (GUI) TmoleX for the quantum chemical program package TURBOMOLE. TmoleX allows users to execute the complete workflow of a quantum chemical investigation from the initial building of a structure to the visualization of the results in a user friendly graphical front end. The purpose of TmoleX is to make TURBOMOLE easy to use and to provide a high degree of flexibility. Hence, it should be a valuable tool for most users from beginners to experts. The program is developed in Java and runs on Linux, Windows, and Mac platforms. It can be used to run calculations on local desktops as well as on remote computers.

Abstract: Ambient vibrations are nowadays considerably used worldwide for numerous types of engineering applications and scientific research. Geopsy and its companion tools are part of that landscape. Since the first release of the program package in 2005, as outcome of the European Union project Site Effects aSsessment from AMbient noisE, Geopsy has become a mature multiplatform open-source package (released under GNU Public License version 3) that has already been recognized as a reference tool for analyzing ambient vibration data in the context of site characterization studies. The community of users has grown from a core group of researchers up to thousands of seismologists and engineers on every career level and on all continents. The versatility of geopsy allows for the processing of all kinds of data needed in site characterization studies, that is, from single station single trace to three-component array recordings. In all of the aforementioned cases, the steps from field acquisition to the production of publication-ready figures are covered and supported by user-friendly graphical user interfaces or corresponding command-line tools for the automation of the complete processing chain. To avoid black-box usage, a number of lower-level tools guarantee maximum flexibility in accessing and controlling processing results at any stage of the analysis.