High-throughput Binding Affinity Calculations at Extreme Scales

Resistance to chemotherapy and molecularly targeted therapies is a major factor in limiting the effectiveness of cancer treatment. In many cases, resistance can be linked to genetic changes in target proteins, either pre-existing or evolutionarily selected during treatment. Key to overcoming this challenge is an understanding of the molecular determinants of drug binding. Using multi-stage pipelines of molecular simulations we can gain insights into the binding free energy and the residence time of a ligand, which can inform both stratified and personal treatment regimes and drug development. To support the scalable, adaptive and automated calculation of the binding free energy on high-performance computing resources, we introduce the High- throughput Binding Affinity Calculator (HTBAC). HTBAC uses a building block approach in order to attain both workflow flexibility and performance. We demonstrate close to perfect weak scaling to hundreds of concurrent multi-stage binding affinity calculation pipelines. This permits a rapid time-to-solution that is essentially invariant of the calculation protocol, size of candidate ligands and number of ensemble simulations. As such, HTBAC advances the state of the art of binding affinity calculations and protocols

Integrating Data Science and Earth Science

This open access book presents the results of three years collaboration between earth scientists and data scientist, in developing and applying data science methods for scientific discovery. The book will be highly beneficial for other researchers at senior and graduate level, interested in applying visual data exploration, computational approaches and scientifc workflows

Integrating Data Science and Earth Science

This open access book presents the results of three years collaboration between earth scientists and data scientists, in developing and applying data science methods for scientific discovery. The book will be highly beneficial for other researchers at senior and graduate level, interested in applying visual data exploration, computational approaches and scientifc workflows

Improving the translation environment for professional translators

When using computer-aided translation systems in a typical, professional translation workflow, there are several stages at which there is room for improvement. The SCATE (Smart Computer-Aided Translation Environment) project investigated several of these aspects, both from a human-computer interaction point of view, as well as from a purely technological side. This paper describes the SCATE research with respect to improved fuzzy matching, parallel treebanks, the integration of translation memories with machine translation, quality estimation, terminology extraction from comparable texts, the use of speech recognition in the translation process, and human computer interaction and interface design for the professional translation environment. For each of these topics, we describe the experiments we performed and the conclusions drawn, providing an overview of the highlights of the entire SCATE project

Elastic Business Process Management: State of the Art and Open Challenges for BPM in the Cloud

With the advent of cloud computing, organizations are nowadays able to react rapidly to changing demands for computational resources. Not only individual applications can be hosted on virtual cloud infrastructures, but also complete business processes. This allows the realization of so-called elastic processes, i.e., processes which are carried out using elastic cloud resources. Despite the manifold benefits of elastic processes, there is still a lack of solutions supporting them. In this paper, we identify the state of the art of elastic Business Process Management with a focus on infrastructural challenges. We conceptualize an architecture for an elastic Business Process Management System and discuss existing work on scheduling, resource allocation, monitoring, decentralized coordination, and state management for elastic processes. Furthermore, we present two representative elastic Business Process Management Systems which are intended to counter these challenges. Based on our findings, we identify open issues and outline possible research directions for the realization of elastic processes and elastic Business Process Management.Comment: Please cite as: S. Schulte, C. Janiesch, S. Venugopal, I. Weber, and P. Hoenisch (2015). Elastic Business Process Management: State of the Art and Open Challenges for BPM in the Cloud. Future Generation Computer Systems, Volume NN, Number N, NN-NN., http://dx.doi.org/10.1016/j.future.2014.09.00

FACILITATING AQUATIC INVASIVE SPECIES MANAGEMENT USING SATELLITE REMOTE SENSING AND MACHINE LEARNING FRAMEWORKS

The urgent decision-making needs of invasive species managers can be better met by the integration of biodiversity big data with large-domain models and environmental data products in the form of new workflows and tools that facilitate data utilization across platforms. Timely risk assessments allow for the spatial prioritization of monitoring that could streamline invasive species management paradigms and invasive species’ ability to prevent irreversible damage, such that decision makers can focus surveillance and intervention efforts where they are likely to be most effective under budgetary and resource constraints. I present a workflow that generates rapid spatial risk assessments on aquatic invasive species by combining occurrence data, spatially explicit environmental data, and an ensemble approach to species distribution modeling using five machine learning algorithms. For proof of concept and validation, I tested this workflow using extensive spatial and temporal occurrence data from Rainbow Trout (RBT; Oncorhynchus mykiss) invasion in the upper Flathead River system in northwestern Montana, USA. Due to this workflow’s high performance against cross-validated datasets (87% accuracy) and congruence with known drivers of RBT invasion, I developed a tool that generates agile risk assessments based on the above workflow and suggest that it can be generalized to broader spatial and taxonomic scales in order to provide data-driven management information for early detection of potential invaders. I then use this tool as technical input for a management framework that provides guidance for users to incorporate and synthesize the component features of the workflow and toolkit to derive actionable insight in an efficient manner

Technological roadmap on AI planning and scheduling

At the beginning of the new century, Information Technologies had become basic and indispensable constituents of the production and preparation processes for all kinds of goods and services and with that are largely influencing both the working and private life of nearly every citizen. This development will continue and even further grow with the continually increasing use of the Internet in production, business, science, education, and everyday societal and private undertaking. Recent years have shown, however, that a dramatic enhancement of software capabilities is required, when aiming to continuously provide advanced and competitive products and services in all these fast developing sectors. It includes the development of intelligent systems – systems that are more autonomous, flexible, and robust than today’s conventional software. Intelligent Planning and Scheduling is a key enabling technology for intelligent systems. It has been developed and matured over the last three decades and has successfully been employed for a variety of applications in commerce, industry, education, medicine, public transport, defense, and government. This document reviews the state-of-the-art in key application and technical areas of Intelligent Planning and Scheduling. It identifies the most important research, development, and technology transfer efforts required in the coming 3 to 10 years and shows the way forward to meet these challenges in the short-, medium- and longer-term future. The roadmap has been developed under the regime of PLANET – the European Network of Excellence in AI Planning. This network, established by the European Commission in 1998, is the co-ordinating framework for research, development, and technology transfer in the field of Intelligent Planning and Scheduling in Europe. A large number of people have contributed to this document including the members of PLANET non- European international experts, and a number of independent expert peer reviewers. All of them are acknowledged in a separate section of this document. Intelligent Planning and Scheduling is a far-reaching technology. Accepting the challenges and progressing along the directions pointed out in this roadmap will enable a new generation of intelligent application systems in a wide variety of industrial, commercial, public, and private sectors