WIWS: a protein structure bioinformatics Web service collection

The WHAT IF molecular-modelling and drug design program is widely distributed in the world of protein structure bioinformatics. Although originally designed as an interactive application, its highly modular design and inbuilt control language have recently enabled its deployment as a collection of programmatically accessible web services. We report here a collection of WHAT IF-based protein structure bioinformatics web services: these relate to structure quality, the use of symmetry in crystal structures, structure correction and optimization, adding hydrogens and optimizing hydrogen bonds and a series of geometric calculations. The freely accessible web services are based on the industry standard WS-I profile and the EMBRACE technical guidelines, and are available via both REST and SOAP paradigms. The web services run on a dedicated computational cluster; their function and availability is monitored daily

Apparent breeding success drives long-term population dynamics of a migratory swan

Contains fulltext : 226690.pdf (publisher's version ) (Open Access

An active registry for bioinformatics web services

Summary: The EMBRACE Registry is a web portal that collects and monitors web services according to test scripts provided by the their administrators. Users are able to search for, rank and annotate services, enabling them to select the most appropriate working service for inclusion in their bioinformatics analysis tasks

Drug design for ever, from hype to hope

In its first 25 years JCAMD has been disseminating a large number of techniques aimed at finding better medicines faster. These include genetic algorithms, COMFA, QSAR, structure based techniques, homology modelling, high throughput screening, combichem, and dozens more that were a hype in their time and that now are just a useful addition to the drug-designers toolbox. Despite massive efforts throughout academic and industrial drug design research departments, the number of FDA-approved new molecular entities per year stagnates, and the pharmaceutical industry is reorganising accordingly. The recent spate of industrial consolidations and the concomitant move towards outsourcing of research activities requires better integration of all activities along the chain from bench to bedside. The next 25 years will undoubtedly show a series of translational science activities that are aimed at a better communication between all parties involved, from quantum chemistry to bedside and from academia to industry. This will above all include understanding the underlying biological problem and optimal use of all available data

A Reflection on Teaching and Learning in a Community Literacies Graduate Course

Th is article outlines one potential model for a graduate–level course in community literacy studies. Ellen Cushman and Jeffrey Grabill taught this course for the first time at Michigan State University in the spring of 2007. In this article our colleagues with varying disciplinary backgrounds reflect on the course, its readings, and their theoretical and practical understanding surrounding many of the central questions of this new discipline: what is a community? What is literacy? What is community literacy? And what does it mean to practice “community literacy”—to write, to speak, and so on? After a wide discussion of course experience from several student colleagues in the course, Cushman and Grabill reflect on their course objectives and point toward future incarnations of the course

Target and (Astro-)WISE technologies - Data federations and its applications

After its first implementation in 2003 the Astro-WISE technology has been rolled out in several European countries and is used for the production of the KiDS survey data. In the multi-disciplinary Target initiative this technology, nicknamed WISE technology, has been further applied to a large number of projects. Here, we highlight the data handling of other astronomical applications, such as VLT-MUSE and LOFAR, together with some non-astronomical applications such as the medical projects Lifelines and GLIMPS, the MONK handwritten text recognition system, and business applications, by amongst others, the Target Holding. We describe some of the most important lessons learned and describe the application of the data-centric WISE type of approach to the Science Ground Segment of the Euclid satellite.Comment: 9 pages, 5 figures, Proceedngs IAU Symposium No 325 Astroinformatics 201

Confronting Grand Challenges in environmental fluid mechanics

Environmental fluid mechanics underlies a wealth of natural, industrial and, by extension, societal challenges. In the coming decades, as we strive towards a more sustainable planet, there are a wide range of grand challenge problems that need to be tackled, ranging from fundamental advances in understanding and modeling of stratified turbulence and consequent mixing, to applied studies of pollution transport in the ocean, atmosphere and urban environments. A workshop was organized in the Les Houches School of Physics in France in January 2019 with the objective of gathering leading figures in the field to produce a road map for the scientific community. Five subject areas were addressed: multiphase flow, stratified flow, ocean transport, atmospheric and urban transport, and weather and climate prediction. This article summarizes the discussions and outcomes of the meeting, with the intent of providing a resource for the community going forward