PDB-Explorer: a web-based interactive map of the protein data bank in shape space

Background The RCSB Protein Data Bank (PDB) provides public access to experimentally determined 3D-structures of biological macromolecules (proteins, peptides and nucleic acids). While various tools are available to explore the PDB, options to access the global structural diversity of the entire PDB and to perceive relationships between PDB structures remain very limited. Methods A 136-dimensional atom pair 3D-fingerprint for proteins (3DP) counting categorized atom pairs at increasing through-space distances was designed to represent the molecular shape of PDB-entries. Nearest neighbor searches examples were reported exemplifying the ability of 3DP-similarity to identify closely related biomolecules from small peptides to enzyme and large multiprotein complexes such as virus particles. The principle component analysis was used to obtain the visualization of PDB in 3DP-space. Results The 3DP property space groups proteins and protein assemblies according to their 3D-shape similarity, yet shows exquisite ability to distinguish between closely related structures. An interactive website called PDB-Explorer is presented featuring a color-coded interactive map of PDB in 3DP-space. Each pixel of the map contains one or more PDB-entries which are directly visualized as ribbon diagrams when the pixel is selected. The PDB-Explorer website allows performing 3DP-nearest neighbor searches of any PDB-entry or of any structure uploaded as protein-type PDB file. All functionalities on the website are implemented in JavaScript in a platform-independent manner and draw data from a server that is updated daily with the latest PDB additions, ensuring complete and up-to-date coverage. The essentially instantaneous 3DP-similarity search with the PDB-Explorer provides results comparable to those of much slower 3D-alignment algorithms, and automatically clusters proteins from the same superfamilies in tight groups. Conclusion A chemical space classification of PDB based on molecular shape was obtained using a new atom-pair 3D-fingerprint for proteins and implemented in a web-based database exploration tool comprising an interactive color-coded map of the PDB chemical space and a nearest neighbor search tool. The PDB-Explorer website is freely available at www.​cheminfo.​org/​pdbexplorer and represents an unprecedented opportunity to interactively visualize and explore the structural diversity of the PDB.

A distributed, semiotic-inductive and human-Oriented approach to web-scale knowledge retrieval

Web-scale knowledge retrieval can be enabled by distributed information retrieval, clustering Web clients to a large-scale computing infrastructure for knowledge discovery from Web documents. Based on this infrastructure, we propose to apply semiotic (i.e., sub-syntactical) and inductive (i.e., probabilistic) methods for inferring concept associations in human knowledge. These associations can be combined to form a fuzzy (i.e.,gradual) semantic net representing a map of the knowledge in the Web. Thus, we propose to provide interactive visualizations of these cognitive concept maps to end users, who can browse and search the Web in a human-oriented, visual, and associative interface.

Ecosystem service trade-offs and stakeholder claims - a meso-scale study from a Madagascar biodiversity hotspot

The north-eastern escarpment of Madagascar has been labelled a global biodiversity hotspot due to its extremely high rates of endemic species which are heavily threatened by accelerated deforestation rates and landscape change. The traditional practice of shifting cultivation or "tavy" used by the majority of land users in this area to produce subsistence rice is commonly blamed for these threats. A wide range of stakeholders ranging from conservation to development agencies, and from the private to the public sector has therefore been involved in trying to find solutions to protect the remaining forest fragments and to increase agricultural production. Consequently, provisioning, regulating and socio-cultural services of this forest-mosaic landscape are fundamentally altered leading to trade-offs between them and consequently new winners and losers amongst the stakeholders at different scales. However, despite a growing amount of evidence from case studies analysing local changes, the regional dynamics of the landscape and their contribution to such trade-offs remain poorely understood. This study therefore aims at using generalised landscape units as a base for the assessment of multi-level stakeholder claims on ecosystem services to inform negotiation, planning and decision making at a meso-scale. The presented study applies a mixed-method approach combining remote sensing, GIS and socio-economic methods to reveal current landscape dynamics, their change over time and the corresponding ecosystem service trade-offs induced by diverse stakeholder claims on the regional level. In a first step a new regional land cover classification for three points in time (1995, 2005 and 2011) was conducted including agricultural classes characteristic for shifting cultivation systems. Secondly, a novel GIS approach, termed “landscape mosaics approach” originally developed to assess dynamics of shifting cultivation landscapes in Laos was applied. Through this approach generalised landscape mosaics were generated allowing for a better understanding of changes in land use intensities instead of land cover. As a next step we will try to use these landscape units as proxies to map provisioning and regulating ecosystem services throughout the region. Through the overlay with other regional background data such as accessibility and population density and information from a region-wide stakeholder analysis, multiscale trade-offs between different services will be highlighted. The trade-offs observed on the regional scale will then be validated through a socio-economic ground-truthing within selected sites at the local scale. We propose that such meso-scale knowledge is required by all stakeholders involved in decision making towards sustainable development of north-eastern Madagascar.

Keeping citizens, companies, and organizations informed by Web KnowARR

For the main part, electronic government (or e-government for short) aims to put digital public services at disposal for citizens, companies, and organizations. To that end, in particular, e-government comprises the application of Information and Communications Technology (ICT) to support government operations and provide better governmental services (Fraga, 2002) as possible with traditional means. Accordingly, e-government services go further as traditional governmental services and aim to fundamentally alter the processes in which public services are generated and delivered, after this manner transforming the entire spectrum of relationships of public bodies with its citizens, businesses and other government agencies (Leitner, 2003). To implement this transformation, one of the most important points is to inform the citizen, business, and/or other government agencies faithfully and in an accessible way. This allows all the partaking participants of governmental affairs for a transition from passive information access to active participation (Palvia and Sharma, 2007). In addition, by a corresponding handling of the participants' data, a personalization towards these participants may even be accomplished. For instance, by creating significant user profiles as a kind of participants' tailored knowledge structures, a better-quality governmental service may be provided (i.e., expressed by individualized governmental services). To create such knowledge structures, thus known information (e.g., a social security number) can be enriched by vague information that may be accurate to a certain degree only. Hence, fuzzy knowledge structures can be generated, which help improve governmental-participants relationship. The Web KnowARR framework (Portmann and Thiessen, 2013; Portmann and Pedrycz, 2014; Portmann and Kaltenrieder, 2014), which I introduce in my presentation, allows just all these participants to be automatically informed about changes of Web content regarding a- respective governmental action. The name Web KnowARR thereby stands for a self-acting entity (i.e. instantiated form the conceptual framework) that knows or apprehends the Web. In this talk, the frameworks respective three main components from artificial intelligence research (i.e. knowledge aggregation, representation, and reasoning), as well as its specific use in electronic government will be briefly introduced and discussed.

A Case for CDN-as-a-Service in the Cloud: A Mobile Cloud Networking Argument

Content Distribution Networks are mandatory components of modern web architectures, with plenty of vendors offering their services. Despite its maturity, new paradigms and architecture models are still being developed in this area. Cloud Computing, on the other hand, is a more recent concept which has expanded extremely quickly, with new services being regularly added to cloud management software suites such as OpenStack. The main contribution of this paper is the architecture and the development of an open source CDN that can be provisioned in an on-demand, pay-as-you-go model thereby enabling the CDN as a Service paradigm. We describe our experience with integration of CDNaaS framework in a cloud environment, as a service for enterprise users. We emphasize the flexibility and elasticity of such a model, with each CDN instance being delivered on-demand and associated to personalized caching policies as well as an optimized choice of Points of Presence based on exact requirements of an enterprise customer. Our development is based on the framework developed in the Mobile Cloud Networking EU FP7 project, which offers its enterprise users a common framework to instantiate and control services. CDNaaS is one of the core support components in this project as is tasked to deliver different type of multimedia content to several thousands of users geographically distributed. It integrates seamlessly in the MCN service life-cycle and as such enjoys all benefits of a common design environment, allowing for an improved interoperability with the rest of the services within the MCN ecosystem.

A high-resolution map of direct and indirect connectivity of erosion risk areas to surface waters in Switzerland: A risk assessment tool for planning and policy-making

Off-site effects of soil erosion are becoming increasingly important, particularly the pollution of surface waters. In order to develop environmentally efficient and cost effective mitigation options it is essential to identify areas that bear both a high erosion risk and high connectivity to surface waters. This paper introduces a simple risk assessment tool that allows the delineation of potential critical source areas (CSA) of sediment input into surface waters concerning the agricultural areas of Switzerland. The basis are the erosion risk map with a 2 m resolution (ERM2) and the drainage network, which is extended by drained roads, farm tracks, and slope depressions. The probability of hydrological and sedimentological connectivity is assessed by combining soil erosion risk and extended drainage network with flow distance calculation. A GIS-environment with multiple-flow accumulation algorithms is used for routing runoff generation and flow pathways. The result is a high resolution connectivity map of the agricultural area of Switzerland (888,050 ha). Fifty-five percent of the computed agricultural area is potentially connected with surface waters, 45% is not connected. Surprisingly, the larger part of 34% (62% of the connected area) is indirectly connected with surface waters through drained roads, and only 21% are directly connected. The reason is the topographic complexity and patchiness of the landscape due to a dense road and drainage network. A total of 24% of the connected area and 13% of the computed agricultural area, respectively, are rated with a high connectivity probability. On these CSA an adapted land use is recommended, supported by vegetated buffer strips preventing sediment load. Even areas that are far away from open water bodies can be indirectly connected and need to be included in planning of mitigation measures. Thus, the connectivity map presented is an important decision-making tool for policy-makers and extension services. The map is published on the web and thus available for application.