The Phyre2 web portal for protein modeling, prediction and analysis

Phyre2 is a suite of tools available on the web to predict and analyze protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art protein bioinformatics tools. Phyre2 replaces Phyre, the original version of the server for which we previously published a paper in Nature Protocols. In this updated protocol, we describe Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites and analyze the effect of amino acid variants (e.g., nonsynonymous SNPs (nsSNPs)) for a user's protein sequence. Users are guided through results by a simple interface at a level of detail they determine. This protocol will guide users from submitting a protein sequence to interpreting the secondary and tertiary structure of their models, their domain composition and model quality. A range of additional available tools is described to find a protein structure in a genome, to submit large number of sequences at once and to automatically run weekly searches for proteins that are difficult to model. The server is available at http://www.sbg.bio.ic.ac.uk/phyre2. A typical structure prediction will be returned between 30 min and 2 h after submission

Using string-matching to analyze hypertext navigation

A method of using string-matching to analyze hypertext navigation was developed, and evaluated using two weeks of website logfile data. The method is divided into phases that use: (i) exact string-matching to calculate subsequences of links that were repeated in different navigation sessions (common trails through the website), and then (ii) inexact matching to find other similar sessions (a community of users with a similar interest). The evaluation showed how subsequences could be used to understand the information pathways users chose to follow within a website, and that exact and inexact matching provided complementary ways of identifying information that may have been of interest to a whole community of users, but which was only found by a minority. This illustrates how string-matching could be used to improve the structure of hypertext collections

Spatial movement pattern recognition in soccer based on relative player movements

Knowledge of spatial movement patterns in soccer occurring on a regular basis can give a soccer coach, analyst or reporter insights in the playing style or tactics of a group of players or team. Furthermore, it can support a coach to better prepare for a soccer match by analysing (trained) movement patterns of both his own as well as opponent players. We explore the use of the Qualitative Trajectory Calculus (QTC), a spatiotemporal qualitative calculus describing the relative movement between objects, for spatial movement pattern recognition of players movements in soccer. The proposed method allows for the recognition of spatial movement patterns that occur on different parts of the field and/or at different spatial scales. Furthermore, the Levenshtein distance metric supports the recognition of similar movements that occur at different speeds and enables the comparison of movements that have different temporal lengths. We first present the basics of the calculus, and subsequently illustrate its applicability with a real soccer case. To that end, we present a situation where a user chooses the movements of two players during 20 seconds of a real soccer match of a 2016-2017 professional soccer competition as a reference fragment. Following a pattern matching procedure, we describe all other fragments with QTC and calculate their distance with the QTC representation of the reference fragment. The top-k most similar fragments of the same match are presented and validated by means of a duo-trio test. The analyses show the potential of QTC for spatial movement pattern recognition in soccer

A Systematic Approach to Constructing Incremental Topology Control Algorithms Using Graph Transformation

Communication networks form the backbone of our society. Topology control algorithms optimize the topology of such communication networks. Due to the importance of communication networks, a topology control algorithm should guarantee certain required consistency properties (e.g., connectivity of the topology), while achieving desired optimization properties (e.g., a bounded number of neighbors). Real-world topologies are dynamic (e.g., because nodes join, leave, or move within the network), which requires topology control algorithms to operate in an incremental way, i.e., based on the recently introduced modifications of a topology. Visual programming and specification languages are a proven means for specifying the structure as well as consistency and optimization properties of topologies. In this paper, we present a novel methodology, based on a visual graph transformation and graph constraint language, for developing incremental topology control algorithms that are guaranteed to fulfill a set of specified consistency and optimization constraints. More specifically, we model the possible modifications of a topology control algorithm and the environment using graph transformation rules, and we describe consistency and optimization properties using graph constraints. On this basis, we apply and extend a well-known constructive approach to derive refined graph transformation rules that preserve these graph constraints. We apply our methodology to re-engineer an established topology control algorithm, kTC, and evaluate it in a network simulation study to show the practical applicability of our approachComment: This document corresponds to the accepted manuscript of the referenced journal articl

Multiple object tracking using a neural cost function

This paper presents a new approach to the tracking of multiple objects in CCTV surveillance using a combination of simple neural cost functions based on Self-Organizing Maps, and a greedy assignment algorithm. Using a reference standard data set and an exhaustive search algorithm for benchmarking, we show that the cost function plays the most significant role in realizing high levels of performance. The neural cost function’s context-sensitive treatment of appearance, change of appearance and trajectory yield better tracking than a simple, explicitly designed cost function. The algorithm matches 98.8% of objects to within 15 pixels

SODA: Generating SQL for Business Users

The purpose of data warehouses is to enable business analysts to make better decisions. Over the years the technology has matured and data warehouses have become extremely successful. As a consequence, more and more data has been added to the data warehouses and their schemas have become increasingly complex. These systems still work great in order to generate pre-canned reports. However, with their current complexity, they tend to be a poor match for non tech-savvy business analysts who need answers to ad-hoc queries that were not anticipated. This paper describes the design, implementation, and experience of the SODA system (Search over DAta Warehouse). SODA bridges the gap between the business needs of analysts and the technical complexity of current data warehouses. SODA enables a Google-like search experience for data warehouses by taking keyword queries of business users and automatically generating executable SQL. The key idea is to use a graph pattern matching algorithm that uses the metadata model of the data warehouse. Our results with real data from a global player in the financial services industry show that SODA produces queries with high precision and recall, and makes it much easier for business users to interactively explore highly-complex data warehouses.Comment: VLDB201