94,110 research outputs found
An Introduction to Programming for Bioscientists: A Python-based Primer
Computing has revolutionized the biological sciences over the past several
decades, such that virtually all contemporary research in the biosciences
utilizes computer programs. The computational advances have come on many
fronts, spurred by fundamental developments in hardware, software, and
algorithms. These advances have influenced, and even engendered, a phenomenal
array of bioscience fields, including molecular evolution and bioinformatics;
genome-, proteome-, transcriptome- and metabolome-wide experimental studies;
structural genomics; and atomistic simulations of cellular-scale molecular
assemblies as large as ribosomes and intact viruses. In short, much of
post-genomic biology is increasingly becoming a form of computational biology.
The ability to design and write computer programs is among the most
indispensable skills that a modern researcher can cultivate. Python has become
a popular programming language in the biosciences, largely because (i) its
straightforward semantics and clean syntax make it a readily accessible first
language; (ii) it is expressive and well-suited to object-oriented programming,
as well as other modern paradigms; and (iii) the many available libraries and
third-party toolkits extend the functionality of the core language into
virtually every biological domain (sequence and structure analyses,
phylogenomics, workflow management systems, etc.). This primer offers a basic
introduction to coding, via Python, and it includes concrete examples and
exercises to illustrate the language's usage and capabilities; the main text
culminates with a final project in structural bioinformatics. A suite of
Supplemental Chapters is also provided. Starting with basic concepts, such as
that of a 'variable', the Chapters methodically advance the reader to the point
of writing a graphical user interface to compute the Hamming distance between
two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables,
numerous exercises, and 19 pages of Supporting Information; currently in
press at PLOS Computational Biolog
Neurocognitive Informatics Manifesto.
Informatics studies all aspects of the structure of natural and artificial information systems. Theoretical and abstract approaches to information have made great advances, but human information processing is still unmatched in many areas, including information management, representation and understanding. Neurocognitive informatics is a new, emerging field that should help to improve the matching of artificial and natural systems, and inspire better computational algorithms to solve problems that are still beyond the reach of machines. In this position paper examples of neurocognitive inspirations and promising directions in this area are given
CHORUS Deliverable 2.2: Second report - identification of multi-disciplinary key issues for gap analysis toward EU multimedia search engines roadmap
After addressing the state-of-the-art during the first year of Chorus and establishing the existing landscape in
multimedia search engines, we have identified and analyzed gaps within European research effort during our second year.
In this period we focused on three directions, notably technological issues, user-centred issues and use-cases and socio-
economic and legal aspects. These were assessed by two central studies: firstly, a concerted vision of functional breakdown
of generic multimedia search engine, and secondly, a representative use-cases descriptions with the related discussion on
requirement for technological challenges. Both studies have been carried out in cooperation and consultation with the
community at large through EC concertation meetings (multimedia search engines cluster), several meetings with our
Think-Tank, presentations in international conferences, and surveys addressed to EU projects coordinators as well as
National initiatives coordinators. Based on the obtained feedback we identified two types of gaps, namely core
technological gaps that involve research challenges, and “enablers”, which are not necessarily technical research
challenges, but have impact on innovation progress. New socio-economic trends are presented as well as emerging legal
challenges
Rotation-invariant features for multi-oriented text detection in natural images.
Texts in natural scenes carry rich semantic information, which can be used to assist a wide range of applications, such as object recognition, image/video retrieval, mapping/navigation, and human computer interaction. However, most existing systems are designed to detect and recognize horizontal (or near-horizontal) texts. Due to the increasing popularity of mobile-computing devices and applications, detecting texts of varying orientations from natural images under less controlled conditions has become an important but challenging task. In this paper, we propose a new algorithm to detect texts of varying orientations. Our algorithm is based on a two-level classification scheme and two sets of features specially designed for capturing the intrinsic characteristics of texts. To better evaluate the proposed method and compare it with the competing algorithms, we generate a comprehensive dataset with various types of texts in diverse real-world scenes. We also propose a new evaluation protocol, which is more suitable for benchmarking algorithms for detecting texts in varying orientations. Experiments on benchmark datasets demonstrate that our system compares favorably with the state-of-the-art algorithms when handling horizontal texts and achieves significantly enhanced performance on variant texts in complex natural scenes
Challenges in Bridging Social Semantics and Formal Semantics on the Web
This paper describes several results of Wimmics, a research lab which names
stands for: web-instrumented man-machine interactions, communities, and
semantics. The approaches introduced here rely on graph-oriented knowledge
representation, reasoning and operationalization to model and support actors,
actions and interactions in web-based epistemic communities. The re-search
results are applied to support and foster interactions in online communities
and manage their resources
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