Prospective cognition in animals

The debate about whether or not animals have foresight has focused on whether animals can be shown to have episodic future thinking, that is the ability to travel mentally in time and see themselves in the future. This focus has distracted from consideration of other forms of foresight that animals demonstrate. We propose a framework for examining future-oriented behaviours and then discuss the evidence for future thinking in animals. In the final section we examine some perspectives of future thinking and suggest that there are future-oriented capabilities of animals that do not involve mental time travel but may yet involve future thinking which deserve further investigation.     

Reviewing the curriculum

The potential use of IT in secondary biology teaching is enormous, although it is a huge undertaking and fairly daunting to newcomers. Computer learning packages and the web can offer a variety of opportunities for learning, ranging from non-interactive content provision to highly interactive student-centred learning experiences. The learning materials in use in New South Wales (NSW) schools include information web sites, computer learning packages as tutorial or revision material, computer learning packages made by the students, virtual field trips, simulations, and virtual laboratories. In addition, students and teachers are using the web for communicating amongst themselves via email, newsgroups and discussion lists, videoconferencing for both local and global communications, and telecollaborative projects. This article will focus on materials used in student learning, and on the forms of electronic communication in use within the school system. A list of resources is provided.     

The Circulate architecture: avoiding workflow bottlenecks caused by centralised orchestration

As the number of services and the size of data involved in workflows increases, centralised orchestration techniques are reaching the limits of scalability. In the classic orchestration model, all data passes through a centralised engine, which results in unnecessary data transfer, wasted bandwidth and the engine to become a bottleneck to the execution of a workflow. This paper presents and evaluates the Circulate architecture which maintains the robustness and simplicity of centralised orchestration, but facilitates choreography by allowing services to exchange data directly with one another. Circulate could be realised within any existing workflow framework, in this paper, we focus on WS-Circulate, a Web services based implementation. Taking inspiration from the Montage workflow, a number of common workflow patterns (sequence, fan-in and fan-out), input to output data size relationships and network configurations are identified and evaluated. The performance analysis concludes that a substantial reduction in communication overhead results in a 2–4 fold performance benefit across all patterns. An end-to-end pattern through the Montage workflow results in an 8 fold performance benefit and demonstrates how the advantage of using the Circulate architecture increases as the complexity of a workflow grows.

The PSI semantic validator: A framework to check MIAPE compliance of proteomics data

The Human Proteome Organization's Proteomics Standards Initiative (PSI) promotes the development of exchange standards to improve data integration and interoperability. PSI specifies the suitable level of detail required when reporting a proteomics experiment (via the Minimum Information About a Proteomics Experiment), and provides extensible markup language (XML) exchange formats and dedicated controlled vocabularies (CVs) that must be combined to generate a standard compliant document. The framework presented here tackles the issue of checking that experimental data reported using a specific format, CVs and public bio‐ontologies (e.g. Gene Ontology, NCBI taxonomy) are compliant with the Minimum Information About a Proteomics Experiment recommendations. The semantic validator not only checks the XML syntax but it also enforces rules regarding the use of an ontology class or CV terms by checking that the terms exist in the resource and that they are used in the correct location of a document. Moreover, this framework is extremely fast, even on sizable data files, and flexible, as it can be adapted to any standard by customizing the parameters it requires: an XML Schema Definition, one or more CVs or ontologies, and a mapping file describing in a formal way how the semantic resources and the format are interrelated. As such, the validator provides a general solution to the common problem in data exchange: how to validate the correct usage of a data standard beyond simple XML Schema Definition validation. The framework source code and its various applications can be found at http://psidev.info/validator .     

Comparative evaluation of label-free SINQ normalized spectral index quantitation in the central proteomics facilities pipeline

Normalized spectral index quantification was recently presented as an accurate method of label‐free quantitation, which improved spectral counting by incorporating the intensities of peptide MS/MS fragment ions into the calculation of protein abundance. We present SINQ, a tool implementing this method within the framework of existing analysis software, our freely available central proteomics facilities pipeline (CPFP). We demonstrate, using data sets of protein standards acquired on a variety of mass spectrometers, that SINQ can rapidly provide useful estimates of the absolute quantity of proteins present in a medium‐complexity sample. In addition, relative quantitation of standard proteins spiked into a complex lysate background and run without pre‐fractionation produces accurate results at amounts above 1 fmol on column. We compare quantitation performance to various precursor intensity‐ and identification‐based methods, including the normalized spectral abundance factor (NSAF), exponentially modified protein abundance index (emPAI), MaxQuant, and Progenesis LC‐MS. We anticipate that the SINQ tool will be a useful asset for core facilities and individual laboratories that wish to produce quantitative MS data, but lack the necessary manpower to routinely support more complicated software workflows. SINQ is freely available to obtain and use as part of the central proteomics facilities pipeline, which is released under an open‐source license.     

一种基于本体集成的生物医学数据库中语义映射维护方法研究

生物医学数据库到生物医学本体的语义映射是基于本体集成生物医学数据库系统的一个重要环节.而生物医学本体随着学科的发展不断演化,造成了集成系统不稳定.针对这个问题,本文在本体演化条件下,分析并发现了语义映射的变化规律,设计了对应的维护流程和维护方法,并通过计算维护收益率证明了该方法对映射的维护是有效性的,从而增强了集成系统在本体演化条件下的稳定性.     

药用植物保育云服务平台设计与实现

药用植物资源是中医药事业和生物医药产业赖以生存和发展的重要资源,同时也是我国的中医药文化遗产的载体。而药用植物资源的保育工作是药植资源可持续性开发与应用的基础。随着生物信息学与信息化技术的快速发展,利用包括云计算在内的新兴信息化技术,在传统种质资源保护与管理等方面的应用越来越多,然而,在药用植物资源保育方面还有待开发与应用。利用云计算、数据库应用及生物信息学等相关技术,对我国药用植物资源的保育数据进行信息化及平台建设,构建药用植物保育云服务平台系统。该系统通过收集、整理和加工药用植物资源信息,开展药用植物数据信息化与应用开发,完成药用植物保育云服务平台,可提供药用植物保护及新物种培育等方面信息查询服务。该平台对于药用植物研究相关的数据标准化、保育学科研究,以及信息共享与服务,具有较为重要的应用价值与社会意义。     

The Semantic Morphology of Adolf Portmann: A Starting Point for the Biosemiotics of Organic Form?

This paper develops the ideas of the Swiss zoologist Adolf Portmann or, more precisely, his concept of organic self-representation, wherein Portmann considered the outer surface of living organisms as a specific organ that serves in a self-representational role. This idea is taken as a starting point from which to elaborate Portman’s ideas, so as to make them compatible with the theoretical framework of biosemiotics. Today, despite the many theories that help us understand aposematism, camouflage, deception and other phenomena related to the category of mimicry, there still is a need for a general theory of self-representation that would re-synthesize evolutionary, morphogenetic and semiotic aspects of the surface of organisms. Here, Adolf Portmann’s concept of self-representation is considered as an important step towards the biosemiotics of animal form.