IMP: Imperial Metagenomics Pipeline for high-throughput sequence data

We have developed an in-house pipeline for the processing and analyses of sequence data generated during Illumina technology-based metagenomic studies of the human gut microbiota. Each component of the pipeline has been selected following comparative analysis of available tools; however, the modular nature of software facilitates replacement of any individual component with an alternative should a better tool become available in due course. The pipeline consists of quality analysis and trimming followed by taxonomic filtering of sequence data allowing reads associated with samples to be binned according to whether they represent human, prokaryotic (bacterial/archaeal), viral, parasite, fungal or plant DNA. Viral, parasite, fungal and plant DNA can be assigned to species level on a presence/absence basis, allowing – for example – identification of dietary intake of plant-based foodstuffs and their derivatives. Prokaryotic DNA is subject to taxonomic and functional analyses, with assignment to taxonomic hierarchies (kingdom, class, order, family, genus, species, strain/subspecies) and abundance determination. After de novo assembly of sequence reads, genes within samples are predicted and used to build a non-redundant catalogue of genes. From this catalogue, per-sample gene abundance can be determined after normalization of data based on gene length. Functional annotation of genes is achieved through mapping of gene clusters against KEGG proteins, and InterProScan. The pipeline is undergoing validation using the human faecal metagenomic data of Qin et al. (2014, Nature 513, 59–64). Outputs from the pipeline allow development of tools for the integration of metagenomic and metabolomic data, moving metagenomic studies beyond determination of gene richness and representation towards microbial-metabolite mapping. There is scope to improve the outputs from viral, parasite, fungal and plant DNA analyses, depending on the depth of sequencing associated with samples. The pipeline can easily be adapted for the analyses of environmental and non-human animal samples, and for use with data generated via non-Illumina sequencing platforms.

Extending Science Gateway Frameworks to Support Big Data Applications in the Cloud

Cloud computing offers massive scalability and elasticity required by many scien-tific and commercial applications. Combining the computational and data handling capabilities of clouds with parallel processing also has the potential to tackle Big Data problems efficiently. Science gateway frameworks and workflow systems enable application developers to implement complex applications and make these available for end-users via simple graphical user interfaces. The integration of such frameworks with Big Data processing tools on the cloud opens new oppor-tunities for application developers. This paper investigates how workflow sys-tems and science gateways can be extended with Big Data processing capabilities. A generic approach based on infrastructure aware workflows is suggested and a proof of concept is implemented based on the WS-PGRADE/gUSE science gateway framework and its integration with the Hadoop parallel data processing solution based on the MapReduce paradigm in the cloud. The provided analysis demonstrates that the methods described to integrate Big Data processing with workflows and science gateways work well in different cloud infrastructures and application scenarios, and can be used to create massively parallel applications for scientific analysis of Big Data.

Financial media, globalisation, and China’s economic integration: comparing narrative construction of the Economist and Caijing

In June 2015, legal frameworks of the Asian Infrastructural Investment Bank were signed by its 57 founding members. Proposed and initiated by China, this multilateral development bank is considered to be an Asian counterpart to break the monopoly of the World Bank and the International Monetary Fund. In October 2015, China’s Central Bank announced a benchmark interest rate cut to combat the economic slowdown. The easing policy coincides with the European Central Bank’s announcement of doubts over US Fed’s commitment to raise interest rates. Global stock markets responded positively to China’s move, with the exception of the indexes from Wall Street (Bland, 2015; Elliott, 2015). In the meantime, China’s ‘One Belt, One Road’ (or New Silk Road Economic Belt) became atopic of discourse in relation to its growing global economy, as China pledged $40 billion to trade and infrastructure projects (Bermingham, 2015). The foreign policy aims to reinforce the economic belt from western China through Central Asia towards Europe, as well as to construct maritime trading routes from coastal China through the South China Sea (Summers, 2015). In 2012, The Economist launched a new China section, to reveal the complexity of the‘meteoric rise’ of China. John Micklethwait, who was then the chief editor of the magazine, said that China’s emergence as a global power justified giving it a section of its own(Roush, 2012). In July 2015, Hu Shuli, the former chief editor of Caijing, announced the launch of a think tank and financial data service division called Caixin Insight Group, which encompasses the new Caixin China Purchasing Managers Index (PMI). Incooperation with with Markit Group, a principal global provider of PMI, the index soon became a widely cited economic indicator. One anecdote from November’s Caixin shows how much has changed: in a high-profile dialogue between Hu Shuli and Kevin Rudd, Hu insisted on asking questions in English; interestingly, the former Prime Minister of Australia insisted on replying in Chinese. These recent developments point to one thing: the economic ascent of China and its increasing influence on the power play between economics and politics in world markets. China has begun to take a more active role in rule making and enforcement under neoliberal frameworks. However, due to the country’s size and the scale of its economy in comparison to other countries, China’s version of globalisation has unique characteristics. The ‘Capitalist-socialist’ paradox is vital to China’s market-oriented transformation. In order to comprehend how such unique features are articulated and understood, there are several questions worth investigating in the realms of media and communication studies,such as how China’s neoliberal restructuring is portrayed and perceived by different types of interested parties, and how these portrayals are de-contextualised and re-contextualised in global or Anglo-American narratives. Therefore, based on a combination of the themes of globalisation, financial media and China’s economic integration, this thesis attempts to explore how financial media construct the narratives of China’s economic globalisation through the deployment of comparative and multi-disciplinary approaches. Two outstanding elite financial magazines, Britain’s The Economist, which has a global readership and influence, and Caijing, China’s leading financial magazine, are chosen as case studies to exemplify differing media discourses, representing, respectively, Anglo-American and Chinese socio-economic and political backgrounds, as well as their own journalistic cultures. This thesis tries to answer the questions of how and why China’s neoliberal restructuring is constructed from a globally-oriented perspective. The construction primarily involves people who are influential in business and policymaking. Hence, the analysis falls into the paradigm of elite-elite communication, which is an important but relatively less developed perspective in studying China and its globalisation. The comparing of characteristics of narrative construction are the result of the textual analysis of articles published over a ten-year period (mid-1998 to mid-2008). The corpus of samples come from the two media outlets’ coverage of three selected events:China becoming a member of the World Trade Organization, its outward direct investment, and the listing of stocks of Chinese companies in overseas exchanges, which are mutually exclusive in sample collection and collectively exhaustive in the inclusion of articles regarding China’s economic globalisation. The findings help to understand that, despite language, socio-economic and political differences, elite financial media with globally-oriented readerships share similar methods of and approaches to agenda setting, the evaluation of news prominence, the selection of frame, and the advocacy of deeply rooted neoliberal ideas. The comparison of their distinctive features reflects the different phases of building up the sense of identity in their readers as global elites, as well as the different economic interests that are aligned with the corresponding readerships. However, textual analysis is only relevant in terms of exploring how the narratives are constructed and the elements they include; textual analysis alone prevents us from seeing the obstacles and the constrains of the journalistic practices of construction. Therefore, this thesis provides a brief discussion of interviews with practitioners from the two media, in order to understand how similar or different narratives are manifested and perceived, how the concept of neoliberalism deviates from and is justified in the Chinese context, and how and for what purpose deviations arise from Western to Chinese contexts. The thesis also contributes to defining financial media in the domain of elite communication. The relevant and closely interlocking concepts of globalisation, elitism and neoliberalism are discussed, and are used as a theoretical bedrock in the analysis of texts and contexts. It is important to address the agenda-setting and ideological role of elite financial media, because of its narrative formula of infusing business facts with opinions,which is important in constructing the global elite identity as well as influencing neoliberal policy-making. On the other hand, ‘journalistic professionalism’ has been redefined, in that the elite identity is shared by the content producer, reader and the actors in the news stories emerging from the much-compressed news cycle. The professionalism of elite financial media requires a dual definition, that of being professional in the understanding of business facts and statistics, and that of being professional in the making sense of stories by deploying economic logic.