Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?

The organization and mining of malaria genomic and post-genomic data is highly motivated by the necessity to predict and characterize new biological targets and new drugs. Biological targets are sought in a biological space designed from the genomic data from Plasmodium falciparum, but using also the millions of genomic data from other species. Drug candidates are sought in a chemical space containing the millions of small molecules stored in public and private chemolibraries. Data management should therefore be as reliable and versatile as possible. In this context, we examined five aspects of the organization and mining of malaria genomic and post-genomic data: 1) the comparison of protein sequences including compositionally atypical malaria sequences, 2) the high throughput reconstruction of molecular phylogenies, 3) the representation of biological processes particularly metabolic pathways, 4) the versatile methods to integrate genomic data, biological representations and functional profiling obtained from X-omic experiments after drug treatments and 5) the determination and prediction of protein structures and their molecular docking with drug candidate structures. Progresses toward a grid-enabled chemogenomic knowledge space are discussed.Comment: 43 pages, 4 figures, to appear in Malaria Journa

Identifying national security fundamentals in the big data of digital asymmetrical environment communication

This conceptualization article discusses the impact of technology to society from variousperspectives which relates on humanities aspect of social convention, hegemony, generation warfare and intelligence constructs.The narratives provide understandings of the current transition, emphasizing the changing need of intelligence protocols to understand the society in current technological advancement era. Intelligence output is detrimental as information is no longer secluded in this borderless communication spheres. The article narrates generation warfare intelligence in complex information system of digital asymmetrical environment in current generation warfare to digest the social implications and of technology to society and provides appropriate recommendations.Keywords: communication; generation warfare; hegemony; intelligence; society; socialconvention

Natural Abduction: the Bridge between Individuals Choices and the Production of Evolutionary Innovations

Defenders of developmental systems theory have shown the need for a new evolutionary synthesis. However this effort requires a metaphysical evolutionary framework in which such an expanded synthesis can be embedded. I propose to develop a Peircean monist ontology by explaining the six characteristics or facets of reality labeled as: A) spontaneity, B) determinism, C) processing of information, D) statistical law, E) internally driven capricious choices and F) tendency to form habits. A special emphasis will be dedicated to characterize the predicates C and E as they provide the clue to the understanding of nature as a continuously open-ended and unpredictable process, where its inherent creativity is analogized to an abductive inference

A national initiative in data science for health: an evaluation of the UK Farr Institute

ObjectiveTo evaluate the extent to which the inter-institutional, inter-disciplinary mobilisation of data and skills in the Farr Institute contributed to establishing the emerging field of data science for health in the UK.&#x0D; Design and Outcome measuresWe evaluated evidence of six domains characterising a new field of science:&#x0D; &#x0D; defining central scientific challenges,&#x0D; demonstrating how the central challenges might be solved,&#x0D; creating novel interactions among groups of scientists,&#x0D; training new types of experts,&#x0D; re-organising universities,&#x0D; demonstrating impacts in society.&#x0D; &#x0D; We carried out citation, network and time trend analyses of publications, and a narrative review of infrastructure, methods and tools.&#x0D; SettingFour UK centres in London, North England, Scotland and Wales (23 university partners), 2013-2018.&#x0D; Results1. The Farr Institute helped define a central scientific challenge publishing a research corpus, demonstrating insights from electronic health record (EHR) and administrative data at each stage of the translational cycle in 593 papers with at least one Farr Institute author affiliation on PubMed. 2. The Farr Institute offered some demonstrations of how these scientific challenges might be solved: it established the first four ISO27001 certified trusted research environments in the UK, and approved more than 1000 research users, published on 102 unique EHR and administrative data sources, although there was no clear evidence of an increase in novel, sustained record linkages. The Farr Institute established open platforms for the EHR phenotyping algorithms and validations (&gt;70 diseases, CALIBER). Sample sizes showed some evidence of increase but remained less than 10% of the UK population in primary care-hospital care linked studies. 3.The Farr Institute created novel interactions among researchers: the co-author publication network expanded from 944 unique co-authors (based on 67 publications in the first 30 months) to 3839 unique co-authors (545 papers in the final 30 months). 4. Training expanded substantially with 3 new masters courses, training &gt;400 people at masters, short-course and leadership level and 48 PhD students. 5. Universities reorganised with 4/5 Centres established 27 new faculty (tenured) positions, 3 new university institutes. 6. Emerging evidence of impacts included: &gt; 3200 citations for the 10 most cited papers and Farr research informed eight practice-changing clinical guidelines and policies relevant to the health of millions of UK citizens.&#x0D; ConclusionThe Farr Institute played a major role in establishing and growing the field of data science for health in the UK, with some initial evidence of benefits for health and healthcare. The Farr Institute has now expanded into Health Data Research (HDR) UK but key challenges remain including, how to network such activities internationally.</jats:p