Ongoing and future developments at the Universal Protein Resource.

The primary mission of Universal Protein Resource (UniProt) is to support biological research by maintaining a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community. UniProt is produced by the UniProt Consortium which consists of groups from the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. UniProt is updated and distributed every 4 weeks and can be accessed online for searches or download at http://www.uniprot.org

Public or private economies of knowledge: The economics of diffusion and appropriation of bioinformatics tools

The past three decades have witnessed a period of great turbulence in the economies of biological knowledge, during which there has been great uncertainty as to how and where boundaries could be drawn between public or private knowledge especially with regard to the explosive growth in biological databases and their related bioinformatic tools. This paper will focus on some of the key software tools developed in relation to bio-databases. It will argue that bioinformatic tools are particularly economically unstable, and that there is a continuing tension and competition between their public and private modes of production, appropriation, distribution, and use. The paper adopts an ?instituted economic process? approach, and in this paper will elaborate on processes of making knowledge public in the creation of ?public goods?. The question is one of continuously creating and sustaining new institutions of the commons. We believe this critical to an understanding of the division and interdependency between public and private economies of knowledge

Sanitation in the Circular Economy: Transformation to a Commercially Valuable, Self-sustaining, Biological System

In 2016 the Toilet Board Coalition ran a Feasibility Study to explore the potential role of Sanitation in the Circular Economy. The following questions were at the centre of our inquiry:- Are there products or materials of value being upcycled from toilet resources?- Are there scalable business models to deliver sustainable supply of these products to the market?- Is there commercial interest and demand from large industrial operations to become buyers into the system? This paper presents the findings of our study in the form of a thought piece on the topic of sanitation in the Circular Economy. Our intent is to present a number of business opportunity spaces, where we believe that value has been left on the table and customer needs unmet, which we recommend are to be explored further in the decade ahead.

Influenza research database: an integrated bioinformatics resource for influenza research and surveillance.

BackgroundThe recent emergence of the 2009 pandemic influenza A/H1N1 virus has highlighted the value of free and open access to influenza virus genome sequence data integrated with information about other important virus characteristics.DesignThe Influenza Research Database (IRD, http://www.fludb.org) is a free, open, publicly-accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. IRD provides a comprehensive, integrated database and analysis resource for influenza sequence, surveillance, and research data, including user-friendly interfaces for data retrieval, visualization and comparative genomics analysis, together with personal log in-protected 'workbench' spaces for saving data sets and analysis results. IRD integrates genomic, proteomic, immune epitope, and surveillance data from a variety of sources, including public databases, computational algorithms, external research groups, and the scientific literature.ResultsTo demonstrate the utility of the data and analysis tools available in IRD, two scientific use cases are presented. A comparison of hemagglutinin sequence conservation and epitope coverage information revealed highly conserved protein regions that can be recognized by the human adaptive immune system as possible targets for inducing cross-protective immunity. Phylogenetic and geospatial analysis of sequences from wild bird surveillance samples revealed a possible evolutionary connection between influenza virus from Delaware Bay shorebirds and Alberta ducks.ConclusionsThe IRD provides a wealth of integrated data and information about influenza virus to support research of the genetic determinants dictating virus pathogenicity, host range restriction and transmission, and to facilitate development of vaccines, diagnostics, and therapeutics

Contrasting Views of Complexity and Their Implications For Network-Centric Infrastructures

There exists a widely recognized need to better understand and manage complex “systems of systems,” ranging from biology, ecology, and medicine to network-centric technologies. This is motivating the search for universal laws of highly evolved systems and driving demand for new mathematics and methods that are consistent, integrative, and predictive. However, the theoretical frameworks available today are not merely fragmented but sometimes contradictory and incompatible. We argue that complexity arises in highly evolved biological and technological systems primarily to provide mechanisms to create robustness. However, this complexity itself can be a source of new fragility, leading to “robust yet fragile” tradeoffs in system design. We focus on the role of robustness and architecture in networked infrastructures, and we highlight recent advances in the theory of distributed control driven by network technologies. This view of complexity in highly organized technological and biological systems is fundamentally different from the dominant perspective in the mainstream sciences, which downplays function, constraints, and tradeoffs, and tends to minimize the role of organization and design

Emerging Search Regimes: Measuring Co-evolutions among Research, Science, and Society

Scientometric data is used to investigate empirically the emergence of search regimes in Biotechnology, Genomics, and Nanotechnology. Complex regimes can emerge when three independent sources of variance interact. In our model, researchers can be considered as the nodes that carry the science system. Research is geographically situated with site-specific skills, tacit knowledge and infrastructures. Second, the emergent science level refers to the formal communication of codified knowledge published in journals. Third, the socio-economic dynamics indicate the ways in which knowledge production relates to society. Although Biotechnology, Genomics, and Nanotechnology can all be characterised by rapid growth and divergent dynamics, the regimes differ in terms of self-organization among these three sources of variance. The scope of opportunities for researchers to contribute within the constraints of the existing body of knowledge are different in each field. Furthermore, the relevance of the context of application contributes to the knowledge dynamics to various degrees

Solomon Islands: Malaita Hub scoping report

The CGIAR Research Program (CRP) Aquatic Agricultural Systems (AAS) will target five countries, including Solomon Islands. The proposed hubs for Solomon Islands were to cover most provinces, referencing the Western, Central and Eastern regions. Scoping of the initial ‘Central’ hub was undertaken in Guadalcanal, Malaita and Central Islands provinces and this report details findings from all three. As scoping progressed however, it was agreed that, based on the AAS context and priority needs of each province and the Program’s capacity for full implementation, the Central Hub would be restricted to Malaita Province only and renamed “Malaita Hub”. Consistent in each AAS country, there are four steps in the program rollout: planning, scoping, diagnosis and design. Rollout of the Program in Solomon Islands began with a five month planning phase between August and December 2011, and scoping of the first hub began in January 2012. This report, the second to be produced during rollout, describes the findings from the scoping process between January and June 2012. This report marks the transition from the scoping phase to the diagnosis phase in which output from scoping was used to develop a hub level theory of change for identifying research opportunities. Subsequent reports detail in-depth analyses of gender, governance, nutrition and partner activities and discuss Program engagement with community members to identify grass-roots demand for research

The PRIDE database and related tools and resources in 2019: improving support for quantification data

The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's largest data repository of mass spectrometry-based proteomics data, and is one of the founding members of the global ProteomeXchange (PX) consortium. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2016. In the last 3years, public data sharing through PRIDE (as part of PX) has definitely become the norm in the field. In parallel, data re-use of public proteomics data has increased enormously, with multiple applications. We first describe the new architecture of PRIDE Archive, the archival component of PRIDE. PRIDE Archive and the related data submission framework have been further developed to support the increase in submitted data volumes and additional data types. A new scalable and fault tolerant storage backend, Application Programming Interface and web interface have been implemented, as a part of an ongoing process. Additionally, we emphasize the improved support for quantitative proteomics data through the mzTab format. At last, we outline key statistics on the current data contents and volume of downloads, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas

Success Stories in Asian Aquaculture

The stories presented in this book reflect the unique nature of Asian aquaculture, providing first-time insight into how and why it has become so successful. Overall, the book demonstrates how the resiliency, adaptability, and innovation of small-scale aquaculture farmers have been crucial to this success. It also places aquaculture development in Asia into a wider global context, and describes its relationship to natural systems, social conditions, and economics. The book is unique in its in-depth presentation of primary research on Asian aquaculture, and in demonstrating how aquaculture can have a lasting positive impact on livelihoods, food security, and sustainable development