Web services and workflow management for biological resources

BACKGORUND: The completion of the Human Genome Project has resulted in large quantities of biological data which are proving difficult to manage and integrate effectively. There is a need for a system that is able to automate accesses to remote sites and to "understand" the information that it is managing in order to link data properly. Workflow management systems combined with Web Services are promising Information and Communication Technologies (ICT) tools. Some have already been proposed and are being increasingly applied to the biomedical domain, especially as many biology-related Web Services are now becoming available. Information on biological resources and on genomic sequences mutations are two examples of very specialized datasets that are useful for specific research domains. RESULTS: The architecture of a system that is able to access and execute predefined workflows is presented in this paper. Web Services allowing access to the IARC TP53 Mutation Database and CABRI catalogues of biological resources have been implemented and are available on-line. Example workflows which retrieve data from these Web Services have also been created and are available on-line. CONCLUSION: We present a general architecture and some building blocks for the implementation of a system that is able to remotely execute workflows of biomedical interest and show how this approach can effectively produce useful outputs. The further development and implementation of Web Services allowing access to an exhaustive set of biomedical databases and the creation of effective and useful workflows will improve the automation of in-silico analysis

A comprehensive bycatch market: investigating pricing mechanisms for ecosystem accountability

Master's Project (M.S.) University of Alaska Fairbanks, 2015This report takes an ecosystem approach to managing targeted and non-targeted species in the Bering Sea Aleutian Island commercial fisheries. The current regulatory environment sets biological harvest limits across fish stock's entire range, although the individual components of managing fisheries within a stock may lead to economic inefficiencies and difficulties in accounting for social costs due to blunt incentives. The research presented here outlines a model for scenario analysis and pricing mechanisms at each level of harvest across a species range. Due to the modeled indifference of harvesting in targeted or non-targeted fisheries, designations are made for degrees of ownership rights and monetary transfers to balance these rights in the presence of non-target bycatch. This report argues that efficiency gains can be made by managing behavior through pricing incentives at the margin

Evidence-based Decision-making in Canada’s Protected Areas Organizations: Implications for Management Effectiveness

Aichi Biodiversity Target 19 calls on Parties to the United Nations Convention on Biological Diversity (CBD) to improve, share, transfer, and apply knowledge. In this study, we provide an initial assessment of the state of evidence-based decision-making in Canada’s protected areas organizations by examining (1) the value and use of various forms of evidence by managers and (2) the extent to which institutional conditions enable or inhibit the use of evidence in decision-making. Results revealed that although managers value and use many forms of evidence in their decision-making, information produced by staff and their organizations are given priority. Other forms of evidence, such as Indigenous knowledge and peer-reviewed information, are valued and used less. The most significant barriers to evidence-based decision-making were limited financial resources, lack of staff, inadequate timeframes for decision-making, a lack of monitoring programs, and a disconnect between researchers and decision-makers. Overall, our results suggest that the potential benefits of evidence-based approaches are not being maximized in Canada’s protected areas organizations. We propose several recommendations to introduce or improve the use of diverse forms of evidence to enhance management effectiveness of Canada’s protected areas and by extension conservation outcomes

Annotated bibliography on socio-economic and ecological impacts of marine protected areas in Pacific Island countries

The bibliography is to highlight impacts on fisheries and livelihoods attributed to coral reef marine protected areas in Pacific Island countries and territories. Included in this collection is literature that reports various forms of reef area management practiced in Pacific Island countries: reserves, sanctuaries, permanent or temporary closed areas, community and traditional managed areas. (Document contains 36 pages

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.

Lessons for Co-management: Experiences from the Fisheries Management Science Programme (FMSP)

The aim of this document is to communicate lessons for fisheries co-management that have emerged from a series of projects undertaken by the DFID Fisheries Management Science Programme (FMSP). It focuses on three examples of FMSP projects: ParFish, Adaptive learning and designing data collection systems. This document does not aim to give a comprehensive overview of co-management but seeks to provide a viewpoint based on the experiences of the FMSP projects in question. This document is targeted to fisheries decision makers, managers and facilitators including government, industry and non-governmental organisations

Organic agriculture: opportunities and challenges

The organic movement may have gained a place in the spotlight of the mainstream media now, but it has not been like that for long. Since the 1950s, organic farmers operating at a grass roots level have devised, tested and shared production methods. They have codified a set of ideals into a pioneering best practice agricultural management system that addresses multiple community values. Niche markets have gradually been created, commonly based on trust and goodwill (formal certification did not begin until the 1960s and 1970s), and often using novel direct marketing strategies such as box schemes and community supported agriculture. After many years of consumers having to hunt around for their organic produce from several suppliers, perhaps directly from the farmer, the task is now a lot easier with specialist food shops and organic shelf space in supermarkets, in the industrialised world at least. Global links have been forged in all continents as organic agriculture has been seen to be an effective rural development option

Catch Shares in Action: Japanese Common Fishing Rights System

The Japanese Common Fishing Rights System is a comprehensive catch share program that manages the nearshore fisheries along Japan's vast coastline by allocating secure areas, or Territorial Use Rights for Fishing (TURFs), to harvesting Cooperatives. The system has evolved over time and is a model for managing mobile nearshore species through a network of scaled Cooperatives. The program depends upon a coordinated system of co-management, including nested layers of governance from the federal level down to the regional level. The program design has promoted innovative approaches -- especially by fishermen -- including coordination within and across TURFs (and Cooperatives), and pooling of harvesting arrangements to improve economic efficiency and resource sustainability

The state of Florida's estuaries and future needs in estuarine research: Part 2. an academic research agenda (review draft)

As a program supporting academic research that addresses recognized societal needs, the Florida Sea Grant Program is developing a research theme area on estuaries to provide a uniquely academic product that will augment mission-oriented research undertaken by government and by the private sector. This report is not a call for proposals. It does not prescribe a specific research plan. Rather, it is a concept paper designed to focus research on two broad "organizing themes": (1) the hydrology of Florida's estuaries, and (2) the impact of cyclic environmental variability on estuarine function. (46pp.