A notification system model for bioinformatics community of practice

Bioinformatics can be considered as a new field of study and it promises a vast exploration area (Carzaniga., Rosenblum., Wolf ., 2001). In order to expedite the maturity in this area, a proper and supportive portal where all researchers could gather and cooperate in conducting their research need to be established. One of the features in a portal that can assist Bioinformatics researchers in performing their work is the ability of the portal to notify. Notification system is a combination of software and hardware to provide a method of distributing message(s) to a set of recipients. The notification messages could assist the recipients in many ways, from time saving and cost saving till life saving. Notification system can be developed with numerous functions depending on the needs and one of the most beneficial functions in research area is notification on the next most relevant knowledge to be read. This type of notification could lessen the researchers’ time in finding the correct thus enhancing their research efficiency. Another type of notification that could assist researchers is the events reminder. Busy and hectic researchers could forget their pack schedule and put total focus on their research while the reminder prompts them when it is time through Windows’ pop up, email and SMS as the means of delivering the messages. Whilst the knowledge management system (KMS) provides a sturdy basic for the Bioinformatics portal as a whole, the agent technology support the operation of the notification system. Agent technology offers great capabilities in ensuring the recipients is notified accordingly through its autonomous, learning and cooperative characteristics. The objective of this project is to build a notification system for Bioinformatics community of practice (CoP). Researchers in this community could utilize this system to make their research process more efficient

Mare Geneticum : Balancing Governance of Marine Genetic Resources in International Waters

Peer reviewedPublisher PD

Distributed BLAST in a grid computing context

The Basic Local Alignment Search Tool (BLAST) is one of the best known sequence comparison programs available in bioinformatics. It is used to compare query sequences to a set of target sequences, with the intention of finding similar sequences in the target set. Here, we present a distributed BLAST service which operates over a set of heterogeneous Grid resources and is made available through a Globus toolkit v.3 Grid service. This work has been carried out in the context of the BRIDGES project, a UK e-Science project aimed at providing a Grid based environment for biomedical research. Input consisting of multiple query sequences is partitioned into sub-jobs on the basis of the number of idle compute nodes available and then processed on these in batches. To achieve this, we have implemented our own Java-based scheduler which distributes sub-jobs across an array of resources utilizing a variety of local job scheduling systems

Text mining meets community curation: a newly designed curation platform to improve author experience and participation at WormBase

Biological knowledgebases rely on expert biocuration of the research literature to maintain up-to-date collections of data organized in machine-readable form. To enter information into knowledgebases, curators need to follow three steps: (i) identify papers containing relevant data, a process called triaging; (ii) recognize named entities; and (iii) extract and curate data in accordance with the underlying data models. WormBase (WB), the authoritative repository for research data on Caenorhabditis elegans and other nematodes, uses text mining (TM) to semi-automate its curation pipeline. In addition, WB engages its community, via an Author First Pass (AFP) system, to help recognize entities and classify data types in their recently published papers. In this paper, we present a new WB AFP system that combines TM and AFP into a single application to enhance community curation. The system employs string-searching algorithms and statistical methods (e.g. support vector machines (SVMs)) to extract biological entities and classify data types, and it presents the results to authors in a web form where they validate the extracted information, rather than enter it de novo as the previous form required. With this new system, we lessen the burden for authors, while at the same time receive valuable feedback on the performance of our TM tools. The new user interface also links out to specific structured data submission forms, e.g. for phenotype or expression pattern data, giving the authors the opportunity to contribute a more detailed curation that can be incorporated into WB with minimal curator review. Our approach is generalizable and could be applied to additional knowledgebases that would like to engage their user community in assisting with the curation. In the five months succeeding the launch of the new system, the response rate has been comparable with that of the previous AFP version, but the quality and quantity of the data received has greatly improved

Towards trusted volunteer grid environments

Intensive experiences show and confirm that grid environments can be considered as the most promising way to solve several kinds of problems relating either to cooperative work especially where involved collaborators are dispersed geographically or to some very greedy applications which require enough power of computing or/and storage. Such environments can be classified into two categories; first, dedicated grids where the federated computers are solely devoted to a specific work through its end. Second, Volunteer grids where federated computers are not completely devoted to a specific work but instead they can be randomly and intermittently used, at the same time, for any other purpose or they can be connected or disconnected at will by their owners without any prior notification. Each category of grids includes surely several advantages and disadvantages; nevertheless, we think that volunteer grids are very promising and more convenient especially to build a general multipurpose distributed scalable environment. Unfortunately, the big challenge of such environments is, however, security and trust. Indeed, owing to the fact that every federated computer in such an environment can randomly be used at the same time by several users or can be disconnected suddenly, several security problems will automatically arise. In this paper, we propose a novel solution based on identity federation, agent technology and the dynamic enforcement of access control policies that lead to the design and implementation of trusted volunteer grid environments.Comment: 9 Pages, IJCNC Journal 201

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E-BioFlow: Different Perspectives on Scientific Workflows

We introduce a new type of workflow design system called\ud e-BioFlow and illustrate it by means of a simple sequence alignment workflow. E-BioFlow, intended to model advanced scientific workflows, enables the user to model a workflow from three different but strongly coupled perspectives: the control flow perspective, the data flow perspective, and the resource perspective. All three perspectives are of\ud equal importance, but workflow designers from different domains prefer different perspectives as entry points for their design, and a single workflow designer may prefer different perspectives in different stages of workflow design. Each perspective provides its own type of information, visualisation and support for validation. Combining these three perspectives in a single application provides a new and flexible way of modelling workflows

Addendum to Informatics for Health 2017: Advancing both science and practice

This article presents presentation and poster abstracts that were mistakenly omitted from the original publication

Human-computer interaction for development (HCI4D):the Southern African landscape

Human-Computer interaction for development (HCI4D) research aims to maximise the usability of interfaces for interacting with technologies designed specifically for under-served, under-resourced, and under-represented populations. In this paper we provide a snapshot of the Southern African HCI4D research against the background of the global HCI4D research landscape.We commenced with a systematic literature review of HCI4D (2010-2017) then surveyed Southern African researchers working in the area. The contribution is to highlight the context- specific themes and challenges that emerged from our investigation