FuGEFlow: data model and markup language for flow cytometry

<p>Abstract</p> <p>Background</p> <p>Flow cytometry technology is widely used in both health care and research. The rapid expansion of flow cytometry applications has outpaced the development of data storage and analysis tools. Collaborative efforts being taken to eliminate this gap include building common vocabularies and ontologies, designing generic data models, and defining data exchange formats. The Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) standard was recently adopted by the International Society for Advancement of Cytometry. This standard guides researchers on the information that should be included in peer reviewed publications, but it is insufficient for data exchange and integration between computational systems. The Functional Genomics Experiment (FuGE) formalizes common aspects of comprehensive and high throughput experiments across different biological technologies. We have extended FuGE object model to accommodate flow cytometry data and metadata.</p> <p>Methods</p> <p>We used the MagicDraw modelling tool to design a UML model (Flow-OM) according to the FuGE extension guidelines and the AndroMDA toolkit to transform the model to a markup language (Flow-ML). We mapped each MIFlowCyt term to either an existing FuGE class or to a new FuGEFlow class. The development environment was validated by comparing the official FuGE XSD to the schema we generated from the FuGE object model using our configuration. After the Flow-OM model was completed, the final version of the Flow-ML was generated and validated against an example MIFlowCyt compliant experiment description.</p> <p>Results</p> <p>The extension of FuGE for flow cytometry has resulted in a generic FuGE-compliant data model (FuGEFlow), which accommodates and links together all information required by MIFlowCyt. The FuGEFlow model can be used to build software and databases using FuGE software toolkits to facilitate automated exchange and manipulation of potentially large flow cytometry experimental data sets. Additional project documentation, including reusable design patterns and a guide for setting up a development environment, was contributed back to the FuGE project.</p> <p>Conclusion</p> <p>We have shown that an extension of FuGE can be used to transform minimum information requirements in natural language to markup language in XML. Extending FuGE required significant effort, but in our experiences the benefits outweighed the costs. The FuGEFlow is expected to play a central role in describing flow cytometry experiments and ultimately facilitating data exchange including public flow cytometry repositories currently under development.</p

Space station accommodations for life sciences research facilities: Phase A conceptual design and programmatics studies for Missions SAAX0307, SAAX0302 and the transition from SAAX0307 to SAAX0302. Volume 1: Executive summary

The conceptual designs and programmatics for a Space Station Nonhuman Life Sciences Research Facility (LSRF) are highlighted. Conceptual designs and programmatics encompass an Initial Orbital Capability (IOC) LSRF, a growth or Follow-on Orbital Capability (FOC), and the transitional process required to modify the IOC LSRF to the FOC LSRF

The Open AUC Project

Progress in analytical ultracentrifugation (AUC) has been hindered by obstructions to hardware innovation and by software incompatibility. In this paper, we announce and outline the Open AUC Project. The goals of the Open AUC Project are to stimulate AUC innovation by improving instrumentation, detectors, acquisition and analysis software, and collaborative tools. These improvements are needed for the next generation of AUC-based research. The Open AUC Project combines on-going work from several different groups. A new base instrument is described, one that is designed from the ground up to be an analytical ultracentrifuge. This machine offers an open architecture, hardware standards, and application programming interfaces for detector developers. All software will use the GNU Public License to assure that intellectual property is available in open source format. The Open AUC strategy facilitates collaborations, encourages sharing, and eliminates the chronic impediments that have plagued AUC innovation for the last 20 years. This ultracentrifuge will be equipped with multiple and interchangeable optical tracks so that state-of-the-art electronics and improved detectors will be available for a variety of optical systems. The instrument will be complemented by a new rotor, enhanced data acquisition and analysis software, as well as collaboration software. Described here are the instrument, the modular software components, and a standardized database that will encourage and ease integration of data analysis and interpretation software

A Bisociated Domain-Based Serendipitous Novelty-Recommendation Technique for Recommender Systems

Traditional recommendation paradigms such as content-based filtering (CBF) tend to recommend items that are very similar to user profile characteristics and item input, resulting in the classical twin problem of overspecialization and concentration bias of recommendations. This twin problem is prevalent with CBF recommender systems due to the utilisation of accuracy metrics to retrieve similar items, and, limiting recommendation computations to single recognized user-centered domains, rather than cross-domains. &nbsp;This paper proposes a Bisociated domain-based serendipitous novelty recommendation techniques using Bisolinkers exploratory creativity discovery technique. The use of Bisolinkers enables establishing unique links between two seemingly unrelated domains, to enhance recommendation accuracy and user satisfaction. The presence of similar terms in two habitually incompatible domains demonstrates that two seemingly unrelated domains contain elements that are related and may act as a link to connect these two domains. Keywords: recommender systems, novelty, machine learning, outlier detection, bisociation &nbsp

Access to diagnosis and treatment of Chagas disease/infection in endemic and non-endemic countries in the XXI century.

In this article, Médicos Sin Fronteras (MSF) Spain faces the challenge of selecting, piecing together, and conveying in the clearest possible way, the main lessons learnt over the course of the last seven years in the world of medical care for Chagas disease. More than two thousand children under the age of 14 have been treated; the majority of whom come from rural Latin American areas with difficult access. It is based on these lessons learnt, through mistakes and successes, that MSF advocates that medical care for patients with Chagas disease be a reality, in a manner which is inclusive (not exclusive), integrated (with medical, psychological, social, and educational components), and in which the patient is actively followed. This must be a multi-disease approach with permanent quality controls in place based on primary health care (PHC). Rapid diagnostic tests and new medications should be available, as well as therapeutic plans and patient management (including side effects) with standardised flows for medical care for patients within PHC in relation to secondary and tertiary level, inclusive of epidemiological surveillance systems