Towards a Common Standard for Data and Specimen Provenance in Life Sciences

The exchange of biological material and data has become an issue of major importance for research in biotechnology. At the same time, many reports indicate problems with quality, trustworthiness and reproducibility of research results, mainly due to poor documentation of data generation or collection of samples. Consequently, there is an urgent need for improved and standardized documentation of data and specimen used in research studies. In response to these issues, we are developing a provenance information standard for the biotechnology domain within the ISO Technical Committee 276 “Biotechnology”. The major objectives of the standard, now registered as ISO/WD 23494, are improved reproducibility of research results, enabling the assessment of the quality of biological samples and data, traceability and higher reliability of observations. We are convinced that the standardization project is of substantial interest to a broader audience, who we would also invite to comment and contribute to this comprehensive effort.Manuscript under consideration

Towards a European Health Research and Innovation Cloud (HRIC)

The European Union (EU) initiative on the Digital Transformation of Health and Care (Digicare) aims to provide the conditions necessary for building a secure, flexible, and decentralized digital health infrastructure. Creating a European Health Research and Innovation Cloud (HRIC) within this environment should enable data sharing and analysis for health research across the EU, in compliance with data protection legislation while preserving the full trust of the participants. Such a HRIC should learn from and build on existing data infrastructures, integrate best practices, and focus on the concrete needs of the community in terms of technologies, governance, management, regulation, and ethics requirements. Here, we describe the vision and expected benefits of digital data sharing in health research activities and present a roadmap that fosters the opportunities while answering the challenges of implementing a HRIC. For this, we put forward five specific recommendations and action points to ensure that a European HRIC: i) is built on established standards and guidelines, providing cloud technologies through an open and decentralized infrastructure; ii) is developed and certified to the highest standards of interoperability and data security that can be trusted by all stakeholders; iii) is supported by a robust ethical and legal framework that is compliant with the EU General Data Protection Regulation (GDPR); iv) establishes a proper environment for the training of new generations of data and medical scientists; and v) stimulates research and innovation in transnational collaborations through public and private initiatives and partnerships funded by the EU through Horizon 2020 and Horizon Europe

An Efficient Modeling and Execution Framework for Complex Systems Development

International audienc

An Emerging Need for a New Software Engineering Method

International audienc

Foundations of Health Information Engineering and SystemsSecond International Symposium, FHIES 2012, Paris, France, August 27-28, 2012. Revised Selected Papers /

X, 223 p. 85 illus.online resource

Calcul distribué centré resources pour de larges images histopathologiques

International audienceAutomatic cell nuclei detection is a real challenge in medical imagery. The Marked Point Process (MPP) is one of the most promising methods. To handle large histopathology images, the algorithm has to be distributed. A new parallelization paradigm called Ordered Read-Write Locks (ORWL) is presented as a possible solution for solving some of the unwanted side effects of the distribution, namely an imprecision of the results on the internal boundaries of partitioned images. This solution extends a parallel version of MPP that has reached good speedups on GPU cards, but was not scaling to complete images as they appear in practical data.La détection automatique de noyaux cellulaires est un vrai challenge pour l'imagerie médicale et la lutte contre le cancer. L'un des axes de recherche les plus prometteurs est l'utilisation de Processus Ponctuels Marqués (PPM). L'algorithme tiré de cette méthode a été parallélisé et atteint de bonnes performances d'accélération sur carteGPU. Cependant, cette parallélisation ne permet pas de traiter une lame complète issue d'un prélèvement de biopsie. Il est ainsi nécessaire de distribuer les calculs. Cette distribution entraîne toutefois des pertes de précision au niveau des axes de coupe de l'image. Un nouveau paradigme de parallélisation appelé Ordered Read-Write Locks (ORWL) est une solution possible à ce problème