Minimum Information About a Simulation Experiment (MIASE)

The original publication is available at www.ploscompbiol.orgReproducibility of experiments is a basic requirement for science. Minimum Information (MI) guidelines have proved a helpful means of enabling reuse of existing work in modern biology. The Minimum Information Required in the Annotation of Models (MIRIAM) guidelines promote the exchange and reuse of biochemical computational models. However, information about a model alone is not sufficient to enable its efficient reuse in a computational setting. Advanced numerical algorithms and complex modeling workflows used in modern computational biology make reproduction of simulations difficult. It is therefore essential to define the core information necessary to perform simulations of those models. The Minimum Information About a Simulation Experiment describes the minimal set of information that must be provided to make the description of a simulation experiment available to others. It includes the list of models to use and their modifications, all the simulation procedures to apply and in which order, the processing of the raw numerical results, and the description of the final output. MIASE allows for the reproduction of any simulation experiment. The provision of this information, along with a set of required models, guarantees that the simulation experiment represents the intention of the original authors. Following MIASE guidelines will thus improve the quality of scientific reporting, and will also allow collaborative, more distributed efforts in computational modeling and simulation of biological processes.The discussions that led to the definition of MIASE benefited from the support of a Japan Partnering Award by the UK Biotechnology and Biological Sciences Research Council. DW was supported by the Marie Curie program and by the German Research Association (DFG Research Training School ‘‘dIEM oSiRiS’’ 1387/1). This publication is based on work (EJC) supported in part by Award No KUK-C1-013-04, made by King Abdullah University of Science and Technology (KAUST). FTB acknowledges support by the NIH (grant 1R01GM081070- 01). JC is supported by the European Commission, DG Information Society, through the Seventh Framework Programme of Information and Communication Technologies, under the VPH NoE project (grant number 223920). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Publishers versio

The Internet of Things as a Privacy-Aware Database Machine

Instead of using a computer cluster with homogeneous nodes and very fast high bandwidth connections, we want to present the vision to use the Internet of Things (IoT) as a database machine. This is among others a key factor for smart (assistive) systems in apartments (AAL, ambient assisted living), offices (AAW, ambient assisted working), Smart Cities as well as factories (IIoT, Industry 4.0). It is important to massively distribute the calculation of analysis results on sensor nodes and other low-resource appliances in the environment, not only for reasons of performance, but also for reasons of privacy and protection of corporate knowledge. Thus, functions crucial for assistive systems, such as situation, activity, and intention recognition, are to be automatically transformed not only in database queries, but also in local nodes of lower performance. From a database-specific perspective, analysis operations on large quantities of distributed sensor data, currently based on classical big-data techniques and executed on large, homogeneously equipped parallel computers have to be automatically transformed to billions of processors with energy and capacity restrictions. In this visionary paper, we will focus on the database-specific perspective and the fundamental research questions in the underlying database theory

Ranked retrieval of Computational Biology models

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Annotation-based storage and retrieval of models and simulation descriptions in computational biology

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