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  • 1
    Keywords: 3, biotechnology, development, EXPERIENCE, FLEXIBILITY, FORMAT, Genetic, genetics, Guideline, LIFE,
    Abstract: The Functional Genomics Experiment data model (FuGE) has been developed to increase the consistency and efficiency of experimental data modeling in the life sciences, and it has been adopted by a number of high-profile standardization organizations. FuGE can be used: (1) directly, whereby generic modeling constructs are used to represent concepts from specific experimental activities; or (2) as a framework within which methodspecific models can be developed. FuGE is both rich and flexible, providing a considerable number of modeling constructs, which can be used in a range of different ways. However, such richness and flexibility also mean that modelers and application developers have choices to make when applying FuGE in a given context. This paper captures emerging best practice in the use of FuGE in the light of the experience of several groups by: (1) proposing guidelines for the use and extension of the FuGE data model; (2) presenting design patterns that reflect recurring requirements in experimental data modeling; and (3) describing a community software tool kit (STK) that supports application development using FuGE. We anticipate that these guidelines will encourage consistent usage of FuGE, and as such, will contribute to the development of convergent data standards in omics research
    Type of Publication: Journal article published
    PubMed ID: 19441879
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  • 2
    Keywords: CELLS ; CELL ; IN-VIVO ; MICROSCOPY ; MODEL ; MODELS ; imaging ; SYSTEM ; VISUALIZATION ; GENOME ; PROTEIN ; PROTEINS ; COMPONENTS ; MOLECULES ; DNA ; DYNAMICS ; BIOLOGY ; MOLECULE ; FORM ; MOBILITY ; BETA ; LOCALIZATION ; EXCHANGE ; LIVING CELLS ; FLUORESCENCE ; GREEN FLUORESCENT PROTEIN ; DIFFUSION ; DNA TOPOISOMERASES ; GFP ; KINETIC-ANALYSIS
    Abstract: Measuring the mobility of proteins in living cells has become critical to many studies in cell biology and forms the basis for discussion on sub-cellular dynamics. Increasingly localization networks are being put together into compartment models to represent the exchange of molecules, represented mathematically as ordinary differential equations (ODE). The set-up is based on published literature, the "knowledge" of the investigator and 3D visualization of the data. Here we demonstrate this method on the example of a simple distribution model of the molecule Topoisomerase IIbeta (Topo IIbeta), nuclear protein that modifies DNA topology. It is found in high concentration in the nucleolus and diffuse in the nucleoplasm, demonstrating a non-membranous inhomogeneity in its distribution. We expand on the simple model by adding additional components to fit fluorescence recovery after photobleaching (FRAP) experiments for protein (GFP) labeled Topo IIbeta to measure its mobility. This model is then validated by comparing it with alternative scenarios and shown to have predictive power
    Type of Publication: Journal article published
    PubMed ID: 15268774
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