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Completed
Mathematics and Computation for the System Biology of Cells
FunderNetherlands Organisation for Scientific Research (NWO)
Duration01 Aug 2004 - 08 Feb 2011
Project code635.100.007
Identifiers
Project timeline100%
Description
Een belangrijk doel in de computationele biologie is het kunnen doorrekenen, in een computersimulatie, van een hele levende cel of zelfs een heel organisme. Uitgaande van de huidige stand der kennis is hiervoor meer werk nodig in twee richtingen: het verzamelen van meer en gedetailleerdere experimentele gegevens, en het ontwikkelen van technieken voor efficiëntere simulatie. De laatste jaren maken de experimentele meetmethoden, mede door de ontrafeling van het genoom, een spectaculaire ontwikkeling door. Steeds meer aspecten van de levende cel worden voor metingen toegankelijk. De uitdaging is om de bijbehorende computationele technieken te ontwikkelen om de simulatie van een levende cel praktisch mogelijk te maken. In dit voorstel zetten we een belangrijke stap in die richting. Ten eerste ontwikkelen we methoden om dynamisch en automatisch de grote chemische complexiteit van de cel te reduceren. Ten tweede gebruiken we op plaatsen met sterke lokale activiteit een deeltjesmethode om voldoende resolutie te krijgen. Ten derde ontwikkelen we methoden om deze verschillen in benadering in één simulatie te verenigen. Met de technieken van dit voorstel komt de simulatie van een volledige levende cel een stap dichterbij.
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Een belangrijk doel in de computationele biologie is het kunnen doorrekenen, in een computersimulatie, van een hele levende cel of zelfs een heel organisme. Uitgaande van de huidige stand der kennis is hiervoor meer werk nodig in twee richtingen: het verzamelen van meer en gedetailleerdere experimentele gegevens, en het ontwikkelen van technieken voor efficiëntere simulatie. De laatste jaren maken de experimentele meetmethoden, mede door de ontrafeling van het genoom, een spectaculaire ontwikkeling door. Steeds meer aspecten van de levende cel worden voor metingen toegankelijk. De uitdaging is om de bijbehorende computationele technieken te ontwikkelen om de simulatie van een levende cel praktisch mogelijk te maken. In dit voorstel zetten we een belangrijke stap in die richting. Ten eerste ontwikkelen we methoden om dynamisch en automatisch de grote chemische complexiteit van de cel te reduceren. Ten tweede gebruiken we op plaatsen met sterke lokale activiteit een deeltjesmethode om voldoende resolutie te krijgen. Ten derde ontwikkelen we methoden om deze verschillen in benadering in één simulatie te verenigen. Met de technieken van dit voorstel komt de simulatie van een volledige levende cel een stap dichterbij.
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