| At line 156 added 27 lines. |
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| + * Chris Wroe |
| + ** use case from integrative biology |
| + ** oxford and new zealand |
| + ** from dna to whole organism modeling |
| + *** cardiac vulnerability to acute ischemia: step 1; import mechanical model from Aukland Data |
| + *** get mechanical model of heart |
| + **** take slice, place in perfusion bath, top and botttom surfaces isolated, site pacing ... |
| + **** finite elelent approach |
| + *** properties of fusion bath |
| + *** protocol for what they do in the experiment: pace at 250ms, apply shock, repeat with diff. interfals, etc. |
| + *** each simulation takes a week |
| + *** perturb initial conditions; stage 1 hypoxia (lack of oxygen), stage 2 hypoxia |
| + *** data analysis: construct activation map, measure activation potential duration, threshold for fibrillation, file produced every 1ms, big |
| + *** perl/shell scripts for all of this |
| + ** want to e-iffy this. |
| + *** simulation step |
| + *** long running, no other examples of this in myGrid |
| + *** finite element bidomain solver: mechanical model, electrophysio model, simulation protocol, initial conditions, parameters -> result file produced for every 1ms 7.3 mb |
| + *** monitor, stop, checkpoint, discard, restart with different parameters |
| + *** a mesh problem ... so more computation and you still run it for a week |
| + ** [www.GeoDise.org] Simon Cox |
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| + * Jeffrey Grethe |
| + ** BIRN workflow requirements (Biomedical informatics research network) |
| + ** enable new understanding of neurological disease by integrating data across multiple scales from macroscopic brain function etc. |
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