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In-vivo. In-Silico. - PowerPoint PPT Presentation
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Computational Biology
The Potts Model effectively models many complex behaviours of biological systems, from cell sorting and chemotaxis to various lifecycle stages of Dictyostelium and chicken limb development.
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In-vivoIn-vivo In-SilicoIn-Silico
Using the Potts Model, a statistical mechanics simulation technique based on cellular automata, scientists develop in-silico computational models based on in-vivo observations about developmental processes. The OSL researches high-performance software and visualization systems used for Potts Model simulations.
// Acceptance based on probabilitydouble prob = acceptanceFunction->accept(temp, change);if (prob >= 1 || rand->getRatio() < prob) { // Accept the change energy += change; cellField->set(neighbor, cell); flips++;}
Bioinformatics
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Process Ideal Speedup Real Speedup Ideal/Real Throughput
SIMD 8.3x 9.7x 75%
Thread 15x 18.1x 77%
Thread (large data)
13.3 21.2 85%
void GenomeCompare(unsigned char *data, long len, unsigned char *result){ // “Diagnol” sum of all the values in data long i = 0; vector unsigned char score, score1, score2, vperm, newsum; newsum = vec_splat_u8(0); // create a constant for(i = 0; i < len - 16; i++) { // Load each vector if((i & 0x0000000f) == 0) { // aligned case score = vec_ld(0, &(data[i])); } newsum = vec_add(score, newsum); } vec_st(newsum, 0, result); // aligned store return;}
E-Coli …AGGATGACCAGATAGGAGTGACCGATTACCGGATAGC…
Human …AGGATGACCAGATAGGAGTGACCGATTACCGGATAGC…
Rat …AGGATGACCAGATAGGAGTGACCGATTACGGGATAGC…
Salamander …AGGATGACCAGATAGGAGTGACCGATTA---GATAGC…
Vector processors in modern computers enable the direct comparison of large genomes. However, obtaining the results is only the first challenge. Presenting the results in a meaningful way to scientists is difficult.
This research focuses on:• Studying the use of high-performance techniques on common bioinformatics algorithms• Using large format display walls and high-resolution (> 200 dpi) displays to present the results • Developing techniques for abstracting vector and cluster level parallelism to make these techniques accessible to scientists
Large genomes are compared using multiple vector processors
The results are rendered to high-resolution formats
Dictyostelium Simulation