faculty of computer science dalhousie university, canada andrew rau-chaplin, arc parallel...
TRANSCRIPT
![Page 1: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/1.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Parallel Computational Biochemistry
![Page 2: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/2.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Proteins, DNA, etc.
DNA encodes the information necessary to produce proteins
Proteins are the main molecular building blocks of life (for example, structural proteins, enzymes)
![Page 3: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/3.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
• Proteins are formed from a chain of molecules called amino acids
Proteins, DNA, etc.
![Page 4: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/4.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
• The DNA sequence encodes the amino acid sequence that constitutes the protein
Proteins, DNA, etc.
![Page 5: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/5.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
• There are twenty amino acids found in proteins, denoted by A, C, D, E, F, G, H, I, ...
Proteins, DNA, etc.
![Page 6: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/6.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Multiple Sequence Alignment
![Page 7: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/7.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Databases of Biological Sequences
>BGAL_SULSO BETA-GALACTOSIDASE Sulfolobus solfataricus.MYSFPNSFRFGWSQAGFQSEMGTPGSEDPNTDWYKWVHDPENMAAGLVSGDLPENGPGYWGNYKTFHDNAQKMGLKIARLNVEWSRIFPNPLPRPQNFDESKQDVTEVEINENELKRLDEYANKDALNHYREIFKDLKSRGLYFILNMYHWPLPLWLHDPIRVRRGDFTGPSGWLSTRTVYEFARFSAYIAWKFDDLVDEYSTMNEPNVVGGLGYVGVKSGFPPGYLSFELSRRHMYNIIQAHARAYDGIKSVSKKPVGIIYANSSFQPLTDKDMEAVEMAENDNRWWFFDAIIRGEITRGNEKIVRDDLKGRLDWIGVNYYTRTVVKRTEKGYVSLGGYGHGCERNSVSLAGLPTSDFGWEFFPEGLYDVLTKYWNRYHLYMYVTENGIADDADYQRPYYLVSHVYQVHRAINSGADVRGYLHWSLADNYEWASGFSMRFGLLKVDYNTKRLYWRPSALVYREIATNGAITDEIEHLNSVPPVKPLRH
NCBI: 14,976,310 sequences
15,849,921,438 nucleotides
Swiss-Prot: 104,559 sequences
38,460,707 residues
PDB: 17,175 structures
![Page 8: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/8.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Sequence comparison
• Compare one sequence (target) to many sequences (database search)
• Compare more than two sequences simultaneously
![Page 9: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/9.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Applications
• Phylogenetic analysis
• Identification of conserved motifs and domains
• Structure prediction
![Page 10: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/10.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
![Page 11: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/11.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Phylogenetic Analysis
![Page 12: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/12.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Structure Prediction
Genomic sequences
> RICIN GLYCOSIDASEMYSFPNSFRFGWSQAGFQSEMGTPGSEDPNTDWYKWVHDPENMAAGLVSGDLPENGPGYWGNYKTFHDNAQKMGLKIARLNVEWSRIFPNPLPRPQNFDESKQDVTEVEINENELKRLDEYANKDALNHYREIFKDLKSRGLYFILNMYHWPLPLWLHDPIRVRRGDFTGPSGWLSTRTVYEFARFSAYIAWKFDDLVDEYSTMNEPNVVGGLGYVGVKSGFPPGYLSFELSRRHMYNIIQAHARAYDGIKSVSKKPVGIIYANSSFQPLTDKDMEAVEMAENDNRWWFFDAIIRGEITRGNEKIVRDDLKGRLDWIGVNYYTRTVVKRTEKGYVSLGGYGHGCERNSVSLAGLPTSDFGWEFFPEGLYDVLTKYWNRYHLYMYVTENGIADDADYQRPYYLVSHVYQVHRAINSGADVRGYLHWSLADNYEWASGFSMRFGLLKVDYNTKRLYWRPSALVYREIATNGAITDEIEHLNSVPPVKPLRH
Protein sequences
Protein structures
![Page 13: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/13.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Clustal W
![Page 14: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/14.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Progressive Alignment
Scerevisiae [1]Celegans [2] 0.640Drosophia [3] 0.634 0.327Human [4] 0.630 0.408 0.420Mouse [5] 0.619 0.405 0.469 0.289
S.cerevisiaeC.elegans
DrosophilaMouse
Human
1. Do pairwise alignment of all sequences and calculate distance matrix
2. Create a guide tree based on this pairwise distance mat
3. Align progressively following guide tree. • start by aligning most closely related pairs of sequences• at each step align two sequences or one to an existing subalignment
![Page 15: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/15.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Parallel Clustal• Parallel pairwise
(PW) alignment matrix
• Parallel guide tree calculation
• Parallel progressive alignment
Scerevisiae [1]Celegans [2] 0.640Drosophia [3] 0.634 0.327Human [4] 0.630 0.408 0.420Mouse [5] 0.619 0.405 0.469 0.289
S.cerevisiaeC.elegans
DrosophilaMouse
Human
![Page 16: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/16.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Parallel Clustal - Improvements
• Optimization of input parameters– scoring matrices, gap penalties - requires
many repetitive Clustal W calculations with various input parameters.
• Minimum Vertex Cover– use minimum vertex cover to remove
erroneous sequences, and identify clusters of highly similar sequences.
![Page 17: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/17.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Minimum Vertex Cover
Conflict Graph– vertex: sequence– edge: conflict (e.g.
alignment with very poor score)
TASK: remove smallest number of gene sequences that eliminates all conflicts
![Page 18: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/18.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
FPT Algorithms
• Phase 1: Kernelization
Reduce problem to size f(k)
• Phase 2: Bounded Tree Search
Exhausive tree search; exponential in f(k)
![Page 19: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/19.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Kernelization
Buss's Algorithm for k-vertex cover
• Let G=(V,E) and let S be the subset of vertices with degree k or more.
• Remove S and all incident edges
G->G’ k -> k'=k-|S|.
• IF G' has more than k x k' edges THEN no k-vertex cover exists
ELSE start bounded tree search on G'
![Page 20: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/20.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Bounded Tree Search
VC={}
VC+=... VC+=... VC+=...
VC+=... VC+=... VC+=...
VC+=... VC+=... VC+=...
![Page 21: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/21.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Case 1: simple path of length 3
VC+={v,v2}
VC={...}
VC+={v1,v2} VC+={v1,v3}
search tree
v
v1
v2
v3
in graph G'
remove selected vertices from G'k' - = 2
![Page 22: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/22.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Case 2: 3-cycle
v
v1
v2
in graph G'
VC+={v,v1}
VC={...}
VC+={v1,v2} VC+={v,v2}
search tree
remove selected vertices from G'k' - = 2
![Page 23: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/23.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Case 3: simple path of length 2
v
v1
v2
in graph G'
VC={...}
VC+={v1}
search tree
remove v1, v2 from G'k' - = 1
![Page 24: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/24.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Case 4: simple path of length 1
v
v1
in graph G'
VC={...}
VC+={v}
search tree
remove v, v1 from G'k' - = 1
![Page 25: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/25.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Sequential Tree Search
Depth first search
– backtrack when k'=0 and G'<>0 ("dead end" ))
– stop when solution found (G'={}, k'>=0 )
![Page 26: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/26.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Parallel Tree SearchBasic Idea:
– Build top log p levels of the search tree (T ')
– every proc. starts depth-first search at one leaf of T '
– randomize depth-first search by selecting random child
T 'log p
![Page 27: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/27.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Analysis: Balls-in-bins
sequential depth-first search path total length:L, #solutions: m
expected sequential time (rand. distr.): L/(m+1)
parallel search path
expected parallel time (rand. distr.): p + L/(p(m+1))expected speedup: p / (1 + (m+1)/L)if m << L then expected speedup = p
![Page 28: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/28.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Simulation Experiment
number of processors
0 50
50
pre
dict
ed s
pee
dup
L = 1,000,000
m = 10m = 100m = 1,000m = 10,000m = 100,000
100
150
200
100 150 200
L = 1,000,000
![Page 29: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/29.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Implementation
• test platform:– 32 node Beowulf cluster– each node: dual 1.4 GHz Intel Xeon, 512
MB RAM, 60 GB disk– gcc and LAM/MPI on LINUX Redhat 7.2
• code-s: Sequential k-vertex cover
• code-p: Parallel k-vertex cover
![Page 30: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/30.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
HPCVL
High Performance Computing Virtual Laboratory - HPCVL (www.hpcvl.org)
Created by parallel computing researchers fromCarleton U. (Comp. Sci.)Queen's (Engineering)Ottawa U. (Life Sci./Hospital)
Obtained $30M+ in Federal (CFI) and Ontario (OIT, ORDCF) grants
![Page 31: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/31.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Test Data
• Protein sequences
• Same protein from several hundred species
• Each protein sequence a few hundred amino acid residues in length
• Obtained from the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/)
![Page 32: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/32.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Test Data
• Somatostatin
– neuropeptide involved in the regulation of many functions in different organ systems
– Clustal Threshold = 10, |V| = 559, |E| = 33652, k = 273, k' = 255
![Page 33: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/33.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Test Data
• WW
– small protein domain that binds proline rich sequences in other proteins and is involved in cellular signaling
– Clustal Threshold = 10, |V| = 425, |E| = 40182, k = 322, k' = 318
![Page 34: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/34.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Test Data
• Kinase
– large family of enzymes involved in cellular regulation
– Clustal Threshold = 16, |V| = 647, |E| = 113122, k = 497, k' = 397
![Page 35: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/35.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Test Data
• SH2 (src-homology domain 2)
– involved in targeting proteins to specific sites in cells by binding to phosphor-tyrosine
– Clustal Threshold = 10, |V| = 730, |E| = 95463, k = 461, k' = 397
![Page 36: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/36.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Test Data
• Thrombin
– protease involved in the blood coagulation cascade and promotes blood clotting by converting fibrinogen to fibrin
– Clustal Threshold = 15, |V| = 646, |E| = 62731, k = 413, k' = 413
![Page 37: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/37.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Test Data
• PHD (pleckstrin homology domain)
– involved in cellular signaling
– Clustal Threshold = 10, |V| = 670, |E| = 147054, k = 603, k' = 603
![Page 38: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/38.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Test Data
• Random Graph
|V| = 220, |E| = 2155, k = 122, k' = 122
• Grid Graph
|V| = 289, |E| = 544, k = 145, k' = 145
![Page 39: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/39.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Test Data
|VC| ~ |V| / 2 k' = k
![Page 40: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/40.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Sequential Times
Kinase, SH2, Thombin: n/a
![Page 41: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/41.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Code-p on Virtual Proc.
![Page 42: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/42.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Parallel Times
![Page 43: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/43.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Speedup: Somatostatin
![Page 44: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/44.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Speedup: WW
![Page 45: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/45.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Speedup: Rand. Graph
![Page 46: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/46.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Speedup: Grid Graph
![Page 47: Faculty of Computer Science Dalhousie University, Canada Andrew Rau-Chaplin, arc Parallel Computational Biochemistry](https://reader036.vdocuments.mx/reader036/viewer/2022081512/551b3c7a550346ae7a8b47d8/html5/thumbnails/47.jpg)
Faculty of Computer ScienceDalhousie University, Canada Andrew Rau-Chaplin, www.cs.dal.ca/~arc
Thank You!
• Questions?