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| Hello, Hossein Azari Soufiani! This is a welcome message from OpenWetWare. By the way, we've announced you on the [[Main Page|home page]]! You can leave messages to any OWW member by editing their User_talk pages like this one. And don't forget to personalize your [[User:Hossein Azari Soufiani|User Page]] so that we can get to know you better! We've included some tips below to get you started.
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| == Report of Second Homework == | | == Report of Second Homework == |
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| The paper [[Media:Endy2005.pdf|"Foundations for the Engineering Biology"]] was really interesting for me because I am an engineer and I like to see the problems from engineering point of view. | | The paper [[Media:Endy2005.pdf|"Foundations for the Engineering Biology"]] was really interesting. |
| The paper was written in a very classic engineering manner and it made understanding of our position in Bioengineering more clear for me.
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| Installing and preparing Python was very different than the other programs which I used before like Matlab, C++.
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| I enjoyed using it, specially the object oriented programing ability makes it really powerful.
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| Plot for Python is very similar to Matlab and we have same commands with a little bit difference.
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| Here you see a plot for three different growth rates for exponential function plotted with different colors.
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| [[Image:plot1.jpg]]
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| ==Code for Third Homework==
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| import random
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| import numpy as np
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| print
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| print
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| Code='cggagcagctcactattcacccgatgagaggggaggagagagagagaaaatgtcctttaggccggttcctcttacttggcagagggaggctgctattctccgcctgcatttctttttctggattacttagttatggcctttgcaaaggcaggggtatttgttttgatgcaaacctcaatccctccccttctttgaatggtgtgccccaccccccgggtcgcctgcaacctaggcggacgctaccatggcgtagacagggagggaaagaagtgtgcagaaggcaagcccggaggcactttcaagaatgagcatatctcatcttcccggagaaaaaaaaaaaagaatggtacgtctgagaatgaaattttgaaagagtgcaatgatgggtcgtttgataatttgtcgggaaaaacaatctacctgttatctagctttgggctaggccattccagttccagacgcaggctgaacgtcgtgaagcggaaggggcgggcccgcaggcgtccgtgtggtcctccgtgcagccctcggcccgagccggttcttcctggtaggaggcggaactcgaattcatttctcccgctgccccatctcttagctcgcggttgtttcattccgcagtttcttcccatgcacctgccgcgtaccggccactttgtgccgtacttacgtcatctttttcctaaatcgaggtggcatttacacacagcgccagtgcacacagcaagtgcacaggaagatgagttttggcccctaaccgctccgtgatgcctaccaagtcacagacccttttcatcgtcccagaaacgtttcatcacgtctcttcccagtcgattcccgaccccacctttattttgatctccataaccattttgcctgttggagaacttcatatagaatggaatcaggatgggcgctgtggctcacgcctgcactttggctcacgcctgcactttgggaggccgaggcgggcggattacttgaggataggagttccagaccagcgtggccaacgtggtg'
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| RCCode=Code
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| TempCode=Code
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| print 'Code=',Code
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| print
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| print
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| pro1=range(1,339)
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| pro2=range(1,339)
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| pro3=range(1,339)
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| prom1=range(1,339)
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| prom2=range(1,339)
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| prom3=range(1,339)
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| #----------------------Problem one --------------------------------------------
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| GCcontent=0
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| for i in range(0,len(Code)-1):
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| if Code[i]=='c':
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| GCcontent=GCcontent+1
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| elif Code[i]=='g':
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| GCcontent=GCcontent+1
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| print 'GC Content=',GCcontent
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| print
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| print
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| print
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| print
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| #----------------------Problem two---------------------------------------------
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| for i in range(0,len(Code)-1):
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| if Code[len(Code)-1-i]=='c':
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| RCCode=RCCode[:i]+'g'+RCCode[i+1:]
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| if Code[len(Code)-1-i]=='g':
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| RCCode=RCCode[:i]+'c'+RCCode[i+1:]
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| if Code[len(Code)-1-i]=='t':
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| RCCode=RCCode[:i]+'a'+RCCode[i+1:]
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| if Code[len(Code)-1-i]=='a':
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| RCCode=RCCode[:i]+'t'+RCCode[i+1:]
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| print 'Recerse Complement=:', RCCode
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| print
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| print
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| #----------------------Problem Three---------------------------------------------
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| standard = { 'ttt': 'F', 'tct': 'S', 'tat': 'Y', 'tgt': 'C',
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| 'ttc': 'F', 'tcc': 'S', 'tac': 'Y', 'tgc': 'C',
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| 'tta': 'L', 'tca': 'S', 'taa': '*', 'tga': '*',
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| 'ttg': 'L', 'tcg': 'S', 'tag': '*', 'tgg': 'W',
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| 'ctt': 'L', 'cct': 'P', 'cat': 'H', 'cgt': 'R',
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| 'ctc': 'L', 'ccc': 'P', 'cac': 'H', 'cgc': 'R',
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| 'cta': 'L', 'cca': 'P', 'caa': 'Q', 'cga': 'R',
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| 'ctg': 'L', 'ccg': 'P', 'cag': 'Q', 'cgg': 'R',
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| 'att': 'I', 'act': 'T', 'aat': 'N', 'agt': 'S',
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| 'atc': 'I', 'acc': 'T', 'aac': 'N', 'agc': 'S',
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| 'ata': 'I', 'aca': 'T', 'aaa': 'K', 'aga': 'R',
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| 'atg': 'M', 'acg': 'T', 'aag': 'K', 'agg': 'R',
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| 'gtt': 'V', 'gct': 'A', 'gat': 'D', 'ggt': 'G',
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| 'gtc': 'V', 'gcc': 'A', 'gac': 'D', 'ggc': 'G',
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| 'gta': 'V', 'gca': 'A', 'gaa': 'E', 'gga': 'G',
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| 'gtg': 'V', 'gcg': 'A', 'gag': 'E', 'ggg': 'G'
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| }
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|
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| for i in range(0,338):
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| Temp1=Code[3*i]+Code[3*i+1]+Code[3*i+2]
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| Temp2=Code[3*i+1]+Code[3*i+2]+Code[3*i+3]
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| Temp3=Code[3*i+2]+Code[3*i+3]+Code[3*i+4]
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| pro1[i]=standard[Temp1]
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| pro2[i]=standard[Temp2]
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| pro3[i]=standard[Temp3]
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| Temp1=RCCode[3*i]+RCCode[3*i+1]+RCCode[3*i+2]
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| Temp2=RCCode[3*i+1]+RCCode[3*i+2]+RCCode[3*i+3]
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| Temp3=RCCode[3*i+2]+RCCode[3*i+3]+RCCode[3*i+4]
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| prom1[i]=standard[Temp1]
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| prom2[i]=standard[Temp2]
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| prom3[i]=standard[Temp3]
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| print 'Sequence of (+1) frame'
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| print pro1
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| print 'Sequence of (+2) frame'
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| print pro2
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| print 'Sequence of (+3) frame'
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| print pro3
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| print 'Sequence of (-1) frame'
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| print prom1
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| print 'Sequence of (-2) frame'
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| print prom2
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| print 'Sequence of (-3) frame'
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| print prom3
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| #-----------------------------Problem Four---------------------------
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| counter=0
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| for j in range(0,1000):
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| Code=TempCode
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| for i in range(0,10):
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| Te=random.random()
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| Te=np.fix(100*Te)
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| Te2=random.random()
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| Te2=int(np.fix(10*Te2))%3
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|
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|
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|
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|
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| if (Code[100*i+int(Te)]=='c') and (Te2==1):
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| Code=Code[:100*i+int(Te)]+'g'+Code[100*i+int(Te)+1:]
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|
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|
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|
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| elif (Code[100*i+int(Te)]=='c') and (Te2==2):
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| Code=Code[:100*i+int(Te)]+'t'+Code[100*i+int(Te)+1:]
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|
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| elif (Code[100*i+int(Te)]=='c') and (Te2==0):
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| Code=Code[:100*i+int(Te)]+'a'+Code[100*i+int(Te)+1:]
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|
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| elif (Code[100*i+int(Te)]=='t') and (Te2==1):
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| Code=Code[:100*i+int(Te)]+'g'+Code[100*i+int(Te)+1:]
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|
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|
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| elif (Code[100*i+int(Te)]=='t') and (Te2==2):
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| Code=Code[:100*i+int(Te)]+'c'+Code[100*i+int(Te)+1:]
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|
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| elif (Code[100*i+int(Te)]=='t') and (Te2==0):
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| Code=Code[:100*i+int(Te)]+'a'+Code[100*i+int(Te)+1:]
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|
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|
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| elif (Code[100*i+int(Te)]=='g') and (Te2==1):
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| Code=Code[:100*i+int(Te)]+'c'+Code[100*i+int(Te)+1:]
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|
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|
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| elif (Code[100*i+int(Te)]=='g') and (Te2==2):
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| Code=Code[:100*i+int(Te)]+'t'+Code[100*i+int(Te)+1:]
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|
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| elif (Code[100*i+int(Te)]=='g') and (Te2==0):
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| Code=Code[:100*i+int(Te)]+'a'+Code[100*i+int(Te)+1:]
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| elif (Code[100*i+int(Te)]=='a') and (Te2==1):
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| Code=Code[:100*i+int(Te)]+'g'+Code[100*i+int(Te)+1:]
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|
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|
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| elif (Code[100*i+int(Te)]=='a') and (Te2==2):
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| Code=Code[:100*i+int(Te)]+'t'+Code[100*i+int(Te)+1:]
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|
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| elif (Code[100*i+int(Te)]=='a') and (Te2==0):
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| Code=Code[:100*i+int(Te)]+'c'+Code[100*i+int(Te)+1:]
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|
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| pro21=range(1,339)
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| pro22=range(1,339)
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| pro23=range(1,339)
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| for i in range(0,338):
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| Temp1=Code[3*i]+Code[3*i+1]+Code[3*i+2]
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| Temp2=Code[3*i+1]+Code[3*i+2]+Code[3*i+3]
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| Temp3=Code[3*i+2]+Code[3*i+3]+Code[3*i+4]
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| pro21[i]=standard[Temp1]
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| pro22[i]=standard[Temp2]
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| pro23[i]=standard[Temp3]
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|
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| for i in range(0,len(pro21)-1):
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| if pro21[i]=='*' and pro1[i]!='*':
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| counter=counter+1
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|
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| print 'Percent of Premature Termination=',counter,'/1000'
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| print
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| print
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| print 'Before Mutation:', pro1
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| print
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| print
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| print 'After Mutation:', pro21
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| input()
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| == Personal/Lab Info ==
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| We have gone ahead and filled in some information you provided us in your membership application on your [[User:Hossein Azari Soufiani|User Page]]. Please take a moment to embellish this and tell the community a little more about you. Put links to your lab pages, your projects and your interests. If you run out of ideas, take a look at some of the other User pages. For example, check out [[User:Julius_B._Lucks]], [[User:Jason_R._Kelly]] and [[User:Reshma_P._Shetty]].
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| You'll also notice that we have put an 'image' placeholder at the top of your [[User:Hossein Azari Soufiani|User Page]]. We encourage you to upload an image of yourself to give OWW a more personal feel. To upload an image, click on the [[Special:Upload|Upload file]] link on the left-hand side (toolbar). Choose a file from your computer, and remember the file name. After you have uploaded the image, you should see it loaded on its own page. Go back to your [[User:Hossein Azari Soufiani|User Page]], click on edit, and replace 'OWWEmblem.png' with the name of your file that you have uploaded in the second line of this page.
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