Ahyy! $ © Various sources. All rights reserved. This content is excluded from our Creative Commons license. For more information, see http://ocw.mit.edu/help/faq-fair-use/. Computational Biology: Genomes, Networks, Evolution Shvqqhhihrrh pu MIT 6.047 / 6.878 HSPH IMI.231 HST.507 Q rvvr hpvr x Q sHhyvFryyv Brrqyvphv I. Administrivia ! "# $ Introductions # Grp r M ' ()*+ , - .+- / M . , 0 + +10 + 1, +" . + 8 Course Information # * M , M$9 # M :7 . $, M ()<)" #/ – All handouts, lectures, notes, etc will be posted here. # M : + ,3 䇾;98?* 䇿 O;98? P > Goals for the term # , 3 . M 7 ,3 , 3 . M < B6 . M 6 0, , 6 M C how # 3 . M "3 B M " b 5D, < M 7 ,# D, b,, ., b,6 6 6 (+ / ; Course content ? Computation & Biology | Foundations & Frontiers # 2 .E(D5 D/ , - . M D h ryrhp rivyt b , 3 ,3 M Aqhrhypr pvrpr b B+, , # 2 .E(.5 D/7 7 M Aqhv M 56,3 + M 䇺 䇻6 6 M A vr ) M 5, , D+ ,3 +,B M 3 B M ,,# + F Course organized around bio/comp modules # 1 , 0 6 M )8h hvrtrvp)6yvtqrytrr9QCHH M !)BrrhqU hp v)SI6rpyr vt p r M ")Srtyhv)@vtrvpUAHvsIr xvsr rpr M #)Wh vhv)BrrvpChuv ur vhivyvrRUG M $)@yv)Quytrryvh vtXB9hriy M %)A vr )Qr hy9vrhr"9trrQuh hTu # 7 7 6 6 M 2. , + + ++1+ 33) , + + 6 +7 + )G+ 7+D57 +, . +< , +0 . +=)+ ,, # 7 ) 6 6 M 10 . + , .+ H+H 6 .+1, + .+ + 3 .+$2 I 9 Textbook / class notes / resources (Optional) Books for the Course 9 iv@qqF tuHvpuv ErQrr 9qhCh T x © Cambridge University Press. All rights reserved.This © Wiley-Interscience. All rights reserved. This content is excluded from our Creative Commons license. content is excluded from our Creative Commons For more information, see http://ocw.mit.edu/help/faq- !'!#$$%&'( license. For more information, see http://ocw.mit fair-use/. .edu/help/faq-fair-use/. 0 3 .-C,+ (JK895;9/ 30 -C1 3 Courtesy of The MIT Press. Used with permission. New this year!! Book for the Course 8hvhy7vyt) BrrIr x@yv ;98?<;F?F G3 , . HhyvFryyvhyys 3. .M G .+ .M 0 3 .: "27 $ Lectures and Scribing # 1 0 3 M " , 36 3 , # - 6 ,0. M 0 3 3 # , 66 336,0 M C 䇻 6 ,0. ( / # 7 66 3; . 6 M N , ,0 6 ,0. , # ) , 3 # ) 35. # 3 M 16+6 + .+ + M 8 Scribing details – DropBox 6047_book LaTex > Sign up here if you haven’t already ; u)pivvrqrhpuvtuypivA Online material from last year ? Lecture feedback: N 0 , 5> .,5> $ ! .6, M ! .6 5> M 6.6D, 5> M C6 6 5> M =B B . 5> 8 " M 266 .6 .5# 5 M 6 0 5# 5 M " 6 5# 56 > , (6 , / M Q9R+9589R+895;9R+;95F9R+SF9R F Homeworks and quiz I Details on Problem sets # 1 ,3 , (/ M " ,3 D, B+ + + . .+, . + 33 06,3 < M ,3 ,<, ,+D, < < , <, (., . 0 ,3 6;F?F/ # 2 . F, M * , . 6 D3 +0 6 M 6 6 +, + D., . +D ,, # )3 M H 36.䇻0 0 +. . < 0< 0 9 Details on the in-class quiz #䇻 + 䇻 6 D M䇻 B+6 .+6++ +6. # 2 .6 8 M C ., , M C 3 0 , M 3 . ,, . 0, ,3 # .,6B M ' B<7#6.+ , M 2, B M " ,3 , M 2,3 (/< 6 + 3 + Final Project Final Project: Original Research in Comp Bio # # , 6 ,, .6 , 3 . M 7 3 ,3 , . M 0 M ) 0 + M , 3 . # 3 .,. M 6 ,, (6 ,< / M = 6 , . M 0,,, +66 + ,0 M 063 0.,, M =,. 6 , ,6 M " 6 # ,# D, , $ It’s a team project # " 66 .,M # 7 . , .D, 8 73 䇻 Q wrpyhvt Final Project at a Glance Q wrprrpv > Details on the final project # 66 , <63 M )5,6,# . M , . M , . 䇻,# + , , M ", 3 + 0 3 +D, M ,+ ,+ +6 # " M ) , 0 . M , + +63 M "50 . 3,,, + 0 63 <+, B+ # # 5 D, + M <6 ,,, +,0+. .,+ 3 <66+ 3 +, ,+0 ; Finding a research mentor / research advisor # 6 . <- < 0 M M , , , 0 M 1D,(/ , 0 +(/ H+($/ 3 +(8/ ,,+ +0 .(6 6 / # , M : + H+ . 6++ , +, . ( / M , ,-, # N, D, M 3 + M 0 +6 M 0+3 6 ? Putting it all together F Course Grading # Q iyrr" AvhyQ wrp# Hvqr ! Tp vi # 8,3 M 1 ,3 ?59R+ 0$58 + $58,3 M ,3 , (")/ M 0 ,3 # 7 ,# M , 3 .(?M/ M ,50H5. ,, 63 # ! M 5 B(H0>/H6 D # 3 , . M 3 +3. # =, . ,3 36 # = . # 3 H I Why Computational Biology ? $9 Why Computational Biology: Last year䇻s answers # *6 (T 6 / # # " 6 #䇻all 3 # 3 .0 # ) + , , # U06.( ., 6/ # ", < .D, 30 # H< 3 60 3 # 166 .( D, , 0/ # 6 6 ( 3 . 3 / # + 5 , # . 6 ., # *6 6 C $ ATATTGAATTTTCAAAAATTCTTACTTTTTTTTTGGATGGACGCAAAGAAGTTTAATAATCATATTACATGGCATTACCACCATATA TATCCATATCTAATCTTACTTATATGTTGTGGAAATGTAAAGAGCCCCATTATCTTAGCCTAAAAAAACCTTCTCTTTGGAACTTTC TAATACGCTTAACTGCTCATTGCTATATTGAAGTACGGATTAGAAGCCGCCGAGCGGGCGACAGCCCTCCGACGGAAGACTCTCCTC TGCGTCCTCGTCTTCACCGGTCGCGTTCCTGAAACGCAGATGTGCCTCGCGCCGCACTGCTCCGAACAATAAAGATTCTACAATACT CTTTTATGGTTATGAAGAGGAAAAATTGGCAGTAACCTGGCCCCACAAACCTTCAAATTAACGAATCAAATTAACAACCATAGGATG AATGCGATTAGTTTTTTAGCCTTATTTCTGGGGTAATTAATCAGCGAAGCGATGATTTTTGATCTATTAACAGATATATAAATGGAA GCTGCATAACCACTTTAACTAATACTTTCAACATTTTCAGTTTGTATTACTTCTTATTCAAATGTCATAAAAGTATCAACAAAAAAT TTAATATACCTCTATACTTTAACGTCAAGGAGAAAAAACTATAATGACTAAATCTCATTCAGAAGAAGTGATTGTACCTGAGTTCAA CTAGCGCAAAGGAATTACCAAGACCATTGGCCGAAAAGTGCCCGAGCATAATTAAGAAATTTATAAGCGCTTATGATGCTAAACCGG TTTGTTGCTAGATCGCCTGGTAGAGTCAATCTAATTGGTGAACATATTGATTATTGTGACTTCTCGGTTTTACCTTTAGCTATTGAT TGATATGCTTTGCGCCGTCAAAGTTTTGAACGAGAAAAATCCATCCATTACCTTAATAAATGCTGATCCCAAATTTGCTCAAAGGAA TCGATTTGCCGTTGGACGGTTCTTATGTCACAATTGATCCTTCTGTGTCGGACTGGTCTAATTACTTTAAATGTGGTCTCCATGTTG CACTCTTTTCTAAAGAAACTTGCACCGGAAAGGTTTGCCAGTGCTCCTCTGGCCGGGCTGCAAGTCTTCTGTGAGGGTGATGTACCA TGGCAGTGGATTGTCTTCTTCGGCCGCATTCATTTGTGCCGTTGCTTTAGCTGTTGTTAAAGCGAATATGGGCCCTGGTTATCATAT CCAAGCAAAATTTAATGCGTATTACGGTCGTTGCAGAACATTATGTTGGTGTTAACAATGGCGGTATGGATCAGGCTGCCTCTGTTT GGTGAGGAAGATCATGCTCTATACGTTGAGTTCAAACCGCAGTTGAAGGCTACTCCGTTTAAATTTCCGCAATTAAAAAACCATGAA TAGCTTTGTTATTGCGAACACCCTTGTTGTATCTAACAAGTTTGAAACCGCCCCAACCAACTATAATTTAAGAGTGGTAGAAGTCAC CAGCTGCAAATGTTTTAGCTGCCACGTACGGTGTTGTTTTACTTTCTGGAAAAGAAGGATCGAGCACGAATAAAGGTAATCTAAGAG TTCATGAACGTTTATTATGCCAGATATCACAACATTTCCACACCCTGGAACGGCGATATTGAATCCGGCATCGAACGGTTAACAAAG GCTAGTACTAGTTGAAGAGTCTCTCGCCAATAAGAAACAGGGCTTTAGTGTTGACGATGTCGCACAATCCTTGAATTGTTCTCGCGA AATTCACAAGAGACTACTTAACAACATCTCCAGTGAGATTTCAAGTCTTAAAGCTATATCAGAGGGCTAAGCATGTGTATTCTGAAT TTAAGAGTCTTGAAGGCTGTGAAATTAATGACTACAGCGAGCTTTACTGCCGACGAAGACTTTTTCAAGCAATTTGGTGCCTTGATG CGAGTCTCAAGCTTCTTGCGATAAACTTTACGAATGTTCTTGTCCAGAGATTGACAAAATTTGTTCCATTGCTTTGTCAAATGGATC ATGGTTCCCGTTTGACCGGAGCTGGCTGGGGTGGTTGTACTGTTCACTTGGTTCCAGGGGGCCCAAATGGCAACATAGAAAAGGTAA GAAGCCCTTGCCAATGAGTTCTACAAGGTCAAGTACCCTAAGATCACTGATGCTGAGCTAGAAAATGCTATCATCGTCTCTAAACCA ATTGGGCAGCTGTCTATATGAATTATAAGTATACTTCTTTTTTTTACTTTGTTCAGAACAACTTCTCATTTTTTTCTACTCATAACT AGCATCACAAAATACGCAATAATAACGAGTAGTAACACTTTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATA GTTTTCAATGTAAGAGATTTCGATTATCCACAAACTTTAAAACACAGGGACAAAATTCTTGATATGCTTTCAACCGCTGCGTTTTGG ACCTATTCTTGACATGATATGACTACCATTTTGTTATTGTACGTGGGGCAGTTGACGTCTTATCATATGTCAAAGTCATTTGCGAAG CTTGGCAAGTTGCCAACTGACGAGATGCAGTAAAAAGAGATTGCCGTCTTGAAACTTTTTGTCCTTTTTTTTTTCCGGGGACTCTAC GAACCCTTTGTCCTACTGATTAATTTTGTACTGAATTTGGACAATTCAGATTTTAGTAGACAAGCGCGAGGAGGAAAAGAAATGACA AAAATTCCGATGGACAAGAAGATAGGAAAAAAAAAAAGCTTTCACCGATTTCCTAGACCGGAAAAAAGTCGTATGACATCAGAATGA AATTTTCAAGTTAGACAAGGACAAAATCAGGACAAATTGTAAAGATATAATAAACTATTTGATTCAGCGCCAATTTGCCCTTTTCCA TTCCATTAAATCTCTGTTCTCTCTTACTTATATGATGATTAGGTATCATCTGTATAAAACTCCTTTCTTAATTTCACTCTAAAGCAT CCCATAGAGAAGATCTTTCGGTTCGAAGACATTCCTACGCATAATAAGAATAGGAGGGAATAATGCCAGACAATCTATCATTACATT AGCGGCTCTTCAAAAAGATTGAACTCTCGCCAACTTATGGAATCTTCCAATGAGACCTTTGCGCCAAATAATGTGGATTTGGAAAAA GTATAAGTCATCTCAGAGTAATATAACTACCGAAGTTTATGAGGCATCGAGCTTTGAAGAAAAAGTAAGCTCAGAAAAACCTCAATA GCTCATTCTGGAAGAAAATCTATTATGAATATGTGGTCGTTGACAAATCAATCTTGGGTGTTTCTATTCTGGATTCATTTATGTACA CAGGACTTGAAGCCCGTCGAAAAAGAAAGGCGGGTTTGGTCCTGGTACAATTATTGTTACTTCTGGCTTGCTGAATGTTTCAATATC CACTTGGCAAATTGCAGCTACAGGTCTACAACTGGGTCTAAATTGGTGGCAGTGTTGGATAACAATTTGGATTGGGTACGGTTTCG$T GTGCTTTTGTTGTTTTGGCCTCTAGAGTTGGATCTGCTTATCATTTGTCATTCCCTATATCATCTAGAGCATCATTCGGTATTTTCT ATATTGAATTTTCAAAAATTCTTACTTTTTTTTTGGATGGACGCAAAGAAGTTTAATAATCATATTACATGGCATTACCACCATATA TATCCATATCTAATCTTACTTATATGTTGTGGAAATGTAAAGAGCCCCATTATCTTAGCCTAAAAAAACCTTCTCTTTGGAACTTTC TAATACGCTTAACTGCTCATTGCTATATTGAAGTACGGATTAGAAGCCGCCGAGCGGGCGACAGCCCTCCGACGGAAGACTCTCCTC TGCGTCCTCGTCTTCACCGGTCGCGTTCCTGAAACGCAGATGTGCCTCGCGCCGCACTGCTCCGAACAATAAAGATTCTACAATACT CTTTTATGGTTATGAAGAGGAAAAATTGGCAGTAACCTGGCCCCACAAACCTTCAAATTAACGAATCAAATTAACAACCATAGGATG AATGCGATTAGTTTTTTAGCCTTATTTCTGGGGTAATTAATCAGCGAAGCGATGATTTTTGATCTATTAACAGATATATAAATGGAA GCTGCATAACCACTTTAACTAATACTTTCAACATTTTCAGTTTGTATTACTTCTTATTCAAATGTCATAAAAGTATCAACAAAAAAT TTAATATACCTCTATACTTTAACGTCAAGGAGAAAAAACTATAATGACTAAATCTCATTCAGAAGAAGTGATTGTACCTGAGTTCAA CTAGCGCAAAGGAATTACCAAGACCATTGGCCGAAAAGTGCCCGAGCATAATTAAGAAATTTATAAGCGCTTATGATGCTAAACCGG TTTGTTGCTAGATCGCCTGGTAGAGTCAATCTAATTGGTGAACATATTGATTATTGTGACTTCTCGGTTTTACCTTTAGCTATTGAT TGATATGCTTTGCGCCGTCAAAGTTTTGAACGAGAAAAATCCATCCATTACCTTAATAAATGCTGATCCCAAATTTGCTCAAAGGAA TCGATTTGCCGTTGGACGGTTCTTATGTCACAATTGATCCTTCTGTGTCGGACTGGTCTAATTACTTTAAATGTGGTCTCCATGTTG CACTCTTTTCTAAAGAAACTTGCACCGGAAAGGTTTGCCAGTGCTCCTCTGGCCGGGCTGCAAGTCTTCTGTGAGGGTGATGTACC A TGGCAGTGGATTGTCTTCTTCGGCCGCATTCATTTGTGCCGTTGCTTTAGCTGTTGTTAAAGCGAATATGGGCCCTGGTTATCATA .