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archive:spring_2015_syllabus [2015/05/11 09:35]
jolespin
archive:spring_2015_syllabus [2015/10/21 11:46] (current)
karplus Added pdf version of Ed's last slides
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 Class meets M/W/F 9:30-10:40 in PSB 305 Class meets M/W/F 9:30-10:40 in PSB 305
  
-For a list of past/​present lecture notes please see the [[lecture notes]]+For a list of past/​present lecture notes please see the [[about_the_class:​lecture_notes]]
  
 | Number | Date | Topic | Lecturer | Lecture Notes | Note taker 1 | Note taker 2 | Slides | | Number | Date | Topic | Lecturer | Lecture Notes | Note taker 1 | Note taker 2 | Slides |
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 | 3  | 3 Apr | Disection and sequencing libraries | Weber / Green | [[lecture_notes:​04-03-2015]] | Richardson | Hussain | {{lecture_notes:​slug_presentation.pdf|Banana slug genome project}} | | 3  | 3 Apr | Disection and sequencing libraries | Weber / Green | [[lecture_notes:​04-03-2015]] | Richardson | Hussain | {{lecture_notes:​slug_presentation.pdf|Banana slug genome project}} |
 | 4  | 6 Apr | De novo genome assembly I   | Prost | [[lecture_notes:​04-06-2015]] | Kan | Chaves | {{::​genomics_workshop_ucsc.pdf|}} | | 4  | 6 Apr | De novo genome assembly I   | Prost | [[lecture_notes:​04-06-2015]] | Kan | Chaves | {{::​genomics_workshop_ucsc.pdf|}} |
-| 5  | 8 Apr | De novo genome ​assemlby ​II  | Prost | [[lecture_notes:​04-08-2015]] | Hussain |jolespin | {{::​genomics_workshop_ucsc.pdf|}} |+| 5  | 8 Apr | De novo genome ​assembly ​II  | Prost | [[lecture_notes:​04-08-2015]] | Hussain |jolespin | {{::​genomics_workshop_ucsc.pdf|}} |
 | 6  | 10 Apr | De novo genome assembly III | Prost | [[lecture_notes:​04-10-2015]] | Musselman-Brown |jolespin | {{::​genomics_workshop_ucsc.pdf|}} | | 6  | 10 Apr | De novo genome assembly III | Prost | [[lecture_notes:​04-10-2015]] | Musselman-Brown |jolespin | {{::​genomics_workshop_ucsc.pdf|}} |
 | 7  | 13 Apr | Illumina sequencing technology | Green | [[lecture_notes:​04-13-2015]] | Hussain ​ |Eisenhart | {{:​illumina-sequencing-v1.pdf|Illumina slides}} | | 7  | 13 Apr | Illumina sequencing technology | Green | [[lecture_notes:​04-13-2015]] | Hussain ​ |Eisenhart | {{:​illumina-sequencing-v1.pdf|Illumina slides}} |
 | 8  | 15 Apr | k-mer spectra analysis | Green | [[lecture_notes:​04-15-2015]] | Musselman-Brown | Cole | {{::​k-mers-v1.pdf| k-mer slides}}| | 8  | 15 Apr | k-mer spectra analysis | Green | [[lecture_notes:​04-15-2015]] | Musselman-Brown | Cole | {{::​k-mers-v1.pdf| k-mer slides}}|
 | 9  | 17 Apr | Genome assembly - theory and practice | Green | [[lecture_notes:​04-17-2015]] | Hussain |Cole | {{:​dbg-assembly-v1.pdf| DBG-assembly slides}}| | 9  | 17 Apr | Genome assembly - theory and practice | Green | [[lecture_notes:​04-17-2015]] | Hussain |Cole | {{:​dbg-assembly-v1.pdf| DBG-assembly slides}}|
-| 10  | 20 Apr | Team 1 report | Team 1 | [[lecture_notes:​04-20-2015]] | Chaves| Calef |{{bme_235_meraculous_report_1.pdf|Meraculous:​ Team 1 Report}}|+| 10  | 20 Apr | Team 1 report | Team 1 | [[lecture_notes:​04-20-2015]] | Chaves| Calef |{{:bme_235_meraculous_report_1.pdf|Meraculous:​ Team 1 Report}}|
 | 11  | 22 Apr | Team 2 report | Team 2 | [[lecture_notes:​04-22-2015]] | McGovern | Cole | {{:​lecture_notes:​soap_team2_report.pdf| SOAPdenovo: Team 2 Report}}| | 11  | 22 Apr | Team 2 report | Team 2 | [[lecture_notes:​04-22-2015]] | McGovern | Cole | {{:​lecture_notes:​soap_team2_report.pdf| SOAPdenovo: Team 2 Report}}|
 | 12  | 24 Apr | Team 3 report | Team 3 | [[lecture_notes:​04-24-2015]] | Richardson | Houser | {{:​sga_bme235_s15.pdf| SGA: Team 3 Report}}| | 12  | 24 Apr | Team 3 report | Team 3 | [[lecture_notes:​04-24-2015]] | Richardson | Houser | {{:​sga_bme235_s15.pdf| SGA: Team 3 Report}}|
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 | 15  | 1 May | Population genetics / [[http://​www.nature.com/​nature/​journal/​v475/​n7357/​full/​nature10231.html|PSMC]] | Green | [[lecture_notes:​05-01-2015]] | Saremi | Markello | | 15  | 1 May | Population genetics / [[http://​www.nature.com/​nature/​journal/​v475/​n7357/​full/​nature10231.html|PSMC]] | Green | [[lecture_notes:​05-01-2015]] | Saremi | Markello |
 | 16  | 4 May | Mate-pair libraries | Weber/​O'​Connell | [[lecture_notes:​05-04-2015]] | Musselman-Brown | Cole |{{:​slug_mate_pair_presentation.pdf|Mate Pair Libraries}}| | 16  | 4 May | Mate-pair libraries | Weber/​O'​Connell | [[lecture_notes:​05-04-2015]] | Musselman-Brown | Cole |{{:​slug_mate_pair_presentation.pdf|Mate Pair Libraries}}|
-| 17  | 6 May | RNAseq | Katzman | [[lecture_notes:​05-06-2015]] | Dudek | Chaves |{{:​rnaseq.pdf|RNA-seq}}|+| 17  | 6 May | RNAseq | Katzman | [[lecture_notes:​05-06-2015]] | Dudek | Chaves |{{:​rnaseq.pdf|RNA-seq}}; {{:​trapnell_et_al._2010.pdf|Trapnell et al., 2010}}|
 | 18  | 8 May | Strategy session | Karplus/​class | [[lecture_notes:​05-08-2015]] | Saremi | Markello | | 18  | 8 May | Strategy session | Karplus/​class | [[lecture_notes:​05-08-2015]] | Saremi | Markello |
-| 19  | 11 May | Team 1 report | Team 1 | [[lecture_notes:​05-11-2015]] | Eisenhart | Matthew | +| 19  | 11 May | Team 1 report | Team 1 | [[lecture_notes:​05-11-2015]] | Eisenhart | Matthew ​|{{:​bme235_meraculous_report_2.pdf|}}
-| 20  | 13 May | Team 2 report | Team 2 | [[lecture_notes:​05-13-2015]] |Feal | Calef |+| 20  | 13 May | Team 2 report | Team 2 | [[lecture_notes:​05-13-2015]] |Feal | Calef | {{:​soapassembly2_update.pptx.pdf| Team 2 SOAPdenovo2 update}}|
 | 21  | 15 May | Team 3 report | Team 3 | [[lecture_notes:​05-15-2015]] | Chaves| Calef | | 21  | 15 May | Team 3 report | Team 3 | [[lecture_notes:​05-15-2015]] | Chaves| Calef |
 | 22  | 18 May | Team 4 report | Team 4 | [[lecture_notes:​05-18-2015]] | Musselman-Brown | McGovern| | 22  | 18 May | Team 4 report | Team 4 | [[lecture_notes:​05-18-2015]] | Musselman-Brown | McGovern|
-| 23  | 20 May | Team 5 report | Team 5 | [[lecture_notes:​05-20-2015]] | jolespin | Saremi | +| 23  | 20 May | Team 5 report | Team 5 | [[lecture_notes:​05-20-2015]] | jolespin | Saremi ​|{{:​discovar_team_presentation_2.pdf|}} ​
-| 24  | 22 May |  |  | [[lecture_notes:​05-22-2015]] | JaredC | Saremi |+| 24  | 22 May | Assembly of Repeat regions ​|  | [[lecture_notes:​05-22-2015]] | JaredC | Saremi |
 | -  | 25 May | Holiday | N/A | N/A | N/A | N/A | | -  | 25 May | Holiday | N/A | N/A | N/A | N/A |
-| 25  | 27 May |   | [[lecture_notes:​05-27-2015]] | Kan| Feal|+| 25  | 27 May | Genome Annotation {{lecture_notes:​eukgeneannotation.pdf|Annotation Review paper}} ​Prost | [[lecture_notes:​05-27-2015]] | Kan| Feal| {{::​annotation_workshop_ucsc.pdf}}|
 | 26  | 29 May |Jellyfish internals for kmer counting ​ | Karplus | [[lecture_notes:​05-29-2015]] | Kan| JaredC | | 26  | 29 May |Jellyfish internals for kmer counting ​ | Karplus | [[lecture_notes:​05-29-2015]] | Kan| JaredC |
 | 27  | 1 Jun | Burrows-Wheeler transform (guts of most mappers) | Karplus | [[lecture_notes:​06-01-2015]] | JaredC | Markello | | 27  | 1 Jun | Burrows-Wheeler transform (guts of most mappers) | Karplus | [[lecture_notes:​06-01-2015]] | JaredC | Markello |
-| 28  | 3 Jun |  |  | [[lecture_notes:​06-03-2015]] |Feal | Calef| +| 28  | 3 Jun | Presentation for donor & final analysis I |  | [[lecture_notes:​06-03-2015]] |Feal | Calef|  
-| 29  | 5 Jun | Final analysis II | Green | [[lecture_notes:​06-05-2015]] | JaredC | Dudek |+| 29  | 5 Jun | Presentation for donors & final analysis II | Green | [[lecture_notes:​06-05-2015]] | JaredC | Dudek | {{::​finalpresentation_bme235.pdf}} {{lecture_notes:​BS-het-v1.pptx}}{{lecture_notes:​BS-het-v1.pdf}} | 
 +|
archive/spring_2015_syllabus.1431362118.txt.gz · Last modified: 2015/05/11 09:35 (external edit)