archive:spring_2015_syllabus
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archive:spring_2015_syllabus [2015/04/08 22:49] ceisenhart |
archive:spring_2015_syllabus [2015/10/21 18:46] 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 | ||
| - | | Number | Date | Topic | Lecturer | Lecture Notes | Note taker 1 | Note taker 2 | | + | For a list of past/present lecture notes please see the [[about_the_class:lecture_notes]] |
| - | | 1 | 30 Mar | Course overview & introduction | Green/Karplus | [[lecture_notes:03-30-2015]] | Dudeck | Eisenhart | | + | |
| - | | 2 | 1 Apr | The Biology of the Banana Slug | Leonard / Pearse | [[lecture_notes:04-01-2015]] | Matthew | Saremi | | + | | Number | Date | Topic | Lecturer | Lecture Notes | Note taker 1 | Note taker 2 | Slides | |
| - | | 3 | 3 Apr | Disection and Sequencing Libraries | Weber / Green | [[lecture_notes:04-03-2015]] | Richardson | Hussain | | + | | 1 | 30 Mar | Course overview & introduction | Green/Karplus | [[lecture_notes:03-30-2015]] | Dudek | Eisenhart | |
| - | | 4 | 6 Apr | De novo genome assembly I | Prost | | | | | + | | 2 | 1 Apr | The biology of the banana slug | Leonard / Pearse | [[lecture_notes:04-01-2015]] | Matthew | Saremi | |
| - | | 5 | 8 Apr | De novo genome assemlby II | Prost | | Hussain |jolespin | | + | | 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}} | |
| - | | 6 | 10 Apr | De novo genome assembly III | Prost | | Hussain |jolespin | | + | | 4 | 6 Apr | De novo genome assembly I | Prost | [[lecture_notes:04-06-2015]] | Kan | Chaves | {{::genomics_workshop_ucsc.pdf|}} | |
| - | | 7 | 13 Apr | Illumina sequencing technology | Green | | Musselman-Brown |Eisenhart | | + | | 5 | 8 Apr | De novo genome assembly II | Prost | [[lecture_notes:04-08-2015]] | Hussain |jolespin | {{::genomics_workshop_ucsc.pdf|}} | |
| - | | 8 | 15 Apr | k-mer spectra analysis | Green | | Musselman-Brown | | | + | | 6 | 10 Apr | De novo genome assembly III | Prost | [[lecture_notes:04-10-2015]] | Musselman-Brown |jolespin | {{::genomics_workshop_ucsc.pdf|}} | |
| - | | 9 | 17 Apr | Genome assembly - theory and practice | Green | | Hussain | | | + | | 7 | 13 Apr | Illumina sequencing technology | Green | [[lecture_notes:04-13-2015]] | Hussain |Eisenhart | {{:illumina-sequencing-v1.pdf|Illumina slides}} | |
| - | | 10 | 20 Apr | Team 1 Report | Team 1 | | | | | + | | 8 | 15 Apr | k-mer spectra analysis | Green | [[lecture_notes:04-15-2015]] | Musselman-Brown | Cole | {{::k-mers-v1.pdf| k-mer slides}}| |
| - | | 11 | 22 Apr | Team 2 Report | Team 2 | | | | | + | | 9 | 17 Apr | Genome assembly - theory and practice | Green | [[lecture_notes:04-17-2015]] | Hussain |Cole | {{:dbg-assembly-v1.pdf| DBG-assembly slides}}| |
| - | | 12 | 24 Apr | Team 3 Report | Team 3 | | | | | + | | 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}}| |
| - | | 13 | 27 Apr | Team 4 Report | Team 4 | | | | | + | | 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}}| |
| - | | 14 | 29 Apr | Team 5 Report | Team 5 | | | | | + | | 12 | 24 Apr | Team 3 report | Team 3 | [[lecture_notes:04-24-2015]] | Richardson | Houser | {{:sga_bme235_s15.pdf| SGA: Team 3 Report}}| |
| - | | 15 | 1 May | Strategy Session | Green | | | | | + | | 13 | 27 Apr | Team 4 report | Team 4 | [[lecture_notes:04-26-2015]] | Houser |Chaves| {{:abysspresentation1.pdf| ABySS: Team 4 Report}} | |
| - | | 16 | 4 May | Population Genetics / PSMC | Green | | Musselman-Brown | | | + | | 14 | 29 Apr | Team 5 report | Team 5 | [[lecture_notes:04-29-2015]] | Richardson | Kan |{{:team_5_report_1.pdf| Discovar de novo: Team 5 Report}} | |
| - | | 17 | 6 May | RNAseq | Green/? | | Musselman-Brown | | | + | | 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 | |
| - | | 18 | 8 May | Team 1 Report | Team 1 | | | | | + | | 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}}| |
| - | | 19 | 11 May | Team 2 Report | Team 2 | | | | | + | | 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}}| |
| - | | 20 | 13 May | Team 3 Report | Team 3 | | | | | + | | 18 | 8 May | Strategy session | Karplus/class | [[lecture_notes:05-08-2015]] | Saremi | Markello | |
| - | | 21 | 15 May | Team 4 Report | Team 4 | | | | | + | | 19 | 11 May | Team 1 report | Team 1 | [[lecture_notes:05-11-2015]] | Eisenhart | Matthew |{{:bme235_meraculous_report_2.pdf|}}| |
| - | | 22 | 18 May | Team 5 Report | Team 5 | | | | | + | | 20 | 13 May | Team 2 report | Team 2 | [[lecture_notes:05-13-2015]] |Feal | Calef | {{:soapassembly2_update.pptx.pdf| Team 2 SOAPdenovo2 update}}| |
| - | | 23 | 20 May | | | | | | | + | | 21 | 15 May | Team 3 report | Team 3 | [[lecture_notes:05-15-2015]] | Chaves| Calef | |
| - | | 24 | 22 May | | | | | | | + | | 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 |{{:discovar_team_presentation_2.pdf|}} | | ||
| + | | 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 | | | | | | | + | | 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 | | | | | | | + | | 26 | 29 May |Jellyfish internals for kmer counting | Karplus | [[lecture_notes:05-29-2015]] | Kan| JaredC | |
| - | | 27 | 1 Jun | | | | | | | + | | 27 | 1 Jun | Burrows-Wheeler transform (guts of most mappers) | Karplus | [[lecture_notes:06-01-2015]] | JaredC | Markello | |
| - | | 28 | 3 Jun | | | | | | | + | | 28 | 3 Jun | Presentation for donor & final analysis I | | [[lecture_notes:06-03-2015]] |Feal | Calef| |
| - | | 29 | 5 Jun | Final analysis II | Green | | | | | + | | 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}} | |
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archive/spring_2015_syllabus.txt · Last modified: 2015/10/21 18:46 by karplus
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