archive:spring_2015_syllabus
Spring 2015 Syllabus
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
| Number | Date | Topic | Lecturer | Lecture Notes | Note taker 1 | Note taker 2 | Slides |
| 1 | 30 Mar | Course overview & introduction | Green/Karplus | 03-30-2015 | Dudek | Eisenhart | |
| 2 | 1 Apr | The biology of the banana slug | Leonard / Pearse | 04-01-2015 | Matthew | Saremi | |
| 3 | 3 Apr | Disection and sequencing libraries | Weber / Green | 04-03-2015 | Richardson | Hussain | Banana slug genome project |
| 4 | 6 Apr | De novo genome assembly I | Prost | 04-06-2015 | Kan | Chaves | genomics_workshop_ucsc.pdf |
| 5 | 8 Apr | De novo genome assembly II | Prost | 04-08-2015 | Hussain | jolespin | genomics_workshop_ucsc.pdf |
| 6 | 10 Apr | De novo genome assembly III | Prost | 04-10-2015 | Musselman-Brown | jolespin | genomics_workshop_ucsc.pdf |
| 7 | 13 Apr | Illumina sequencing technology | Green | 04-13-2015 | Hussain | Eisenhart | Illumina slides |
| 8 | 15 Apr | k-mer spectra analysis | Green | 04-15-2015 | Musselman-Brown | Cole | k-mer slides |
| 9 | 17 Apr | Genome assembly - theory and practice | Green | 04-17-2015 | Hussain | Cole | DBG-assembly slides |
| 10 | 20 Apr | Team 1 report | Team 1 | 04-20-2015 | Chaves | Calef | Meraculous: Team 1 Report |
| 11 | 22 Apr | Team 2 report | Team 2 | 04-22-2015 | McGovern | Cole | SOAPdenovo: Team 2 Report |
| 12 | 24 Apr | Team 3 report | Team 3 | 04-24-2015 | Richardson | Houser | SGA: Team 3 Report |
| 13 | 27 Apr | Team 4 report | Team 4 | 04-26-2015 | Houser | Chaves | ABySS: Team 4 Report |
| 14 | 29 Apr | Team 5 report | Team 5 | 04-29-2015 | Richardson | Kan | Discovar de novo: Team 5 Report |
| 15 | 1 May | Population genetics / PSMC | Green | 05-01-2015 | Saremi | Markello | |
| 16 | 4 May | Mate-pair libraries | Weber/O'Connell | 05-04-2015 | Musselman-Brown | Cole | Mate Pair Libraries |
| 17 | 6 May | RNAseq | Katzman | 05-06-2015 | Dudek | Chaves | RNA-seq; Trapnell et al., 2010 |
| 18 | 8 May | Strategy session | Karplus/class | 05-08-2015 | Saremi | Markello | |
| 19 | 11 May | Team 1 report | Team 1 | 05-11-2015 | Eisenhart | Matthew | bme235_meraculous_report_2.pdf |
| 20 | 13 May | Team 2 report | Team 2 | 05-13-2015 | Feal | Calef | Team 2 SOAPdenovo2 update |
| 21 | 15 May | Team 3 report | Team 3 | 05-15-2015 | Chaves | Calef | |
| 22 | 18 May | Team 4 report | Team 4 | 05-18-2015 | Musselman-Brown | McGovern | |
| 23 | 20 May | Team 5 report | Team 5 | 05-20-2015 | jolespin | Saremi | discovar_team_presentation_2.pdf |
| 24 | 22 May | Assembly of Repeat regions | 05-22-2015 | JaredC | Saremi | ||
| - | 25 May | Holiday | N/A | N/A | N/A | N/A | |
| 25 | 27 May | Genome Annotation Annotation Review paper | Prost | 05-27-2015 | Kan | Feal | annotation_workshop_ucsc.pdf |
| 26 | 29 May | Jellyfish internals for kmer counting | Karplus | 05-29-2015 | Kan | JaredC | |
| 27 | 1 Jun | Burrows-Wheeler transform (guts of most mappers) | Karplus | 06-01-2015 | JaredC | Markello | |
| 28 | 3 Jun | Presentation for donor & final analysis I | 06-03-2015 | Feal | Calef | ||
| 29 | 5 Jun | Presentation for donors & final analysis II | Green | 06-05-2015 | JaredC | Dudek | finalpresentation_bme235.pdf bs-het-v1.pptxbs-het-v1.pdf |
archive/spring_2015_syllabus.txt · Last modified: 2015/10/21 18:46 by karplus
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Discussion
Is it just on my machine, or are others seeing the PDF versions of Ed's slides as having been badly converted from the original format, resulting in bad line breaks?
I converted them from .ppt format on a mac machine, so there may be some formatting issues but the content is all there.
Do we have a copy of Stefan's lecture slides?