User Tools

Site Tools


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

Discussion

, 2015/04/20 11:51

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?

, 2015/04/20 18:06

I converted them from .ppt format on a mac machine, so there may be some formatting issues but the content is all there.

, 2015/04/20 10:22

Do we have a copy of Stefan's lecture slides?

You could leave a comment if you were logged in.
archive/spring_2015_syllabus.txt · Last modified: 2015/10/21 11:46 by karplus