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about_the_class:lecture_notes

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====== Notes ====== ===== Spring 2015 ===== For syllabus and note taker schedule please see the [[spring 2015 syllabus]] ^ Date ^ Topic ^ | Mon Mar 30 09:30-10:40 | [[lecture_notes:03-30-2015|Course outline]] | | Wed Apr 1 09:30-10:40 | [[lecture_notes:04-01-2015|Banana slug biology]] | | Fri Apr 3 09:30-10:40 | [[lecture_notes:04-03-2015|Dissection, extraction, and library preparation]] | | Mon Apr 6 09:30-10:40 | [[lecture_notes:04-06-2015|Denovo-assembly part:1]] | | Wed Apr 8 09:30-10:40 | [[lecture_notes:04-08-2015|Denovo-assembly part:2]] | | Fri Apr 10 09:30-10:40 | [[lecture_notes:04-10-2015|Denovo-assembly part:3]] | | Mon Apr 13 09:30-10:40 | [[lecture_notes:04-13-2015|Illumina sequencing technology]] | | Wed Apr 15 09:30-10:40 | [[lecture_notes:04-15-2015|K-mer spectra analysis]] | | Fri Apr 17 09:30-10:40 | [[lecture_notes:04-17-2015|Genome assembly - theory and practice]] | | Mon Apr 20 09:30-10:40 | [[lecture_notes:04-20-2015|Team 1 report]] | | Wed Apr 22 09:30-10:40 | [[lecture_notes:04-22-2015|Team 2 report]] | | Fri Apr 24 09:30-10:40 | [[lecture_notes:04-24-2015|Team 3 report]] | | Mon Apr 27 09:30-10:40 | [[lecture_notes:04-27-2015|Team 4 report]] | | Wed Apr 29 09:30-10:40 | [[lecture_notes:04-29-2015|Team 5 report]] | | Fri May 1 09:30-10:40 | [[lecture_notes:05-01-2015|Strategy session]] | | Mon May 4 09:30-10:40 | [[lecture_notes:05-04-2015|Population genetics]] | | Wed May 6 09:30-10:40 | [[lecture_notes:05-06-2015|RNAseq]] | | Fri May 8 09:30-10:40 | [[lecture_notes:05-08-2015|Team 1 report]] | | Mon May 11 09:30-10:40 | [[lecture_notes:05-11-2015|Team 2 report]] | | Wed May 13 09:30-10:40 | [[lecture_notes:05-13-2015|Team 3 report]] | | Fri May 15 09:30-10:40 | [[lecture_notes:05-15-2015|Team 4 report]] | | Mon May 18 09:30-10:40 | [[lecture_notes:05-18-2015|Team 5 report]] | | Wed May 20 09:30-10:40 | [[lecture_notes:05-20-2015|Lecture title]] | | Fri May 22 09:30-10:40 | [[lecture_notes:05-22-2015|Lecture title]] | | Mon May 25 09:30-10:40 | Holiday | | Wed May 27 09:30-10:40 | [[lecture_notes:05-27-2015|Lecture title]] | | Fri May 29 09:30-10:40 | [[lecture_notes:05-29-2015|Jellyfish internals for kmer counting]] | | Mon Jun 1 09:30-10:40 | [[lecture_notes:06-01-2015|Burrows-Wheeler transform]] | | Wed Jun 3 09:30-10:40 | [[lecture_notes:06-03-2015|Lecture title]] | | Fri Jun 5 09:30-10:40 | [[lecture_notes:06-05-2015|Final analysis II]] | ===== Spring 2011 ===== ^ Date ^ Topic ^ | Mon Mar 28 14:00-15:10 | [[lecture_notes:03-28-2011|Course Outline]] | | Wed Mar 30 14:00-15:10 | [[lecture_notes:03-30-2011|Sequencing Technologies]] | | Fri Apr 1 14:00-15:10 | [[lecture_notes:04-01-2011|Guest Lecture: Nader Pourmand on Sequencing Technologies]] | | Mon Apr 4 14:00-15:10 | [[lecture_notes:04-04-2011|Assembly Overview]] | | Wed Apr 6 14:00-15:10 | [[lecture_notes:04-07-2011|Jellyfish]] | | Fri Apr 8 14:00-15:10 | [[lecture_notes:04-08-2011|Jellyfish Results]] | | Mon Apr 11 14:00-15:10 | [[lecture_notes:04-11-2011|Guest Lecture: Graham Ruby on PRICE]] | | Wed Apr 13 14:00-15:10 | [[lecture_notes:04-13-2011|Guest Lecture: Daniel Zerbino on Velvet]] | | Fri Apr 15 14:00-15:00 | [[lecture_notes:04-15-2011|Resources]] | | Mon Apr 18 14:00-15:00 | [[lecture_notes:04-18-2011|Game Plan]] | | Wed Apr 20 14:00-15:00 | [[lecture_notes:04-20-2011|More Jellyfish]] | | Fri Apr 22 14:00-15:00 | [[lecture_notes:04-22-2011|Burrows-Wheeler Transform]] | | Mon Apr 25 14:00-15:00 | [[lecture_notes:04-25-2011|More Burrows-Wheeler Transform]] | | Wed Apr 27 14:00-15:00 | [[lecture_notes:04-27-2011|454 Presentation]] | | Fri Apr 29 14:00-15:00 | [[lecture_notes:04-29-2011|Guest Lecture: Janet Leonard and John Pearse on Banana Slug Biology]] | | Mon May 9 14:00-15:00 | [[lecture_notes:05-09-2011|Quake paper: Edward Liaw]] | | Wed May 11 14:00-15:00 | [[lecture_notes:05-11-2011|SOAP-denovo paper: Sam Vohr]] | | Fri May 13 14:00-15:00 | [[lecture_notes:05-13-2011|BWA results, insert length analysis]] | | Mon May 16 14:00-15:00 | [[lecture_notes:05-16-2011|Seqprep]] | | Wed May 18 14:00-15:00 | [[lecture_notes:05-18-2011|K-mer Counting Theory]] | | Fri May 20 14:00-15:00 | [[lecture_notes:05-20-2011|Sanger String Graph Assembler]] | | Mon May 23 14:00-15:00 | [[lecture_notes:05-23-2011|Guest Lecture: Patricia Chan on setting up the UCSC Genome Browser]] | | Wed May 25 14:00-15:00 | [[lecture_notes:05-25-2011|Paired End Assembler]] | | Fri May 27 14:00-15:00 | [[lecture_notes:05-27-2011|Review]] | | Fri June 3 14:00-15:00 | [[lecture_notes:06-03-2011|SARUMAN Paper: Sam Vohr]] | ===== Spring 2010 ===== ^ Date ^ Topic ^ | Mon Mar 29 14:00-15:10 | [[lecture_notes:03-29-2010|Course Outline]] | | Wed Mar 31 14:00-15:10 | [[lecture_notes:03-31-2010|Sequencing Technologies]] | | Fri Apr 02 14:00-15:10 | [[lecture_notes:04-02-2010|Resources]] | | Mon Apr 05 14:00-15:10 | [[lecture_notes:04-05-2010|Assembly Overview]] | | Wed Apr 07 14:00-15:10 | [[lecture_notes:04-07-2010|Base Space, Flow Space, Color Space]] | | Fri Apr 09 14:00-15:10 | [[lecture_notes:04-09-2010|Assembler Graphs]] | | Mon Apr 12 14:00-15:10 | [[lecture_notes:04-12-2010|Sample Preparation]] | | Wed Apr 14 14:00-15:10 | [[lecture_notes:04-14-2010|Library Construction]] | | Fri Apr 16 14:00-15:10 | [[lecture_notes:04-16-2010|Newbler Assembly on POG]] | | Mon Apr 19 14:00-15:10 | [[lecture_notes:04-19-2010|Presentation on Assemblers and Velvet]] | | Wed Apr 21 14:00-15:10 | [[lecture_notes:04-21-2010|Newbler Assembly on POG and using Solid Mate Pair Data]] | | Fri Apr 23 14:00-15:10 | [[lecture_notes:04-23-2010|Banana Slug Biology - Guest Lecture]] | | Mon Apr 26 14:00-15:10 | [[lecture_notes:04-26-2010|Tool Review: Galt and Velvet]] | | Wed Apr 28 14:00-15:10 | [[lecture_notes:04-28-2010|Tool Review: Euler-SR (John) and MIRA (Michael)]] | | Fri Apr 30 14:00-15:10 | [[lecture_notes:04-30-2010|map-colorspace5 and contig ordering; Estimating Genome Size]] | | Mon May 03 14:00-15:10 | [[lecture_notes:05-03-2010|Burrows Wheeler Transform]] | | Wed May 05 14:00-15:10 | [[lecture_notes:05-05-2010|Mate-paired data to fix assembly]] | | Fri May 07 14:00-15:10 | [[lecture_notes:05-07-2010|Approximate Search and BWA]] | | Mon May 10 14:00-15:10 | [[lecture_notes:05-10-2010|Tool Review : SSAKE by John Kim, and Slug locomotion by Jenny]] | | Wed May 12 14:00-15:10 | [[lecture_notes:05-12-2010|Tool Review : PCAP by Shyamini]] | | Fri May 14 14:00-15:10 | No class | | Mon May 17 14:00-15:10 | [[lecture_notes:05-17-2010|Genome Annotation with RAST and Artemis by Jeff Long]]| | Wed May 19 14:00-15:10 | [[lecture_notes:05-19-2010|Thomas Juetteman on ALLPATHS, Michael on Mira Internals]]| | Fri May 21 14:00-15:10 | [[lecture_notes:05-21-2010|Patricia Chan on setting up a genome browser]]| | Mon May 24 14:00-15:10 | [[lecture_notes:05-24-2010|Slug assemblies and pluck-scripts]]| | Wed May 26 14:00-15:10 | [[lecture_notes:05-26-2010|pluck-scripts]]| | Fri May 28 14:00-15:10 | [[lecture_notes:05-28-2010|pluck-scripts cont.]]| | Wed Jun 02 14:00-15:10 | [[lecture_notes:06-02-2010|Looking at related de-novo assemblies: Sea Hare and Panda]]| | Fri Jun 04 14:00-15:10 | [[lecture_notes:06-04-2010|Pcap Pog Assembly and Colorspace Python Script]]|

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about_the_class/lecture_notes.1429287157.txt.gz · Last modified: 2015/04/17 16:12 by ceisenhart