about_the_class:lecture_notes
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about_the_class:lecture_notes [2010/03/30 15:48] juettemann |
about_the_class:lecture_notes [2010/06/06 22:19] galt adding a title |
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| ====== Notes ====== | ====== Notes ====== | ||
| - | * [[lecture_notes:Mar29|Mon Mar 29 14:00-15:10]] | + | ^ Date ^ Topic ^ |
| - | + | | Mon Mar 29 14:00-15:10 | [[lecture_notes:03-29-2010|Course Outline]] | | |
| - | ====== Mon Mar 29 14:00-15:10 ====== | + | | Wed Mar 31 14:00-15:10 | [[lecture_notes:03-31-2010|Sequencing Technologies]] | |
| - | Kevin outlined the content of the course. The course webpage for Spring 2010 can be found [[http://users.soe.ucsc.edu/~karplus/bme235/s10/index.html|here]]. | + | | 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]] | | |
| - | Students will be graded according to their contributions to this wiki. | + | | Fri Apr 09 14:00-15:10 | [[lecture_notes:04-09-2010|Assembler Graphs]] | |
| - | Everyone with an SOE user account is able edit the wiki. Weblinks to the terms of agreement that has to be signed before an account is created can be found on the course webpage. | + | | 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]] | | |
| - | The very first assignment for all students is to create a scaffold for each section of the wiki. The sections were assigned on a voluntary basis. | + | | 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]] | | |
| - | Kevin emphasised the importance of avoiding plagiarism. All content that is someone else's idea/product has to cited properly and credit has to be given to the original author. Sentences have to be quoted if they differ only in a few words, pictures taken from other people's webpages have to be licensed under creative commons and the source must be added immediately. Intellectual property without proper credit on the wiki is not acceptable. | + | | 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]] | | |
| - | Team work is allowed, but students should keep in mind that their grade depends on their contribution to the wiki and should take turns in writing (meaning logging in with their SOE account) when working in teams. | + | | 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|Comparing 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]]| | ||
about_the_class/lecture_notes.txt · Last modified: 2015/07/28 06:01 by ceisenhart
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