This is an old revision of the document!
===== About the class ===== Welcome! This is the main wiki page for the UCSC class BME235. Currently BME235 is entirely supported through donations, in 2014 there was a very successful [[https://crowdfund.ucsc.edu/project/5424db950920652635292bae|crowdfunding campaign]]. The 2015 spring class was taught by Kevin Karplus and Ed Green. Previously Kevin Karplus organized and taught the class in spring of 2012. ==== Spring 2015 ==== The 2015 spring class consisted of 18 students, graduate and proven undergraduates, that were split apart into five groups. Each group was assigned a modern assembly program (chosen by Kevin and Ed). The groups were then asked to research, install and run the assembly programs. The class met three times weekly where groups could collaborate and share data. ==== Spring 2012 ==== The 2012 spring class was lead by Kevin Karplus. ==== Modifying the wiki ==== Resources and links that will explain how to modify the wiki. The wiki is entirely supported by past and current students from BME235. Please take the extra time to ensure that your posts to the wiki match the [[Style guide | style guide ]]. Additionally take extra care to ensure that your posts are in the right [[https://www.dokuwiki.org/namespaces | name space]] throughout the site. This makes navigation using the sitemap (see the top right of the wiki) much easier, and it will allow the wiki to expand and support future efforts. Welcome! Following the successful [[https://crowdfund.ucsc.edu/project/5424db950920652635292bae|crowdfunding campaign]], this class and effort will be continued. * [[Spring 2015 syllabus]] The lecture schedule and registered note takers. * [[Data overview]] Raw data and associated analysis. * [[Teams]] Each team is attempting an assembly with a different program. * [[Summer 2015]] A page to organize summer work. * [[Style Guide|Complete guide for modifying the wiki]] * [[computer_resources:campusrocks|Complete guide to campusRocks and SGE]] * [[Budget]] * [[Specific task]] * [[Banana slug genome browser]] A guide for accessing and setting up the banana slug hub. * [[Backup directory]] Paths on Charles' hive account where assembly and raw data files are backed-up. ==== Important pages of this wiki ==== * [[Computer resources]] describes the computers and file systems available for this class, how to get an account, how the directories are organized, how to get file permissions set correctly, and so forth. * [[Style guide]] will have suggestions for organizing content on the wiki. * [[Lecture notes]] will have pointers to notes taken by the students for each lecture. Two students will be designated each lecture to take notes, but others are encouraged to add their own notes to the wiki pages. * [[Other mollusk genomes]] has a list of other mollusks that have been sequenced, and where the data for them is. Prior mollusk genomes may be very useful in annotating the banana slug. * [[Euchromatin and Heterochromatin]] ==== Archived pages of the wiki ==== These links are several years old. Due to the speed in which bioinformatics moves, most if not all of this information will be outdated. * [[RNA]] * [[computer_resources:data|Data available]] lists the datasets that we have to assemble and annotate the genome. The data will not appear on the wiki itself (due to the size of the files), but descriptions of it and pointers to the files will. * [[computer_resources:assemblies|Assemblies]] lists the attempted assemblies (separated into subdirectories by organism). * [[Lab protocols]] will describe how the slugs were collected, the DNA extracted, and all the wet-lab work was done to produce the data files. * [[Sequencing technologies]] lists the platforms used for getting data on the banana slug. From there, we'll have pages on each technology explaining how it works, what sort of data it produces, what its common errors modes are, and other information needed to work with the data. * [[Bioinformatic tools]] lists the available tools for assembly and annotation. Each tool will have its own web page describing its strengths and weaknesses, and what we managed to do using that tool. * [[Banana slug biology]] collects the information we can find about the biology of //Ariolimax dolichophallus// (and other //Ariolimax// species). * [[Banana slugs in popular culture]] collects random information about banana slugs that can't really be classified as "biology". This will probably contain mainly information about the slug as the UCSC mascot. * [[Contributors]] will list the main contributors to this project (providing pictures and links to their own pages as appropriate). * [[Review Articles]] will list helpful review articles discovered.
