Banana Slug Genomics

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===== About the class =====

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 Due to the speed in which bioinformatics moves, most if not all of this information will be outdated.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.
Banana Slug Genomics

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