Banana Slug Genomics

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This is the archive for pages that are no longer being supported.  Ideally these pages will be renamed into the 'archive' namespace. 


**Archived files**
  * [[Archive::bioinformatic_tools | bioinformatic_tools]] 
  * [[Archive::banana_slugs_in_popular_culture | banana_slugs_in_popular_culture]]
  * [[Archive::euchromatin_and_heterochromatin | Euchromatin and heterochromatin ]] 


**Deprecated links (things to be archived)**
  * [[Spring 2015 syllabus]]  The lecture schedule and registered note takers. 
  * [[Summer 2015]] A page to organize summer work.
  * [[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.
  * [[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]]
  * [[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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