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--- start [2015/04/15 18:05]
ceisenhart
+++ start [2015/07/15 18:44]
ceisenhart Major changes under way, please let me finish before doing more
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-[[feed.php|{{ :feed-icon-28x28.png}}]]
+====== Banana slug genomics ======
-====== Banana Slug Genomics ======
+{{http://users.soe.ucsc.edu/~karplus/cyberslugs/slug-dreaming-300x400.jpg }}((The Cyberslug is **not** licensed under Creative Commons.  It is licensed exclusively to the Jack Baskin School of Engineering at the University of California, Santa Cruz, and may not be used by others.  Furthermore, the slug-dreaming icon here is only for use by the Banana Slug Genomics project—contact Kevin Karplus for permission to use it.))
-===== Reborn - Spring 2015 =====
-Welcome back, Banana Slug Genomics! Following the successful [[https://crowdfund.ucsc.edu/project/5424db950920652635292bae|crowdfunding campaign]], this class and effort will be rebooted.
-  * [[Spring 2015 Syllabus]]  The lecture schedule and registered note takers.
+**This is the home page for the Banana Slug Genomics wiki.**
-  * [[Data overview]]  Raw data and associated analysis.
-  * [[Teams]] Each team is attempting an assembly with a different program.
-  * [[Style Guide|A guide for modifying the wiki]] A guide for modifying the wiki.
-  * [[computer_resources:campusrocks]] Complete guide to campusRocks and SGE.
+**We are working to assemble and annotate the genome of the UCSC mascot //Ariolimax dolichophallus//, the slender banana slug. Additionally we are collecting and hosting as much information as we can find about the biology of the banana slug.**
+Our wonderful faculty created a [[https://www.youtube.com/watch?t=11&v=hF8IkJpq6OI | video ]] for our 2014 crowdfunding campaign.  See how the project started and follow along at a high level, a great place to start for those uninitiated in genomics!
+This wiki is publicly readable, but editable only by people with UCSC School of Engineering computer accounts.
+Contact Kevin Karplus (karplus@soe.ucsc.edu) if you need to edit these pages and do not have such an account.
+In addition to page-specific discussions on each page, there is a separate [[http://forums.soe.ucsc.edu/viewforum.php?f=102|forum]] for discussions about the class.  The discussion forum is intended for more transient discussions than this wiki---such as where new material should go into the wiki, discussions of re-organizing the wiki or alerts about time-sensitive material.
+===== Assemblies =====
-----
+[[Full_genome_assemblies | Full genome assemblies ]]
+[[Mitochondrion_assemblies | Mitochondrion assemblies ]]
-{{http://users.soe.ucsc.edu/~karplus/cyberslugs/slug-dreaming-300x400.jpg }}((The Cyberslug is **not** licensed under Creative Commons.  It is licensed exclusively to the Jack Baskin School of Engineering at the University of California, Santa Cruz, and may not be used by others.  Furthermore, the slug-dreaming icon here is only for use by the Banana Slug Genomics project—contact Kevin Karplus for permission to use it.))
-This is the home page for the Banana Slug Genomics wiki.
+===== Data =====
-Material on these pages will mainly be created by students of the [[http://users.soe.ucsc.edu/~karplus/bme235|BME235 course]].  We hope to be able to assemble and annotate the genome of the UCSC mascot //Ariolimax dolichophallus//, the slender banana slug, as well as collecting all the information we can find about the biology of the banana slug.
-This wiki should be publicly readable, but editable only by people with UCSC School of Engineering computer accounts.
+[[Data overview | Access to the raw and processed data]]
-Contact Kevin Karplus (karplus@soe.ucsc.edu) if you need to edit these pages and do not have such an account.
-In addition to page-specific discussions on each page, there is a separate [[http://forums.soe.ucsc.edu/viewforum.php?f=102|forum]] for discussions about the class.  The discussion forum is intended for more transient discussions than this wiki---such as where new material should go into the wiki, discussions of re-organizing the wiki or alerts about time-sensitive material.
+===== About the class =====
-===== Important pages of this wiki =====
+[[About the class | General information about the class and 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.
-  * [[Banana Slug Genome Browser]] will have a UCSC genome browser, once we get to the point of having few enough contigs that building a browser makes sense.
+[[Teams | Pages for each assembly team ]]
-  * [[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.
+[[Budget | The budget for our project]]
+Currently we **are not** accepting donations. Thanks to all our current and previous donors!
+----
-===== Old pages of this 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.
-  * [[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.
-  * [[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.
-  * [[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.

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