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 ====== 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.))
+{{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 [[https://www.soe.ucsc.edu/people/karplus | Kevin Karplus]] for permission to use it.))
-**This is the home page for the Banana Slug Genomics wiki.**
-**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.**
+**This is the home page for the Banana Slug Genomics wiki. **
-This wiki is publicly readable, but editable only by people with UCSC School of Engineering computer accounts.
+**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 about the biology of the banana slug.**
-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.
+Researchers and staff at UCSC created this [[https://www.youtube.com/watch?t=11&v=hF8IkJpq6OI | video ]] for the 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!
-===== Assemblies =====
-[[Full_genome_assemblies | Full genome assemblies ]]
+This project is hosted at UCSC as a graduate class BME235. All information is publicly accessible and free to use, please cite the authors when possible and the wiki as a whole. Please contact [[https://www.soe.ucsc.edu/people/karplus | Kevin Karplus]] with general questions. For questions on specific assemblies please identify the team that created the assembly and email them directly.
+===== About the slug =====
-[[Mitochondrion_assemblies | Mitochondrion assemblies ]]
+//Ariolimax Dolicophallus// is a relatively unstudied species. Here we aim to provide concise and accurate biological information about //Ariolimax Dolicophallus//.
+[[About the slug | Biological information about the slug ]]
 ===== Data =====
+Links to the raw [[Data overview | data]], as well as processed data are provided [[Data overview | here]]. The data includes mate-pair data, raw Illumina reads, and RNA-seq.
-[[Data overview | Access to the raw and processed data]]
+[[Data overview | Data]]
-===== About the class =====
-[[About the class | A more detailed look at the class, students, and teachers ]]
+===== Assemblies =====
+The [[Assemblies | assemblies ]] are available for annotation, merging and other bioinformatics uses.  The assemblies include full nuclear assemblies as well as mitochondrion assemblies.
-[[Teams | Pages for each assembly team ]]
+[[Assemblies | Assemblies ]]
-[[Budget | The budget for our project. Currently we **are not** accepting donations.   ]]
+===== Post-assembly analysis =====
+Our [[Post-assembly_analysis|analysis]] of the completed assemblies.  Includes the [[Banana slug genome browser |UCSC track hub for the banana slug]], analysis of heterozygosity and any annotation results.
+[[Post-assembly_analysis | Post-assembly analysis ]]
-[[feed.php|{{ :feed-icon-28x28.png}}]]
-===== 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.
-  * [[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]]
-====Team pages and results ====
+===== About the class =====
-The mitochondrion for the banana slug was assembled!
+The project is supported at UCSC as the BME235 Banana Slug Genomics class.  More information about the class can be found in the [[About the class | general information]] link. To see which students have worked on the project view the [[Contributors | contributors ]] link.   The budget for the project is publicly viewable using the [[Budget | budget]] link.  Old pages, pages that do not follow the style guide, and pages that cannot be assimilated into the main wiki are archived [[Archive | here]].
-[[mitochondrion_2015 | 2015 Mitochondrion assembly ]]
+[[About the class | General information ]]
-Each team is attempting to assemble the banana slug genome with a different assembly program.  The results are posted in the team pages below.
+[[Contributors | Contributors]]
+[[Budget | Budget]]
+[[Archive | Archive]]
+Currently we **are not** accepting donations. Thanks to all our past donors!
+----
+This wiki is publicly readable, but editable only by people with UCSC School of Engineering computer accounts.
+Contact [[https://www.soe.ucsc.edu/people/karplus | Kevin Karplus]] 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.
-----

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