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| - | ====== Banana Slug Genomics ====== | + | ====== Banana slug genomics ====== |
| ===== Reborn - Spring 2015 ===== | ===== 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. | 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. | + | * [[Spring 2015 syllabus]] The lecture schedule and registered note takers. |
| - | * [[Data overview]] Raw data (fastq format) | + | * [[Data overview]] Raw data and associated analysis. |
| - | * [[Teams]] | + | * [[Teams]] Each team is attempting an assembly with a different program. |
| - | * [[Results]] Processed information, FASTQC | + | * [[Style Guide|Complete guide for modifying the wiki]] |
| - | * [[Changing the Wiki]] A guide for modifying the wiki. | + | * [[computer_resources:campusrocks|Complete guide to campusRocks and SGE]] |
| + | * [[Budget]] | ||
| + | * [[RNA]] | ||
| + | * [[Specific Task]] | ||
| + | |||
| + | ===== 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. | ||
| + | * [[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. | ||
| + | * [[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. | ||
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| + | |||
| + | ====Team pages and results ==== | ||
| + | Each team is attempting to assemble the banana slug genome with a different assembly program. The results are posted in the team pages below. | ||
| + | |||
| + | [[team_1_page| Meraculous: Team 1 page]] | ||
| + | |||
| + | [[soapdenovo2|SOAPdenovo2: Team 2 page]] | ||
| + | |||
| + | [[0.10.13|SGA: Team 3 page]] | ||
| + | |||
| + | [[team_4_page| ABySS: Team 4 page]] | ||
| + | |||
| + | [[team_5_page| Discovar de novo: Team 5 page]] | ||
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| 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. | 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. | ||
| - | ===== Top-level pages of this wiki ===== | + | ===== 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]] 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. | + | |
| * [[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: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). | * [[computer_resources:assemblies|Assemblies]] lists the attempted assemblies (separated into subdirectories by organism). | ||
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| * [[Banana slug biology]] collects the information we can find about the biology of //Ariolimax dolichophallus// (and other //Ariolimax// species). | * [[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. | * [[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. | ||
| - | * [[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. | ||
| - | * [[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. | ||
| - | * [[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. | ||
| * [[Contributors]] will list the main contributors to this project (providing pictures and links to their own pages as appropriate). | * [[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. | * [[Review Articles]] will list helpful review articles discovered. | ||
| - | ===== Very useful pages of this wiki ===== | + | |
| - | * [[http://www.rocksclusters.org/rocks-documentation/4.1/]] Rocks Cluster Distribution: Users Guide | + | |
start.txt · Last modified: 2015/10/07 03:14 by karplus
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