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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.)) | ||
| + | |||
| + | **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 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 ]] | ||
| + | |||
| + | |||
| + | ===== Data ===== | ||
| + | |||
| + | [[Data overview | Access to the raw and processed data]] | ||
| + | |||
| + | ===== About the class ===== | ||
| + | |||
| + | About the class | ||
| + | |||
| + | Team pages | ||
| + | |||
| + | Budget | ||
| + | |||
| + | |||
| + | [[feed.php|{{ :feed-icon-28x28.png}}]] | ||
| + | |||
| ===== Reborn - Spring 2015 ===== | ===== Reborn - Spring 2015 ===== | ||
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| * [[Spring 2015 syllabus]] The lecture schedule and registered note takers. | * [[Spring 2015 syllabus]] The lecture schedule and registered note takers. | ||
| * [[Data overview]] Raw data and associated analysis. | * [[Data overview]] Raw data and associated analysis. | ||
| - | * [[Teams]] Each team is attempting an assembly with a different program. | + | * [[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]] | * [[Style Guide|Complete guide for modifying the wiki]] | ||
| * [[computer_resources:campusrocks|Complete guide to campusRocks and SGE]] | * [[computer_resources:campusrocks|Complete guide to campusRocks and SGE]] | ||
| * [[Budget]] | * [[Budget]] | ||
| * [[Specific task]] | * [[Specific task]] | ||
| - | * [[Banana slug genome browser]] A guide for accessing and setting up the banana slug hub. | + | * [[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 ===== | ===== Important pages of this wiki ===== | ||
| Line 19: | Line 52: | ||
| * [[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. | * [[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. | * [[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. | ||
| - | * [[RNA]] | ||
| * [[Euchromatin and Heterochromatin]] | * [[Euchromatin and Heterochromatin]] | ||
| Line 27: | Line 59: | ||
| [[mitochondrion_2015 | 2015 Mitochondrion assembly ]] | [[mitochondrion_2015 | 2015 Mitochondrion assembly ]] | ||
| - | Each team is attempting to assemble the banana slug genome with a different assembly program. The results are posted in the team pages below. The assemblies are in the /campusdata/BME235/S15_assemblies/ folder on the campusrocks server. | + | 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 page | Contig N50 | Scaffold N50 | Total bases | Path | | + | |
| - | |[[team_1_page| Meraculous: Team 1 page]]| N/A | N/A | N/A | N/A | | + | |
| - | |[[soapdenovo2|SOAP: Team 2 page]]| 1,388 | 12,629 | 2,140,710,711 | SOAPdenovo2/assemblyTask/SOAPdenovo2_allAssembly_1/soapdenovo2_allAssembly_1.scafSeq| | + | |
| - | |[[0.10.13|SGA: Team 3 page]]| N/A | N/A | N/A | N/A | | + | |
| - | |[[team_4_page| ABySS: Team 4 page]]| 2,669 | 3,063 | 2,446,362,204| | + | |
| - | |[[team_5_page| Discovar de novo: Team 5 page]]| 9,513 | 10,634 | 2,245,788,654 | DiscovarDeNovo/firstFullRun/discovarDeNovoAssembly.fasta | | + | |
| Line 43: | Line 69: | ||
| ---- | ---- | ||
| - | |||
| - | {{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. | ||
| - | 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. | ||
| - | 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. | ||
| - | |||
| - | ===== 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. | ||
| - | * [[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. | ||
start.txt · Last modified: 2015/10/07 03:14 by karplus
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Noncommercial-Share Alike 3.0 Unported
