about_the_class:about_the_class
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| - | ===== Reborn - Spring 2015 ===== | + | ===== About the class ===== |
| + | Welcome! | ||
| - | Welcome back, Banana Slug Genomics! Following the successful [[https://crowdfund.ucsc.edu/project/5424db950920652635292bae|crowdfunding campaign]], this class and effort will be rebooted. | + | This is the main wiki page for the UCSC class BME235. Currently BME235 is entirely supported through donations, in 2014 there was a very successful [[https://crowdfund.ucsc.edu/project/5424db950920652635292bae|crowdfunding campaign]]. The 2015 spring class was taught by [[https://www.soe.ucsc.edu/people/karplus | Kevin Karplus]] and [[https://www.soe.ucsc.edu/people/ed | Ed Green ]]. Previously [[https://www.soe.ucsc.edu/people/karplus | Kevin Karplus]] organized and taught the class in spring of 2012. |
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| + | ==== Spring 2015 ==== | ||
| + | The 2015 spring class consisted of 18 students, graduate and proven undergraduates, that were split apart into five groups. Each group was assigned a modern assembly program (chosen by [[https://www.soe.ucsc.edu/people/karplus | Kevin Karplus]] and [[https://www.soe.ucsc.edu/people/ed | Ed Green ]]). The groups were then asked to research, install and run the assembly programs. The class met three times weekly where groups could collaborate and share data. | ||
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| + | ==== Spring 2012 ==== | ||
| + | The 2012 spring class was lead by [[https://www.soe.ucsc.edu/people/karplus | Kevin Karplus]]. | ||
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| + | ==== Modifying the wiki ==== | ||
| + | The wiki is entirely supported by past and current students from BME235. Please take the extra time to ensure that your posts to the wiki match the [[Style guide | style guide ]]. Additionally take extra care to ensure that your posts are in the right [[https://www.dokuwiki.org/namespaces | name space]] throughout the site. This makes navigation using the sitemap (see the top right of the wiki) much easier, and it will allow the wiki to expand and support future efforts! | ||
| + | * [[Style Guide|Complete guide for modifying the wiki]] | ||
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| + | Important notes about modifying the wiki; | ||
| + | * **Use the 'Preview' button before submitting.** | ||
| + | * **Always provide an edit summary.** | ||
| + | * **For minor changes, click the 'Minor Changes' box** | ||
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| + | The wiki stores past revisions of every page. They can be accessed through the side bar using the 'Old revisions' tab. This can be used as a last resort, when a page is altered beyond recognition or accidentally deleted. | ||
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| + | ==== Computer servers ==== | ||
| + | The servers and resources that have been used so far in the project. The most universal resource is UCSC's [[https://support.soe.ucsc.edu/craigslist | campusrocks server]], which requires a UCSC Cruz Blue ID and password to login. | ||
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| + | * [[computer_resources:campusrocks|Complete guide to campusRocks and SGE]] | ||
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| + | During the Spring 2015 [[https://www.soe.ucsc.edu/people/ed | Ed Green ]] was able to let students use his server edser (edser2.ucsc.edu). The server has 390 G of RAM, which is necessary for certain assembly algorithms (Discovar //de novo//). | ||
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| + | In both the Spring 2012 and Spring 2015 classes the server Kolossus was accessed. Kolossus is a 1TB RAM machine that the UCSC Genome Browser group uses. Access is restricted, but students interested in using it can contact the [[http://genome.ucsc.edu/staff.html | UCSC Genome Browser system administration staff]]. | ||
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| + | Welcome! | ||
| + | Following the successful [[https://crowdfund.ucsc.edu/project/5424db950920652635292bae|crowdfunding campaign]], this class and effort will be continued. | ||
| * [[Spring 2015 syllabus]] The lecture schedule and registered note takers. | * [[Spring 2015 syllabus]] The lecture schedule and registered note takers. | ||
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| * [[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. | * [[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]] | * [[Budget]] | ||
| * [[Specific task]] | * [[Specific task]] | ||
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| * [[Backup directory]] Paths on Charles' hive account where assembly and raw data files are backed-up. | * [[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 ==== |
| * [[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]] 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. | * [[Style guide]] will have suggestions for organizing content on the wiki. | ||
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| * [[Euchromatin and Heterochromatin]] | * [[Euchromatin and Heterochromatin]] | ||
| + | ==== Archived pages of the 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. | These links are several years old. Due to the speed in which bioinformatics moves, most if not all of this information will be outdated. | ||
| * [[RNA]] | * [[RNA]] | ||
about_the_class/about_the_class.txt · Last modified: 2015/09/11 22:04 by 5.9.83.211
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Noncommercial-Share Alike 3.0 Unported
