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===== About the class ===== | ===== About the class ===== | ||
+ | Welcome! | ||
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+ | 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]] | ||
+ | |||
+ | 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** | ||
+ | |||
+ | 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! | Welcome! | ||
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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]] |