Banana Slug Genomics

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====== About the class ======
Welcome! 

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.   

===== 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. 
  * [[Spring 2015 syllabus]]  The lecture schedule and registered note takers. 


===== Spring 2012 =====
The 2012 spring class was lead by [[https://www.soe.ucsc.edu/people/karplus | Kevin Karplus]]. 

===== 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. 

===== Computer servers =====
===CampusRocks===
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. 

  * [[computer_resources:campusrocks|Complete guide to campusRocks and SGE]] 

**Note that this is a computer cluster, please do not run programs on the head node!**

When you log in you will be on the 'head' node, this node is not meant for running programs! The head node is a very limited machine with only one job, assigning programs to other machines in the cluster. If you try and run programs on the head node the system administration will kill your program and send you an angry email.  To run programs you must use the Sun Grid Engine (SGE). 

The SGE takes in very simple shell scripts and assigns them to a non-head node in the cluster.  You can provide commands when you submit the shell scripts (request a bigger node, parallelize across multiple nodes, etc).  As the scripts are submitted they are queued, if there is heavy usage on the server your script may not run immediately.  

===Edser===

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//). 

===Kolossus===

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, students interested in using it should explain their request to the [[http://genome.ucsc.edu/staff.html | UCSC Genome Browser system administration staff]].
Banana Slug Genomics

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