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--- about_the_class:about_the_class [2015/07/15 17:41]
ceisenhart created
+++ about_the_class:about_the_class [2015/07/28 06:37]
ceisenhart
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-These links are several years old. Due to the speed in which bioinformatics moves, most if not all of this information will be outdated.
+====== About the class ======
-  * [[RNA]]
+Welcome!
-  * [[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).
+**If it is your first time here and you are enrolled in the class, please see [[about_the_class::the_basics| this page]]. **
-  * [[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.
+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.
-  * [[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.
+===== 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.
+  * [[archive: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]].
+===== Spring 2010 =====
+The first class during spring 2010 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 [[about_the_class: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!
+  * [[about_the_class: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]].

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