Banana Slug Genomics

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====== Mon Mar 29 14:00-15:10 ======
**Some of this material copied from [[lecture_notes:Mar29|this original source]]**

Kevin outlined the content of the course. The course webpage for Spring 2010 can be found [[http://users.soe.ucsc.edu/~karplus/bme235/s10/index.html|here]].


Students will be graded according to their contributions to this wiki. 
Everyone with an SOE user account is able edit the wiki. Weblinks to the terms of agreement that has to be signed before an account is created can be found on the course webpage. 

The very first assignment for all students is to create a scaffold for each section of the wiki. The sections were assigned on a voluntary basis.

Kevin emphasised the importance of avoiding plagiarism. All content that is someone else's idea/product has to cited properly and credit has to be given to the original author. Sentences  have to be quoted if they differ only in a few words, pictures taken from other people's webpages have to be licensed under creative commons and the source must be added immediately. Intellectual property without proper credit on the wiki is not acceptable. 

Team work is allowed, but students should keep in mind that their grade depends on their contribution to the wiki and should take turns in writing (meaning logging in with their SOE account) when working in teams.


  - Studying //Ariolimax Dolichophallus//, otherwise known as Banana Slug. Scientific name stems from Latin for "Long Penis"
  - This class is not a competitive course-- all written work will be done in the wiki. No private papers will be turned in. All work done will be done on the campus-rocks and should be accessible to all members of the course.
    - Credit wil be given for creation of original material as well as bettering existing contents.
  - Three parts to this class
    - Underlying Sequencing Technology
    - Bioinformatics
      - What tools are out there, when do they break?
    - ?
  - Reading List
    - No assigned reading in the class.
    - Individuals will create their own reading list for the course.
  - Some work has already been done on assembling small genomes at UCSC.
    - Archaeal and Bacterial genomes around 4 mb in length.
  - Homework
    - By the end of the week, create a scaffolding of all the weblinks available from the start page of the wiki.
    - Computer resources page
      - Should contain technical information: Number of processor cores, memory available per node, etc.
      - What version of programs are installed (i.e. perl, python, gcc, etc)
      - Organization of file directory
      - Installed files
  - Will need to utilize both UCSC and SOE accounts.
    - SOE accounts will be used for accessing this wiki.
      - Undergrads that don't have SOE accounts, you must create one. Google "Terms of agreement soe.ucsc.edu" and find the form. Get Kevin or another SOE faculty to sign it. [edit] Link available in the syllabus
    - UCSC accounts will be used to access the UCSC campus rocks cluster.
  - All data should be documented on the data available page[insert link].
    - Secondary sequence data along with quality measurements are considered to be raw data. Image files from seqeuncing machines will not be analyzed.
  - [[wiki:lab_protocols|Lab Protocols]]
    - All information about lab protocols used to create the sequencing should be gathered and documented in the wiki.
    - Information of the original slug.
    - DNA extraction techniques.
    - Sample Library preparation.
  - [[sequencing_technologies|Sequencing technologies]]
    - Background of the platforms.
    - Cross comparison of the platforms to compare error rates and error types.
    - Other 
  - [[bioinformatics_tools|Bioinformatics Tools]]
    - The cluster is barebones and has no existing bioinformatics tools.
    - Main page should list all existing programs available on the web for genome assembly.
    - Individual pages will document the local installation.
  - Small test organisms
    - //Pyrobacullum OG// [find scientific name]
    - //Vibrio cholera//
    - About 2-4mb in size.
    - Used as test data for benchmarking available tools.
  - Banana Slug biology
    - Guest speaker (or two) will give organism information of the Banana slug.
    - Web Literature searches on the Banana Slug should be done.
      - ~40 papers, many are difficult to find.
    - Information about other types of banana slugs may be helpful. There is data on another species found in regions north of UCSC.
    - Summaries and references of the papers should be put in the wiki.
  - Banana Slugs in popular culture
    - Miscellaneous facts and other fun things should be put in this section.
    - Should be kept out of scientific sections of the wiki.
  - Genome Browser
    - If a quality assembly can be produced, a genome browser will be created. 
    - Following years may shift their focus onto annotations.
  - Style Guide
    - As the wiki fills with information, how will the style of the wiki change?
  - Lecture Notes
    - Should be taken by rotating members of the course. Allows for students to get a feel for the information being conveyed to the audience. Alterations to the notes can be made by journal club presenters.
  - Volunteers for filling out wiki pages
    - Computer Resources - Thomas
    - Data Available - [insert name]
    - Lab Protocols - John Kim
    - Sequencing Technology - Jenny Draper
    - Bioinformatic Tools - ?
    - Banana slug biology - ?
    - Banana slugs in popular culture - No one
    - other mollusc genomes - ?
    - style guide - Chris
    - Lecture Notes - John and Thomas
  - Academic Integrity
    - DO NOT add any information unless the source is known-- Sources should be added at the same time as information.
    - Direct copying is not allowed.
    - Direct quotations is allowed but should be limited.
  - Additional Information
    - SOE accounts will be used to access this wiki.
    - Permission codes are available from Kevin Karplus.
    - There is no required programming language. Python is recommended for rapid prototyping. C or C++ is recommended for large datasets.
    - parallel processing is done using sunGrid
    - All data must be off the cluster 2-3 weeks after the course.
Banana Slug Genomics

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