lecture_notes:03-29-2010
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| - | - Studying //Ariolimax Dolichophallus//, otherwise known as Banana Slug. Scientific name stems from Latin for "Long Penis" | + | * 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. | + | * 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. | + | * Credit wil be given for creation of original material as well as bettering existing contents. |
| - | - Three parts to this class | + | * Three parts to this class |
| - | - Underlying Sequencing Technology | + | * Underlying Sequencing Technology |
| - | - Bioinformatics | + | * Bioinformatics |
| - | - What tools are out there, when do they break? | + | * What tools are out there, when do they break? |
| - | - ? | + | * ? |
| - | - Reading List | + | * Reading List |
| - | - No assigned reading in the class. | + | * No assigned reading in the class. |
| - | - Individuals will create their own reading list for the course. | + | * Individuals will create their own reading list for the course. |
| - | - Some work has already been done on assembling small genomes at UCSC. | + | * Some work has already been done on assembling small genomes at UCSC. |
| - | - Archaeal and Bacterial genomes around 4 mb in length. | + | * Archaeal and Bacterial genomes around 4 mb in length. |
| - | - Homework | + | * Homework |
| - | - By the end of the week, create a scaffolding of all the weblinks available from the start page of the wiki. | + | * By the end of the week, create a scaffolding of all the weblinks available from the start page of the wiki. |
| - | - Computer resources page | + | * Computer resources page |
| - | - Should contain technical information: Number of processor cores, memory available per node, etc. | + | * 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) | + | * What version of programs are installed (i.e. perl, python, gcc, etc) |
| - | - Organization of file directory | + | * Organization of file directory |
| - | - Installed files | + | * Installed files |
| - | - Will need to utilize both UCSC and SOE accounts. | + | * Will need to utilize both UCSC and SOE accounts. |
| - | - SOE accounts will be used for accessing this wiki. | + | * 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 | + | * 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. | + | * UCSC accounts will be used to access the UCSC campus rocks cluster. |
| - | - All data should be documented on the data available page[insert link]. | + | * 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. | + | * 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]] | + | * [[wiki:lab_protocols|Lab Protocols]] |
| - | - All information about lab protocols used to create the sequencing should be gathered and documented in the wiki. | + | * All information about lab protocols used to create the sequencing should be gathered and documented in the wiki. |
| - | - Information of the original slug. | + | * Information of the original slug. |
| - | - DNA extraction techniques. | + | * DNA extraction techniques. |
| - | - Sample Library preparation. | + | * Sample Library preparation. |
| - | - [[sequencing_technologies|Sequencing technologies]] | + | * [[sequencing_technologies|Sequencing technologies]] |
| - | - Background of the platforms. | + | * Background of the platforms. |
| - | - Cross comparison of the platforms to compare error rates and error types. | + | * Cross comparison of the platforms to compare error rates and error types. |
| - | - Other | + | * Other |
| - | - [[bioinformatics_tools|Bioinformatics Tools]] | + | * [[bioinformatics_tools|Bioinformatics Tools]] |
| - | - The cluster is barebones and has no existing 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. | + | * Main page should list all existing programs available on the web for genome assembly. |
| - | - Individual pages will document the local installation. | + | * Individual pages will document the local installation. |
| - | - Small test organisms | + | * Small test organisms |
| - | - //Pyrobacullum OG// [find scientific name] | + | * //Pyrobacullum OG// [find scientific name] |
| - | - //Vibrio cholera// | + | * //Vibrio cholera// |
| - | - About 2-4mb in size. | + | * About 2-4mb in size. |
| - | - Used as test data for benchmarking available tools. | + | * Used as test data for benchmarking available tools. |
| - | - Banana Slug biology | + | * Banana Slug biology |
| - | - Guest speaker (or two) will give organism information of the Banana slug. | + | * Guest speaker (or two) will give organism information of the Banana slug. |
| - | - Web Literature searches on the Banana Slug should be done. | + | * Web Literature searches on the Banana Slug should be done. |
| - | - ~40 papers, many are difficult to find. | + | * ~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. | + | * 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. | + | * Summaries and references of the papers should be put in the wiki. |
| - | - Banana Slugs in popular culture | + | * Banana Slugs in popular culture |
| - | - Miscellaneous facts and other fun things should be put in this section. | + | * Miscellaneous facts and other fun things should be put in this section. |
| - | - Should be kept out of scientific sections of the wiki. | + | * Should be kept out of scientific sections of the wiki. |
| - | - Genome Browser | + | * Genome Browser |
| - | - If a quality assembly can be produced, a genome browser will be created. | + | * If a quality assembly can be produced, a genome browser will be created. |
| - | - Following years may shift their focus onto annotations. | + | * Following years may shift their focus onto annotations. |
| - | - Style Guide | + | * Style Guide |
| - | - As the wiki fills with information, how will the style of the wiki change? | + | * As the wiki fills with information, how will the style of the wiki change? |
| - | - Lecture Notes | + | * 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. | + | * 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 | + | * Volunteers for filling out wiki pages |
| - | - Computer Resources - Thomas | + | * Computer Resources - Thomas |
| - | - Data Available - [insert name] | + | * Data Available - [insert name] |
| - | - Lab Protocols - John Kim | + | * Lab Protocols - John Kim |
| - | - Sequencing Technology - Jenny Draper | + | * Sequencing Technology - Jenny Draper |
| - | - Bioinformatic Tools - ? | + | * Bioinformatic Tools - ? |
| - | - Banana slug biology - ? | + | * Banana slug biology - ? |
| - | - Banana slugs in popular culture - No one | + | * Banana slugs in popular culture - No one |
| - | - other mollusc genomes - ? | + | * other mollusc genomes - ? |
| - | - style guide - Chris | + | * style guide - Chris |
| - | - Lecture Notes - John and Thomas | + | * Lecture Notes - John and Thomas |
| - | - Academic Integrity | + | * Academic Integrity |
| - | - DO NOT add any information unless the source is known-- Sources should be added at the same time as information. | + | * 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 copying is not allowed. |
| - | - Direct quotations is allowed but should be limited. | + | * Direct quotations is allowed but should be limited. |
| - | - Additional Information | + | * Additional Information |
| - | - SOE accounts will be used to access this wiki. | + | * SOE accounts will be used to access this wiki. |
| - | - Permission codes are available from Kevin Karplus. | + | * 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. | + | * 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 | + | * parallel processing is done using sunGrid |
| - | - All data must be off the cluster 2-3 weeks after the course. | + | * All data must be off the cluster 2-3 weeks after the course. |
lecture_notes/03-29-2010.txt · Last modified: 2010/04/01 19:49 by svasili
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