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Topics in Teaching web:
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Changed: now 02:34 GMT
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Changed by:
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WebStatistics
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17 Mar 2010 - 02:27 - r1.1281
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TWikiGuest
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// Statistics for Web // Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads: // // Mar 2010 13763 15 0 2575 1842 WebRss 353 350 BioE241 347 342 WebChanges 310 242 WebIndex 224 213 ArraysAndHashesLab 163 WebSearch 15 Main.IanHolmes // Feb 2010 23658 5 0 4036 3308 WebRss 1238 626 BioE241 577 478 BioE131 338 279 WebSearch 253 201 LizXiaSecondaryStructurePairwiseAlignmentGraduateProject 181 PatternMatchingLab ...
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BioE241
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15 Mar 2010 - 10:16 - r1.188
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IanHolmes
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// BioE241 // Class info // Title: Probabilistic Modeling, Genomics and Jurassic Park // Instructor: Main.IanHolmes // Class: !BioE 241 // When: Spring semester, 2010 // Lectures: Tue/Thurs 3-5:30, 115 Kroeber // Instructor blog please do post comments/questions. //
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BioE241XRateLab
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15 Mar 2010 - 10:09 - r1.5
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IanHolmes
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// BioE241 xrate lab // The purpose of this lab is to get basic familiarity with the xrate software and to use it as an independent check of the previous labs. // Some links to get you started: // Main.XRATE main program page // Main.XrateFormat description of xrate's file format, including a list of sample grammar files // Kimura transition/transversion model // The Kimura 2-parameter model that you have been working with is implemented as an example grammar ...
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BioE241SubstitutionLab
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01 Mar 2010 - 11:04 - r1.20
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IanHolmes
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// Substitution model lab // Model // A point substitution model with uniform base frequencies that distinguishes between transitions (purine-to-purine or pyrimidine-to-pyrimidine substitutions) and transversions (all other nucleotide substitutions). // Kimura's two-parameter model () // Transition rate A // Transversion rate B // Alignment length L // Time T // The rate matrix for this model, over the alphabet (A,C,G,T), is $R \left(\begin{array}{llll}-K B ...
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BioE241PhyloHMMLab
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01 Mar 2010 - 10:34 - r1.15
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IanHolmes
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// BioE241 phylo-HMM lab // Model // A hidden Markov model (HMM) with N states, where each state emits columns of a multiple sequence alignment, according to the following generative model... // a phylogenetic tree, T // a Kimura 2-parameter substitution rate matrix (see substitution lab). To begin with try A .8 (transitions) and B .1 (transversions) // a state-specific scaling on the rate matrix. These should span an "appropriate" set R of rate multipliers ...
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BioE241PruningLab
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05 Feb 2010 - 15:03 - r1.2
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IanHolmes
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// BioE241 pruning lab // Model // Kimura model (see substitution lab) // Phylogenetic tree // Goals // Write code to implement the Felsenstein pruning algorithm to calculate the (log-)likelihood of a multiple sequence alignment under the Kimura 2-parameter model. // At this stage, you can represent tree and alignment as internal data structures; the next step involves writing parsers, but that's a bit more involved // You should allow for // 1 ambiguous character ...
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BioE131
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26 Jan 2010 - 21:25 - r1.384
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TWikiGuest
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// BioE131/231 // Introduction to Computational Biology. // Course info // Code: Bioe131/231 // Title: Introduction to computational biology // Instructor: Ian Holmes (follow the link to my page for my office hours) // GSI: Oscar Westesson (office hours: During lab time. I will have additional O.H. if there is sufficient demand) // When: //
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BioE241Modalities
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19 Jan 2010 - 15:00 - r1.50
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IanHolmes
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// Probabilistic Modeling in Computational Biology // Class meets thirty times. // Programming exercises // Five Programming Exercises. // (One due every 3 weeks.) // Model solutions are in C++. // Any language is OK, but C, C++, Perl or Java is recommended. // Numerical scripting languages (Main.MatLab, R...) and algebraic languages (Mathematica, Maple...) come with powerful built-in mathematical libraries // which can help with some of the statistics, but ...
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BioE131Policies
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20 Nov 2009 - 14:15 - r1.21
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IanHolmes
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// Teaching.BioE131 policies // Key dates // Academic calendar (Fall 2009) // Exams: // Midterm 1: Wednesday September 30, 3:10-4pm // Midterm 2: Wednesday November 18, 3:10-4pm // Take-home final // Final project deadlines: see project page // Grading scheme // 40 homework assignments //
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InformationContentOfDNA
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17 Nov 2009 - 08:51 - r1.136
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IanHolmes
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// Before we begin // This lab assumes you are now comfortable navigating through a linux environment and manipulating and using perl files. If you run into basic problems, consult previous labs, a neighbor, or if needed the GSI. // Several new tools are introduced in this lab. Spend a little bit of time familiarizing yourself with them both by reading about them on their source websites, and by tinkering with them. // Goals // Get a feel for the information ...
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BayesianInferenceHomework
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13 Nov 2009 - 13:55 - r1.5
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IanHolmes
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// Bayesian inference exercise. // These programming exercises also develop your understanding of Bayesian statistical inference procedures. // Background reading // First read the Wikipedia article on Wikipedia:Bayesian inference. // Specifically, be sure to read the section titled // Simple examples of Bayesian inference. // Open reading frames submit as hw6a.pl // Suppose that S is a sequence of N codons. Equivalently, S can be thought of as a sequence of ...
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InformationContentHomework
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09 Nov 2009 - 16:48 - r1.5
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TWikiGuest
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// Information content programming exercise. // In addition to building on your programming skills, this exercise tests your understanding of the entropy concepts that have been covered in class. // The goal of the exercise is to write a Perl program that does the following (grading shown in red italics ): // 1 Read in a multiple sequence alignment in format (you may assume the file is correctly formatted); (10) Relevant points of the stockholm format for this ...
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BacterialGenePrediction
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28 Oct 2009 - 11:11 - r1.158
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TWikiGuest
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// Bacterial Gene Prediction // Goals // Find open reading frames (ORFs) in a bacterial genome // Find the protein translations // Compare different gene prediction methods: // Compare predicted ORFs to "trusted" annotation // Compare to a bacterial genefinding program (Glimmer) // Compare to a translated-protein homology search program (exonerate) // Build experience manipulating genomes and genome annotations // some basic guided data-processing tasks // ...
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NussinovAlgorithmHomework
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21 Oct 2009 - 17:24 - r1.22
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TWikiGuest
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// Nussinov Algorithm homework // Implement the Nussinov algorithm // Implement the Nussinov algorithm; specifically, a Perl program that does the following: // 1 Takes (as input) exactly one command-line argument, which is an RNA sequence (in upper- or lower-case, or a mixture of both); // Alternatively, you may have the program read the RNA sequence from standard input, as you prefer. Be sure to specify how the RNA sequence is input when you submit your program ...
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SequenceAlignmentLab
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21 Oct 2009 - 17:11 - r1.73
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TWikiGuest
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// Sequence Alignments // By the end of this lab, you should: // be able to find similar proteins to your protein of interest // have an idea of how to perform sequence alignments using available online tools // know where to look for further help on using these tools // Scroll down to the end of the page for the (two-part) homework. // // 0. Before we get started... //
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PerlSequenceSimulator
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08 Oct 2009 - 23:04 - r1.10
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IanHolmes
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// Perl sequence simulator // For this assignment you are asked to write a sequence "simulator" that generates random FASTA sequence files with similar statistics to a real (experimentally sequenced) FASTA file. // Your program should be able to // calculate length nucleotide composition statistics from a FASTA file; // optionally // save those length composition statistics to a named parameter file, or // load length composition statistics from a previously ...
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SampleMidterm
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29 Sep 2009 - 11:33 - r1.124
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IanHolmes
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// Sample midterm questions // Sample questions for the Teaching.BioE131 midterm exam. // Multiple-choice questions // (1) Which of the following are all Perl keywords that can be used to manipulate strings? // (a) foreach, each, for // (b) reverse, uc, chop //
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MidtermFall2008
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29 Sep 2009 - 11:26 - r1.11
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IanHolmes
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// 2008 midterm answers // midterm2008.pdf: Midterm exam // midterm2008-answers.doc: Midterm answer sheet // Please note that the answer sheet is intended as a reference for grading, not a worked discussion. // Some of the "answers" are quite terse; others are merely outlines. // For example, question 26 refers to a Google search. // We obviously did not expect you to Google during the exam (an examination which allowed free access to Google would have its merits ...
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ArraysAndHashesLab
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28 Sep 2009 - 12:07 - r1.138
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TWikiGuest
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// Arrays and Hashes in Perl // By the end of this lab, you should know: // how to use arrays and hashes in Perl // one way to write the reverse complement exercise // some things to keep in mind when doing error-checking // // 0. Before we get started... // In the following lab, we will use a $ symbol to signify a UNIX prompt. The prompt you see in your terminal window may/may not end in a $ , but just remember that you don't actually type in the $ , just the ...
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RNALogicHomework
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14 Sep 2009 - 17:18 - NEW
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IanHolmes
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// Homework // This homework comes in three parts. // Hammerhead ribozyme YES gate // Verify the properties of the YES-1 gate in Figure 2 of the RNA logic gates paper by Breaker and Penchovsky, covered in class: // // NB: the relevant RNA sequence is given in Figure 2. // You should report the following for both the OFF and ON positions of the switch (NB these are exactly the results reported for Fig2a of the Breaker-Penchovsky paper): // 1 Predicted MFE structure ...
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RNAFoldingLab
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14 Sep 2009 - 17:18 - r1.31
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IanHolmes
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// RNA folding lab // In this lab you will learn to use the Main.VIENNA package and various related tools for analyzing, predicting the secondary structure of visualizing RNA sequences. // Predict the structure of the nanos translational control element // To begin with you will predict the secondary structure of the translational control element (TCE) found in the 3'UTR of the nanos gene in the fruitfly, Drosophila melanogaster . // This element is described ...
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BioE131Labs
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14 Sep 2009 - 17:14 - r1.47
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IanHolmes
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// Teaching.BioE131 Labs // Lab Date Comment // 01: Unix 08/30/06 // 02: Biological Databases 09/6/06 // 03: Perl Basics 09/13/06 // 04: Sequence Alignment 09/20/06 // 05: Perl Array Hashes 09/27/06 // 06: Perl Pattern Matching 10/04/06 // 07: Information content of DNA, Teaching.DNAInfoContentHW 10/11/06 // No lab. 10/18, 10/23, 10/25 // 08: gene prediction 10/30/06 // 09: Primate phylogeny 11/06/06 // 10: Pathway mining 11/13/06 //
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PairwiseAlignmentHomework
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14 Sep 2009 - 17:14 - r1.7
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IanHolmes
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// Pairwise alignment homework // NOTE This homework may take you significantly longer than the previous ones, as it is substantially harder. Get started soon! Ask questions! // While you've seen that there are a number of tools that help you compare sequences, it's important to understand what's going on behind the scenes. To that end, you'll be implementing the first dynamic programming string alignment algorithm discussed in class (the Wikipedia:Needleman ...
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BrokenTelephoneTree
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14 Sep 2009 - 17:14 - r1.41
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IanHolmes
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// Broken Telephone Tree // You are the director of a secret police agency, pitted against an imaginary organization using the nefarious tactic of a phone tree. You decide how much information to share with other secret police agencies in reconstructing the structure of the network... // Message analysis from a telephone tree with noise (in the form of edit-distance paths between dictionary words). // Equivalent to certain problems in molecular evolution phylogenetic ...
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HW1_Sol2
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14 Sep 2009 - 17:14 - r1.2
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IanHolmes
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// Set ALLOWTOPICVIEW Main.GraduateStudentInstructorGroup // hw2.pl // # hw2.pl compares the contents of two fasta files // # It will note any sequence names that: // # 1) Are present in the first file, but not the second // # 2) Are present in the second file, but not the first // # 3) Are present in both files, but are associated with different sequencess // # Expected input: // # Two filenames for fasta files in valid fasta format // # Produces an error ...
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PatternMatchingLab
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14 Sep 2009 - 17:07 - r1.105
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IanHolmes
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// Pattern Matching in Perl // By the end of this lab, you should know: // how to write some simple regular expressions in Perl // how to read/interpret a regular expression you see in Perl // how to "capture" information from regular expressions // // Before we get started... // In the following lab, we will use a $ symbol to signify a UNIX prompt. The prompt you see in your terminal window may/may not end in a $ , but just remember that you don't actually ...
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PerlDiff
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14 Sep 2009 - 16:57 - r1.2
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IanHolmes
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// Now, you get to try writing another Perl program, which is a custom version of the Unix diff command. Here are the requirements: // Your task is to compare two FASTA files and determine whether they contain the same set of sequence names and sequence data. If the files are equivalent, the program should exit without printing anything. Otherwise, it should print out the sequence names which... // 1 are present in the first file, but not in the second; // 1 ...
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PerlConceptGraph
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14 Sep 2009 - 14:59 - r1.46
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IanHolmes
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// A graph of concept dependencies in basic Perl for BioE131 // digraph { // Interpreter shape doublesquare,label "Perl Interpreter" ; // OS shape double square,label "Operating System" ; // Scalars shape square ; // Filehandles shape square ; // Regexps shape square ; // Arrays shape square ; // Hashes shape square ; // References shape square ; // Subroutines shape square ; //
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UsingWiki
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08 Sep 2009 - 08:02 - r1.56
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IanHolmes
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// Wiki lab practical // Before this lab, you should already have registered an account on biowiki.org and emailed your username to Main.IanHolmes. If you haven't, please do this now. Be sure to include the text "bioe131" in the subject line of your email. Your account should then be authorized for adding URLs and attaching files. // This lab and the associated homework are pretty straightforward. On the other hand, after the first year of running wiki-based ...
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UnixTutorial
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31 Aug 2009 - 17:03 - r1.62
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IanHolmes
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// (Thank you to the course staff of Bioengineering 144 for this great UNIX tutorial!) // Lab Assignment 1 – Welcome to the world of UNIX // Goals for this lab – By the end of this lab assignment, you will: // Know how to login and out of the DECF machines in Etcheverry. // Feel comfortable with basic UNIX commands // Key to following this lab: Everywhere there is text in Courier font means that it is displayed on screen. Anything in bold Courier that follows ...
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LabSchedule
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31 Aug 2009 - 14:21 - r1.3
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IanHolmes
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// For the times when 1171 Etcheverry is reserved, see here: // http://www.decf.berkeley.edu/help/info/1171-cal.fl.html // Note that the supervised lab times are a subset of the reserved times (see Teaching.BioE131 for details). // The lab assistant hours and office location (for help getting your account) can be found here: // http://www.decf.berkeley.edu/labasst.html // Main.IanHolmes 26 Aug 2008 //
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PerlBasicsLab
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31 Aug 2009 - 14:18 - r1.80
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IanHolmes
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// Perl Basics // By the end of this lab, you should know how to: // write and execute simple Perl scripts in the UNIX environment // use arguments passed in from the command line in your Perl scripts // read data from text files and user input // use the NCBI website to create FASTA files // // 0. Before we get started... // The prompt you get depends on the UNIX shell you're running and other things like preference files. In the following lab, I will use a ...
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LabArraysHashesF05
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31 Aug 2009 - 14:17 - r1.5
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IanHolmes
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// Back to Teaching.UndergraduateClass // Lab 4: Arrays and Hashes in Perl (9/28/2005) // By the end of this lab, you should know: // how to use arrays and hashes in Perl // one way to write the reverse complement exercise // some things to keep in mind when doing error-checking // This lab is a bit long because I want to go through the solutions to the reverse complement exercise in a lot of details, given that it's the first Perl script many of you have written ...
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LabRegExpF05
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31 Aug 2009 - 14:17 - r1.5
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IanHolmes
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// Back to Teaching.UndergraduateClass // Lab 5: Regular Expressions in Perl (10/5/2005) // By the end of this lab, you should know: // how to write some simple regular expressions in Perl // how to read/interpret a regular expression you see in Perl // how to "capture" information from regular expressions // // 0. Before we get started... // In the following lab, I will use a $ symbol to signify a UNIX prompt. The prompt you see in your terminal window may ...
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UnixCheatsheet
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31 Aug 2009 - 14:07 - r1.22
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IanHolmes
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// UNIX cheatsheetBioE 131/231 // (Note: bold words are arguments you specify to the command, i.e. don't type 'file' if you see file …use the filename you want) // Special Directories/Shortcuts // . current directory // .. parent directory // ~username your home directory // wildcard character (eg ' ls .fna ' lists all files ending in .fna ) // Accounts // whoami show user who’s currently logged in // passwd change password // chmod flags file change permissions ...
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UnixLab
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31 Aug 2009 - 14:07 - r1.19
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IanHolmes
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// UNIX // For this lab, follow the Teaching.UnixTutorial. The Teaching.UnixCheatsheet has a nice summary of Unix commands. // Here is a list of other useful UNIX links: // DECF Unix Help page // A short, very basic UNIX tutorial // A list of useful commands, grouped by category // The Webmonkey guide to some of the basic UNIX commands //
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LabBlastEtc
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31 Aug 2009 - 13:58 - r1.19
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IanHolmes
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// Back to Teaching.UndergraduateClass // Lab 7: Sequence Alignments (10/28/2005) // By the end of this lab, you should: // be able to find similar proteins to your protein of interest // have an idea of how to perform sequence alignments using available online tools // know where to look for further help on using these tools // // 0. Before we get started... //
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ProtVizLab
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31 Aug 2009 - 13:58 - r1.81
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IanHolmes
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// Protein Visualization Lab // // // Purpose // To find and visualize functional residues using ET and DARV, two different methods for amino acid conservation detection. // By the end of this lab... // By the end of this lab, you should be able to: //
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BiologicalDatabases
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31 Aug 2009 - 13:58 - r1.52
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IanHolmes
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// Biological Databases // By the end of this lab, you should have: // visited some of the more commonly-used databases in computational biology // know how to search for information on these databases // gotten an idea of the huge amount of biological data that's out there!! // // 0. Before we get started... // This lab only requires the use of a web browser. To make things easier, it might be good to have two browser windows open one kept on this page so ...
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Number of topics: 50
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