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Topics in Teaching web:
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Changed: now 01:26 GMT
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Changed by:
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WebStatistics
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07 Oct 2008 - 07:57 - r1.270
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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: // // Oct 2008 4423 19 0 311 304 WebStatistics 137 135 LabArraysHashes 116 90 WebIndex 85 84 PerlSequenceSimulator 77 76 LabPerlBasics 61 MesoscaleMolecularDynamicsSimulationOfRnai 17 Main.TWikiGuest 1 Main.AllisonBerke 1 Main.IanHolmes // Sep 2008 28978 52 0 2125 1791 BioE131 1291 1113 UsingWiki 777 591 WebRss 533 470 ...
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PerlSequenceSimulator
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06 Oct 2008 - 15:07 - r1.4
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AllisonBerke
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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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NussinovAlgorithm
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06 Oct 2008 - 15:06 - r1.4
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TWikiGuest
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// This lab and homework will involve implementing the 1978 Nussinov algorithm for RNA folding. // Lab for 12/8 and 12/10 // Nussinov R, Piecznik G, Grigg JR and Kleitman DJ (1978) Algorithms for loop matchings. SIAM Journal on Applied Mathematics. // DurbinBook // Graduates will implement more sophisticated versions of the algorithm, e.g. Nussinov 1980: // // Main.IanHolmes 27 Aug 2007 //
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ProtVizLab
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06 Oct 2008 - 15:06 - r1.76
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TWikiGuest
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// Protein Visualization Lab // Lab for 12/1 and 12/3, due a week later (12/10) // // // 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... //
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PathwayMining
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06 Oct 2008 - 15:05 - r1.44
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TWikiGuest
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// NOTE this lab is not currently working. Someone needs to go through this and make sure the right databases with the right types of accessions/names are set up. There's currently a disconnect somewhere. // Pathway Mining // Lab for 11/24 and 11/26, due a week later (12/3) // Tools // This practical involves using getuniprot.pl, // a script that extracts, in FASTA format, the subset of Main.UniProt that // 1 has one or more annotations descended from a given ...
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PrimatePhylogeny
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06 Oct 2008 - 15:05 - r1.106
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TWikiGuest
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// Primate phylogeny practical // Lab for 11/17 and 11/19, due a week later (11/26) // Goals // Investigate whether humans are, indeed, related to apes // Brief exposure to phylogenetic tree-building software // Procedure //
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BacterialGenePrediction
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06 Oct 2008 - 15:04 - r1.141
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TWikiGuest
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// Bacterial Gene // Lab for 11/10 and 11/12, due a week later (11/19) // 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 ...
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InformationContentOfDNA
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06 Oct 2008 - 15:04 - r1.130
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TWikiGuest
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// Lab for 11/3 and 11/5, due a week later (11/12) // 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 ...
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LabSeqAlign
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06 Oct 2008 - 15:04 - r1.65
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TWikiGuest
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// Sequence Alignments // Lab for 10/27 and 10/29, due a week later (11/5) // 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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RNAFolding
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06 Oct 2008 - 15:03 - r1.5
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TWikiGuest
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// RNA folding lab // Lab for 10/20 and 10/22, due a week later (10/29) // 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. // Fold a hammerhead ribozyme sequence // Data: // Rfam:RF00163 // Wikipedia:Hammerhead ribozyme // Genbank:AF404053.1 // Outline: //
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LabRegExp
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06 Oct 2008 - 15:03 - r1.102
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TWikiGuest
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// Pattern Matching in Perl // Lab for 10/13 and 10/15, due a week later (10/22) // 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 ...
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UsingWiki
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15 Sep 2008 - 13:07 - r1.42
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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. Your account should now be authorized for adding URLs and attaching files. // The purpose of this lab is to familiarize yourself with the general concept of a wiki, the specific syntax of biowiki.org (which is slightly different from the syntax of other wikis, such as Wikipedia, that you may have encountered) and ...
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BioE131
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12 Sep 2008 - 10:52 - r1.279
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AllisonBerke
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// BioE131/231 // Introduction to Computational Biology. // Course info // Code: Bioe131/231 // Title: Introduction to computational biology // Instructor: Ian Holmes (office hours: 11am-noon Wednesdays, 1-2pm Fridays, 374C Stanley Hall) // GSI: Allison Berke (office hours: 11am-noon Mondays, 12-1pm Fridays, 6112 Etcheverry, and by appt (berke at berkeley.edu )) // When: //
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WebPreferences
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15 Aug 2008 - 12:37 - r1.21
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IanHolmes
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// Web Preferences // The following settings are web preferences of the web. These preferences overwrite the site-level preferences in ., and can be overwritten by user preferences (your personal topic, eg: .TWikiGuest in the web). // Preferences: // Top buttons // Set TOPBUTTONS // Koala skin: // Set SKIN koala // Set NAVBARH // Set NAVBARF // Set NOWEBSBAR //
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WebHome
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31 Jul 2008 - 11:58 - r1.39
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IanHolmes
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// Teaching links // Links on this page refer mostly to classes taught by Ian Holmes in the Department of Bioengineering at UC Berkeley. // Classes // Please select one of the following links: // Class wikis: // class wiki // Computational Biology class pages (more info): // Teaching.BioE131 //
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BioE241
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10 Dec 2007 - 10:00 - r1.160
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IanHolmes
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// BioE241 // Class info // Title: Probabilistic modeling in computational biology // Instructor: Main.IanHolmes // Class: !BioE 241 // When: Fall semester // Lectures: MF 11-12:30, 621 Stanley Hall // Note room change (previously 425 Hearst Mining Building) //
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RGBColors
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18 Nov 2007 - 19:26 - NEW
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JoshKittleson
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// white 255 255 255 // red 255 0 0 // green 0 255 0 // blue 0 0 255 // magenta 255 0 255 // cyan 0 255 255 // yellow 255 255 0 // black 0 0 0 // aquamarine 112 219 147 // blueviolet 159 95 159 // brass 181 166 66 // brightgold 217 217 25 // brown 166 42 42 //
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TempLab
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10 Oct 2007 - 20:02 - r1.60
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JoshKittleson
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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) // 1 For each column $i$ in the alignment: // 1 ...
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StyleGuidelines
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12 Sep 2007 - 02:05 - r1.10
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JoshKittleson
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// Overview and Rationale // Most programming languages provide a great deal of flexibility in the syntax they allow. Different programmers have different styles, and this freedom allows each person to program in a style that he/she is comfortable with. However, without the careful application of some set of consistent guidelines, the clarity of a program may suffer. Consider this example from the wikipedia entry on obfuscation: // The following program is a ...
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UnixTutorial
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29 Aug 2007 - 14:06 - r1.60
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JoshKittleson
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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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ToDoList
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25 Jun 2007 - 15:53 - r1.43
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IanHolmes
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// List of teaching tasks for Fall 2007 semester // Teaching.BioE131 // Refer to Teaching.BioE131Modalities for more detailed class plan. // Put together the reader // Organize "Biophysical Principles" slides: HACKING, DOGMA, PROTEINS, MOTIFS, NUSSINOV // Prepare PROTEINS NUSSINOV labs; wikipages for DOGMA/DATABASES reading homework (e.g. DogmaReview, TranscriptionReview, TranslationReview, ProteinSecondaryStructureReview, ProteinDomainStructureReview, NucleicAcidSecondaryStructureReview ...
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UnixCheatsheet
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18 Jun 2007 - 14:48 - r1.21
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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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UndergraduateClassComments
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18 Jun 2007 - 14:29 - r1.24
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IanHolmes
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// Click here to add a comment to this page: // All parties are invited to comment on the Teaching.UndergraduateClass proposal. // UCB Bioengineering faculty and student comments are especially welcomed. // Please endeavor to make the comments brief, positive and specific. // // Kimmen Sjolander, 28 Feb 2005: I also recommend including at least one lecture on different aspects of Main.ExperimentalDesign. // This could touch on Main.SyntheticBiology... IanHolmes ...
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YeastRegulatoryNetworkAnalysis
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18 Jun 2007 - 14:25 - r1.4
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IanHolmes
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// Goals // Introduction to microarrays, functional genomics, systems biology // Get a feel for large-scale datasets e.g. in yeast // Analyze classic yeast cell cycle data: // Use Main.KMeansClustering to partition microarray data // Use TavazoieChurch algorithm to find DNA-protein binding sites in promoters // Data // Spellman et al (what else?) // Software //
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WikiPrize
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18 Jun 2007 - 14:25 - r1.25
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IanHolmes
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// Wikiprize award for UCB Bioengineering website design // The WikiPrize will be awarded annually to teams or individuals, // comprised of Main.IanHolmes' Teaching.GraduateClass and Teaching.UndergraduateClass members, // for the creation of an outstanding science website. // Competitors (teams or individuals) will design and build a scientific website // (database, browser, wiki, blog, chatroom, newswire; whatever) and run it for 6 months. // Competitors will ...
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VisualizingNucleicAcidStructure
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18 Jun 2007 - 14:25 - r1.11
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IanHolmes
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// Goals // Visualize concepts of DNA/RNA topology and geometry such as // major and minor groove; DNA- and RNA-protein interactions // propellor twist; sequence dependence of DNA structure // winding number, supercoiling // tRNA structure // Gain exposure to molecular visualization software (Pymol) // Data // DNA // A-form DNA: PDB:1ANA // Identify the major and minor grooves //
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SimulatingGenomeEvolution
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18 Jun 2007 - 14:25 - r1.9
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IanHolmes
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// Goals // Simulate the evolution of a genomic DNA sequence using realistic rules // Understand forward simulation with a Markov chain // Investigate the ability of algorithms like Main.SmithWaterman and Main.NeedlemanWunsch to detect homology // ...at the sequence level ("are these sequences related"?) // ...and at the residue level ("are these residues aligned"?) // (Optional) Make an animation of an evolving DNA sequence // Software // grammar.pl // Main ...
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RecommendedGraduateClasses
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18 Jun 2007 - 14:25 - r1.12
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IanHolmes
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// Here are a few links to RecommendedGraduateClasses for this Spring. // Probably too late for most of your Telebears decision processes but oh well. // Stat 246 with Terry Speed. A highly statistical class covering population genetics, RH mapping and microarrays, as well as sequence analysis // Math 127 with Bernd Sturmfels, pursuing the mathematical connections of these compbio models in more depth // MCB 145, Steve Brenner and Mike Eisen's Genomics class ...
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SpikesBook
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18 Jun 2007 - 14:09 - r1.5
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IanHolmes
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// Rieke, Warland, de Ruyter van Steveninck and Bialek. // Spikes: Exploring the Neural Code. // ISBN:0262681080 // Link to the publishers' page. // Summary: Neural computation in terms of information theory and statistical decision theory. //
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UndergraduateClass
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18 Jun 2007 - 14:00 - r1.204
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IanHolmes
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// BIOE 131/231 Introduction to Computational Biology Fall 2005 // Note: this is the page for the Fall 2005 class. For Fall 2006, please go to the new Teaching.BioE131 page. // Announcements // (12/8/05 Main.AngiChau): Please be sure to check the UndergraduateClassProject page for some updated details about the final project report. Your final project report should be emailed to both Main.AngiChau and IanHolmes. // (11/30/05 Main.AngiChau): This week's lab ...
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RevComp
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18 Jun 2007 - 13:59 - r1.7
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IanHolmes
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// back to Teaching.UndergraduateClass // Remember that there are many ways to write a program in Perl, so this is just one possible way to write it // Reverse complement a FASTA file. // (a) Write a Perl program to do the following: // Open a file, whose filename is specified by the user as a single command-line argument. That is, if the name of your Perl script is programname and the name of the file is filename, then the script should be run by typing the ...
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RelativeEntropy
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18 Jun 2007 - 13:57 - r1.32
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IanHolmes
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// Some notes on relative entropy and information content // Shannon information content // The "Shannon information content" of outcome x under probability distribution p is // $h p(x) \log 2 p(x)$ // Shannon entropy // The "Shannon entropy", or average information content, is // $H p \langle h p(x) \rangle p$ //
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SampleMidterm
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18 Jun 2007 - 13:55 - r1.119
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IanHolmes
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// Sample midterm questions // Sample questions for the Teaching.BioE131 midterm exam. // Please note that calculators will be required for the exam. // Multiple-choice questions // (1) Which of the following are all Perl keywords that can be used to manipulate strings? // (a) foreach, each, for //
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SubmissionInstructions
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18 Jun 2007 - 13:50 - r1.9
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IanHolmes
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// Back to Teaching.UndergraduateClass // BIOE 131/231 Electronic Homework Submission Instructions // First of all, please note that if your files you want to submit are not on a DECF be131-XX account you received during the first week, you will have to email your files to the GSI, since the submission script currently cannot handle transferring of files outside of the be131-XX set of accounts. // Login to a DECF machine, then at the terminal prompt, type: ...
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UndergraduateClassProject
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18 Jun 2007 - 13:49 - r1.46
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IanHolmes
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// Back to Teaching.UndergraduateClass main page // // Project description: Bacterial Genome Analysis, Bioe131/231 Fall 2005 // // In this project you will be asked to analyse an anonymous bacterial genome for clues about the biology of the organism. // The genome in question was sequenced by the Joint Genome Institute in Walnut Creek for one of their experimental collaborators. // It has not yet been released to Genbank, EMBL or any other public database. ...
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UndergraduateClassFeedback
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18 Jun 2007 - 13:49 - r1.15
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IanHolmes
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// // i think the perl lectures should be moved to the lab sessions. that way, people who already know how to program can choose not to attend and people who don't know how to program can learn while being able to play with code at the same time. the other alternative is to require dr. arkin's class (be142?) or an ability to program in perl as a prerequisite. in any case, i don't think teaching perl syntax during lecture is a great idea and the lectures can ...
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Number of topics: 50
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