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Biowiki's Fall07 web
http://biowiki.org/twiki/bin/view/Fall07
The Fall07 web of TWiki. TWiki is a Web-Based Collaboration Platform for the Corporate World.en-usBiowiki content is in the public domain.IanHolmes [wikigardener@postbox.biowiki.org]IanHolmes [wikigardener@postbox.biowiki.org]BiowikiTWiki.Fall07Biowiki.Fall07
http://biowiki.org/twiki/bin/view/Fall07
http://biowiki.org/twiki/pub/TWiki/TWikiLogos/BioWikiLogo.pngWebChangesGroup
http://biowiki.org/view/Fall07/WebChangesGroup
Pages most recently changed in this group of webs: // URLPARAM{"web"} "} // 2008-10-04T21:05Zroot1.1updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Fall07/WebChangesGrouphttp://biowiki.org/twiki/bin/rdiff/Fall07/WebChangesGroupFinalPresentationSchedule
http://biowiki.org/view/Fall07/FinalPresentationSchedule
Presentations for the !BioE131 FinalProject will take place during the last 3 lectures of the semester (Wednesday 12/5, Friday 12/7 and Monday 12/10). // Please edit this page to sign up for a time. // If there is more than one person in your group (remember that your presentation should be 5 minutes per person ), please sign up for a block of time, using the name of each person in your group. // Name Time Date // Brent Satterfield 3:10 12/5 // 3:15 12/5 // 3:20 12/5 // 3:25 12/5 // 3:30 12/5 // 3:35 12/5 // 3:40 12/5 // 3:45 12/5 // Nikit Kumar 3:10 12/7 // Bushra Samad 3:15 12/7 // Fan Li 3:20 12/7 // Adam Luce 3:25 12/7 // Brian Kim 3:30 12/7 // 3:35 12/7 // Matthew Johnson 3:40 12/7 // Hank Shih 3:45 12/7 // Michael Motion 3:10 12/10 // Sheng-Ying Pao 3:15 12/10 // Thomas Larsson 3:20 12/10 // Jason Keller 3:25 12/10 // Katie Harding 3:30 12/10 // Raffi Hagopian 3:35 12/10 // Simina Ticau 3:40 12/10 // Leland Wong 3:45 12/10 // 2007-11-28T07:14Zyam1.22updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Fall07/FinalPresentationSchedulehttp://biowiki.org/twiki/bin/rdiff/Fall07/FinalPresentationScheduleFinalExam
http://biowiki.org/view/Fall07/FinalExam
Take-home .FinalExam will be given out on Friday 11/30 (at end of class) and must be returned by Monday 12/3 (also at end of class). Main.IanHolmes 27 Nov 2007 // Review on 11/28. // 2007-11-27T12:41Zyam1.3updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Fall07/FinalExamhttp://biowiki.org/twiki/bin/rdiff/Fall07/FinalExamGraduateFinal
http://biowiki.org/view/Fall07/GraduateFinal
BioE241 "final" // The following is a proposal for the loosely styled Teaching.BioE241 in-class "final", to be held on the last day of instruction (Monday December 10th). // The general theme is a discussion of probabilistic computational biology algorithms, methods or models applicable to any/all sections of the following paper: // // Particular examples of discussion topics: // how is "adaptation to radiotolerance" hypotheses II ruled out? // how is the RDRM motif identified? // can you imagine a probabilistic model for the CRISPR or SNR repeats? // how might one construct a sequence analysis workflow for one (or more) of the various tables, in terms of the algorithms concepts covered in class (sequence analysis, HMMs, phylogeny, stochastic processes, ontologies etc.)? // Also note the JgiTour page: BioE241'ers are welcome to sign up. // 2007-11-04T23:26Zyam1.7updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Fall07/GraduateFinalhttp://biowiki.org/twiki/bin/rdiff/Fall07/GraduateFinalFinalProject
http://biowiki.org/view/Fall07/FinalProject
Final project // Brief summmary of rules // The idea of the final project is to expand on one of the homework exercises, labs or lectures. // You will give a 5-minute presentation on this work in class. // Credit // The final presentation will be worth 25 of the final grade. // Teams // You are encouraged to form teams, in which case you will get 5 minutes per person in the team. // You also need to clearly identify the separate contributions of team members. // Multimedia // The idea of the "elaboration" is to extend or riff on the original homework idea: to think about previously undiscussed algorithms or theory issues (or generalizations of the algorithm); to visualize it by showing some previously unseen pictures; or to do a Karaoke song or a standup routine or a videogame pitch... all of these are admissible (though bear in mind that you will be assessed on both scientific content as well as presentation, so do bear this in mind if you choose to go for a multimedia extravaganza...) // You will have full access to the class AV equipment (including speakers) and you can bring your laptop. The time limits will be strictly enforced, with 2- and 4-minute warnings. // 2007 theme // A suggested theme (and this is just a suggestion you're free to pursue other ideas) is the following recent paper from JGI: // // How the theme connects to topics covered in class // This paper discusses the comparative genomics of radiation-tolerant Wikipedia:extremophiles. // The paper contains a lot of bioinformatics analysis and there are many opportunities for you to apply the ideas and algorithms in the class syllabus // (alignment, phylogeny, ontologies, pathway mining, gene prediction, probabilistic analysis, protein structure visualization...) // General idea of projects // The suggestion here is that you describe, analyze, reconstruct or extend some small part of the analysis in this paper using the ideas that we have covered in class or lab. // For example, you could use a program that you have written and compare the results to the ones shown here; // or you could discuss an analysis from the paper, explaining the algorithms together with the biological implications of the results. // Specific hints for starting points // Read papers (e.g. this one) on bioengineering Deinococcus geothermalis for bioremediation of hot nuclear waste dumps // Download Genbank entries for Deinococcus geothermalis and Deinococcus radiodurans // Note that there may be multiple entries, e.g. the D.geothermalis genome spans several plasmids // Make alignments and/or sequence logos for the palindromic "radiation/desiccation response motif" (RDRM) located in upstream regions of radiation-resistance genes // According to the paper, such genes include DR0326, DR0423, DRA0346, DR0070, DR0219, DR0906, DR1913, DR0659 ... // Reproduce the part of the analysis where genes common to both thermophiles are identified // As above, try to identify genes common to both thermophiles, but restrict the search to genes that are implicated in radiation resistance in D.radiodurans // Build phylogenetic trees for gene families of interest // e.g. one of the families in the gene-gains-and-losses figure (Fig 3) or the conserved-gene-alignments figure (Fig 5) // compare the "gene tree" to the "species tree" of the organisms from whence the genes were taken. Are they in agreement? (Sometimes, in bacteria, they aren't: for example, in the lactic acid bacteria, the phylogeny for proteins associated with the transcription/translation machinery is different from the phylogeny of the fermentation-related proteins, suggesting horizontal gene transfer possibly associated with an ecological adaptation) // Look in each genome for genes connected to a particular Gene Ontology term, and make a prediction about the biology of the organisms based on the number of genes you find in that pathway // e.g. are there any genes for tryptophan biosynthesis? If not, the bacterium may be a tryptophan Wikipedia:auxotroph // a starting point might be the metabolic or other processes referred to in the paper, e.g. GO:0005996 (monosaccharide metabolism), GO:0016491 (oxidoreductase activity), GO:0006281 (DNA repair) ... // Caveat // Note (again) that you are free to choose a different topic other than those listed. // Dates // Final presentations will take place during the last 3 lectures of the semester // (Wednesday 12/5, Friday 12/7 and Monday 12/10). // Please sign up on the FinalPresentationSchedule. // 2007-11-04T09:27Zyam1.18updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Fall07/FinalProjecthttp://biowiki.org/twiki/bin/rdiff/Fall07/FinalProjectJgiTour
http://biowiki.org/view/Fall07/JgiTour
Tour of the Joint Genome Institute // On Friday 11/16 there will be no afternoon BioE131 class. Instead there will be an afternoon tour of the Joint Genome Institute, the !DoE sequencing center in Walnut Creek. A bus will leave from the east side of Evans Hall at 1:10pm. // Please click here to edit this page and add your name, if you can attend the JGI tour on 11/16/2007. // Ian Holmes // Josh Kittleson // Raffi Hagopian // Bushra Samad // Simina Ticau // Jason Keller // Matthew Johnson // Oscar Westesson // Lei Qi // Michael Motion // Katie Harding // Lars Barquist // Kristin Robrock // 2007-11-02T17:14Zguest1.13updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Fall07/JgiTourhttp://biowiki.org/twiki/bin/rdiff/Fall07/JgiTourJoshuaArribere
http://biowiki.org/view/Fall07/JoshuaArribere
// Name: Joshua Arribere // Email: jaarribere@gmail.com // Interests: Computational and Molecular Biology, Genetics // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.JoshuaArribereSandbox just for me // Related topics // Main.ChangePassword // 2007-10-28T21:32Zguest1.1updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Fall07/JoshuaArriberehttp://biowiki.org/twiki/bin/rdiff/Fall07/JoshuaArribereNikitKumar
http://biowiki.org/view/Fall07/NikitKumar
// Name: Nikit Kumar // Email: nik4221@berkeley.edu // Interests: Programming and biomedicine. // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.NikitKumarSandbox just for me // Related topics // Main.ChangePassword // 2007-10-14T20:15Zguest1.1updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Fall07/NikitKumarhttp://biowiki.org/twiki/bin/rdiff/Fall07/NikitKumarIvyLin
http://biowiki.org/view/Fall07/IvyLin
// Name: Ivy Lin // Email: i.ifan.lin@gmail.com // Interests: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.IvyLinSandbox just for me // Related topics // Main.ChangePassword // 2007-10-14T20:08Zguest1.1updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Fall07/IvyLinhttp://biowiki.org/twiki/bin/rdiff/Fall07/IvyLinKevinMathews
http://biowiki.org/view/Fall07/KevinMathews
// Name: KevinMathews // Email: kevcbe@yahoo.com // Interests: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.KevinMathewsSandbox just for me // Related topics // Main.ChangePassword // 2007-10-08T19:03Zguest1.1updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Fall07/KevinMathewshttp://biowiki.org/twiki/bin/rdiff/Fall07/KevinMathewsKofiBoakye
http://biowiki.org/view/Fall07/KofiBoakye
// Name: Kofi Boakye // Email: kaboakye@eecs.berkeley.edu // Interests: Learning how techniques from my research area (speech and natural language) are being applied to computational biology. // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.KofiBoakyeSandbox just for me // Related topics // Main.ChangePassword // 2007-09-22T17:09Zguest1.1updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Fall07/KofiBoakyehttp://biowiki.org/twiki/bin/rdiff/Fall07/KofiBoakyeShengYingPao
http://biowiki.org/view/Fall07/ShengYingPao
// Name: Sheng-Ying Pao // Email: pao@berkeley.com // Interests: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.ShengYingPaoSandbox just for me // Related topics // Main.ChangePassword // 2007-09-19T15:33Zguest1.1updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Fall07/ShengYingPaohttp://biowiki.org/twiki/bin/rdiff/Fall07/ShengYingPaoPeterBattaglino
http://biowiki.org/view/Fall07/PeterBattaglino
// Name: Peter Battaglino // Email: pbb@berkeley.edu // Interests: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.PeterBattaglinoSandbox just for me // Related topics // Main.ChangePassword // 2007-09-07T13:39Zguest1.1updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Fall07/PeterBattaglinohttp://biowiki.org/twiki/bin/rdiff/Fall07/PeterBattaglinoAdamLuce
http://biowiki.org/view/Fall07/AdamLuce
// Name: Adam Luce // Email: aluce@berkeley.edu // Interests: My research/academic interests are related to the field of tissue engineering. // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.AdamLuceSandbox just for me // Related topics // Main.ChangePassword // 2007-09-03T17:21Zguest1.1updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Fall07/AdamLucehttp://biowiki.org/twiki/bin/rdiff/Fall07/AdamLuceGloL
http://biowiki.org/view/Fall07/GloL
// Name: GloL // Email: gleinh@berkeley.edu // Interests: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.GloLSandbox just for me // Related topics // Main.ChangePassword // 2007-09-01T14:04Zguest1.1updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Fall07/GloLhttp://biowiki.org/twiki/bin/rdiff/Fall07/GloLBushraSamad
http://biowiki.org/view/Fall07/BushraSamad
// Name: Bushra Samad // Email: bushra@berkeley.edu // Interests: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.BushraSamadSandbox just for me // Related topics // Main.ChangePassword // 2007-08-30T22:09Zguest1.1updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Fall07/BushraSamadhttp://biowiki.org/twiki/bin/rdiff/Fall07/BushraSamadSiminaTicau
http://biowiki.org/view/Fall07/SiminaTicau
// Name: Simina Ticau // Email: simina ticau@berkeley.edu // Interests: I'm currently thinking I want to focus on proteomics/genomics so I'm taking the class to get an introduction to the field. // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.SiminaTicauSandbox just for me // Related topics // Main.ChangePassword // 2007-08-30T13:18Zguest1.1updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Fall07/SiminaTicauhttp://biowiki.org/twiki/bin/rdiff/Fall07/SiminaTicauJasonKeller
http://biowiki.org/view/Fall07/JasonKeller
// Name: Jason Keller // Email: jasonkeller@berkeley.edu // Interests: I'm taking this course in the hopes of figuring out whether or not I might want to specialize in this field. I am especially interested in protein informatics. // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.JasonKellerSandbox just for me // Related topics // Main.ChangePassword // 2007-08-29T20:18Zguest1.1updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Fall07/JasonKellerhttp://biowiki.org/twiki/bin/rdiff/Fall07/JasonKellerRaffiHagopian
http://biowiki.org/view/Fall07/RaffiHagopian
// Name: Raffi Hagopian // Email: RHagopian@Berkeley.edu // Interests: Programming and genetics. // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.RaffiHagopianSandbox just for me // Related topics // Main.ChangePassword // 2007-08-29T19:38Zguest1.1updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Fall07/RaffiHagopianhttp://biowiki.org/twiki/bin/rdiff/Fall07/RaffiHagopianMatthewJohnson
http://biowiki.org/view/Fall07/MatthewJohnson
// Name: Matthew Johnson // Email: matthewjohnson@berkeley.edu // Interests: Tissue engineering primarily, everything else to a slightly lesser degree. I don't know that much about computational biology so I figured I should learn! // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.MatthewJohnsonSandbox just for me // Related topics // Main.ChangePassword // 2007-08-29T18:44Zguest1.1updatedmajorhttp://biowiki.org/twiki/bin/rdiff/Fall07/MatthewJohnsonhttp://biowiki.org/twiki/bin/rdiff/Fall07/MatthewJohnson
