Last modified by varvio@helsinki_fi on 2024/03/27 10:43
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1 = (% style="color: rgb(0,51,102);" %)Biometry and bioinformatics I, fall 2014(%%) =
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5 === (% style="color: rgb(0,51,102);" %)Lecturer(%%) ===
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7 [[Sirkka-Liisa Varvio>>doc:mathstatHenkilokunta.Varvio, Sirkka-Liisa]]
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9 === (% style="color: rgb(0,51,102);" %)Scope, type and prerequisites(%%) ===
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11 * 5 cr (-> 10 cr by additional work)
12 * Intermediate / advanced studies in statistics
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14 At least basic courses on probability and statistical inference are assumed as prerequisites
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17 === (% style="color: rgb(0,51,102);" %)Time schedule(%%) (% style="color: rgb(0,51,102);" %)and content scheme and relationships to other courses
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20 * Tuesdays 14-18 in computer class C128, Exactum
21 * I period. **The first session will be 9.9**
22 * The course consists of tutorial lectures during computer sessions, assignments initiated during computer session (completed during student´s own, additional, time).
23 * The spirit of the course is  learning by doing (data-analysis) and reading scientific papers, rather than listening lectures. The general topic is: how to work with sequence data, collecting data from databases - the first steps which are need in the next course, Biometry and bioinformatics II. BB_II.
24 * Assignments 1, 2 and 3 to be submitted 7.10 at the latest. They will be inspected and commented. Assignments 4 and 5 to be submitted 13.10.
25 * Home-exam.
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27 |(% class="highlight-blue" data-highlight-colour="blue" %)(((
28 ==== (% style="color: rgb(0,51,102);" %)Computer session 9.9.14 in C128,  14.15 ->
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31 (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)We familiarize with (%%)[[http:~~/~~/www.ncbi.nlm.nih.gov/>>url:http://www.ncbi.nlm.nih.gov/||shape="rect"]], [[attach:NCBI BLAST.pdf]]. Examples.
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33 Introduction to sequence alignment by ClustalX, [[http:~~/~~/www.clustal.org/>>url:http://www.clustal.org/||shape="rect"]], (installed in C128, ); also [[http:~~/~~/mafft.cbrc.jp/alignment/server/>>url:http://mafft.cbrc.jp/alignment/server/||shape="rect"]] will be introduced
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35 * [[attach:Assignment 1_BB_I_corrections added.pdf]], [[attach:Initial_dataset_for_assignment_1.txt]],[[attach:Initial_dataset_for_assignment_1_aligned.txt]]
36 * [[attach:Assignment 2_BB_I.pdf]], [[http:~~/~~/www.ncbi.nlm.nih.gov/genomes/FLU/aboutdatabase.html>>url:http://www.ncbi.nlm.nih.gov/genomes/FLU/aboutdatabase.html||shape="rect"]]
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38 The plan is that after this session you are prepared to start data collection to assignments 1 and 2. Next session, 16.9 is a tutorial session for data collection for these two assignments.
39 Submit your collected data for assignment 1 to course Moodle-area. It will be checked and commented by Mitja or Siru. No data pre-checking for assignment 2.
40 During the session 23.9 there is a lecture about sequence clustering methods.
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43 (% style="color: rgb(0,51,102);" %)**Computer session 16.9 in C128, 14.15 ->**
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45 Data-collection for assignments 1, 2 and 3.
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47 [[attach:Assignment 3_ BB_I.pdf]], Human mitochondrial genome database: [[http:~~/~~/www.mtdb.igp.uu.se/>>url:http://www.mtdb.igp.uu.se/||shape="rect"]]
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50 (% style="color: rgb(0,51,102);" %)**Lecture session 23.9 in C128, 14.15 ->**
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52 * [[attach:Background for data-analysis.pdf]] (% style="color: rgb(153,51,0);" %) (%%), [[attach:Short tutorial article.pdf]], [[attach:The original NJ-algorithm paper.pdf]]
53 * Demonstration of the software package [[MEGA5>>url:http://www.megasoftware.net/||shape="rect"]].
54 * Data analysis of assignments 1, 2 and 3
55 * [[attach:Assignment 4_BB_I.pdf]], [[attach:Mammalian phylogenetics.pdf]], [[attach:H1N1 phylogenetics.pdf]], [[attach:EBOLA phylogenetics.pdf]], [[attach:Human mtDNA and New World arctic population histories.pdf]], [[attach:Human mtDNA and first dispersals across Africa.pdf]]. Submit your essays 13.10 at the latest.
56 * [[attach:Assignment 5_BB_I.pdf]] Submit this assignment 13.10 at the latest.
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59 (% style="color: rgb(0,51,102);" %)**Data-analysis session 30.9 in C128, 14.15 ->**
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61 * (% style="color: rgb(0,0,0);" %)The session is for practical data-analysis with MEGA5. You should have your data for assignments 1, 2 and 3 collected, and ready to perform phylogeny analyses.(%%) Next Tuesday, 6.10 you are supposed to submit your reports.
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65 (% style="color: rgb(0,51,102);" %)**Session 14.10 in C128, **(% style="color: rgb(255,0,0);" %) (%%)
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67 * (% style="color: rgb(0,0,0);" %)Assignment 1,2 and 3 presentations
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71 * (% style="color: rgb(0,51,102);" %)**[[attach:Exam 211014_31114.pdf]], **[[attach:exam_gene.txt]], [[attach:bact_genedata1.txt]], [[attach:bact_genedata2.txt]](%%)
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76 === **[[MOODLE>>url:https://moodle.helsinki.fi/course/view.php?id=14108||shape="rect"]]** ===
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81 === [[Registration>>url:https://oodi-www.it.helsinki.fi/hy/opintjakstied.jsp?html=1&Tunniste=57795||shape="rect"]] ===
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84 Did you forget to register? [[ What to do?>>doc:mathstatOpiskelu.Kysymys4]]
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