Wiki source code of Biometry and bioinformatics I, fall 2014
Last modified by varvio@helsinki_fi on 2024/03/27 10:43
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1.1 | 1 | = (% style="color: rgb(0,51,102);" %)Biometry and bioinformatics I, fall 2014(%%) = | |
2 | |||
3 | ---- | ||
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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]] | ||
8 | |||
9 | === (% style="color: rgb(0,51,102);" %)Scope, type and prerequisites(%%) === | ||
10 | |||
11 | * 5 cr (-> 10 cr by additional work) | ||
12 | * Intermediate / advanced studies in statistics | ||
13 | * ((( | ||
14 | At least basic courses on probability and statistical inference are assumed as prerequisites | ||
15 | ))) | ||
16 | |||
17 | === (% style="color: rgb(0,51,102);" %)Time schedule(%%) (% style="color: rgb(0,51,102);" %)and content scheme and relationships to other courses | ||
18 | (%%) === | ||
19 | |||
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. | ||
26 | |||
27 | |(% class="highlight-blue" data-highlight-colour="blue" %)((( | ||
28 | ==== (% style="color: rgb(0,51,102);" %)Computer session 9.9.14 in C128, 14.15 -> | ||
29 | (%%) ==== | ||
30 | |||
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. | ||
32 | |||
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 | ||
34 | |||
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"]] | ||
37 | |||
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. | ||
41 | ))) | ||
42 | |(% class="highlight-blue" data-highlight-colour="blue" %)((( | ||
43 | (% style="color: rgb(0,51,102);" %)**Computer session 16.9 in C128, 14.15 ->** | ||
44 | |||
45 | Data-collection for assignments 1, 2 and 3. | ||
46 | |||
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"]] | ||
48 | ))) | ||
49 | |(% class="highlight-blue" data-highlight-colour="blue" %)((( | ||
50 | (% style="color: rgb(0,51,102);" %)**Lecture session 23.9 in C128, 14.15 ->** | ||
51 | |||
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. | ||
57 | ))) | ||
58 | |(% class="highlight-blue" data-highlight-colour="blue" %)((( | ||
59 | (% style="color: rgb(0,51,102);" %)**Data-analysis session 30.9 in C128, 14.15 ->** | ||
60 | |||
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. | ||
62 | (% style="color: rgb(0,0,0);" %) | ||
63 | ))) | ||
64 | |(% class="highlight-blue" data-highlight-colour="blue" %)((( | ||
65 | (% style="color: rgb(0,51,102);" %)**Session 14.10 in C128, **(% style="color: rgb(255,0,0);" %) (%%) | ||
66 | |||
67 | * (% style="color: rgb(0,0,0);" %)Assignment 1,2 and 3 presentations | ||
68 | |||
69 | ))) | ||
70 | |(% class="highlight-blue" data-highlight-colour="blue" %)((( | ||
71 | * (% style="color: rgb(0,51,102);" %)**[[attach:Exam 211014_31114.pdf]], **[[attach:exam_gene.txt]], [[attach:bact_genedata1.txt]], [[attach:bact_genedata2.txt]](%%) | ||
72 | (% style="color: rgb(0,51,102);" %)\\ | ||
73 | ))) | ||
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75 | |(% class="highlight-yellow" data-highlight-colour="yellow" %)((( | ||
76 | === **[[MOODLE>>url:https://moodle.helsinki.fi/course/view.php?id=14108||shape="rect"]]** === | ||
77 | ))) | ||
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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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