Support materials biomedicine master March 2019

6-18 March 2019

SB II, Colonel-Kleinmann-Weg 2,

3. Stock, Raum-Nr. 03-544

Please, note that eating in the room where we will teach is strictly forbidden. In the SB II building there is a room across the main entrance that you can use for eating.

 

Note: seminar day (18 March Monday) is at Biozentrum I, BZ1-HS (room 00.187), Hans-Dieter-Hüsch-Weg 15

 

Day 1 / 6 March Wednesday / 9:00 - 17:00

Biostatistics / Statistical genetics

Presentations available at the Jogustine Reader.

Day 2 / 7 March Thursday / 9:00 - 17:00

Teachers: Dr. Jean-Fred Fontaine, Mr. Steffen Albrecht

Programming I

  1. Prerequisites
    1. software: RStudio
    2. packages (to install within RStudio): tidyverse and ggvis
  2. Introduction: R-Course-2019-Intro
  3. Tutorial:
    1. Data files (to unzip in your user directory): datasets_danalysis.zip
    2. Lecture notes
      1. Online: http://cbdm-01.zdv.uni-mainz.de/~galanisl/danalysis/
      2. Offline: tidyverse_tutorial_GA2018

Programming II

Day 3 / 8 March Friday / 9:00 - 17:00

Teachers: Dr. Jean-Fred Fontaine, Mr. Steffen Albrecht

Programming III

  1. Lecture notes
    1. 06_additional.pdf
  2. Data files
    1. records.csv.gz
    2. users.csv.gz
    3. users2018.tsv.gz
    4. AVGduration.tsv.gz

Programming IV

Day 4 /  11 March Monday / 9:00 - 17:00

Kinetic modeling of protein dynamics

Course materials: 20190311_JGU_ProteinBC | 20190311_JGU_ProteinBC.ipynb

Day 5 / 12 March Tuesday / 9:00 - 17:00 

Summary: MuroMB2019

Protein coding genes in genomic sequences, Homology I

Exercises --> 1-UCSC&UniProt

Homology II, Multiple sequence alignment I

Exercises --> 2-Homology

 

Day 6 / 13 March Wednesday / 9:00 - 17:00

Multiple sequence alignment II

Exercises --> 3-MSA

Phylogenetic analysis

Exercises --> 4-Phylogeny

Data files: file1.fasta | file2.fasta | file3.fasta | file4.fasta

 

Day 7 / 14 March Thursday / 9:00 - 17:00

Protein structure, homology modelling

Low complexity regions / repeats

Presentations: lesson1_chimera_4 | lesson2_domains_5 | lesson3_model3D_6 | lesson4_repeats_2 | lesson5_repeatsdbs_2

Data files: MR1_fasta

 

Day 8 / 15 March Friday / 9:00 - 17:00

Networks

Presentation: ComplexNetworks_Lecture_ML20190315

Exercises: Networks_Exercise 1

Protein interactions

File: genes_Exercise2

Exercises: Exercise2_HIPPIE

 

Day 9 / 18 March Monday / 10:00 - 17:00

Seminars day

Different room!

Biozentrum I,

BZ1-HS (room 00.187),

Hans-Dieter-Hüsch-Weg 15

Location room for seminars day (March 18th Monday 10:00)

 

 

Files:

tutorial_scientific_article_presentation

 

Links:

Get a random human sequence from Uniprot

Protein Data Bank (PDB): http://www.rcsb.org/

PFAM: https://pfam.xfam.org/

UniProt: https://www.uniprot.org/

ClustalOmega: https://www.ebi.ac.uk/Tools/msa/clustalo/

T-Coffee: http://tcoffee.crg.cat/

T-REX: http://www.trex.uqam.ca/

Repeats db: http://repeatsdb.bio.unipd.it/

dAPE: http://cbdm-01.zdv.uni-mainz.de/~munoz/polyx/

Dotlet: http://dotlet.vital-it.ch

Aquaria: http://aquaria.ws/

Polyphen2: http://genetics.bwh.harvard.edu/pph2/