12-23 March 2018
SB II, Colonel-Kleinmann-Weg 2,
3. Stock, Raum-Nr. 03-544
Day 1 / 12 March Monday / 9:00 - 17:00
Biostatistics / Statistical genetics
Presentations: biostatistics course
Day 2 / 13 March Tuesday / 9:00 - 17:00
Protein coding genes in genomic sequences
Homology I
Homology II
Multiple sequence alignment I
Exercises day 2: 1-UCSC&UniProt / 2-Homology
Day 3 / 14 March Wednesday / 9:00 - 17:00
Multiple sequence alignment II
Phylogenetic analysis
Exercises day 3: 3-MSA / 4-Phylogeny
Support files: file1.fasta file2.fasta file4.fasta file3.fasta
Day 4 / 15 March Thursday / 9:00 - 17:00
Protein structure
Protein structure representation
Protein domains
Protein structure homology modelling
Non-globular proteins
Summary theory (sequence analysis, phylogeny, MSA, structure): MuroMB2018
Day 5 / 16 March Friday / 11:00 - 17:00
Protein interactions
Lecture notes: http://cbdm-01.zdv.uni-mainz.de/~galanisl/netbio/
Seminar session I
Day 6 / 19 March Monday / 9:00 - 17:00
Programming I
Part 1 - Introduction (PDF): R-Course-2018-Intro
Part 1 - Tutorial (PDF): R-Course-2018-Part-1
Programming II
Day 7 / 20 March Tuesday / 9:00 - 17:00
Programming III
Part 1 - Long Exercise 1 (PDF): Migraine
Part 1 - Long Exercise 1 (CSV files): records / users
Part 1 - Long Exercise 2 (PDF): GenesProteins
Part 1 - Long Exercise 2 (CSV files): genes / uniprot
Programming IV
Prerequisites: Packages tidyverse and ggvis
Data files: datasets_danalysis.zip
Lecture notes on "Data Analysis with the tidyverse": http://cbdm-01.zdv.uni-mainz.de/~galanisl/danalysis/
Day 8 / 21 March Wednesday / 9:00 - 17:00
Programming V
Programming VI
Day 9 / 22 March Thursday / 9:00 - 17:00
Kinetic modeling of protein dynamics
Support files: JGU_ProteinBC_22-3-18 / JGU_ProteinBC_22-3-18.ipynb
Seminar session II
Day 10 / 23 March Friday / 9:00 - 17:00
RNAseq
Support files are available at: https://owncloud-ext.charite.de/owncloud/index.php/s/4SVFqEby1sqHo3j
Location:
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.
Files:
tutorial_scientific_article_presentation
Links:
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/