Day 1 / 20 March Monday / 14:00 - 17:00 / Hörsaal Anthropologie
Biostatistics/Statistical Genetics
Lecture slides: Biomedicine_course_Day1_Biostatistics_v2
Day 2 / 21 March Tuesday / 9:00 - 17:00 / Hörsaal Anthropologie
Supervised & unsupervised learning/Clustering/PCA
Lecture slides:
Biomedicine_course_Day2_Statistical_genetics
http://prezi.com/vcfyx2ckvazi/?utm_campaign=share&utm_medium=copy
http://prezi.com/ihptuzuecepm/?utm_campaign=share&utm_medium=copy
Programming
Support files: Literals.ipynb
Lecture slides: Python4Biologists.pdf
Day 3 / 22 March Wednesday / 9:00 - 17:00 / Hörsaal Anthropologie
Programming
Support files: Sequences.ipynb | shrub_dimensions.csv | Conditionals.ipynb
Lecture slides: see Day 2
Day 4 / 23 March Thursday / 9:00 - 17:00 / Hörsaal Anthropologie
Programming
Support files:
Regex.ipynb | sequences.tsv | IfForWhileRevisited_v2.ipynb | Python4Biologists2
Lecture slides: see Day 2
Day 5 / 24 March Friday / 14:00 - 17:00 / Hörsaal Anthropologie
Programming
Support files: Python4Biologists_Regex
Lecture slides: see Day 2
Day 6 / 27 March Monday / 9:00 - 17:00 / Hörsaal Anthropologie
Programming
Support files: python-stats.ipynb | python-stats_exercises_corrected.ipynb | geno_chr1 | FORMULAS | phenos map_chr1
6.1 Sequence analysis, homology (block 1)
Support files: exercises_UCSC+uniprot
Day 7 / 28 March Tuesday / 9:00 - 12:45 / 15:15 - 17:00 / Hörsaal Anthropologie
7.1 Sequence analysis, homology (block 2)
Support files: exercises_homology
7.2 Multiple sequence alignments
Exercises and solutions: exercises_alignments
7.3 Phylogenetic analyses (block 1)
Support files: file1_fasta.txt | file2_fasta.txt | file3_fasta.txt | file4_fasta.txt
Exercises and solutions: exercises_phylogeny
Day 8 / 29 March Wednesday / 9:00 - 17:00 / Hörsaal Anthropologie
8.1 Phylogenetic analyses (block 2)
Support file: file5.fasta
8.2 Protein structure, Chimera
Main points (Enrique Muro): Muro_MB2017
8.3 Repeats and homorepeats
Lecture slides: lesson_bias_6_short
Day 9 / 30 March Thursday / 9:00 - 17:00 / Hörsaal Anthropologie
9.1 Protein interaction networks
Presentation: http://cbdm-01.zdv.uni-mainz.de/~galanisl/netbio/
Support tools: HIPPIE | UniProt
9.2 Dynamics / Modeling
Support file: Biomedicine Master 2017, dynamic modeling-Students.ipynb
Slides: JGU_ProteinBCshort
Solutions to exercises: https://github.com/baumgast/Biomedicine-teaching
Day 10 / 31 March Friday / 10:15 - 16:00 / Seminar room, Institute of Genetics
Seminars 15 to 27.
Links:
timetree: http://timetree.org/
UniProt: http://www.uniprot.org
Genome browser (UCSC): https://genome.ucsc.edu/
BLAT (UCSC): https://genome.ucsc.edu/cgi-bin/hgBlat
BLAST (PDB): http://www.rcsb.org/pdb/secondary.do?p=v2/secondary/search.jsp#search_sequences
BLAST (NCBI): http://blast.ncbi.nlm.nih.gov/
BLASTp (NCBI): https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
PFAM: http://pfam.xfam.org/
Dotlet: http://dotlet.vital-it.ch
Aquaria: http://aquaria.ws/
Polyphen2: http://genetics.bwh.harvard.edu/pph2/
TMHMM: http://www.cbs.dtu.dk/services/TMHMM/
RepeatsDB: http://repeatsdb.bio.unipd.it/
dAPE: http://cbdm-01.zdv.uni-mainz.de/~munoz/polyx/
HIPPIE: http://cbdm-01.zdv.uni-mainz.de/~mschaefer/hippie/index.php