Support materials biomedicine master March 2017

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

Lecture slides: chimera_3 | lesson_domains_2 | lesson_model3D_4_short

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:

PDB: http://www.rcsb.org/pdb/

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

 

Files:

tutorial_scientific_article_presentation