5-16 December 2022
00-445 (N33) NatFak Hauptgebäude
Day 1 / 5 December Monday / 9:00 - 17:00
Fundamentals of programming in Molecular Biomedicine
Solutions to Python exercises:
Day 2 / 6 December Tuesday / 9:00 - 17:00
Biostatistics/Statistical genetics
R-script: Basics_in_R_1.R (download and rename to remove the .txt extension)
Software required: R / RStudio Desktop
Solutions to the exercises: Solutions_Basics_in_R.R (download and rename to remove the .txt extension)
Presentation: biostatistics course_WS_2022_2023
Day 3 / 7 December Wednesday / 9:00 - 17:00
Protein annotation and protein-coding genes in the genome
Sequence Homology
Multiple sequence alignment
Phylogenetic trees
Summary of the classes: Muro Summary
Extra exercises:
- Exercises -> MIER-Exercises-Master2022_upload
- File needed for exercises -> snakes.fasta
Day 4 / 8 December Thursday / 9:00 - 17:00
Protein structure, representation, Protein domains, disorder
Software required: Chimera / JalView
Presentations: lesson1_chimera_7 | lesson2_domains_8 | idp_course
Day 5 / 9 December Friday / 9:00 - 17:00
Protein interaction networks
Files: Kaplanis_28_genes_annotated | Kaplanis_285_genes | Kaplanis_285_genes_annotated | Kaplanis_285_IntAct.cys | Cytoscape_tasks
Software required: Cytoscape
Presentations: PPI_networks (folder in MS teams) | Machine Learning _pdf
Day 6 / 12 December Monday / 9:00 - 17:00
Protein structure prediction, low complexity, repeats
Data files: MR1_fasta
Presentations: lesson3_model3D_9 | lesson4_repeats_5 | lesson5_repeatsdbs_6
Day 7 / 13 December Tuesday / 9:00 - 17:00
RNAseq
Presentations: TranscriptomeAnalysis (folder in MS teams)
Dynamic modelling, miRNA prediction
Data files: sequences_mirna.fa (download and rename to remove the .txt extension)
Presentations: DynamicModelling_ProteinKinetics (1) | mirna_lecture
Day 8 / 14 December Wednesday / 9:00 - 17:00
Programming with R (I)
Software required: R / RStudio Desktop
Here you will find the Introduction Slides
For most of the time we will work with a comprehensive tutorial containing introductions and exercises. You can open this tutorial via this link
Day 9 / 15 December Thursday / 9:00 - 17:00
Programming with R (II)
Software required: R / RStudio Desktop
Additional exercises are available to practice the skills you just learned and to get more routine in using R. The extra exercises are available here
Day 10 / 16 December Friday / 9:00 - 17:00
Proteomics
Presentations: Proteomics (folder in teams)
Software required:
Please, install in your remote desktop and test prior to the corresponding lesson using https://apps.zdv.uni-mainz.de/. If you have problems installing any of the indicated software then email the corresponding contact person (in brackets).
Chimera: (protein 3D representation; Miguel Andrade)
JalView: (alignment and structure representation; Miguel Andrade)
Cytoscape: (Protein networks; Katja Luck)
R: (Programming with R; Max Sprang)
RStudio Desktop: (Programming with R; Max Sprang)
Links:
Protein Data Bank (PDB): http://www.rcsb.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
BLAT (UCSC): https://genome.ucsc.edu/cgi-bin/hgBlat
BLAT (UCSC european mirror): https://genome-euro.ucsc.edu/cgi-bin/hgBlatcommand=start
Blastp (NCBI): https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&BLAST_SPEC=&LINK_LOC=blasttab&LAST_PAGE=blastp
Timetree: http://www.timetree.org/