Day 1 / 27 November Monday / 9:00 - 17:00

Fundamentals of Programming in Molecular Biomedicine

Enrique M. Muro's e-book "Fundamentals of Programming for Molecular Biologists with Python

Before the course starts, be sure that you are ready to run Python and you are familiar with the JGU Jupyter server: http://cbdm-01.zdv.uni-mainz.de/~muro/teaching/p4b/mod1-a/WiSe23/c0_set_up/c0_jgu_jupyter_notebook_server.html

Material provided after the class:

On-site exercises

On-site exercises (solutions)

Day 2 / 28 November Tuesday / 9:00 - 17:00

Main points explained during the class today (also PS and PDB):

Main_points.txt

You are expected to take notes during the class. Bring paper and a pen to do (quickly) some exercises during the class. There will be many lectures on:

Protein annotation and protein-coding genes (genomics)/Sequence Homology/ Multiple sequence alignment

We will also work on applied bioinformatics and exercises: technology/databases/programs:

Files needed for some exercises: file1.fasta | file2.fasta | file3.fasta | file4.fasta | snakes.fasta
Solutions to the exercises -> MIER-Exercises-Master2023_SHORT
Some links:
- UniProt -> https://www.uniprot.org/
- NCBI BLAST -> https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins
- Clustal Omega -> https://www.ebi.ac.uk/jdispatcher/msa/clustalo
- T-Coffee -> https://tcoffee.crg.eu/
- Seaview -> https://doua.prabi.fr/software/seaview
- Dotlet: http://dotlet.vital-it.ch
- UCSC: https://genome.ucsc.edu/
- 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/

Day 3 / 29 November Wednesday / 9:00 - 17:00

Protein structure, representation, Protein domains, disorder

Software required: Chimera / JalView

Dr Grynberg's slides -> Low Complexity World - Master Students talk Mainz 2023
Prof Andrade's slides -> lesson1_chimera_7.pdf | lesson2_domains_10.pdf
Ms. Gonvales-Kulik materials -> idp_course_2023 | idp_course_questions_answers_2023

Day 4 / 30 November Thursday / 9:00 - 17:00

Protein structure prediction, low complexity, repeats

Data files: MR1_fasta

Materials: lesson3_model3D_11_MSc.pdf | lesson4_repeats_5.pdf | lesson5_repeatsdbs_6.pdf

Mr. Schumbera's slides -> mastermodule_phasesep_301123 (phase separation)

Day 5 / 1 December Friday / 9:00 - 17:00

Protein interaction networks

Software required: Cytoscape

Ms. Vagiona's slides -> Prediction_PTMS_master_2023

Day 6 / 4 December Monday / 9:00 - 17:00

Biostatistics/Statistical genetics

Software required: R / RStudio Desktop

R-script: Basics_in_R_2023.R (download and rename to remove the .txt extension)

Slides: biostatistics course_WS_2022_2023

Exercises: excercises biostatistics

Solutions: Solutions_Basics_in_R

Day 7 / 5 December Tuesday / 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 8 / 6 December Wednesday / 9:00 - 17:00

Dr Marini's slides and additional material -> https://seafile.rlp.net/d/7f5a7fd9bbd24f269848/

Day 9 / 7 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 / 8 December Friday / 9:00 - 17:00

Dr Distler's slides -> https://seafile.rlp.net/f/ac644093c54e4ea1acdc/?dl=1
Prof Tenzer's slides (1) -> https://seafile.rlp.net/f/a359d2cda3cd4b638c1e/
Prof Tenzer's slides (2) -> https://seafile.rlp.net/f/a9c12c05783c4c9b9e6a/

Software required:

Run Python from the JGU Jupyter server: http://cbdm-01.zdv.uni-mainz.de/~muro/teaching/p4b/mod1-a/WiSe23/c0_set_up/c0_jgu_jupyter_notebook_server.html

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).

Notepad++ and Python: (Fundamentals of programming in Molecular Biomedicine; Enrique M. Muro)

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)