Day 1 / 7 March Monday / 9:00 - 17:00

Introduction slides: intro_1

Fundamentals of programming in Molecular Biomedicine (with Python)

Guidelines: c0_set_up_v1.0

Day 2 / 8 March Tuesday / 9:00 - 17:00

Sequence Homology

Multiple sequence alignment

Summary of the day:

MuroMB2022.txt

For the exercises:

Files needed for exercises:
- File1 -> file1.fasta
- File2 -> file2.fasta
- File3 -> file3.fasta
- File4 -> file4.fasta
- Snakes.fasta -> snakes.fasta
Solutions -> SHORT-Exercises-Master2022

Day 3 / 9 March Wednesday / 9:00 - 17:00

Protein structure, homology modelling

Low complexity regions / repeats

Presentations: lesson1_chimera_6 | lesson2_domains_7 | lesson3_model3D_8 | lesson4_repeats_4

Data files: MR1_fasta

Software required:

Chimera: install current production release from https://www.cgl.ucsf.edu/chimera/download.html (protein 3D representation; Miguel Andrade)

JalView: install from http://www.jalview.org/getdown/release/ (alignment and structure representation; Miguel Andrade)

Day 4 / 10 March Thursday / 9:00 - 17:00

Repeat databases / Disorder in proteins

Presentations: lesson5_repeatsdbs_5 | idp_course_with_answers_2022

Proteomics

Presentations: 20220310_Proteomics_Intro_UD | Lecture MS2022_Part1_MassSpectrometryIntro-compressed

Day 5 / 11 March Friday / 9:00 - 16:00

Protein interaction networks

Presentations: Master_ProteinBiochemBioinfo_2022_PPIs_1_2_KL | Master_ProteinBiochemBioinfo_2022_PPIs_3_KL | Master_ProteinBiochemBioinfo_2022_PPIs_4_KL | Master_ProteinBiochemBioinfo_2021_PPIs_5_KL

Software required:

Cytoscape: (Protein networks; Katja Luck)

Day 6 / 14 March Monday / 9:00 - 17:00

Biostatistics / Statistical genetics

R-script: Basics_in_R_1.R (download and rename to remove the .txt extension) | Solutions_Basics_in_R.R (download and rename to remove the .txt extension)

Presentation: biostatistics course_2022

Software required:

R: https://cran.r-project.org/

RStudio Desktop: https://rstudio.com/products/rstudio/download/ (the free version!)

Day 7 / 15 March Tuesday / 9:00 - 16:30

RNAseq

Software required:

CRAN and Bioconductor (https://bioconductor.org/) packages: (RNAseq analysis, Federico Marini)

For the bulk transcriptome analysis:
# install the Bioc installer
install.packages("BiocManager")
# install Bioc version 3.14
BiocManager::install(version = "3.14")
# install specific Bioconductor packages
BiocManager::install(c("pcaExplorer", "ideal", "GeneTonic", "macrophage", "org.Hs.eg.db", "clusterProfiler", "iSEE"), dependencies = TRUE)

Check all packages are installed by calling library("package_name") e.g.
library("DESeq2")
library("pcaExplorer")
library("ideal")
library("GeneTonic")
library("iSEE")
... should return no error

Day 8 / 16 March Wednesday / 9:00 - 17:00

Programming with R (I)

Introduction slides: R-Course-2021-Intro

Tutorial: click here (includes all material)

If the link to the tutorial is broken, you can use the following link to download a ZIP archive containing the tutorial and required data files: 20210310_R_tuto_ggplot

Day 9 / 17 March Thursday / 9:00 - 17:00

Programming with R (II)

Extra exercises: click here

Software required:

Please, install in your computer and test prior to the corresponding lesson. If you have problems installing any of the indicated software then email the corresponding contact person (in brackets).

Chimera: install current production release from https://www.cgl.ucsf.edu/chimera/download.html (protein 3D representation; Miguel Andrade)

JalView: install from http://www.jalview.org/getdown/release/ (alignment and structure representation; Miguel Andrade)

Cytoscape: (Protein networks; Katja Luck)

R: https://cran.r-project.org/

RStudio Desktop: https://rstudio.com/products/rstudio/download/ (the free version!)