University of Malta

Training Material
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Below is a list of training material which can be viewed/downloaded:

Summer School in Epigenomics

Summer School in Model Systems

2nd TrainMALTA Networking Event

EMBL-EBI Roadshow

HTS Bioinformatics School

[R]efresh - Introductory Course to R

Data Carpentry Workshop 


The summer school on Epigenomics will be organized between the 23rd and 27th July 2018. It will focus on Epigenomics and will cover aspects of transcription factor binding, chromatin modifications, chromosome conformation, DNA methylation and nucleosome positioning, and the integration of this data type with other HTS data, such as gene expression and variation. You can download the protocols that shall be followed throughout the summer school. 



The summer school on Model Systems was organized between the 18th and 22nd September 2017. Two days of the summer school included presentations on iPSCs and model systems given by researchers from UCAM, KU Leuven and UOM. The abstracts of the various presentations can be viewed from here. The remaining three days of the summer school was lab-based and participants performed CRISPR which is a technology used for gene editing. You can download the protocols followed and the results obtained during the summer school. 


The 2nd TrainMALTA Networking Event was organized on the 1st and 2nd of June 2017 at the University of Cambridge UK. On day 1, participants gave presentations on their past and current research. On day 2, genes of interest were analysed during a gene-centred workshop using different data sets (genomic, transcriptomic, epigenomic etc.) generated by research projects at UCAM. Course material from day 2 can be found here

Course Material covered during EMBL-EBI Roadshow which occurred on the 2nd and 3rd of February 2017. Course material covers the following modules: 

1) Ensembl Genomes browsing 

2) Genetic Variation Databases (European Variation Archive)

3) Standards and Ontologies (GO, OLS)

4) Interactions & Pathways (Reactome, IntAct)


NB: Introductory training videos on Ensembl browser can be found in the following links:



Course Material for High Throughput Sequence Bioinformatics Summer School that took place on 12th - 16 September 2016. 

Instructions for downloading and installing RGV, R Studio and SSHFS

Lectures and Presentations

Practical Exercises and Resources - To follow the practical exercises, you will need to download the data files which can be accessed from here


Course Material covered during [R]efresh - Introductory Course to R. The material covers:

  1. An introduction to R - installation of R and introducing basic features
  2. Vectors and Matrices in R
  3. Introduction to functions and basic programming principles in R
  4. Introduction to Data Frames and functions used to load/save data from/to files
  5. Manipulating Data Frames in R - Using dplyr to manipulate data frames
  6. Basic Visualisation - Using the Base Package in R to visualise data
  7. Advanced Visualisations using ggplot2 and R

Note that R and RStudio software are required to follow this course material. 

R can be downloaded 

RStudio can be downloaded from



Course Material covered during Data Carpentry WorkshopCourse material provides instructions on:

  1. How to use spreadsheet programs (such as Excel) more effectively, and the limitations of such programs
  2. Getting data out of spreadsheets and into more powerful tools (such as RStudio)
  3. Data management and manipulation
  4. Data visualisation
  5. Workflows and automating repetitive tasks, in particular using the command line shell
  6. The use of OpenRefine
  7. The use of SQLite
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Last Updated: 17 July 2018

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