Resources and opportunities

Resources and opportunities

This project focuses on planning and delivering a suite of training, mentoring and coaching activities.

UM, UCAM and KU Leuven will organise three summer schools which will be held at the University of Malta (UM). Summer schools will run yearly and will last for 1 - 2 weeks and will consist of lectures and hands-on sessions. Each summer school will focus on a different aspect of training.

Summer School in HTS bioinformatics score skills was held between 12 and 16 September 2016 and focused on basic bioinformatics, statistics and related aspects including introduction to experimental design, commandline open-source tools in UNIX, data handling and visualisation using R, accessing high throughput data from public repositories and good practice for reproducible data analysis. Summer school participants will have the opportunity to handle RNA-seq and human variation (such as exome sequencing) data. Access the course material.

Summer School in Model Systems which was held between 18 and 22 September 2017 focused on imparting the basics in the utilisation of model systems for the elucidation of the function of genes or mutations within candidate genes. The summer school was both lecture based and lab based. Researchers from the University of Cambridge, KU Leuven and the University of Malta gave presentations on model systems including the zebrafish (Danio rerio) and the common house fly (Drosophila melanogaster) and their use for gene silencing and gene up-regulation. Another session was dedicated to presentations on iPSCs and their uses and applications for cell re-programming in order to induce adult somatic cells to revert to the pluripotent stage as well as induction mechanisms that can push cells down various differentiation pathways. With regards to the lab-based sessions, participants learned how to perform CRISPR which is a technique used for gene editing. Access the Summer School material.

Summer School in Epigenomics was held between 23 and 27 July 2018 at the University of Malta Campus. The summer school covered 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.

The Bioinformatics Training Facility of the UCAM’s School of the Biological Sciences has an established bioinformatics training programme of short courses and workshops which provide practical training in the latest biomedical research techniques and bioinformatics tools for researchers and clinicians. All courses take place in Cambridge, UK and are open to all members of the TrainMALTA project.

This will provide additional opportunities to members of the UM for training in basic programming (R, Python, Perl), in how to get the most out of widely used data resources such as European Bioinformatics Institute databases and in downstream analysis approaches (such as network analysis with Cytoscape). All of these topics would be complementary to HTS training and help participants develop bioinformatics skills crucial to their future scientific carrier.

A Data Carpentry Workshop was organised on the 16 and 17 May 2016 to teach basic concepts, skills and tools for managing, analysing and sharing more effectively large amounts of data collected during research. The event was open to University of Malta students and researchers who were trained by our collaborators from UCAM. Access the course material.

A Training Workshop in R, [R]efresh, was held between 31 August and 2 September 2016 which also served as a refresher course in preparation for the HTS summer school which was held in September 2016. Access the course material.

An EMBL-EBI Roadshow was held on 2 and 3 February 2017. Experienced EBI training experts provided a combined presentations and hands-on practical sessions guiding attendees through the use of selected databases and tools. Access the course material.

A Policy Meeting on Genomic Medicine on 19 September 2017 at the University of Malta Valletta Campus. This policy meeting brought together leading academic scientists and researchers, consultants, and policy makers with a series of presentations and open discussion surrounding policy making in a genomics era.

The Train the Trainer (TtT) event was held on 24 July 2018 at the University of Malta Msida Campus. This workshop was meant to provide new trainers with guidance and tips for developing and delivering training; exploring the motivations behind learning, reviewing a range of methods to engage learners and keep them actively learning, examining the requirements for a successful course and acquiring appropriate feedback.Resources csn. Download the presentation.  

A Genomics Workshop was held from 17 to 20 September 2018 in Cambridge, UK. The three-day workshop tackled these challenges through seminars, discussions and hands on training on long-range sequencing, analysis of whole genome data, non-coding space, machine learning and AI, variant calling using machine learning and protein-protein interactions.

Yearly networking meetings will be organised throughout the project. The aim of these meetings is for scientists and students to meet, present their ongoing work, their results and their plans for taking forward their current research in an environment that will help foster the building of networks that can serve as a basis to future collaborative projects.

The First Annual TrainMALTA Networking Event was held on 25 and 26 April 2016 at the University of Malta Valletta Campus. A number of students and researchers from all three universities gave presentations about their research. Download the abstracts of the works presented  .

The Second Annual TrainMALTA Networking Event was held on 1 and 2 June 2017 at the University of Cambridge, UK. On the first day, researchers from UM, UCAM and KU Leuven gave short presentations of their past and present work. Download the abstracts of the work presented  . On the second day, genes of interest were analysed during a gene-centred workshop using different data sets (genomic, transcriptomic, epigenomic etc.) generated by research projects at UCAM. All expenses were covered by the TrainMALTA funds.

The consortium will run an active exchange programme, whereby students and staff from UM will spend extended time periods with the other partner institutions to learn and apply unique methods and technologies.

At the host institutions participants will integrate within the relevant research groups such as the groups of Prof. Willem Ouwehand, Dr Cedric Ghevaert and Prof. Anne Ferguson Smith at UCAM and Prof. Kathleen Freson at KU Leuven participating in all aspects of research activities within that group. The aim of these exchanges is to provide UM researchers with hands-on experience of Bioinfomatic techniques (Work Package 2) as well as laboratory techniques such as zebrafish manipulation (Work Package 4), the study of epigenetic changes (Work Package 3) and establishing and handling IPSCs lines (work Package 4) which they can then take back to the UM and disseminate amongst other active researchers there.

If you are interested in participating in an exchange programme contact us by email.

Funding for Courses and Conferences

The TrainMALTA grant can fund students and researchers to attend courses and conferences that are related to the scope of this project, such as conferences and courses offered by:

  • The Bioinformatics School in UCAM
  • Wellcome Genome Campus
  • The European Bioinformatics Institute, EBIas well as other national and international conferences in related areas.
  • European Society of Human Genetics, ESHG

Follow the instructions if you are interested in applying for funding.

Subscription to relevant software programs and databases can be funded by TrainMALTA.

Current subscriptions/licence include:
NextGENe - Next Generation Sequencing Software for Biologists
BioDiscovery -  A comprehensive tool for genetic data analysis and management for clinical labs
Strand NGS - An integrated platform that provides analysis, management and visualization tools for next-generation sequencing data
Sequencher DNA sequence analysis software

For more information contact us on email.