TrainMALTA is a collaborative training action between the University of Cambridge (UCAM), the Katholieke Universiteit Leuven (KU Leuven) and the University of Malta (UM).
The specific focus of this action is to provide training on best-practices in bioinformatic analysis, integration of High Throughput Sequencing (HTS) data, and robust quantitative analytical methods as well as training in the use of model systems such as the zebrafish model and induced pluripotent stem cells (IPSCs).
The specific objectives are:
- acquire a solid understanding of the basis of data analysis enabling life scientists to analyse and interpret HTS data within a biological and clinical context
- appreciate the limitations of each technique and analysis pipeline
- enhance collaborations between life scientists, bioinformaticians and statisticians
- develop the skill set necessary to validate HTS data using model systems, all pre-requisites to transitioning HTS from the research lab to the clinic.
Work Package 1 Management: The objective of this WP is the overall management of the project from scientific, administrative, legal and financial aspects; monitoring and reporting on project progress, achievement of milestones and deliverables; coordination of communication between the partners and the EU; organisation of training activities, progress meetings, networking events and the setting up and maintenance of a project website. All 3 partners will play an active role in the execution of this WP.
Work Package 2 Introduction to bioinformatics and statistics for life scientists: This WP will provide an introduction to basic bioinformatics and statistics concepts, which are key for the analysis and interpretation of HTS data. The main aim of this WP is to equip life scientists with a core set of skills which are indispensable to build complex data processing pipelines (WP3)
Work Package 3 Interpreting whole genome sequencing and the epigenetic landscape: This WP will focus on the skill set necessary to interpret data from whole genome sequencing (WGS), the statistical methods required to interrogate both coding and non-coding areas, and methods (biological, mathematical and informatical) to investigate the epigenome.
Work Package 4 From gene discovery to mechanisms – model systems: The focus of this WP will be on the use of model systems to validate candidates identified through HTS.
The model organism Danio renio (zebrafish) has been widely utilised as a model organism for vertebrate development. This WP will focus on the use of morpholinos and CRISPR technology for gene silencing, and gene up-regulation via the injection of capped and polyadenylated wild type or mutant mRNAs in zebrafish.
Another aspect of this WP is training in induced pluripotent stem cells (IPSCs). IPSCs are a newly emerging model system. They can be established from human adult somatic cells and have the ability to grow almost indefinitely and differentiate into different cell types. Training activities within this WP will teach scientists at UoM how to establish and differentiate human IPSC lines using established and novel approaches.
Work Package 5 Dissemination, Networking & Communication: This WP outlines the dissemination, communication and networking events that will be carried out during this project and in the months immediately following the end of the project. These include dissemination events to both the scientific community and the general public, attendance at conferences, publication of scientific literature and networking events.
