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Network-wide training

OPATHY will provide ESRs with state-of-the-art network-wide training activities. To avoid fragmentation, existing international courses (e.g. T1 Online Research Skills, I3 Creative Thinking and Innovation) will be integrated into the program. Most network training will be based around three 7 to 9-day summer schools that combine research workshops (W), academic modules (A), transferable skills (T), and innovation and entrepreneurship sessions (I). We will invite external speakers and renowned experts in the respective fields and encourage trainees to interact with them.


The follwong courses will be offered during the OPATHY summer schools:


Summer School 1, University of Aberdeen, UK



Date: August 28 - September 2, 2016



Course A1. Introductory course on clinically important yeasts (P2), 0,5 day

Topics include introductory seminars on the biology of important yeast pathogens, their physiology, biochemistry, phylogeny and phylogenomics, clinical aspects, biosafety aspects, immunological interactions with the host, phenotypic versus molecular diagnostics, identification and typing, and immunological/serological detection tools.


Course W1. In vivo and in vitro infection models (P5, P6), 2 days 

Study of infection in microbial pathogenesis, including the assessment of strain virulence. Different models (e.g. rabbit, mouse, fruit fly, and zebra fish) and their specific pro and cons will be discussed. We will cover the 3Rs strategy (Reduce, Refine, Replace), and the legislation and ethics surrounding use of animals in research. Alternative cell-based approaches will be presented.


Course A2. Gender in research training (Yellow WIndow), 1 day 

The training and its materials give the research community practical tools to integrate gender aspects into research in general, and referring to Horizon 2020’s specificities. The training comprises topics as promoting equal opportunities for women and men in research teams (including in decision-making positions) AND integrating a gender dimension in research and innovation. Both topics contribute to excellence in research.


Course T1b. Time and project management, 0,5 day

Time and project management skills in academia and private sector, including setting timelines and targets,
prioritizing, organizing and reporting, using online tools to and achieving higher efficiency.



Winter School 1, Centre for Genomic Regulation, Barcelona, Spain


Date: March 1-4, 2017


Course T1A. Improvement of science communication skills (P2, P1, P4, P5, P9), 2 days

Topics covered in the course:

  • How to make the focus sentence?

  • Storytelling techniques

  • How to simplify a scientific concept by using different analogies?

  • How to make scientific talk engaging by using communication toolbox?

  • How to deal with stage fright and body language when you are presenting?

  • Preparation for the Science Slam


Summer School 2, Hans-Knoell-Institute, Jena, Germany 



Date: August 27 - September 1, 2017



Course W2. Functional genomics and cellular analysis of infection models (P6, P5), 3 days

This course, based on W1, will cover the use of functional genomics and cellular approaches to analyse the different stages of infection, using established in vitro and ex vivo models and alternative in vivo models. ESRs will learn quantification of fungal adhesion, invasion and damage, routes of invasion (discrimination between induced endocytosis and active penetration), cellular and molecular analysis of interactions with host cells (e.g. RNAseq).


Course A3. Clinical Mycology: From bench to bed-side (P8), 2 days

Theoretical and practical knowledge of current practices in how to apply bed side tests, to manage human specimens, interpret results, assess the risk of infections, monitor treatment, check for fungal outbreaks and how to best prevent fungal infections.


Course I1b. Valorisation, IP and entrepreneurial skills (P10, P1, P4, OP2), 0,5 day

It is highly important for OPATHY trainees to become aware of the valorisation potential of their work, and know the potential pitfalls in this challenging process. This course has three parts: A) (Summer School 1): Half-day introduction to increase the trainee’s awareness on the general aspects of valorisation and company creation. B) (Summer School 2): 2-day course to introduce the business plan. The course will cover the process of company creation, including legal forms, business development, sources of capital, market penetration, IP strategies, FDA approval. C) (Final Symposium): Half-day session in which trainees will present and discuss their business cases with experts, and representatives of the four companies in OPATHY will share their experience.


Summer School 3, Valencia, Spain 



Date: 2018


Course W3. Applied bioinformatics and post-genomics techniques (P1-4, P7, PO1, PO2), 5 days, 5 ECTS credits.

Training in post-genomics techniques, in silico data analysis, and applications in diagnosis. Topics will include proteomics and sequencing technologies, analysis of ‘omics’ data, functional analyses, comparative genomics, transcriptomics and proteomics, probe optimisation, data formats, and relevant databases. The course will include basic training in the UNIX environment and a representative programming language (Python). The format will be flexible to accommodate the diverse background of the ESRs so that they can effectively advance their skills.


Course T1C. Grant writing (P1), 1 day

Introduction to science policy and writing successful fellowships. The course will offer lectures on fellowship application and a hands-on exercise in the form of writing a 4-page proposal, evaluated by OPATHY PIs.


Course T2. Ethical, legal and social aspects of clinical research (P9, P2), 2 days

Divided in three modules: A) Biosafety aspects, legislation and ethical aspects of scientific publishing. B) Ethical aspects of the use of animals in clinical research experiments. C) Ethical use of human samples. European and national legislation will be discussed.


Course T1B. Time and Project Management (P1, P4, P7, P10), 1 day

Time and project management skills in academia and private sector, including setting timelines and targets, prioritizing, organizing and reporting, using online tools to and achieving higher efficiency.



Final Symposium, Barcelona, Spain 



Date: 2019


This will be a scientific and learning-by-doing training event. The ESRs will organize the open final symposium on “Fungal Infections” and will be involved in all aspects regarding the organization, including selection of a venue, scientific and social programs, fundraising and finances, advertisement, abstract book, website, etc.  

A number of recognized scientists have already agreed to participate as speakers, and all ESRs of the ETN will deliver scientific talks. This symposium will be open for other researchers in the fields. Since P8 is board member of the European Society for Clinical Microbial Infectious Diseases and P6 is vice-president of the International Society for Human and Animal Mycology, this symposium will be open to the participation of these two societies, which will serve to connect the trainees with practising scientist and clinicians outside OPATHY.



Further Courses 



Course I2. Company development, automation and management (P7, P4, P10, P9), 2 days

Location: Bremen, Germany. Introduction to needs and conditions in a company with commercial goals and customer-related obligations. The implementation of modern tools, such as robotics, into clinical laboratories will be demonstrated and discussed.


Course I3. Creative thinking and innovation (P1) 10 ECTS credits. 3 weeks

Instructors: Variety of individuals from public and private sector. Location: Dublin, Ireland. Schedule: Several offerings per year.

This is an interdisciplinary module run by UCD for mixed groups of ESRs. The aim is to help ESRs to access their ability for independent, creative thinking and innovation. Mechanisms for developing effective multidisciplinary teams are explored using short challenges with varying team composition. Participants gain first-hand experience in how to form and develop creative ideas. They are introduced to cycles of risk, failure, self-evaluation and change. All participants embark on a 1-week intensive project with a public or private host, and share their outcomes in an event called “The Pitch”. All ESRs will have the opportunity to complete a 30 credit Postgraduate Certificate in Innovation and Entrepreneurship at UCD (including course I3), offered in two additional two week blocks over the three year programme.