Training programme

To fully exploit emerging single-cell technologies for the understanding of developmental mechanisms, it is essential to train a fully proficient new generation of scientists in data science next to fundamental biology. Through individual thesis projects, secondments and a common training programme, the Doctoral Candidates will be trained in the essential enabling technologies that are urgently needed in the field: single cell technologies, liquid biopsy, deep profiling, spatial data analysis, multi-omic data integration and systems immunology. 

They will also develop complementary transferable skills regarding communication, dissemination, intellectual property and entrepreneurship, that will foster their carrier in research and contribute to the long-term deployment of the project objectives. 

Network-Wide Training Events

The training programme will include common training events and conferences. 

TE1: Kick-off meeting

Project Kick-off meeting in Stockholm.

TE2: Conference “Genomics of Complex Diseases: New Challenges (FPS) 

This 2-day Symposium (1 ECTS) aims to overview genetic, epigenetic, regulatory and functional aspects of genomics studies as well as the new challenges posed by new advances in sequencing of the microbiome and its relationship with the immuno metabolome and the integration of various sources of “omics” data in the understanding of complex diseases, focused on systemic autoimmune diseases. The scientific program will include microbiome studies in lupus and other autoimmune diseases, studies on the immuno metabolome and strategies for the clustering and integration of omics data for the reclassification of autoimmune diseases using single-cell analyses.

TE2: Ethical considerations in experimental research (FPS)

This 1-day workshop (0.3 ECTS) will cover the basic principles of ethics in animal experimentation and personalized medicine, how to use Systematic Reviews and meta-analysis in fundamental and preclinical studies and the use of human material and data. This will stimulate best practices and increase awareness of applicable ethical principles and guidelines.

TE3: Virtual journal club (FPS)

An online journal club will be organized once a month, with the aim to create a common forum for bioinformaticians and wet lab scientists to learn to speak a common language. This journal club will run throughout the program, and will be organized by a rotating system of all partners involved.

TE4: Experimental design (UBO)

This 3-day course (1 ECTS) will teach DCs the basics of setting up experiments for single-cell research. In addition to the logistic aspects of planning experiments on human and mouse tissues, special care will be given to the statistical aspects of experiment design.

TE5: Single-cell data generation and analysis (CRG-CERCA, OMNISCOPE)

This 10-day course (2 ECTS) will teach DCs what it takes to prepare, generate and process single-cell genomics data. The first part will teach different methods for single cell library preparation for sequencing. In addition, the logistical aspects and statistical underpinnings of current single cell methods, including uncertainties and limitations, will be discussed. The second part will span the entire process from the gene expression quantification, quality control to different data analysis types. A focus will be on the integration of data from single-cell and spatial (including in situ) sequencing to derive spatially resolved transcriptome maps.

TE6: Personal development and career plan (LUMC)

This 0.5-day workshop (0.5 ECTS, including individual preparation time) will help the new researchers map out their career plan for the duration of this project and beyond (where they want to go next). It will look at the sets of key skills they will have to acquire as young scientists, and how these will be developed during the project.

TE7: Mass cytometry and imaging (DRFZ, FLUIDIGM, VIB)

This training event (5 days) will cover a basic introduction to the CyTOF technology, followed by an in-depth training on the actual experimental set-up and operational use of CyTOF systems. This will include a session on panel-design, best practices and general troubleshooting guidelines. The last part of the training session will provide the participants with the basics of state of-the-art computational analysis of mass cytometry data. DCs will first learn how to export and import FCS files, perform quality control, automated gating and advanced data visualization. Finally, some more advanced data mining tasks, such as clustering of patients based on cytometry data will be tackled. This training event will be organized as a joint event with the German Society for Cytometry, in particular the German Mass Cytometry User Forum25.

TE8: Basics of machine learning and bioinformatics (VIB, UNICT)

This 5-day course (2 ECTS) will introduce DCs to basic computational methods for data analysis and bioinformatics. Participants will first learn the basics of data pre-processing, quality control and the different types of machine learning tasks that can be performed. Next, they will acquire expertise in working with simple command line tools, simple scripting, using third party tools for complex tasks, integrating tools and tasks to build pipelines, and programming. At the end of the meeting hackathons of biologists and bioinformaticians will introduce technological challenges to the participants and will create a favorable environment for the development of novel and additional solutions not yet included at this point in time.

TE9: Data integration and spatial omics (UNICT, CRG-CERCA )

This 3-day workshop (1 ECTS) will teach DCs how to use more advanced computational approaches to integrate various types of (omics) data and how to integrate it with spatial data (e.g. as generated by spatial omics/CyTOF imaging).

TE10: Public communication (UBO, ATRYs)

This 2-day workshop (1 ECTS) will address approaches to tune the communication to different audiences in terms of level of knowledge and cognitive skills, and cover the do’s and don’ts of social media communication. Several tangible outputs will be produced. First, the workshop will coach participants to write (or improve) a Wikipedia entry which relates to their work. Next, it will focus on two types of social media to be used in public communication: Twitter and YouTube. The DCs will produce their first SIGNATURE tweets and write a short script for a movie about their research.

TE 12: Starting a biotech company (ALTRABIO, OMNISCOPE)

This 1-day workshop (0.5 ECTS) will teach DCs what it takes to set up a company in biotech. Founders of ALTRABIO and OMNISCOPE will talk about setting up a company, making a business plans and dealing with customers.

Local training

While network events will be carried out in English, DCs will be also encouraged to learn the local language of their primary host laboratory to facilitate their rapid integration into their host institution and the local community. Suitable language courses can be available through most of the universities at which the DCs are registered for their PhD. Health and safety training will be provided locally by each individual hosting institution or laboratory (including secondments), immediately after DC recruitment. Moreover, specific training in the use of experimental techniques requiring specialized instrumentation will require an additional local training.