Overview of the COSMIC workshops

 

Scientific workshops

 

Systems medicine.
Organisers: B1a (AMC), B2 (INRIA), B6 (ANX), B8 (HZI), B9 (IBM), ET5 (Kersten).
Setup: Preparatory e-lectures, presentations, literature discussion, computer labs, patient seminar.
Duration: 3 days e-learning, 2 day workshop.
Topics: Systems medicine, (big) data integration and analysis, bioinformatics, mathematical modelling. Top-down/bottom-up approaches, differential equations, agent-based models, mechanistic models. Computer labs will be provided to the fellows (package ‘R/deSolve’ and ‘CompuCell3D’). Fellows will attend a patient seminar to learn the patient perspective of an immune disorder.
 
Experimental methodologies in immunology.  
Organisers: B1a,b,c (AMC), B3 (KI), B4 (BI), B5 (IFOM), B10 (CER), PO7 (VB).
Setup: Preparatory e-lectures, presentations, literature discussion, discussion of (expected) experiments and data, computer lab.
Duration: 3 days e-learning, 2 day workshop.
Topics: Familiarise and train fellows in the applicability, advantages and pitfalls of the different laboratory techniques used by the partners. Multiparameter flow-cytometry, NGS, and laser-aided microdissection. Immunogenetics, transcriptional and epigenetic (single cell) profiling (RNAseq, ATACseq and ChipSeq). Mouse models to study GC biology. Drug screening. Computer lab statistical OMICS data analysis. Laboratory standardisation. Ethics and research integrity.
 
Immune related diseases.
Organisers:B1b,c (AMC), B3 (KI), B5 (IFOM), B7 (RDX), B10 (CER), PO6 (IW).
Setup: Presentations, patient seminar.
Duration: 1 day.
Topics: Prevention, diagnostic, and (personalised) treatment of patients with BCL and RA. Using animal models for validation of new drugs. Patients and physicians lecture about BCL and RA, also covering socio-economic consequences.
 
 
Bring-your-own systems medicine
Organisers: B1a (AMC), B8 (Helmholtz), B6 (ANX), B4 (BI), B5 (IFOM).
Setup: Discussion and reflection on project cases.
Duration: 2 days.
Topics : Cross-fertilisation between experimental and computational fellows. Experimental fellows are asked to bring a case from their research that they would like to approach with modelling. Vice versa, computational fellows will bring ideas for new experiments as a basis for new models or validation of existing models. During the workshop, proposed models and experiments will be discussed and refined. These experiments/models may be implemented in COSMIC.
 
 
Transferable skills workshops
 
Modern research: Open Science and Advanced ICT
Organisers: B1a (AMC), PO3 (SURFsara), B9 (IBM) (KNIME), ET1 (Dr. Boiten), ET4 (Prof. Lovis)
Setup: Preparatory e-lectures, presentations, computer lab.
Duration: 3 days e-learning, 2 day workshop.
Topics : Principles of Open Science, Open Access, Open Source, Open Education.  Data stewardship. Data standardisation. Open Access clinical and patient data. FAIR Research Data Management. Advanced ICT infrastructures (e.g., Cloud, supercomputing). Cloud tutorial for the analysis of NGS data. Guided tour at the Dutch Computer Center SURFsara. HIPSTER for reconstruction of comprehensive molecular maps based on patient data, public datasets and biomedical literature.
 
Communication and socio-public aspects of research  
Organisers: B1a (AMC), PO4 (BioTecture), PO5 (NBIC), PO6 (IW).
Setup: Preparatory e-learning, presentations, video, Science Cafe.
Duration: 2 days e-learning, 3 day workshop.
Topics: communication of research to non-scientists (general public, patients). Fellows prepare a presentation and short layman video to present their research. Practice their presentation and communication skills. To put the acquired skills to practice, a Science Café is organised for which the general public, students, and patient are invited. Fellows present their work and discuss with the audience societal expectations, animal studies, etc. Fellows make teaching material for secondary school students. Each Fellow will visit a local secondary school to stimulate interest of these students for systems medicine.
 
 
Beyond the university
Organisers: B6 (ANX), B7 (RDX), B9 (IBM), PO2 (KNIME), PO3 (SURFsara), PO7 (VB).
Setup: Presentations, discussion of business cases.
Duration: 1 day.
Topics: skills important for careers in a company. Translational research and different commercialisation models. Open source business models. New business models for the health/systems medicine/P4 medicine sector in the context of High Performance Computing and Big Data technologies. Research-based entrepreneurship. Project planning. Standardisation in industry. Technology transfer between universities and companies.
 
Presenting, explaining, convincing and debating
Organisers: B1a,c (AMC), PO4 (Biotecture), PO6 (IW), ET3 (Ascenion), all COSMIC participants,
Setup: Presentation of project proposal; Science Café. 
Duration:  2 days.
Topics: Project management, risk management, and reporting.  IPR related issues. The proposal from the e-learning course will be further refined through face-to-face meetings Project presentation (e-Learning course 3, 4; see below) to COSMIC scientific researchers (academia/companies). Train the fellows to prepare presentations and review sessions. Presentation styles for different audiences. Defence from questions posed by audience. Science Café where fellows present the relevance of their proposal to the general public, patients, and other stakeholders.

 

Presenting, explaining, convincing and debating
Organisers: B1a,c (AMC), PO4 (Biotecture), PO6 (IW), ET3 (Ascenion), all COSMIC participants,
Setup: Presentation of project proposal; Science Café.
Duration:  2 days.
Topics: Project management, risk management, and reporting.  IPR related issues. The proposal from the e-learning course will be further refined through face-to-face meetings Project presentation (e-Learning course 3, 4; see below) to COSMIC scientific researchers (academia/companies). Train the fellows to prepare presentations and review sessions. Presentation styles for different audiences. Defence from questions posed by audience. Science Café where fellows present the relevance of their proposal to the general public, patients, and other stakeholders.
 
 
Company workshops
 
Redoxis company workshop
Redoxis will run a 1-day workshop at their premises in Lund (Sweden) about potential career prospects that young scientists can have in both industry and SME. Different positions will be discussed by heads of academic departments as well as senior scientists and executives from companies. This will offer fellows the opportunity to pitch a business case for a startup company and have a recorded mock interview with invited business advisors; as well as receive personal feedback on their project, career ambitions, business aspects, IP, trademarks and commercialisation of life science technologies. Representatives from major pharma industries will be invited through contacts within our European Collaboration Networks.
 
IBM company workshop
IBM runs a 1-day workshop at their premises in Zurich (Switzerland) about ‘Research in a company’. With personnel from human resources and applied researchers with different career tracks at IBM. Discussion about differences between research universities and companies.

 

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