Overview of the COSMIC workshops


Scientific workshops


Systems medicine - January 21st,  2019.
Organisers: B1a (AMC), B2 (INRIA), B6 (ANX), B8 (HZI), B9 (IBM), ET5 (Kersten).
Setup: Presentations, patient seminar.
Duration: 1 day workshop.
Topics: Systems medicine, ordinary differential equations, stochastic modelling, Gillespie algorithm, agent-based modelling, protein functional interaction networks, gene regulatory network interference. Fellows will attend a patient seminar to learn the patient perspective of an immune disorder.
Experimental methodologies in immunology-  January 22nd, 2019  
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: 1 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- ‘The Lymphoma Concept’ & ‘Research Proposal Assignment’ - October 7th, 2019
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 - September 15th 2020
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-  January 25th, 2019
Organisers: B1a (Antoine van Kampen; AMC), PO3 (Anwar Osseyran, Carlos Teijeiro Barjas;SURFsara), ET1 (Dr. Boiten; Lygature), ET4 (Prof. Lovis; University of Geneva)
Setup:  Presentations, Guided tour at SURFsara (national computer center).
Duration:  1 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), Clinical data re-use, working succesfully in public-private projects, new business models for health. Guided tour at the Dutch Computer Center SURFsara. 
Communication and socio-public aspects of research  - October 10th, 2019
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 - October 11th, 2019
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.
Fair and data stewardship - September 18th, 2020
Organiser: PO5 (DTL)
Setup:  Virtual meeting (corona-pandemic)
Duration:  1 day
Topics:  Introduction; The relevance of research data management  (Research data management and the data life cycle, Open science, open access and open data, FAIR guiding principles, Data stewardship). Planning data (Data management plans, informed consent procedures, Funder and journal requirements, Costing data management). ollecting data (Finding data (and the importance of FAIR data), Capture data (importance of metadata, pre-registration), Data security and privacy). Processing and analysing data (Tools for processing and analysing data, Infrastructure for storing and sharing data, Organising data, Versioning and documenting data, Anonymisation, pseudonymisation and personal data). Publishing, preserving data & reusing data (What data should be archived, Archiving for scientific integrity, Archiving for reuse, Archiving non-digital data, FAIR data, Data rights)

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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