COSMIC Mission

COSMIC delivers the next generation of systems medicine professionals who successfully combat complex human disorders. We will focus on B-cell lymphoma and rheumatoid arthritis, diseases that originate from abnormal functioning of the adaptive immune system, in particular the germinal center. COSMIC develops and integrates experimental and computational approaches, and establish a unique cross-fertilization between oncology and auto-immunity. 
 
Download: COSMIC Summary
 
  • COSMIC in numbers

    10 Beneficiaries
    7 Partner Organisations
    14 Early Stage Researchers (ESRs)
        -13 PhD students
        -1 Industrial researcher
    5 Companies
    9 European countries
        -NL, FR, SE, UK, IT, ES, DE, CH, EL
    5 Visiting Scientists
    4 External Trainers
    5 Members of External Advisory Board
    1 Ethics Advisor
  • COSMIC Research Background

    Systems Medicine

    One of the key question in systems biology is how biological systems (e.g., cells, molecular networks, germinal center) operate upon interaction with their external environment. Answering this question will generate knowledge about the dy­namics of complex systems and quantitative and explanatory computer models based on ex­perimental data.

    Systems medicine implements systems biology approaches in medical research and practice. This involves iterative and reciprocal feedback between clinical investigations and practice with computational, statistical and mathematical multiscale analysis and modelling of pathogenetic mechanisms, disease progression and remission, treatment responses, and adverse events as well as disease prevention at the individual patient level.

    Systems medicine aims at a measurable improvement of patient health through systems-based approaches and practice.

    Source: CASyM
    See also: EASyM
    Further reading: Schmitz, U., and Wolkenhauer, O. eds. (2016). Systems Medicine (New York: Springer)

    Adaptive immunity
    Germinal Center
    B-cell lymphoma
    Rheumatoid Arthritis
    Computational modelling
  • COSMIC Systems Medicine

    Through collaboration with existing systems medicine initiatives (e.g. EASyM, ISBE) COSMIC researchers contribute to systems medicine infrastructure and best practices that reduce time and costs to address clinical needs.

    At the same time this will promote Europe’s position in the health domain.
  • COSMIC Training

    An important aim of the Marie Sklodowska-Curie Action European Training Network (ETN) is to train young researchers (Early Stage Researchers, ESRs) with multi-disciplinary and multi-sectorial scientific and transferable skills required in systems medicine and translational medicine (WP2).

    COSMIC delivers 14 highly skilled systems medicine professionals who are able to address and solve complex clinical questions and to shape the next generation of systems medicine scientists.

 

Overview of the COSMIC workshops

 

Scientific workshops

 

Systems medicine.
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.  
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.
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 (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  
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.

COSMIC NEWS

29 April 2018 3359

EASyM conference

2nd Conference of the European Association of Systems Medicine (EASYM) This conference is…
27 January 2018 2968

Andien Vaes: new controller

New controller: Andien Vaes. Andien Vaes (AMR) takes over the tasks of Don van Velzen.…
23 December 2017 852

Biotecture becomes Science Matters

Biotecture becomes Science Matters Our Partner Organisation Biotecture changed their name…

COSMIC Highlights

29 September 2019 74

LINK - Extremadura en el Mundo

LINK - Extremadura en el Mundo Our fellow, Rodrigo Garcia Valiente took part as an…
22 February 2019 301

CERTH Highschool students

Highschool students at CERTH Rerun by popular demand. Bastien of PLANT.ID did so well…
11 February 2018 1865

COSMIC Coffee Mug

First COSMIC Merchandise During the kickoff meeting (8-9 February) all participants…

Events

06 May 2018 763

5th European Congress of Immunology

5th European Congress of Immunology 2-5 september 2018 | Amsterdam RAI Exhibition and…
29 April 2018 1267

EASyM 2nd conference

2nd Conference of the European Association of Systems Medicine (EASYM) 7 - 9 November…
16 March 2018 2510

Workshop Applying bioinformatics and data science competency frameworks to ELIXIR Training

Workshop Applying bioinformatics and data science competency frameworks to ELIXIR…

 

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    Project coordination

    Prof. dr. A.H.C. van Kampen (Antoine)
    Bioinformatics Laboratory
    E: a.h.vankampen at amc.uva.nl
    P: +31 20 5667096

    Project management:
    Dr. Laurian Jongejan
    Department of Experimental Immunology
    E: l.zuidmeer at amc.uva.nl
    P: +31 20 5666819

    The Netherlands
    Academic Medical Center, University of Amsterdam

    Marie Skłodowska-Curie Actions

    The Marie Skłodowska-Curie actions (MSCA), named after the double Nobel Prize winning Polish-French scientist famed for her work on radioactivity, support researchers at all stages of their careers. One type of action is the European Training Network (ETN) aimed at joint research training by partners from academia, industry, and other organisation. ETNs facilitate the the researcher to experience different sectors and develop their transferable skills by working on joint research projects.

    H2020

    COSMIC is a European Training Network funded from the European Union's Horizon 2020 research and innovation programme under grant agreement No 765158.









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