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.

 

COSMIC Annual Meeting. An impression

 
21-25 January, 2019
Amsterdam
 
Workshop Systems Medicine
On 21 January 2019 we kicked off with the Workshop Systems Medicine and computational modelling. The lecturers talked about Systems medicine, ordinary differential equations, stochastic modelling, Gillespie algorithm, agent-based modelling, protein functional interaction networks, gene regulatory network interference. 
 
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The ESRs are listening to a lecture of Sebastian Binder
 
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Sebastian Binder talks about a agent based model about wolves that eat sheep.
 
 
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Judith Farres talks about protein interaction networks and how they can be used to study disease.
 
 
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Olivier Gandrillon talks about computational approaches for gene regulatory network interference
 
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 Maria Martinez introduces the ESRs to noise and stochastic modelling.
 
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 Finalizing the workshop Systems Medicine with a very nice dinner in Amsterdam
 
 
Workshop Advanced experimental methodologies in Immunology
On 22 January 2019 we continued with the Workshop Methodologies in Immunology. Presentations about antibody technology, advanced imaging technologies, advanced Flow-cytometry and novel FACS applications, high throughput analysis of BCR and TCR repertoires, transcriptomics and Epigenetics (single-cell & long-read), and transgenic, reporter and knockout mice in immunology.
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Jeroen Guikema talks about antibody technology
 
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Prof. Eric Reits (Cell Biology, AMC) talks about Advanced Imaging technologies in Immunology.
 
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Berend Hooijbrink talks advanced Flow-cytometry and novel FACS
 
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Dr. Andreas Agathangelidis & Prof. dr. Niek de Vries (MD) explain repertoire sequencing of T-cells and B-cells

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Martin Turner explains transcriptomics and epigenetics (single-cell & long-read) approaches
 
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Rikard Holmdahl and Stefano Casola explain the development and use of transgenic, reporter and knockout mice in immunology
 
During this workshop the ESRs also attended a patient seminar during which a patient with rheumatoid arthritis was interviewed by Niek de Vries. Through this interview the ESRs were informed about the experience of a patient with a severe form of this disease.
 
 
Mid-term review meeting
On 23 January 2019 we continued with the mid-term review meeting during which the EU project officer (Charalampos Moschopoulos) and the COSMIC External Advisory Board were also present. During this meeting the coordinator gave an overview over COSMIC and its current status. Subsequently, the ESRs briefly presented their research projects. Finally, the Project Officer had a private meeting with the ESRs while the PIs and the External Advisory Board discussed various organizational aspects of the project, and received first feedback from the EAB. The feedback received from the EAB was positive although they advised to put more effort to link to experimental work with the computational modelling. The Project Officer was also positive about COSMIC but stressed to keep an close eye on the implementation of the seconment program and to finalize the consortium agreement. 
 
 
Annual meeting
On 24 January 2019 we continued with the annual meeting during which the PIs gave a short update about the research they were planning to do with their ESR(s). Subsequently, the research projects were discussed in smaller groups. Impresssion of the meeting:
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Niek
Michael
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Workshop Modern Research: Open Science and Advanced ICT
On 24 January 2019 we concluded the week with a Workshop about modern research. We had several very interesting talks and discussion about various aspects of scientific projects. The workshop was concluded with a tour at the national computer center SURFsara in Amsterdam. Antoine van Kampen kicked-off with a presentation about Open Science in which we had interesting discussion about open access publishing and data.
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Very tired after a stressfull night
 
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We had a very interesting and entertaining presentation (Clinical Data Reuse or Secondary Use: Current Status and Potential Future Progress) from Prof. dr. Christian Lovis of the University of Geneve. One thing he talked about was the correlation between chocolate consumption and number of nobel Laureates (published in the high impact journal the New England Journal of Medicine)
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Dr. Jan Willem Boiten from Lygature talked about working successfully in public-private consortia 
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New business models for health Prof. dr. Anwar Osseyran University of Amsterdam / SURFsara
 
 
Subsequently, the group went to the Data Tower where they got a guided tour at SURFsara by Dr. Carlos Teijeiro Barjas.  After a check of our ID and giving away our finger print we could enter the building. An impression is shown below. 
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COSMIC NEWS

29 April 2018 2414

EASyM conference

2nd Conference of the European Association of Systems Medicine (EASYM) This conference is…
27 January 2018 1856

Andien Vaes: new controller

New controller: Andien Vaes. Andien Vaes (AMR) takes over the tasks of Don van Velzen.…
23 December 2017 566

Biotecture becomes Science Matters

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

COSMIC Highlights

22 February 2019 69

CERTH Highschool students

Highschool students at CERTH Rerun by popular demand. Bastien of PLANT.ID did so well…
11 February 2018 1318

COSMIC Coffee Mug

First COSMIC Merchandise During the kickoff meeting (8-9 February) all participants…
11 February 2018 697

Kickoff meeting

COSMIC kickoff meeting. 8-9 February, 2018 Amsterdam COSMIC officially started 1st of…

Events

06 May 2018 457

5th European Congress of Immunology

5th European Congress of Immunology 2-5 september 2018 | Amsterdam RAI Exhibition and…
29 April 2018 858

EASyM 2nd conference

2nd Conference of the European Association of Systems Medicine (EASYM) 7 - 9 November…
16 March 2018 1276

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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