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Systems Chemistry School 2015, Jena, 19 - 25 September 2015

COST Action CM1304 Systems Chemistry School 2015
The  COST action CM1304 - Emergence and Evolution of Complex Chemical Systems - invites for their international summer school on computational systems chemistry taking place in Jena, Germany,  from 19 - 25 September 2015 under the auspice of Friedrich Schiller University Jena and the COST action CM1304 .



The Systems Chemistry School offers an intensive 6 days introduction to modern computational systems chemistry for experimentally working scientists from all levels. It will provide theoretical background and hands-on experience that will help to setup a theoretical and computational foundation for experimental work in the area of systems chemistry.

Target Audience

Experimentally working scientists from all levels (Phd students, postdoctoral and senior researchers, etc.).

If you are from a formal background and would like to study the exciting methods listed below in more detail, you are welcome as well.


The program consists of seven courses, each providing the theoretical background and two sets of practical exercises using selected tools. The teaching will consist of  a mix of lectures and hands on exercises with a strong focus on educating the participants on how to apply the learned modelling approaches and software tools to concrete example problems. A wide range of modeling techniques ranging from discrete to continuous and from deterministic to stochastic approaches will be covered by the summer school program.

The planned topics are (subject to change):

ODEs (xpp auth): students will learn to translate chemical reaction equation into ODEs and to integrate them to get the time behaviour. study signal-response curves of small networks of coupled linear modules (buzzer, sniffer, etc).

Petri-nets (lola): students will learn how to translate reaction equations into a Petri-net and how to analyse their properties using Petri-net theory.

Gillespie-type Simulations (stochkit): students will learn to setup stochastic simulations. In particular examples will be used that show different behaviour from Process algebras including small and large particle numbers. How to check the correctness of a stochastic simulation will be also discussed.

Process Algebras (SPiM): students will learn what a process algebra is and will formulate and simulate chemical reaction systems as well as infection-biology models in pi-calculus.

Graph Grammars (MØD): students will learn how to write a chemical graph grammar and to generate hypergraph of the possible molecules and reactions spanned by the grammar. The hypergraph will be used as input for deterministic and/or stochastic simulation of the network's time behavior. 

Reaction-diffusion Systems (t.b.d.): Students will learn how to model and simulate spatial chemical reaction-diffusion systems.

Autocatalytic Sets and Chemical Organization Theory (OrgAnalysis): students will learn how to identify the hierarchical structure of a complex reaction network and how to describe its qualitative dynamics as a movement in the space of chemical organizations. In hands on exercises students will investigate examples from autocatalytic sets and chemical computing.

Optional topic: Self-assembly and rule-based modeling (kapa, BioNetGen, SR-Sim): Students learn how to setup and simulate a rule-based model and how to simulate self-assembly processes with it in 3D space.



Saturday, 19 September 2015
   18:00 Welcome Reception Buffet at the Akademiehotel
             Am Stadion 1, 07749 Jena

Sunday, 20 September 2015

   09:00 Lectures begin, Accouchierhaus, Jenergasse 8

Friday, 25 September 2015

   13:00 Lectures end

   13:00 - 14:00  Farewell lunch


Accouchierhaus, FSU Jena, Jenergasse 8

Fees and funding

Participation is free of charge. However, you have to apply to get admission (see below).

Fellowships are available for participants from COST countries, approved NNC Institutions, and from approved European RTD Organisations.
The that cover the hotel (in double rooms, double occupancy, which we book for you) and also travel support up to approx. 340,- EUR (exceptions can be made on request and availability). For single room occupation an extra cost applies (approx. 20 - 30 EUR / night).

Trainees not eligible to be reimbursed:
  1. Trainees from approved IPC institutions
  2. Trainees from approved IO, the EC and EU Agencies
  3. Any other Trainees not specifically mentioned as being eligible

We welcome participants from all levels, e.g..,  Phd students, postdocs and experienced scientists.


Application is closed now.

If you wish to participate, please contact the organizer directly.

General Notes

Applicants are welcome from all countries. Enrollment is limited. Language is English.

Laptops and Posters

Participants should bring their laptops for the practical exercises.

Participants are welcome to bring posters.



We strongly recommend to travel by train:

Note that booking in advance can save a significant amount of money. A discount usually implies that you are bound to a specific train.


If you need to fly, there are many target airports more or less close to Jena. They are all well connected by fast trains. We recommend to combine a single air trip with a train trip.


Erfurt (60min)

Leipzig (90min)

Berlin (3h)

Frankfurt (3h)

(You can reach Frankfurt and Berlin (Schönefeld Airport) after the summer school ends on Friday at 16:00, i.e., you can take back a plane leaving from Berlin or Frankfurt from 17:30 on Friday)

Altenburg (3h)

Hannover (3h; on Friday there at 16:40)

Nürnberg (3h)


Participants (trainer and trainees) will stay together at the  Akademie Hotel with a short walk through the Paradies to the summer school venue near the Phyletic Museum.


If you have any questions concerning the local organization, please contact the local organizer

    Peter Dittrich

If you have questions concerning the COST action funding, please contact the COST action coordinator.


The summer school is financially supported by the EU COST action CM1304 - Emergence and Evolution of Complex Chemical Systems  .