2016 Summer School

Whole-cell models are promising tools for predicting phenotype from genotype by accounting for every individual gene and cell function. Whole-cell modeling has the potential to enable rational bioengineering and precision medicine. However, significant work remains to develop fully complete and accurate whole-cell models. The goal of the 2016 Whole-Cell Modeling Summer School is to provide young investigators cutting-edge training in large-scale dynamical modeling and model integration.

Why participate?
The course will be the first course focused on multi-algorithm whole-cell modeling. It will teach strategies for building and managing large models which aren't covered by any other course including multi-algorithm modeling, model organism database curation, surrogate modeling, and software development. The five-day course will feature didactic lectures, interactive hands-on tutorials, and student research talks. The mornings will feature lectures on modeling individual pathways. The afternoons will feature interactive hands-on tutorials on building and analyzing multi-algorithm models to generate and evaluate hypotheses. Throughout the course, students will work toward building a small whole-cell model. In addition, the course will include student talks to enable students to share their own research.

Who is the course for?
The course is designed for PhD students and postdoctoral scholars who wish to gain training in large-scale dynamical modeling. See the pre-requesites section below for more information.

More info
Date & location | Speakers & instructors | Organizers | Schedule | Apply | Fees | Scholarships | Contact

Date and location

The summer school will be held April 3-8, 2016 at the Center for Regulatory Genomics in Barcelona, Spain.


  • James Faeder
    Associate Professor, University of Pittsburgh
    Signaling, rule-based modeling

  • Tim Gardner
    CEO, Riffyn
    Automated experimentation

  • Anne-Claude Gavin
    Group Leader, EMBL Heidelberg
    Protein-protein interactions

  • Peter Karp
    Director, SRI International
    Data curation, pathway/genome databases

  • Edda Klipp
    Professor, Humboldt University of Berlin
    Cell cycle regulation, ODE modeling

  • Julio Saez-Rodriguez
    Group Leader, European Bioinformatics Institute
    Signaling, logical modeling

  • Ian Stansfield
    Professor, University of Aberdeen
    Translational regulation, stochastic modeling

  • Jörg Stelling
    Professor, ETH Zürich
    Central metabolism, ODE modeling

  • Bas Teusink
    Professor, VU University Amsterdam
    Global metabolism, flux balance analysis

  • Barbara Di Ventura
    Group Leader, University of Heidelberg
    Cell division, spatial modeling


  • Yin Hoon Chew
    Postdoctoral Scholar, Icahn School of Medicine at Mount Sinai

  • Verónica Lloréns-Rico
    PhD Student, Center for Regulatory Genomics

  • Samuel Miravet-Verde
    PhD Student, Center for Regulatory Genomics

  • Marie Trussart
    PhD Student, Center for Regulatory Genomics

  • Marc Weber
    Postdoctoral Fellow, Center for Regulatory Genomics


  • Javier Carrera
    Postdoctoral Fellow, Stanford University
    Integrative modeling

  • Jonathan Karr
    Fellow, Icahn School of Medicine at Mount Sinai
    Integrative modeling

  • Maria Lluch-Senar
    Staff Scientist, Center for Regulatory Genomics
    Genomic profiling

  • Luis Serrano
    Group Leader and Director, Center for Regulatory Genomics
    Genomic profiling

Content and schedule

The course will be six days long. Day 2-5 will feature 2-1 h morning lectures, 2-2 h hands-on afternoon tutorials, and student talks. In addition, we will tour the city on the final day.

The course will focus on teaching students theory and techniques for large-scale dynamical modeling. Both computational and experimental researchers are encouraged to apply. However, due to the limited time of the course, the tutorials will assume prior knowledge of dynamical modeling (e.g. ordinary differential equations) and computer programming (e.g. MATLAB or Python). Participants who do not have experience with computer programming and/or dynamical modeling will be paired with participants who do to complete the tutorials. Similarly, participants who do not have extensive biological knowledge will be paired with participants who do.

Unfortunately, due to the limited time of the course, the tutorials will not have time to provide introductions to computer programming and dynamical modeling. There are several other courses which provide introductions to these topics:

  • Coursera Systems Biology courses
  • Advanced Lecture Course on Systems Biology
  • Dresden Summer School in Systems Biology
  • In Silico Systems Biology
  • qBio Summer School


5:30-6:00 pm Welcome
Maria Lluch-Senar
6:00-7:00 pm Lecture
Jonathan Karr
Introduction to whole-cell modeling
7:00-8:00 pm Lecture
Luis Serrano
Genomic profiling
8:00- pm Welcome dinner
9:00-10:00 am Lecture
Peter Karp
Data curation and pathway/genome databases
10:00-11:00 am Lecture
Tim Gardner
Automated experimentation
11:00-11:15 am Coffee
11:15-12:15 pm Lecture
Edda Klipp
Systems biology standards including SBML
12:15-12:45 pm Team building activity
12:45-1:30 pm Lunch
1:30-2:45 pm Tutorial
Peter Karp
2:45-4:00 pm Tutorial
Maria Lluch-Senar
Experimental genome annotation
4:00-4:15 pm Coffee
4:15-6:15 pm Tutorial
Samuel Miravet
Software engineering and testing
6:15 pm Community discussion
What should whole-cell models represent and predict?
9:00-10:00 am Lecture
Jörg Stelling
Central dynamics and ODE modeling
10:00-11:00 am Lecture
Bas Teusink
Global metabolism and FBA
11:00-11:15 am Coffee
11:15-12:45 pm Student talks
12:45-2:00 pm Lunch
2:00-4:00 pm Tutorial
Veronica Llorens
Pathway modeling using ordinary differential equations
4:00-4:15 pm Coffee
4:15-6:15 pm Tutorial
Marc Weber
Genome-scale metabolic modeling using FBA
6:15 pm Community discussion
What can we learn and design with whole-cell models?
9:00-10:00 am Lecture
James Faeder
Cell signaling and rule-based modeling
10:00-11:00 am Lecture
Ian Stansfield
Translational regulation and stochastic modeling
11:00-11:15 am Coffee
11:15-12:45 pm Student talks
12:45-2:00 pm Lunch
2:00-4:00 pm Tutorial
Marie Trussart
Rule-based modeling
4:00-4:15 pm Coffee
4:15-6:15 pm Tutorial
Yin Hoon Chew
Model composition
6:15 pm Poster session
9:00-10:00 am Lecture
Barbara Di Ventura
Cell division and spatial modeling
10:00-11:00 am Lecture
Edda Klipp
Cell cycle regulation and ODE modeling
11:00-11:15 am Coffee
11:15-12:45 pm Student talks
12:45-2:00 pm Lunch
2:00-4:00 pm Tutorial
Jonathan Karr
Whole-cell modeling
4:00-4:15 pm Coffee
4:15-6:15 pm Tutorial
Jonathan Karr
Whole-cell modeling (continued)
6:15 pm Poster session
9:00-10:00 am Lecture
Julio Saez-Rodriguez
Cell signaling and logical modeling
10:00-11:00 am Lecture
Anne-Claude Gavin
Protein-protein interactions
11:00-11:15 am Coffee
11:15-12:15 pm Lecture
Jonathan Karr
Systemizing and accelerating whole-cell modeling
12:15-12:45 pm Closing
Maria Lluch-Senar
12:45- Lunch and tour

Recommended reading

Whole-cell modeling

  • Karr JR, Takahasi K & Funahashi A. The principles of whole-cell modeling. Curr Opin Microbiol 27, 18–24 (2015).
  • Carrera J & Covert MW. Why Build Whole-Cell Models?. Trends Cell Biol 25, 719–22 (2015).
  • Macklin DN, Ruggero NA & Covert MW. The future of whole-cell modeling. Curr Opin Biotechnol 28, 111–115 (2014).
  • Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B Jr, Assad-Garcia N, Glass JI & Covert MW. A whole-cell computational model predicts phenotype from genotype. Cell 150, 389–401 (2012).
  • Tomita M, Hashimoto K, Takahashi K, Shimizu TS, Matsuzaki Y, Miyoshi F, Saito K, Tanida S, Yugi K, Venter JC et al. E-CELL: software environment for whole-cell simulation. Bioinformatics 15, 72–84 (1999).

Metabolic modeling

  • Murabito E, Verma M, Bekker M, Bellomo D, Westerhoff HV, Teusink B & Steuer R. Monte-Carlo modeling of the central carbon metabolism of Lactococcus lactis: insights into metabolic regulation. PLoS One 9, e106453 (2014).
  • Maarleveld TR, Khandelwal RA, Olivier BG, Teusink B & Bruggeman FJ. Basic concepts and principles of stoichiometric modeling of metabolic networks. Biotechnol J 8, 997–1008 (2013).

Intracellular signaling

  • Klipp E & Liebermeister W. Mathematical modeling of intracellular signaling pathways. BMC Neurosci 7, S10 (2006).

Translation regulation

  • Gorgoni B, Marshall E, McFarland MR, Romano MC & Stansfield I. Controlling translation elongation efficiency: tRNA regulation of ribosome flux on the mRNA. Biochem Soc Trans 42, 160–5 (2014).

Cell cycle and division regulation

  • Di Ventura B, Knecht B, Andreas H, Godinez WJ, Fritsche M, Rohr K, Nickel W, Heermann DW & Sourjik V. Chromosome segregation by the Escherichia coli Min system. Mol Syst Biol 9, 686 (2013).
  • Di Ventura B & Sourjik V. Self-organized partitioning of dynamically localized proteins in bacterial cell division. Mol Syst Biol 7, 457 (2011).

Integrative modeling

  • Carrera J, Estrela R, Luo J, Rai N, Tsoukalas A & Tagkopoulos I. An integrative, multi-scale, genome-wide model reveals the phenotypic landscape of Escherichia coli. Mol Syst Biol 10, 735 (2014).

Logical modeling

  • Morris MK, Saez-Rodriguez J, Sorger PK & Lauffenburger DA. Logic-based models for the analysis of cell signaling networks. Biochemistry 49, 3216–3224 (2010).

Rule-based modeling

  • Sekar JA & Faeder JR. Rule-based modeling of signal transduction: a primer. Methods Mol Biol 880, 139-218 (2012).

Pathway/genome databases

  • Keseler IM, Mackie A, Peralta-Gil M, Santos-Zavaleta A, Gama-Castro S, Bonavides-Martínez C, Fulcher C, Huerta AM, Kothari A, Krummenacker M, Latendresse M, Muñiz-Rascado L, Ong Q, Paley S, Schröder I, Shearer AG, Subhraveti P, Travers M, Weerasinghe D, Weiss V, Collado-Vides J, Gunsalus RP, Paulsen I & Karp PD. EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res 41, D605-12 (2013).
  • Reed JL, Famili I, Thiele I & Palsson BO. Towards multidimensional genome annotation. Nat Rev Genet 7, 130-41 (2006).


  • Lluch-Senar M, Delgado J, Chen WH, Lloréns-Rico V, O'Reilly FJ, Wodke JA, Unal EB, Yus E, Martínez S, Nichols RJ, Ferrar T, Vivancos A, Schmeisky A, Stülke J, van Noort V, Gavin AC, Bork P & Serrano L. Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium. Mol Syst Biol 11, 780 (2015).
  • Güell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kühner S, Rode M, Suyama M, Schmidt S, Gavin AC, Bork P & Serrano L. Transcriptome complexity in a genome-reduced bacterium. Science 326, 1268–1271 (2009).
  • Yus E, Maier T, Michalodimitrakis K, van Noort V, Yamada T, Chen WH, Wodke JA, Güell M, Martínez S, Bourgeois R, Kühner S, Raineri E, Letunic I, Kalinina OV, Rode M, Herrmann R, Gutiérrez-Gallego R, Russell RB, Gavin AC, Bork P & Serrano L. Impact of genome reduction on bacterial metabolism and its regulation. Science 326, 1263–1268 (2009).
  • Kühner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P, Castaño Diez D, Chen WH, Devos D, Güell M, Norambuena T, Racke I, Rybin V, Schmidt A, Yus E, Aebersold R, Herrmann R, Böttcher B, Frangakis AS, Russell RB, Serrano L, Bork P & Gavin AC. Proteome organization in a genome-reduced bacterium. Science 326, 1235–1240 (2009).

Synthetic biology

  • Gardner TS. Synthetic biology: from hype to impact. Trends Biotechnol 31, 123–5 (2013).
  • Marchisio MA & Stelling J. Computational design tools for synthetic biology. Curr Opin Biotechnol 20, 479–85 (2009).

Important dates

  • Application posted: September 1, 2015
  • Application due: December 15, 2015
  • Notification of application decisions: Early January, 2016
  • Oral abstract submission: Winter 2016
  • Notification of oral presentation decisions: Winter 2016
  • Summer school: April 3-8, 2016

How to apply

An online application will be available in September 2015. The application will ask for brief descriptions of why you want to participate in the course, your background, and your current research, as well as your CV.

Selection criterion
Students will be selected based on the prior knowledge and research experience and their desire to participate in the course.

The online application is available here and due December 15, 2015.

Oral abstract submissions

Accepted students will have the opportunity to apply for 12-minute oral presentations. An online application will be available in early winter 2016. The body of the abstract, including references, will be limited to 4,000 characters including spaces.

Registration fee

The registration free includes all materials needed for the course, lunches, coffee breaks, a welcome dinner, and the city tour. Students are responsible for their lodging, breakfasts, and dinners.

  • Academia: €400 ($440)
  • Industry: €1000 ($1100)


Numerous hotels are available nearby (see Hotels.com map).

Travel scholarships

Several scholarships will be available. We expect to be able to give approximately $1,000 to trainees from a US-based institutions. We expect to be able to award two additional scholarships for registration fees for non-US-based participants. To apply for a scholarship, answer "yes" to the question "Would you like to apply for travel grant?" in the application form.

How to get to the school @ The Center for Genomic Regulation (CRG)

The course will be held at the Center for Genomic Regulation (CRG) at the Parc de Recerca Biomedica de Barcelona (PRBB) at 88 Carrer del Doctor Aiguader, Barcelona 08003, Spain.

The CRG is accessible by taxi and bus/train from the Barcelona-El Prat Airport

  • Taxi (15 min)
  • Bus (1 h): (1) Take bus A1 toward Catalunya Place to Espanya Place. (2) Take bus D20 toward Passeig Maritim to Carrer Trewalny. (3) The PRBB is across the street.

Contact and more information

Please contact Sharon Bel Nieto with any logistical questions. Please contact the organizers with any content questions.


Last updated Jan 18, 2016.
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