2017 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 2017 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 | Organizers | Instructors | Schedule | Fees | Scholarships | Apply | Directions | Accomodations | Course materials | Photos | Contact

Date and location

The summer school will be held September 4-7, 2017 at the Center for Regulatory Genomics in Barcelona, Spain.


  • 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


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

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

  • Saahith Pochiraju
    Bioinformatician, Icahn School of Medicine at Mount Sinai

  • Yosef Roth
    Research Assistant, Icahn School of Medicine at Mount Sinai

  • Balázs Szigeti
    Postdoctoral Scholar, Icahn School of Medicine at Mount Sinai

  • Marie Trussart
    Postdoctoral Fellow, Walter and Eliza Hall Institute of Medical Research

  • Marc Weber
    Postdoctoral Fellow, Center for Regulatory Genomics

Content and schedule

The course will be four days long. The first day will feature an introductory lecture and ice-breaker activites. Day 2-4 will feature a combination of lectures, hands-on tutorials, and group discussions.

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. 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 Computational Systems Biology
  • Dresden Summer School in Systems Biology
  • In Silico Systems Biology
  • qBio Summer School


10:00-1:00 pm Tutorial
Samuel Miravet-Verde
1:pm-3:00 pm Lunch
3:00-3:30 pm Welcome
Maria Lluch-Senar
3:30-5:00 pm Ice breaker
Damjana Kastelic
5:00-5:30 pm Lecture
Introduction to whole-cell modeling
Jonathan Karr
5:30-6:00 pm Lecture
Experimental methods and data analysis for understanding whole cells
Maria Lluch-Senar
7:30-10:00 pm Dinner party
15 Carrer de la Fusina
+34 932 68 12 53
9:00-10:30 am Tutorial
Modeling the 3-D structure of the chromosome
Marie Tussart
10:30-11:00 am Coffee break
11:00-12:30 pm Tutorial
Modeling the 3-D structure of the chromosome
Marie Tussart
12:30-2:00 pm Lunch
2:00-3:30 pm Tutorial
Pathway modeling using ordinary differential equations
Verónica Lloréns-Rico
3:30-4:00 pm Coffee break
4:00-5:30 pm Tutorial
Pathway modeling using ordinary differential equations
Verónica Lloréns-Rico
5:30-6:00 pm Discussion
9:00-10:30 am Tutorial
Genome-scale metabolic modeling using FBA
Marc Weber
10:30-11:00 am Coffee break
11:00-12:30 pm Tutorial
Genome-scale metabolic modeling using FBA
Marc Weber
12:30-2:00 pm Lunch
2:00-3:30 pm Tutorial
Stochastic simulation
Jonathan Karr
3:30-4:00 pm Coffee break
4:00-5:30 pm Tutorial
Stochastic simulation
Jonathan Karr
5:30-6:00 pm Discussion
9:00-10:30 am Tutorial
Model composition
Jonathan Karr
10:30-11:00 am Coffee break
11:00-12:30 pm Tutorial
Model composition
Jonathan Karr
12:30-2:00 pm Lunch
2:00-3:00 pm Tutorial
Rule-based modeling
Samuel Miravet-Verde
3:00-4:00 pm Tutorial
Data aggregation
Yosef Roth and Saahith Pochiraju
4:00-4:30 pm Coffee break
4:30-5:30 pm Tutorial
Model testing and validation
Jonathan Karr
5:30-6:00 pm Closing
Maria Lluch-Senar and Jonathan Karr

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).

Registration fee

The registration fee 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 ($430)
  • Industry: €800 ($860)

Travel scholarships

Several scholarships will be available. We expect to be able to give several $1,000 to trainees from non-European institutions.

How to apply

The course application is available online . The application asks 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.

Important dates
  • Application posted: Spring, 2017
  • Application due: May 18, 2017
  • Notification of application decisions: June 2, 2017
  • Summer school: September 4-7, 2017

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.


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

Course materials

All of the slides and course materials are available to the course participants at http://www.wholecell.org/school-2017/private. Please use the username and password provided by the course organizers.


Contact and more information

Please contact Damjana Kastelic or Anna Sole Amat with any logistical questions. Please contact the organizers with any content questions.


Last updated Aug 24, 2017.
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