2016 Summer School

Date and location

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

Speakers

• 
  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

Instructors

• 
  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

Organizers

• 
  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.

Pre-requisites
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

Schedule

• Day 1
• Day 2
• Day 3
• Day 4
• Day 5
• Day 6

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).

Genomics

• 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.

Apply
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)

Accommodations

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.

Sponsors