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.
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.
Date and location
Fellow, Icahn School of Medicine at Mount Sinai
Staff Scientist, Center for Regulatory Genomics
Group Leader and Director, Center for Regulatory Genomics
PhD Student, Center for Regulatory Genomics
PhD Student, Center for Regulatory Genomics
PhD Student, Center for Regulatory Genomics
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, student talks, and group discussions. 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. 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
Introduction to whole-cell modeling
Genomics and pathway/genome databases
Pathway modeling using ordinary differential equations
Stochastic and rule-based modeling
|TBD||ClosingJonathan Karr and Maria Lluch-Senar|
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- Application posted: Spring, 2017
- Application due: May 18, 2017
- Notification of application decisions: End of May, 2017
- Summer school: September 4-7, 2017
How to apply
Students will be selected based on the prior knowledge and research experience and their desire to participate in the course.
Accepted students will have the opportunity to give an approximately 10 minute presentation on their research.
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)
Numerous hotels are available nearby (see Hotels.com map).
Several scholarships will be available. We expect to be able to give several $1,000 to trainees from non-European institutions.
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.