CANCELLED: Building minimal cells: From non-essential genes identification to genome engineering, March 27-29, 2018 @ Bordeaux, FR

Minimal cells are extremely significant scientific objects, as their study will bring us closer to understanding what life really is. In addition to this fundamental question, minimal cells are also a keystone of the development of synthetic biology and biotechnology. Indeed, the ability to remove non-essential genes from a genome is crucial to the production of a streamlined organism. Building these minimal cells, perfectly tailored for a given task, promises significant improvement in a wide array bioprocesses ranging from metabolite production to the creation of synthetic cells. The goal of the MiniCell Workshop on “Building Minimal Cells” is to provide young investigators cutting-edge training in the design and production of genome-reduced micro-organisms, for both fundamental and applied sciences.

Why participate?

The course will revolve around two axes: the identification of essential and non-essential genes in a given micro-organism; and the design, validation and implementation of genome engineering tools to produce genome-reduced cells. Participants will be trained in the production and sequencing of transposon libraries in bacteria, Tn-seq data analysis, and the in vitro rapid prototyping and testing of CRISPR-Cas9 genome edition tools. The course will feature a complete day of seminar, with didactic presentations by scientists at the forefront of their fields. This seminar will introduce the participants to the core concepts underlying the production of genome-reduced cells, in the model bacterium Bacillus subtilis and Mycoplasma genitalium. The next two days will be dedicated to hands-on tutorials and experiments in both wet and in silico biology.

Who is the course for?

The course is designed for PhD students and postdoctoral scholars who wish to gain training in genome engineering and genome minimization. Students should already have a good foundation in molecular biology.


The course will focus on teaching students theory and techniques for essential genes identification and genome engineering. Participation in the course requires prior knowledge of basic molecular biology, in particular the manipulation of nucleic acids (DNA & RNA), as well as a basic knowledge of the principles of high-throughput sequencing.


Yonathan Arfi, Bordeaux University, Bordeaux, France
Alain Blanchard, Bordeaux University, Bordeaux, France
Damjana Kastelic, CRG, Barcelona, Spain
Carole Lartigue, INRA, Bordeaux, France
Maria Lluch-Senar, CRG, Barcelona, Spain
Luis Serrano-Pubul, CRG, Barcelona, Spain
Pascal Sirand-Pugnet, Bordeaux University, Bordeaux, France

Instructors and speakers

Mickey Gjerris, Copehaguen University, Denmark
John Glass, JCVI, San Diego, USA
Jonathan Karr, Icahn School of Medicine at Mount Sinai, New York, USA
Jochen Hecht, CRG, Barcelona, Spain
Carole Lartigue, INRA, Bordeaux, France
Samuel Miravet, CRG, Barcelona, Spain
Pascal Sirand-Pugnet, Bordeaux University, Bordeaux, France
Jörg Stülke, Georg-August-Universität, Göttingen, Germany


Duration of the course: The course will start on Tuesday March 27th at 9 am and finish on Thursday March 29th at 5pm.

Number of participants



ISVV –Institute of Vine & Wine Science
210 Chemin de Leysotte, 33140 Villenave-d'Ornon, France

Registration fee

250€ (+ 21% VAT) for academic researchers and 500€ (+21% VAT) for industry.

How to apply

The application is available at the course website . The application deadline is March 1, 2018.

Participants will be selected according to their CV, motivation letter and description of their work. Participants will be notified if they have been selected for the course by the beginning of March, 2018.

More information

Please visit the course website or contact

Whole-cell modeling summer school, September 4-7, 2017 @ CRG, Barcelona ES

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.


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.

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.

More information

Please visit the course website for more information.

Whole-cell modeling summer school, April 3-8, 2016 @ CRG, Barcelona ES

The summer school will teach students how to build whole-cell models through didactic lectures and hands-on active learning exercises on biological pathways, dynamical modeling, hybrid modeling, and strategies for managing model complexity. Students will learn about key intracellular pathways, methods for modeling biological pathways, and the latest methods for constructing models which represent multiple pathways.


The course will be five days long. Each morning will include 2 lectures that will introduce students to biological concepts in metabolism, cellular signaling, and cell cycle regulation, as well as computational concepts in logical, constraint-based, ordinary differential equation, and hybrid modeling. Each afternoon will feature 2 tutorials which will provide students hands-on instruction in model building, model composition, and simulation. The course will also provide students opportunities to present their research, as well as network with the other students and faculty.

How to apply

The summer school will be open to graduate students and postdoctoral scholars. An online application will be available on the course website in Fall 2015.

More information

Please visit the course website for more information.

Graduate and postdoctoral training

The Minicell project will provide hands-on graduate and postdoctoral training in genomics, whole-cell modeling, and genome engineering. Our trainees will also receive professional training in oral and written communication, as well as career counseling.

Please contact the individual partner laboratories for more information and to apply:

  • Experimental genomics @ Center for Regulatory Genomics, Barcelona ES: Luis Serrano
  • Genome engineering @ National Institute for Agricultural Research, Bordeaux FR: Alain Blanchard
  • Microbial pathogenesis @ University of Göttingen, Göttingen DE: Jörg Stülke
  • Whole-cell modeling @ Mount Sinai School of Medicine, New York US: Jonathan Karr

Laboratory exchanges

Our graduate and postdoctoral trainees will also have opportunities for training outside their primary field through exchanges with the other partner laboratories. Trainees will be encouraged to do at least one two-week exchange. The exchanges will enable students to learn additional skills, network with other scientists, and share knowledge from their primary lab.

  • Samuel Miravet from the Center for Genomic Regulation visited Mount Sinai from January to April, 2017.
  • Yosef Roth from Mount Sinai visited the Center for Genomic Regulation from May to June, 2018.
© Minicell Consortium 2015. Last updated March 30, 2018, 9:10 a.m..