Parisian Master of Research in Computer Science
Master Parisien de Recherche en Informatique (MPRI)

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cours:c-1-36 [2019/09/10 14:16]
phs [WG2 Atelier “Loop-Elimination in FIFO automata” / Ph. Schnoebelen]
cours:c-1-36 [2019/10/01 16:15] (current)
mfuegger [WG1 Atelier “Distributed synthetic microbiology” / M. Függer]
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 **Langue:** Anglais  **Langue:** Anglais 
  
-**Salle:** TBA+**Salle:** C311
  
 **Mots clés:** distributed systems, microbiology, synthetic biology, circuit design, dynamic systems **Mots clés:** distributed systems, microbiology, synthetic biology, circuit design, dynamic systems
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 **Estimation du volume de travail personnel demandé:** Approximately 5h/week (2h/week in class). **Estimation du volume de travail personnel demandé:** Approximately 5h/week (2h/week in class).
  
-**Participants:** +**Participants:** Bourreau Y., Crepon P.-A., Fournis d'Albiat J., Lecroel M., Le Mogne L., Yax N.
  
 **News:** **News:**
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       * Todo until next time:       * Todo until next time:
          * Write me a subscribe mail          * Write me a subscribe mail
 +
 +  * Literature:
 +      * If you cannot access a paper let me know.
 +      * From class (//lac// operon)
 +          * Díaz-Hernández and Santillán "Bistable behavior of the lac operon in E. coli when induced with a mixture of lactose and TMG", Frontiers in Physiology, 2010
 +      * Components & tutorials on design:
 +          * iGEM [[http://parts.igem.org/Catalog]] 
 +      * Single cell:
 +          * Brophy and Voigt "Principles of Genetic Circuit Design", Nature Methods, 2014
 +          * Nielsen et al. "Genetic circuit design automation" Science, 2016
 +          * Cello compiler [[http://cellocad.org/about.html]]
 +          * Siuti et al. "Synthetic circuits integrating logic and memory in living cells", Nature Biotechnology, 2013
 +          * Guiziou et al. "Hierarchical composition of reliable recombinase logic devices", Nature Communications, 2019
 +          * Gorochowski et al. "Genetic circuit characterization and debugging using RNA‐seq", Mol Syst Biol., 2017
 +      * Distributed:
 +          * Liao et al. "Rock-paper-scissors: Engineered population dynamics increase genetic stability", Science, 2019
 +          * Omar Din et al. "Synchronized cycles of bacterial lysis for in vivo delivery", Nature, 2017 & Chowdhury et al. "Programmable bacteria induce durable tumor regression and systemic antitumor immunity", Nature Medicine, 2019
 +          * Regot et al. "Distributed biological computation with multicellular engineered networks", Nature, 2011
 +          * Sardanyés et al. "Computational implementation of a tunable multicellular memory circuit for engineered eukaryotic consortia", Frontiers in physiology, 2015
 +          * Cummings et al. "Probability 1 computation with chemical reaction networks", International Workshop on DNA-Based Computers, 2014
 +          * Esvelt et al. "A system for the continuous directed evolution of biomolecules" Nature, 2011 
                    
-  * Sept. 24, 14.00-16.00: Discussion of research questions in class+  * Sept. 24, 14.00-16.00: Discussion of research questions in class. Formed 2 groups working on //ML in E. coli// and //Fast Gates in E. coli//. Todo until next time: progress on research question
      
-  * Oct. 1, 14.00-16.00: tba+  * Oct. 1, 14.00-16.00: Presentation and discussion of current research state in class. Timeline for next 3 weeks.
      
-  * Oct. 10, 14.15-16.00: tba+  * Oct. 8, 14.00-16.00: Work in groups. Q&A in class.
      
-  * Oct. 15, 14.15-16.00: Meeting shifted to ... (tba)+  * Oct. 15, 14.00-16.00: Meeting shifted to ... (tba)
    
   * Oct. 22, group-wise, 1h each: final presentations   * Oct. 22, group-wise, 1h each: final presentations
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 **Langue:** English as soon as one participant is not fluent French speaker. All documents will be in English. **Langue:** English as soon as one participant is not fluent French speaker. All documents will be in English.
  
-**Salle:** TBA.+**Salle:** C402
  
 **Mots clés:** theory of automata, computer-aided verification of programs. **Mots clés:** theory of automata, computer-aided verification of programs.
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 **Description:** By loop-elimination we mean computing the effect of repeating a sequence of instructions an arbitrary number of times. Loop elimination is possible for FIFO automata (Boigelot & Godefroid 1999, Bouajjanni & Habermehl 1999) and for lossy FIFO automata (Abdulla et al., 2004). The goal of this working group is to try to extend these two results by developping a common generalization. In summary we will tackle an open problem in theoretical computer science. The group will meet weekly and will use emails, chats, .. for exchanges between two meetings. **Description:** By loop-elimination we mean computing the effect of repeating a sequence of instructions an arbitrary number of times. Loop elimination is possible for FIFO automata (Boigelot & Godefroid 1999, Bouajjanni & Habermehl 1999) and for lossy FIFO automata (Abdulla et al., 2004). The goal of this working group is to try to extend these two results by developping a common generalization. In summary we will tackle an open problem in theoretical computer science. The group will meet weekly and will use emails, chats, .. for exchanges between two meetings.
  
-**Les objectifs pédagogiques:** The working group will be an opportunity for attacking a research problem while working *as a group*. We will see how tasks like bibliographical research, understanding complex results, inventing new techniques, validating them, writing down proofs, checking the proofs, can be done collectively.+**Les objectifs pédagogiques:** The working group will be an opportunity for attacking a research problem while working *as a group*. We will see how tasks like gathering bibliography, understanding complex results, inventing new techniques, validating them, writing down proofs, checking the proofs, can be done collectively.
  
 **Les attentes individuelles et collectives:** It is expected that each participant will contribute his/her ideas, time & energy, ensuring group success.  **Les attentes individuelles et collectives:** It is expected that each participant will contribute his/her ideas, time & energy, ensuring group success. 
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 **Estimation du volume de travail demandé:** at least 5 hours per week (including the weekly meetings). **Estimation du volume de travail demandé:** at least 5 hours per week (including the weekly meetings).
  
-**Participants:** TBA+**Participants:** Bonnet P., Durand S., El Husseini A., Gaudin S., Hadjoudj M., Huriot Tattegrain S., Petitjean Q.
  
 **Planning:** Six meeting on Tuesday at 14h, starting Sep 17th. **Planning:** Six meeting on Tuesday at 14h, starting Sep 17th.
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 **Langue:** French or English as soon as it is better for one student. **Langue:** French or English as soon as it is better for one student.
  
-**Salle:** TBA.+**Salle:** C419
  
 **Mots clés:** Bibliography, search of existing (or new) proofs of famous results, comparison of their respective advantages. **Mots clés:** Bibliography, search of existing (or new) proofs of famous results, comparison of their respective advantages.
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 **Le travail sera:** partly individual and partly collective, depending on the team and the specific situations we will face. **Le travail sera:** partly individual and partly collective, depending on the team and the specific situations we will face.
  
-**Participants:** TBA+**Participants:** Callard A., Chanus B., Guermond N., Long Quan, Soulier G. 
  
 **Planning:** 6 réunions hebdomadaires le mardi de 14h à 16h, début le 17 septembre 2018.  **Planning:** 6 réunions hebdomadaires le mardi de 14h à 16h, début le 17 septembre 2018. 
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 **Langue:** English as soon as one participant is not fluent French speaker. All documents will be in English. **Langue:** English as soon as one participant is not fluent French speaker. All documents will be in English.
  
-**Salle:** TBA.+**Salle:** C522
  
 **Mots clés:** security, quantum cryptanalysis and post-quantum cryptography **Mots clés:** security, quantum cryptanalysis and post-quantum cryptography
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 **Estimation du volume de travail demandé:** around 5 hours per week (including the weekly meetings). **Estimation du volume de travail demandé:** around 5 hours per week (including the weekly meetings).
  
-**Participants:** TBA+**Participants:** Blanc M., Costes M., Dardilhac V., Fievet B., Harington E., Mirwasser S., Rémond U.
  
 **Planning:** Six meeting on Tuesday at 14h, starting Sep 17th. **Planning:** Six meeting on Tuesday at 14h, starting Sep 17th.
  
 **Modalités d'évaluation:** 50% for collective involvement during the discussions, and 50% for personal contribution (presenting/writing, looking for new related articles)  **Modalités d'évaluation:** 50% for collective involvement during the discussions, and 50% for personal contribution (presenting/writing, looking for new related articles) 
 +
 ====== Ateliers 2ème session: du 12 nov. au 17 déc. ====== ====== Ateliers 2ème session: du 12 nov. au 17 déc. ======
  
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 **Language:** French by default, English on request **Language:** French by default, English on request
  
-**Room:** TBA+**Room:** C311
  
 **Mots clés:** State of the art, synthesis, bibliography, identification of new research problems **Mots clés:** State of the art, synthesis, bibliography, identification of new research problems
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 **The research topic** will be chosen by the students and validated by the teacher. **The research topic** will be chosen by the students and validated by the teacher.
  
-**Participants:**  +**Participants:**  Callard A., Crepon P.-A., Durand S., Fievet B., Mirwasser S., Petitjean Q., Rémond U.
  
 **Planning:** every Tuesday from November 12 to December 17, 14:00-16:00 **Planning:** every Tuesday from November 12 to December 17, 14:00-16:00
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 1/4 write an introduction to an article 1/4 write an introduction to an article
  
-==== WG6 Atelier “Cell Fate prediction: The Boolean Approach" / Stefan Haar ====+==== WG6 Atelier “Faces of Causality" / Stefan Haar ====
  
 **Encadrant:** [[http://www.lsv.ens-cachan.fr/~haar|Stefan Haar]]. **Encadrant:** [[http://www.lsv.ens-cachan.fr/~haar|Stefan Haar]].
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 **Langue:** Anglais **Langue:** Anglais
  
-**Salle:** TBA+**Salle:** C402
  
 **Mots clés:** bibliographie; bioinformatics **Mots clés:** bibliographie; bioinformatics
  
 **Description:**  **Description:** 
-In this module, the students will study the state of the art in the interdisciplinary field of epigenetic prediction. +Reasoning that gives causal explanations for observed factsrather than logging temporal succession, is central in a number of disciplins where the 'post hoc ergo proper hoc (after this, hence because of this)'-fallacy is inadmissible. At the same time, there is an astonishing variety of  formalisations for 'causal relation' or 'causal history' in the literature on formal methods. The participants are expectedin first round,  to investigate  and present one facet of this domainand then to select one of the problems emerging in the discussion for further investigation. Presenting the findings, and leads for future research if not all questions have been answered, in a second talk will conclude the module.
-The problem is: derivefrom available knowledge about cell's regulatory networkwhat are the accessible phenotypes, and potentially  what are the factors that decide between those. Based on selected authoritative articles - complemented by their own literature search where appropriate -  from systems biology and from formal bio-informatics (boolean networks)they are expected to cooperate  for preparing a sound and comprehensive in-class presentation of the topic+
  
-**Participants:**  
  
-**Planning:** 4-5 réunions hebdomadaires le mercredi de 14h à 16h, début le ou 22 novembre 2018 (les dates seront précisées ultérieurement). +**Participants:** Chanus B., Costes M., Dardilhac V., Fournis d'Albiat J., Long Quan, Soulier G.  
 + 
 +**Planning:** 4-5 réunions hebdomadaires le mardi de 14h à 16h, début le 12 ou 19 novembre 2019 (les dates seront précisées ultérieurement). 
  
 **Modalités d'évaluation:**  **Modalités d'évaluation:** 
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     * 60% présentation (~30min) ou équivalent.     * 60% présentation (~30min) ou équivalent.
  
-**Articles (further reading will be announced later):** + 
-    * Andrey ZinovyevLaurence Calzone, Simon Fourquet and Emmanuel Barillot[[https://doi.org/10.1007/978-3-642-20164-6_16|How cell decides between life and death: mathematical modeling of epigenetic landscapes of cellular fates]]VCapasso et al. (eds.), Pattern Formation in Morphogenesis, Springer Proceedings in Mathematics 15. +**References:** (to be completed later, depending on the number of participants and on the nature of their requests; pdfs will be provided where available) 
-    * Calzone LTournier L, Fourquet S, Thieffry D, Zhivotovsky B, et al. (2010). [[https://doi.org/10.1371/journal.pcbi.1000702|Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement]]PLoS Comput Biol 6(3): e1000702.  + 
-    * DemongeotJ. and GolesE. and MorvanM. and NoualMand SenéS.,  [[ https://doi.org/10.1371/journal.pone.0011793 +    * J. PearlDMackenzieThe Book of WhyBasic Books, New York. 
-|Attraction basins as gauges of the robustness against boundary conditions in biological complex systems]]PLoS One vol.5 no 82010+    * Gregor Gössler, Daniel Le Métayer. A General Framework for Blaming in Component-Based Systems. (INRIA report
-    * M. Noual & S. Sené . Synchronism vs asynchronism in monotonic Boolean automata networks. 
Natural Computing, 17:393-402, 2018  (Preprint [[https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&cad=rja&uact=8&ved=2ahUKEwiBnKbmp7LdAhVJOhoKHeq-ChIQFjABegQICBAB&url=https%3A%2F%2Fhal.archives-ouvertes.fr%2Fhal-01479438&usg=AOvVaw1lR0edfsI-7lacItDtLp2d|here]])+    * Eric FabreAlbert Benveniste:Partial Order Techniques for Distributed Discrete Event Systems: Why You Cannot Avoid Using ThemDiscrete Event Dynamic Systems 17(3): 355-403 (2007) 
 +    * Prakash Panangaden : Causality in Physics and Computation. 
 +    * Javier Esparza, Christian KernReactive and Proactive Diagnosis of Distributed Systems Using Net Unfoldings. ACSD 2012: 154-163 
 +    * Eric Fabre: Trellis Processes : A Compact Representation for Runs of Concurrent SystemsDiscrete Event Dynamic Systems 17(3): 267-306 (2007) 
 +    * Paolo BaldanRoberto BruniAndrea Corradini Fabio Gaducci, Hernan Melgratti and Ugo Montanari. Event Structures for Petri Nets with persistence. Logical Methods in Computer ScienceVol14(3:25)2018pp1–30 
 +    * César RodríguezStefan Schwoon, Victor KhomenkoContextual Merged ProcessesPetri Nets 2013: 29-48 
 +    * Glynn WinskelEvent Structures, Stable Families and GamesENS Lyon2017
 +    * Marc de Visme  and Glynn Winskel     Strategies with Parallel CausesCSL 2017 Causal UnfoldingsCalco 2019
  
 ==== WG7 Atelier "Autour d’un article scientifique fondateur" / L. Fribourg ==== ==== WG7 Atelier "Autour d’un article scientifique fondateur" / L. Fribourg ====
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 **Langue:** Français sauf si anglais demandé **Langue:** Français sauf si anglais demandé
  
-**Salle:** TBA+**Salle:** C419 
 + 
 +**Participants:** Bonnet P., Guermond N., Hadjoudj M., Harington E., Lecroel M., Le Mogne L.
  
 **Description:** **Description:**
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 **Langue:** French or English as soon as it is better for one student. **Langue:** French or English as soon as it is better for one student.
  
-**Salle:** TBA.+**Salle:** C522
  
 **Mots clés:** Bibliography, search of existing famous results. **Mots clés:** Bibliography, search of existing famous results.
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 **Le travail sera:** partly individual and partly collective, depending on the team and the specific situations we will face. **Le travail sera:** partly individual and partly collective, depending on the team and the specific situations we will face.
  
-**Participants:** TBA+**Participants:** Blanc M., Bourreau Y., El Husseini A., Gaudin S., Huriot Tattegrain S., Yax N.
  
 **Planning:** 6 réunions hebdomadaires le mardi de 14h à 16h, début le 12 novembre 2018.  **Planning:** 6 réunions hebdomadaires le mardi de 14h à 16h, début le 12 novembre 2018. 
 
Universités partenaires Université Paris-Diderot
Université Paris-Saclay
ENS Cachan École polytechnique Télécom ParisTech
ENS
Établissements associés Université Pierre-et-Marie-Curie CNRS INRIA CEA