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start [2018/09/06 10:38]
Nicolas Schabanel [My current researches include]
start [2023/10/23 09:57] (current)
Nicolas Schabanel [Internship proposal]
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 {{ :​ma_pomme.png?​440x348 |Ma pomme}}\\ {{ :​ma_pomme.png?​440x348 |Ma pomme}}\\
-{{ :email-cnrs.png?250x70 ​|Courriel}}+{{::email-ens.png?300x88|}}
  
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 69364 Lyon Cedex 07\\ 69364 Lyon Cedex 07\\
 France\\ France\\
-Office: **332** //(Site Monnod - Main building - 3rd floor - South)//​\\ +Office: **322** //(Site Monnod - Main building - 3rd floor - South)//​\\ 
-Phone: +33 4 72 72 80 00 / +33 4 26 23 39 67 / +33 4 72 72 87 42+Phone: +33 4 72 72 80 00 / +33 4 26 73 14 55
  
 Resident member of the\\ Resident member of the\\
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 ==== Past Event  ==== ==== Past Event  ====
 +  * **[[https://​remila60.sciencesconf.org/​|Conférence en l'​honneur d'​Éric Rémila pour ses 60 ans]]**, ÉNS de Lyon, France, May 28, 2019\\ //​(Co-organizer with Kevin Perrot) Founded by ANR, LIP and Codrin Nichitiu.//  ​
   * **[[%%siteRoot%%/​workshop/​ComputingWithMolecularGeometry/​|Workshop:​ Computing with molecular geometry]]**,​ Villa Finaly, Florence, Italie, Nov. 20-23, 2017\\ //​(Co-organizer with Claire Lesieur and Damien Woods) Founded by [[http://​www.ixxi.fr|IXXI]],​ [[https://​tapdance.inria.fr/​|Tapdance]] and la [[http://​www.cnrs.fr/​mi/​|mission pour l'​interdisciplinarité du CNRS]]//   * **[[%%siteRoot%%/​workshop/​ComputingWithMolecularGeometry/​|Workshop:​ Computing with molecular geometry]]**,​ Villa Finaly, Florence, Italie, Nov. 20-23, 2017\\ //​(Co-organizer with Claire Lesieur and Damien Woods) Founded by [[http://​www.ixxi.fr|IXXI]],​ [[https://​tapdance.inria.fr/​|Tapdance]] and la [[http://​www.cnrs.fr/​mi/​|mission pour l'​interdisciplinarité du CNRS]]//
   * **[[http://​www.irif.univ-paris-diderot.fr/​~nschaban/​GT-COA/​Journees_2017|6èmes journées]] du [[http://​www.irif.univ-paris-diderot.fr/​~nschaban/​GT-COA/​|GT CoA]]** (Complexités et Algorithmes),​ LIP, Lyon, Nov. 27-28, 2017   * **[[http://​www.irif.univ-paris-diderot.fr/​~nschaban/​GT-COA/​Journees_2017|6èmes journées]] du [[http://​www.irif.univ-paris-diderot.fr/​~nschaban/​GT-COA/​|GT CoA]]** (Complexités et Algorithmes),​ LIP, Lyon, Nov. 27-28, 2017
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     * **Random systems** ​     * **Random systems** ​
  
-My work is currently ​supported by the LIP Installation BQR (2017-18), MoPrExProgMol (2018) and AMARP (2018-20) CNRS Mission pour l'​interdisplinarité,​ and IXXI CalcASMol(2018-19) grants.+My work is supported by the ANR Scalmazène (2022-2026),​ ANR NanoShapeLearn (2023-2027), ​the LIP Installation BQR (2017-18), MoPrExProgMol (2018) and AMARP (2018-20) ​by CNRS Mission pour l'​interdisplinarité,​ and IXXI CalcASMol (2018-19) grants.
  
 +==== Internship proposal ====
 +
 +:!: **__2024 Internship proposal:__ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​stage/​2021_internship.pdf|DNA computing: Theory, Models and wet lab experiments]]**
 ==== Students ==== ==== Students ====
-  * Nicolas **Blanchard** (M2, 2015; PhD advisor 2016-)+  ​* Amaury **Jacques** (M1, 2021) 
 +  * Octave **Hazard** (M2, 2021) 
 +  ​* Nicolas ​**Levy** (M2, 2020; PhD advisor 2020-) 
 +  * Pierre **Marcus** (M2, 2020; 4A, 2021)  
 +  * Daria **Pchelina** (M1, 2019) [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​publications/​2019/​2019-M1-report-Pchelina.pdf|Report]] ] 
 +  * Enka (Nikola) ​**Blanchard** (M2, 2015; PhD co-advisor ​with Ted Selker ​2016-2019**:!: Prix de thèse PSL SHS //"​Interface Sciences/​Humanités"//​** [ [[http://​www.ens-lyon.fr/​actualite/​recherche/​enka-blanchard-laureate-du-prix-de-these-psl-shs?​ctx=contexte|web]] ​ | [[https://​www.youtube.com/​watch?​v=Rlps2gkKb-A&​feature=youtu.be|Remise du prix]] ]
   * Alberto **Vera Azócar** (U. Chile, several research internships 2013, 2015)   * Alberto **Vera Azócar** (U. Chile, several research internships 2013, 2015)
   * Damien **Regnault** (PhD co-advisor with Éric Thierry, 2005-2008)   * Damien **Regnault** (PhD co-advisor with Éric Thierry, 2005-2008)
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   * Sandeep **Dey** (Master thesis advisor, 2005)    * Sandeep **Dey** (Master thesis advisor, 2005) 
  
 +==== Teaching ====
 +  * **[[http://​www.ens-lyon.fr/​DI/​en/​informations-m2-2019-2020/​|M2IF]] CR07 [[lecturemolecularprogramming|Molecular programming:​ Theory & wet-lab experiments]]** [ [[lecturemolecularprogramming#​past_lectures_summary|past lectures]] ]
 +  * **[[https://​wikimpri.dptinfo.ens-cachan.fr/​doku.php?​id=start|MPRI]] 2.11.1 [[mpri2-11-1|Approximation Algorithms & Molecular Algorithms]]** ​
 +  * :!: **__2022 Internship proposal:__ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​stage/​2021_internship.pdf|DNA computing: Theory, Models and wet lab experiments]]**
 +
 +==== Softwares ====
 +  * :!: **[[http://​www.ens-lyon.fr/​ensnano|ENSnano]]**:​ a 3D DNA nanostructure design software for Windows, Mac OS and linux\\ codeveloped with [[http://​perso.ens-lyon.fr/​nicolas.levy|Nicolas Levy]], 2021 [ [[http://​www.ens-lyon.fr/​ensnano|website]] |  [[https://​www.youtube.com/​channel/​UC-5XMNJouMPsB9pW5Q9UVcA|youtube channel]] ]
 +  * :!: **[[http://​perso.ens-lyon.fr/​nicolas.schabanel/​OSsimulator|OS simulator]]**:​ a fast and memory-efficient iPad app that simulates arbitrary Oritatami Systems //(works with limitations on Apple silicon M1 too)//, 2021 [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​OSsimulator|website]] | [[https://​apps.apple.com/​us/​app/​simple-os-simulator/​id1530162352|download]] ]
 +  * **[[https://​apps.apple.com/​us/​app/​caos-simulator/​id1488203962|CAOS simulator]]**:​ an iOS app implementing our Oritatami cellular automata simulation, 2020 \\ [ [[https://​hub.darcs.net/​nikaoOoOoO/​CAOSSimulator|source code]] ]
 +  * **[[https://​itunes.apple.com/​us/​app/​id1335581323|Scary Pacman]]**: an iOS app implementing our Oritatami scaling algorihms, 2018\\ [ [[https://​hub.darcs.net/​nikaoOoOoO/​OritatamiScaling|source code]] ]
 +  * **[[https://​apps.apple.com/​app/​clean-scan/​id995830264|Clean scan]]**: an iOS app to take printable pictures of white, green and black board, 2015
 ==== Publications ==== ==== Publications ====
 +  *  **2022**
 +     * **Rule-of-thumb-free geometry-driven design of arbitrary complex curved DNA origami with ENSnano (Abstract)**\\ ​ [[https://​thenlevy.github.io/​perso.ens-lyon-nicolas.levy/​|Nicolas Levy]], Allan Mills, [[http://​www.cbs.cnrs.fr/​index.php/​fr/​personnel?​PERS=Gaetan%20Bellot|Gaëtan Bellot]]*, Nicolas Schabanel*. //​[[https://​dna28.cs.unm.edu/​|DNA28]]//,​ New Mexico, Aug. 2022. \\
 +     * **Turedo a new computational model for molecular nanobots?​**,​ Nicolas Schabanel.\\ Invited talk at the special session «Computing with bio-molecules» at //​[[https://​cs.swansea.ac.uk/​cie2022/​|CiE 2022]]//, Swansea, Jul 2022.
 +     * **[[%%publiRoot%%/​2022/​2022-PchelinaSchabanelSekiTheyssier-STACS.pdf|Oritatami systems assemble shapes no less
 +complex than tile assembly model (aTAM)]]** \\  Daria Pchelina, Nicolas Schabanel, Shinnosuke Seki, Guillaume Theyssier. //​[[https://​stacs2022.sciencesconf.org/​|STACS]]//,​ 26:1-23, 2022. \\ Supplementary material: [ [[https://​hub.darcs.net/​turedo2oritatami/​turedo2oritatami/​python|Turedo2oritatami compiler]] | [[%%publiRoot%%/​2021/​2021-PchelinaSchabanelSekiTheyssier.pdf|Full version]] ]
 +  *  **2021**
 +     * **[[%%publiRoot%%/​2021/​2021-LevySchabanel.pdf|ENSnano:​ a 3D modeling software for DNA nanostructures]]** \\  Nicolas Levy, Nicolas Schabanel. //In [[http://​dna27.iopconfs.org/​home|DNA27]]//,​ LIPIcs, vol. 205, pp.5:1-23, doi:​10.4230/​LIPIcs.DNA.27.5,​ 2021.\\ **:!: best student paper & best presentation award.** ​ \\ :!: Download ENSnano at: [ [[https://​www.ens-lyon.fr/​ensnano|ENSnano website]] ] [ [[https://​www.youtube.com/​channel/​UC-5XMNJouMPsB9pW5Q9UVcA|Youtube channel]] ]
 +  *  **2020**
 +     * **[[%%publiRoot%%/​2020/​2020-LATIN-PchelinaSchabanelSekiUbukata.pdf|Simple Intrinsic Simulation of Cellular Automata in Oritatami Molecular Folding Model]]** [ [[https://​hal.archives-ouvertes.fr/​hal-02410874/​document|Full version]] ] \\  Daria Pchelina, Nicolas Schabanel, Shinnosuke Seki, Yuki Ubukata. In //​[[http://​latin2020.ime.usp.br/​|LATIN]]//,​ LNCS 12118:​425-436,​ Sao Paulo, 2020. doi:​10.1007/​978-3-030-61792-9_34 [[https://​hal.archives-ouvertes.fr/​hal-02410874v1|hal-02410874]]\\ //:!: Download the iOS app [[https://​apps.apple.com/​us/​app/​caos-simulator/​id1488203962|CAOS simulator]] implementing our simulation [ [[https://​hub.darcs.net/​nikaoOoOoO/​CAOSSimulator|source code]] ]//
 +  *  **2019**
 +     * **[[https://​www.mdpi.com/​1422-0067/​20/​9/​2259|Oritatami:​ A Computational Model for Molecular Co-Transcriptional Folding ]]** [ [[%%publiRoot%%/​2019/​2019-IJMS-GearyMeunierSchabanelSeki.pdf|PDF]] & [[%%publiRoot%%/​2019/​2019-IJMS-GearyMeunierSchabanelSeki-s1.pdf|supplementary materials]] ]\\ Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki. [[https://​www.mdpi.com/​journal/​ijms|IJMS (Int. J. of Molecular Sciences)]],​ Special Issue Nucleic Acid Nanotechnology,​ 2019, 20(9), 2259.\\ [[https://​doi.org/​10.3390/​ijms20092259]] ​
   *  **2018**    *  **2018**
-     * **[[%%publiRoot%%/​2018/​2018-ISAAC-OritatamiTuring-GearyMeunierSchabanelSeki.pdf|Proving the Turing Universality of Oritatami Co-Transcriptional Folding]]** [ [[http://​www.irif.fr/​~nschaban/​oritatami/​|Supplementary materials]] ]\\ Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki. [[http://​isaac2018.ie.nthu.edu.tw/​|ISAAC 2018]], Jiaoxi, Yilan County, Taiwan, Dec. 2018. +     * **[[%%publiRoot%%/​2018/​2018-ISAAC-OritatamiTuring-GearyMeunierSchabanelSeki.pdf|Proving the Turing Universality of Oritatami Co-Transcriptional Folding]]** [ [[http://​www.irif.fr/​~nschaban/​oritatami/​|Supplementary materials]] ]\\ Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki. [[http://​isaac2018.ie.nthu.edu.tw/​|ISAAC 2018]], LIPIcs.ISAAC.2018.23:​1-23:​13, Jiaoxi, Yilan County, Taiwan, Dec. 2018. [ [[https://​arxiv.org/​abs/​1508.00510|Arxiv]] ] 
-     * **[[%%publiRoot%%/​2018/​2018-DNA24-OritatamiShapes-DemaineHendricksOlsenPatitzRogersSchabanelSekiThomas.pdf|Know When to Fold ’Em: Self-Assembly of Shapes by Folding in Oritatami]]**\\ Erik D. Demaine, Jacob Hendricks, Meagan Olsen, Matthew J. Patitz, Trent A. Rogers, Nicolas Schabanel, Shinnosuke Seki, and Hadley Thomas. [[http://​dna24sdnu.com/​|DNA24]],​ Jinan, China, Oct. 2018.\\ Invited talk at [[https://​ucnc2018.lacl.fr/​self-assembly/​|UCNC2018 Self-assembly,​ geometry and computation workshop]], Fontainebleau,​ June 2018. +     * **[[%%publiRoot%%/​2018/​2018-DNA24-OritatamiShapes-DemaineHendricksOlsenPatitzRogersSchabanelSekiThomas.pdf|Know When to Fold ’Em: Self-Assembly of Shapes by Folding in Oritatami]]**\\ Erik D. Demaine, Jacob Hendricks, Meagan Olsen, Matthew J. Patitz, Trent A. Rogers, Nicolas Schabanel, Shinnosuke Seki, and Hadley Thomas. [[http://​dna24sdnu.com/​|DNA24]], LNCS 11145:19-36, Jinan, China, Oct. 2018.\\ Invited talk at [[https://​ucnc2018.lacl.fr/​self-assembly/​|UCNC2018 Self-assembly,​ geometry and computation workshop]], Fontainebleau,​ June 2018. \\ //:!: Download the iOS app [[https://​itunes.apple.com/​us/​app/​id1335581323|Scary Pacman]] implementing our algorithms [ [[https://​hub.darcs.net/​nikaoOoOoO/​OritatamiScaling|source code]] ]//
   *  **2017**    *  **2017**
-     * **[[%%publiRoot%%/​2017/​2017-Oritatami-GearyMeunierSchabanelSeki|Proving the Turing Universality of Oritatami Co-Transcriptional Folding]]**\\ Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki. //​Submitted//,​ 65 pages, july 2017. [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​oritatami/​|Supplementary materials]] ] 
      * **[[%%publiRoot%%/​2017/​2017-Walcom-BlanchardSchabanel.pdf|Dynamic Facility Location: Minimizing the Sum of Radii]]**\\ Nicolas K. Blanchard, Nicolas Schabanel. //​[[http://​walcom2017.nctu.edu.tw/​index.html|WALCOM]]//,​ LNCS 10167:​30-41,​ march 2017.      * **[[%%publiRoot%%/​2017/​2017-Walcom-BlanchardSchabanel.pdf|Dynamic Facility Location: Minimizing the Sum of Radii]]**\\ Nicolas K. Blanchard, Nicolas Schabanel. //​[[http://​walcom2017.nctu.edu.tw/​index.html|WALCOM]]//,​ LNCS 10167:​30-41,​ march 2017.
   * **2016**   * **2016**
     * **[[%%publiRoot%%/​2016/​2016-Automata-Schabanel.pdf|Oritatami systems: a computational model for co-transcriptional folding]]**\\ Nicolas Schabanel. **Invited plenary talk** at //​[[http://​automata2016.ini.uzh.ch/​|Automata]]//,​ Jun. 2016.      * **[[%%publiRoot%%/​2016/​2016-Automata-Schabanel.pdf|Oritatami systems: a computational model for co-transcriptional folding]]**\\ Nicolas Schabanel. **Invited plenary talk** at //​[[http://​automata2016.ini.uzh.ch/​|Automata]]//,​ Jun. 2016. 
     * **[[%%publiRoot%%/​2016/​2016-MFCS-GearyMeunierSchabanelSeki.pdf|Programming biomolecules that fold greedily during transcription]]**\\ Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki. //​[[http://​mfcs.ki.agh.edu.pl|MFCS]]//,​ LIPIcs 58, 43:1-43:14, Aug. 2016.     * **[[%%publiRoot%%/​2016/​2016-MFCS-GearyMeunierSchabanelSeki.pdf|Programming biomolecules that fold greedily during transcription]]**\\ Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki. //​[[http://​mfcs.ki.agh.edu.pl|MFCS]]//,​ LIPIcs 58, 43:1-43:14, Aug. 2016.
-    * **[[%%publiRoot%%/2016/2016-HALG-GearyMeunierSchabanelSeki.pdf|Folding Turing is hard but feasible]]**\\ Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki.//​[[http://​highlightsofalgorithms.org/​program/​|HALG]]//,​ Jun. 2016.+    * **[[https://arxiv.org/​abs/​1508.00510|Folding Turing is hard but feasible]]**\\ Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki.//​[[http://​highlightsofalgorithms.org/​program/​|HALG]]//,​ Jun. 2016.
  
   *  **2015**    *  **2015**
-    * **[[%%publiRoot%%/​2015/​2015-DNA21-GearyMeunierSchabanelSeki.pdf|Efficient universal computation by molecular co-transcriptional folding (Short announcement)]]**\\ Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki. //​[[http://​dna21.wyss.harvard.edu/​|DNA21]]//,​ 1 page, 2015.  (Full version in submission, see above) +    * **[[%%publiRoot%%/​2015/​2015-DNA21-GearyMeunierSchabanelSeki.pdf|Efficient universal computation by molecular co-transcriptional folding (Short announcement)]]**\\ Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki. //​[[http://​dna21.wyss.harvard.edu/​|DNA21]]//,​ 1 page, 2015. 
- +
-  *  **2014**+
     * **[[%%publiRoot%%/​2014/​2014-ICALP-EisenstatMathieuSchabanel.pdf|Facility Location in Evolving Metrics]]**\\ with David Eisenstat and Claire Mathieu. //ICALP,// pages 459-470, 2014.     * **[[%%publiRoot%%/​2014/​2014-ICALP-EisenstatMathieuSchabanel.pdf|Facility Location in Evolving Metrics]]**\\ with David Eisenstat and Claire Mathieu. //ICALP,// pages 459-470, 2014.
  
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     * **[[%%publiRoot%%/​2003/​2003.04-Minotaure-Schabanel.pdf|Thèse idiote: le hasard fabrique des certitudes]]** (in French)\\ //Le minotaure// (trimenstrial journal, 20 000ex), 1:66-69, april-june 2003.     * **[[%%publiRoot%%/​2003/​2003.04-Minotaure-Schabanel.pdf|Thèse idiote: le hasard fabrique des certitudes]]** (in French)\\ //Le minotaure// (trimenstrial journal, 20 000ex), 1:66-69, april-june 2003.
  
-==== Teaching ==== 
-  
-  * **MPRI 2.11.1 [[https://​wikimpri.dptinfo.ens-cachan.fr/​doku.php?​id=cours:​c-2-11-1|Approximation Algorithms & Molecular Algorithms]]** 
- 
-==== Other ==== 
  
-  *  **Algoseum:​** “Bringing scientific interactive games and exhibitions to science museum” ​