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start [2020/02/18 15:01]
Nicolas Schabanel [Publications]
start [2023/10/23 09:57] (current)
Nicolas Schabanel [Internship proposal]
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 France\\ France\\
 Office: **322** //(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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     * **Random systems** ​     * **Random systems** ​
  
-My work is currently ​supported by the LIP Installation BQR (2017-18), MoPrExProgMol (2018) and AMARP (2018-20) by 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 ==== ==== Internship proposal ====
  
-:!: **__2020 M2 Internship proposal:__ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​stage/​2020_M2_Internship.pdf|DNA computing: Theory, Models and wet lab experiments]]**+:!: **__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 **Levy** (M2, 2020) +  ​* Amaury **Jacques** (M1, 2021) 
-  * Pierre **Marcus** (M2, 2020) +  * 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]] ]   * Daria **Pchelina** (M1, 2019) [ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​publications/​2019/​2019-M1-report-Pchelina.pdf|Report]] ]
-  * Nikola **Blanchard** (M2, 2015; PhD advisor 2016-2019)+  * 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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 ==== Teaching ==== ==== Teaching ====
-  * **[[http://​www.ens-lyon.fr/​DI/​en/​informations-m2-2019-2020/​|M2IF]] ​SCR1 [[lecturemolecularprogramming|Molecular programming:​ Theory & wet-lab experiments]]** [ [[lecturemolecularprogramming#​past_lectures_summary|past lectures]] ] +  * **[[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 [[https://wikimpri.dptinfo.ens-cachan.fr/doku.php?id=cours:c-2-11-1|Approximation Algorithms & Molecular Algorithms]]** [ [[https://wikimpri.dptinfo.ens-cachan.fr/doku.php?​id=cours:c-2-11-1#​course_summary_2019-20molecular_programming_lectures_5-8|past lectures]] ] +  * **[[https://​wikimpri.dptinfo.ens-cachan.fr/​doku.php?​id=start|MPRI]] 2.11.1 [[mpri2-11-1|Approximation Algorithms & Molecular Algorithms]]**  
-  * :!: **__2020 M2 Internship proposal:__ [[http://​perso.ens-lyon.fr/​nicolas.schabanel/​stage/2020_M2_Internship.pdf|DNA computingTheoryModels and wet lab experiments]]**+  * :!: **__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 simulation2020 \\ [ [[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**    *  **2020**
-     * **[[https://hal.archives-ouvertes.fr/​hal-02410874/​document|Simple Intrinsic Simulation of Cellular Automata in Oritatami Molecular Folding Model]]**\\ ​ Daria Pchelina, Nicolas Schabanel, Shinnosuke Seki, and Yuki UbukataLATIN, Sao Paulo, 2020. [[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]] ]//+     * **[[%%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**    *  **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]] ​      * **[[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]]** ​{{anchor:​oritatamituring2018:​}} ​[ [[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-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]],​ 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]] ]//      * **[[%%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**
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   *  **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.  ​[[#​oritatamituring2018|Full version published at ISAAC 2018]]  +    * **[[%%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.