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--- start [2021/05/14 18:46]
Nicolas Schabanel [Softwares]
+++ start [2024/04/09 16:16]
Nicolas Schabanel [Students]
@@ Line 45: / Line 45: @@
     * **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 ====
-:!: **__2021 Internship proposal:__ [[http://perso.ens-lyon.fr/nicolas.schabanel/stage/2021_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 ====
-  * Nicolas **Levy** (M2, 2020; PhD advisor 2020-)
+  * Amaury **Jacques** (M1, 2021)
+  * Octave **Hazard** (M2, 2021)
+  * Nicolas **Levy** (M2, 2020; PhD advisor 2020-2023)
   * 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]] ]
@@ Line 62: / Line 64: @@
 ==== 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]]**
-  * :!: **__2021 Internship proposal:__ [[http://perso.ens-lyon.fr/nicolas.schabanel/stage/2021_internship.pdf|DNA computing: Theory, Models 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|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 ====
+  * **2023**
+    * **[[https://doi.org/10.1007/978-981-19-9891-1_13|Ok: A Kinetic Model for Locally Reconfigurable Molecular Systems]]**\\
+Pierre Marcus, Nicolas Schabanel and Shinnosuke Seki.
+In: Jonoska, N., Winfree, E. (eds) //Visions of DNA Nanotechnology at 40 for the Next 40.// Natural Computing Series. Springer, Singapore.
+  *  **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. Submitted, 2021. [ [[https://www.ens-lyon.fr/ensnano|ENSnano website]] ]
+     * **[[%%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]] ]
-     * **[[%%publiRoot%%/2021/2021-PchelinaSchabanelSekiTheyssier.pdf|Oritatami simulates self-avoiding 2D Turing machines]]** \\  Daria Pchelina, Nicolas Schabanel, Shinnosuke Seki, Guillaume Theyssier. Submitted, 2021. [[%%publiRoot%%/2021/oritatami-turedo-rule.pdf|Supplementary material]]
   *  **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]]//, 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**
      * **[[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**
-     * **[[%%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]] ]//
   *  **2017**
@@ Line 88: / Line 101: @@
   *  **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.