Differences

This shows you the differences between two versions of the page.

--- start [2018/03/16 10:58]
Nicolas Schabanel
+++ start [2023/10/23 09:57]
Nicolas Schabanel [Internship proposal]
@@ Line 4: / Line 4: @@
 </const>
-<columns 100% center 440 left - >
+<columns 100% center 440 center - >
 {{ :ma_pomme.png?440x348 |Ma pomme}}\\
-{{ :email-cnrs.png?250x70 |Courriel}}
+{{::email-ens.png?300x88|}}
 <newcolumn>
@@ Line 16: / Line 16: @@
 Lyon Cedex 07\\
 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\\
@@ Line 24: / Line 24: @@
-[ [[#My current researches include|Research]] | [[http://www.irif.univ-paris-diderot.fr/~nschaban/GT-COA/|GT CoA]] | [[#Students|Students]] | [[#Publications|Publications]] | [[#Popularization|Popularization]] | [[#Teaching|Teaching]] | [[#Other|Other]] ]
+[ [[#My current researches include|Research]] | [[http://www.irif.fr/gt-coa/|GT CoA]] | [[#Students|Students]] | [[#Publications|Publications]] | [[#Popularization|Popularization]] | [[#Teaching|Teaching]] | [[#Other|Other]] ]
@@ Line 30: / Line 30: @@
 ==== 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]]//
   * **[[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
@@ Line 44: / Line 45: @@
     * **Random systems**
-My work is currently supported by the LIP Installation BQR and MOPREXPROGMOL CNRS MI 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.
-=== Students ===
+==== Internship proposal ====
-  * Nicolas **Blanchard** (M2, 2015; PhD advisor 2016-)
+:!: **__2024 Internship proposal:__ [[http://perso.ens-lyon.fr/nicolas.schabanel/stage/2021_internship.pdf|DNA computing: Theory, Models and wet lab experiments]]**
+==== Students ====
+  * 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)
   * Damien **Regnault** (PhD co-advisor with Éric Thierry, 2005-2008)
@@ Line 54: / Line 63: @@
   * Sandeep **Dey** (Master thesis advisor, 2005)
-=== Publications ===
+==== 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 ====
+  *  **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**
+     * **[[%%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**
-     * **[[%%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.
   * **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-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**
-    * **[[%%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.
@@ Line 83: / Line 114: @@
   *  **2010**
     * **[[%%publiRoot%%/2010/2010-WAOA-PruhsRobertSchabanel.pdf|Minimizing Maximum Flowtime of Jobs with Arbitrary Parallelizability]]**\\ with Kirk Pruhs and Julien Robert. //WAOA,// LNCS 6534:237–248, 2010.
-    * **[[%%publiRoot%%/2010/HdR-Schabanel.pdf|Systèmes complexes & algorithmes]]** (in French)\\ //Habilitation à diriger des recherches,// Université Paris Diderot, 2010. %%publiRoot%%/2010/HDR-Defense-Schabanel.pdf|Slides}}
+    * **[[%%publiRoot%%/2010/HdR-Schabanel.pdf|Systèmes complexes & algorithmes]]** (in French)\\ //Habilitation à diriger des recherches,// Université Paris Diderot, 2010. [[%%publiRoot%%/2010/HDR-Defense-Schabanel.pdf|Slides]]
     * **[[%%publiRoot%%/2010/2010-DMTCS-RegnaultSchabanelThierry.pdf|On the analysis of “simple” 2D stochastic cellular automata]]**\\ with Damien Regnault and Éric Thierry. //Invited publication to the special issue of DMTCS in honor of Philippe Flajolet,// 12(2):263–294, 2009.
@@ Line 153: / Line 184: @@
     * **[[%%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”