Difference between revisions of "OxDNA users and developers workshop"

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(Attendees)
 
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and test simpler utilities). Make detailed plans for future development and collaborations.
 
and test simpler utilities). Make detailed plans for future development and collaborations.
 
Users to get help in utilizing more advanced code features.
 
Users to get help in utilizing more advanced code features.
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The programme is now available
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[http://doye.chem.ox.ac.uk/abstracts/oxDNA_programme.pdf here]
  
 
===Registration===
 
===Registration===
There are no registration fees. There will be a workshop dinner on Tuesday 3 September, and a wine-tasting event led by Domen Prešern on Wednesday 4 September.
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There are no registration fees. There will be a workshop dinner on Tuesday 3 September at Jesus College, and a wine-tasting event led by Domen Prešern on Wednesday 4 September at 8pm at Ard's home. There will also be the possibility to go on a Tolkien tour of Oxford led by Megan Engel.
 
 
To register for the workshop fill in this [https://forms.gle/GgmQBVb92KBpcPeM6 form]
 
  
 
===Accommodation options===
 
===Accommodation options===
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Erik Benson, University of Oxford; Evolutionary refinement of DNA nanostructures using coarse-grained molecular dynamics simulations
 
Erik Benson, University of Oxford; Evolutionary refinement of DNA nanostructures using coarse-grained molecular dynamics simulations
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Joakim Bohlin, University of Oxford
  
 
Keitel Cervantes-Salguero, Queen Mary University of London
 
Keitel Cervantes-Salguero, Queen Mary University of London
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Jonathan Doye, University of Oxford
 
Jonathan Doye, University of Oxford
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Megan Engel, Harvard University; Internal forces in oxDNA
  
 
Hannah Fowler, University of Oxford
 
Hannah Fowler, University of Oxford
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Ard Louis, University of Oxford
 
Ard Louis, University of Oxford
  
Christopher Maffeo, University of Illinois; multi-resolution DNA
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Christopher Maffeo, University of Illinois; A Python framework for multi-resolution modeling of nanoscale DNA objects
  
 
Michael Matthies, Arizona State University; General-Purpose analysis package for coarse-grained simulations of DNA/RNA nanotechnology
 
Michael Matthies, Arizona State University; General-Purpose analysis package for coarse-grained simulations of DNA/RNA nanotechnology
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Behnam Najafi, University of Oxford; Characterising DNA T-motifs
  
 
Thomas Ouldridge, Imperial College; Non-equilibrium information processing: modelling with oxDNA
 
Thomas Ouldridge, Imperial College; Non-equilibrium information processing: modelling with oxDNA
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Domen Prešern, University of Oxford
 
Domen Prešern, University of Oxford
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Ferdinando Randisi, FarbricNano; FabricNano: a DNA-nanotech/bio-catalysis startup
  
 
Flavio Romano, Universitá Ca Foscari di Venezia
 
Flavio Romano, Universitá Ca Foscari di Venezia
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Jiaming Yu, University of Cambridge, Numerical Study on the Effect of Flexibility in DNA Building Blocks
 
Jiaming Yu, University of Cambridge, Numerical Study on the Effect of Flexibility in DNA Building Blocks
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[[Image:oxDNAworkshop.jpeg|440px]] [[Image:oxDNAworkshop_Jesus.jpeg|380px]] [[Image:oxDNAworkshop_dinner.jpeg|215px]]
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===Remote participants===
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Carlos Castro, Ohio State University; Design Automation for DNA Origami Mechanisms
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Elisa de Llano, Austrian Institute of Technology; Adenita: Customizable modeling and visualization of DNA nanostructures
 
__NOTOC__
 
__NOTOC__

Latest revision as of 18:59, 5 September 2019

We are planning to hold an oxDNA users and developers workshop in Oxford from September 2-5 2019. The aim of the workshop is to bring together both developers and users of the oxDNA and oxRNA models not only to share current research projects, but also to set the agenda for the future development of the oxDNA and oxRNA models, code and infrastructure, as well as to identify (and begin to address) current shortcomings. Particular foci are likely to be inter-operability of DNA design and simulation tools, user-friendly tools to improve oxDNA accessibility for non-expert users.

Location

Beecroft Building, Department of Physics, University of Oxford (map).

Beecroft2.jpg Beecroft3.jpg Beecroft7.jpg

Schedule

All attendees are welcome to give a short research presentation as part of the workshop.

Monday, Tuesday am: Short research presentations from all/most attendees. These will help to highlight the range of work for which oxDNA is being used, tools that have been developed, and wish lists for future development.

Tuesday pm: Discussion-based sessions to define the agenda for future development and to identify key targets and outline plans for implementation.

Wednesday, Thursday: "Hackathon": Begin to address the simpler targets (e.g. improve documentation of newer features, incorporation of existing external utilities into oxDNA infrastructure, develop and test simpler utilities). Make detailed plans for future development and collaborations. Users to get help in utilizing more advanced code features.

The programme is now available here

Registration

There are no registration fees. There will be a workshop dinner on Tuesday 3 September at Jesus College, and a wine-tasting event led by Domen Prešern on Wednesday 4 September at 8pm at Ard's home. There will also be the possibility to go on a Tolkien tour of Oxford led by Megan Engel.

Accommodation options

A number of rooms (not en suite) have been reserved at The Queen's College on their main site. These would cost £57.60 per night. These rooms can be booked here. To access these rooms the code DOYE2019 needs to be entered before selecting the dates.

Bed and breakfast rooms at other colleges can be booked here.

Travel

The closest airport to Oxford is Heathrow, and the quickest transport from Heathrow airport to Oxford is via coach. More travel information can be found here.

Sponsors

We are grateful for support from the John Fell Fund.

Attendees

Matteo Becchi, SISSA Trieste

Erik Benson, University of Oxford; Evolutionary refinement of DNA nanostructures using coarse-grained molecular dynamics simulations

Joakim Bohlin, University of Oxford

Keitel Cervantes-Salguero, Queen Mary University of London

Hemani Chhabra, University of Oxford

Lorenzo Di Michele, University of Cambridge

Jonathan Doye, University of Oxford

Megan Engel, Harvard University; Internal forces in oxDNA

Hannah Fowler, University of Oxford

Oliver Henrich, University of Strathclyde; Using oxDNA in the LAMMPS code

Sieun Jung, Korea University

Fabian Kohler, Technische Universität München; Cryo-EM Studies of Multilayer DNA Origami Objects

Maximilian Nicolas Honemann, TU Munich

Will Kaufhold, University of Cambridge; Rapid in silico prototyping of proximity sensitive DNA nanostructures

Jaewon Lee, Korea University

Ard Louis, University of Oxford

Christopher Maffeo, University of Illinois; A Python framework for multi-resolution modeling of nanoscale DNA objects

Michael Matthies, Arizona State University; General-Purpose analysis package for coarse-grained simulations of DNA/RNA nanotechnology

Behnam Najafi, University of Oxford; Characterising DNA T-motifs

Thomas Ouldridge, Imperial College; Non-equilibrium information processing: modelling with oxDNA

Matthew Patitz, University of Arkansas; A web-based front end for oxDNA

SungHun Park, Korea University

Domen Prešern, University of Oxford

Ferdinando Randisi, FarbricNano; FabricNano: a DNA-nanotech/bio-catalysis startup

Flavio Romano, Universitá Ca Foscari di Venezia

Lorenzo Rovigatti, Sapienza Universitá di Roma

Michael Selby, University of Oxford

Rahul Sharma, École polytechnique fédérale de Lausanne; The cgDNA family of coarse grain models of DNA: cgDNA+, cgDNAweb, and cgDNAmc

Enrico Skoruppa, KU Leuven; Torsional properties of DNA

Petr Šulc, Arizona State University; Towards simulations and design of large DNA/RNA systems with oxDNA/oxRNA

Antonio Suma, University of Bari / Temple University, Accessibility of endonuclease to DNA origami: role of local and global fluctuations

Jiaming Yu, University of Cambridge, Numerical Study on the Effect of Flexibility in DNA Building Blocks

OxDNAworkshop.jpeg OxDNAworkshop Jesus.jpeg OxDNAworkshop dinner.jpeg

Remote participants

Carlos Castro, Ohio State University; Design Automation for DNA Origami Mechanisms

Elisa de Llano, Austrian Institute of Technology; Adenita: Customizable modeling and visualization of DNA nanostructures