OxDNA users and developers workshop 2024: Difference between revisions

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(Created page with "e 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 o...")
 
 
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e are planning to hold an oxDNA users and developers workshop in Oxford from September 2-5 2019.  
We are planning to hold an oxDNA users and developers workshop in Oxford <b>September 2-5 2024</b>.  
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,
The aim of the workshop is to bring together both developers and users of the oxDNA, oxRNA and oxNA models to share current research projects and 
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
to set the agenda for the future development of the oxDNA family of 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.
shortcomings. Particular foci are likely to be inter-operability of DNA design and other simulation tools, see for example those listed on [http://tacoxdna.sissa.it/ tacoxdna], and user-friendly tools to improve oxDNA accessibility for non-expert users, see for example  [https://sulcgroup.github.io/oxdna-viewer/ oxview]


===Location===
===Location===
[https://www2.physics.ox.ac.uk/the-beecroft-building Beecroft Building], Department of Physics, University of Oxford ([https://goo.gl/maps/U61yvrBi1Zn9VKBr7 map]).
Lindemann lecture theatre, [https://www.physics.ox.ac.uk/ Department of Physics], University of Oxford ([https://maps.app.goo.gl/Q2vm7Cfisj1NGFus5 map]).


<div style="text-align:left">
<div style="text-align:left"> [[Image:Beecroft-keble.jpg|700px]]
[[Image:Beecroft2.jpg|440px]]  [[Image:Beecroft3.jpg|520px]] [[Image:Beecroft7.jpg|162px]]
</div>
</div>


===Schedule===
===Schedule===


All attendees are welcome to give a short research presentation as part of the workshop.
The conference will start the morning of Monday 2 September, and end the afternoon of Thursday 5 September.


Monday, Tuesday am: Short research presentations from all/most attendees. These will help to highlight the range of work for which
The programme will be similar to our previous [[OxDNA users and developers workshop 2019]] and contain:
 
1) Short research presentations from 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.
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
2)  Discussion-based sessions to define the agenda for future development and to identify
key targets and outline plans for implementation.
key targets and outline plans for implementation.


Wednesday, Thursday: "Hackathon": Begin to address the simpler targets (e.g. improve documentation
3) A conference dinner and other social events.
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
[https://docs.google.com/document/d/1Rp0thnxet5gMsmbSuFqaMrDA4RXpmwtvlTVz67vX7jM/edit?usp=sharing, CONFERENCE-SCHEDULE].
[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 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.
There are no registration fees. There will be a workshop dinner on Tuesday 3 September.
 
<b> Apply for conference participation at this [https://docs.google.com/forms/d/1JBvnF6-0pFAMOme4hwuLISc7nkjpCZEmq7yTnQmt3fs/viewform?  link]</b> You will receive confirmation of participation within a few weeks of application.
 
For further questions you can email us at oxdnacommittee@gmail.com


===Accommodation options===
===Accommodation options===


A number of rooms (not en suite) have been reserved at [http://www.queens.ox.ac.uk The Queen's College] on their main site. These would cost £57.60 per night. These rooms can be booked [https://www.queens.ox.ac.uk/bed-breakfast here]. To access these rooms the code DOYE2019 needs to be entered before selecting the dates.
Bed and breakfast rooms at colleges can be booked [http://conference-oxford.com/bb-self-catering here].  There are also many hotels and airbnbs in Oxford.
 
Bed and breakfast rooms at other colleges can be booked [http://conference-oxford.com/bb-self-catering here].


===Travel===
===Travel===
The closest airport to Oxford is Heathrow, and the quickest transport from Heathrow airport to Oxford is via [https://airline.oxfordbus.co.uk/ coach]. More travel information can be found [https://www2.physics.ox.ac.uk/contacts/how-to-find-us here].
Oxford is well served by public transport. From Europe, the Eurostar goes to London st Pancras, from which you can reach Oxford by train.  The closest airport to Oxford is Heathrow, and the quickest transport from Heathrow airport to Oxford is via [https://airline.oxfordbus.co.uk/ coach] or by [https://www.thetrainline.com/ train]. Other airports include (roughly in order of ease of getting to Oxford)  Birmingham, London Gatwick, London Luton, and London Stansted. More travel information can be found [https://www2.physics.ox.ac.uk/contacts/how-to-find-us here].


===Sponsors===
===Sponsors===
We are grateful for support from the [https://innovation.ox.ac.uk/award-details/john-fell-fund/ John Fell Fund].
We are grateful for support from EPSRC under grant EP/V06231X/1


===Attendees===
===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
Photos of attendees from the [[OxDNA users and developers workshop 2024 ]] below:


[[Image:oxDNAworkshop.jpeg|440px]] [[Image:oxDNAworkshop_Jesus.jpeg|380px]] [[Image:oxDNAworkshop_dinner.jpeg|215px]]
[[Image:OxDNAworkshop2024b.jpg|440px]] [[Image:oxDNAworkshop_Brasenose.jpg|360px]] [[Image:oxDNAworkshop_dinner2024.jpeg|333px]]


===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
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Latest revision as of 21:31, 5 September 2024

We are planning to hold an oxDNA users and developers workshop in Oxford September 2-5 2024. The aim of the workshop is to bring together both developers and users of the oxDNA, oxRNA and oxNA models to share current research projects and to set the agenda for the future development of the oxDNA family of 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 other simulation tools, see for example those listed on tacoxdna, and user-friendly tools to improve oxDNA accessibility for non-expert users, see for example oxview

Location

Lindemann lecture theatre, Department of Physics, University of Oxford (map).

Beecroft-keble.jpg

Schedule

The conference will start the morning of Monday 2 September, and end the afternoon of Thursday 5 September.

The programme will be similar to our previous OxDNA users and developers workshop 2019 and contain:

1) Short research presentations from 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.

2) Discussion-based sessions to define the agenda for future development and to identify key targets and outline plans for implementation.

3) A conference dinner and other social events.

CONFERENCE-SCHEDULE.

Registration

There are no registration fees. There will be a workshop dinner on Tuesday 3 September.

Apply for conference participation at this link You will receive confirmation of participation within a few weeks of application.

For further questions you can email us at oxdnacommittee@gmail.com

Accommodation options

Bed and breakfast rooms at colleges can be booked here. There are also many hotels and airbnbs in Oxford.

Travel

Oxford is well served by public transport. From Europe, the Eurostar goes to London st Pancras, from which you can reach Oxford by train. The closest airport to Oxford is Heathrow, and the quickest transport from Heathrow airport to Oxford is via coach or by train. Other airports include (roughly in order of ease of getting to Oxford) Birmingham, London Gatwick, London Luton, and London Stansted. More travel information can be found here.

Sponsors

We are grateful for support from EPSRC under grant EP/V06231X/1

Attendees

Photos of attendees from the OxDNA users and developers workshop 2024 below:

OxDNAworkshop2024b.jpg OxDNAworkshop Brasenose.jpg OxDNAworkshop dinner2024.jpeg


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