OxDNA - User contributions [en]

OxDNA users and developers workshop 2024

2024-09-05T21:31:23Z

Louis: /* Attendees */

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, 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 [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===
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"> [[Image:Beecroft-keble.jpg|700px]]
</div>

===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.

[https://docs.google.com/document/d/1Rp0thnxet5gMsmbSuFqaMrDA4RXpmwtvlTVz67vX7jM/edit?usp=sharing, CONFERENCE-SCHEDULE].

===Registration===
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===

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.

===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 [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===
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:

[[Image:OxDNAworkshop2024b.jpg|440px]] [[Image:oxDNAworkshop_Brasenose.jpg|360px]] [[Image:oxDNAworkshop_dinner2024.jpeg|333px]]

__NOTOC__

OxDNA users and developers workshop 2024

2024-09-05T21:30:55Z

Louis: /* Attendees */

File:OxDNAworkshop2024b.jpg

2024-09-05T21:30:28Z

Louis:

File:OxDNAworkshop dinner2024.jpeg

2024-09-05T21:28:41Z

Louis:

File:OxDNAworkshop Brasenose.jpg

2024-09-05T21:26:34Z

Louis:

File:OxDNAworkshop2024.jpg

2024-09-05T21:25:12Z

Louis:

OxDNA users and developers workshop 2024

2024-09-05T21:21:49Z

Louis: /* Attendees */

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, 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 [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===
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"> [[Image:Beecroft-keble.jpg|700px]]
</div>

===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.

[https://docs.google.com/document/d/1Rp0thnxet5gMsmbSuFqaMrDA4RXpmwtvlTVz67vX7jM/edit?usp=sharing, CONFERENCE-SCHEDULE].

===Registration===
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===

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.

===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 [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===
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:

[[Image:oxDNAworkshop.jpeg|440px]] [[Image:oxDNAworkshop_Jesus.jpeg|380px]] [[Image:oxDNAworkshop_dinner.jpeg|215px]]

__NOTOC__

OxDNA users and developers workshop 2024

2024-08-29T20:09:36Z

Louis: /* Schedule */

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, 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 [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===
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"> [[Image:Beecroft-keble.jpg|700px]]
</div>

===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.

[https://docs.google.com/document/d/1Rp0thnxet5gMsmbSuFqaMrDA4RXpmwtvlTVz67vX7jM/edit?usp=sharing, CONFERENCE-SCHEDULE].

===Registration===
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===

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.

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

===Attendees===

Photos of attendees from the [[OxDNA users and developers workshop 2019]] below:

[[Image:oxDNAworkshop.jpeg|440px]] [[Image:oxDNAworkshop_Jesus.jpeg|380px]] [[Image:oxDNAworkshop_dinner.jpeg|215px]]

__NOTOC__

OxDNA users and developers workshop 2024

2024-08-03T12:24:47Z

Louis: /* Schedule */

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, 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 [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===
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"> [[Image:Beecroft-keble.jpg|700px]]
</div>

===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) "Hackathon" sessions where we begin to address the simpler targets and make detailed plans for future development and collaborations.

4) A conference dinner and other social events.

A full schedule will be posted here closer to the conference date, but here is a [https://drive.google.com/file/d/1TejIy_1DkSoRni182ofws4JX9aORD098/view?usp=sharing, draft schedule].

===Registration===
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===

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.

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

===Attendees===

Photos of attendees from the [[OxDNA users and developers workshop 2019]] below:

[[Image:oxDNAworkshop.jpeg|440px]] [[Image:oxDNAworkshop_Jesus.jpeg|380px]] [[Image:oxDNAworkshop_dinner.jpeg|215px]]

__NOTOC__

OxDNA users and developers workshop 2024

2024-08-03T12:20:39Z

Louis: /* Schedule */

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, 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 [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===
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"> [[Image:Beecroft-keble.jpg|700px]]
</div>

===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) "Hackathon" sessions where we begin to address the simpler targets and make detailed plans for future development and collaborations.

4) A conference dinner and other social events.

A full schedule will be posted here closer to the conference date, but here is a draft schedule.

===Registration===
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===

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.

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

===Attendees===

Photos of attendees from the [[OxDNA users and developers workshop 2019]] below:

[[Image:oxDNAworkshop.jpeg|440px]] [[Image:oxDNAworkshop_Jesus.jpeg|380px]] [[Image:oxDNAworkshop_dinner.jpeg|215px]]

__NOTOC__

OxDNA users and developers workshop 2024

2024-04-27T20:27:33Z

Louis:

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, 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 [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===
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"> [[Image:Beecroft-keble.jpg|700px]]
</div>

===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) "Hackathon" sessions where we begin to address the simpler targets and make detailed plans for future development and collaborations.

4) A conference dinner and other social events.

A full schedule will be posted here closer to the conference date.

===Registration===
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===

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.

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

===Attendees===

Photos of attendees from the [[OxDNA users and developers workshop 2019]] below:

[[Image:oxDNAworkshop.jpeg|440px]] [[Image:oxDNAworkshop_Jesus.jpeg|380px]] [[Image:oxDNAworkshop_dinner.jpeg|215px]]

__NOTOC__

OxDNA users and developers workshop 2024

2024-04-27T17:59:51Z

Louis:

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, 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 [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===
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"> [[Image:Beecroft-keble.jpg|700px]]
</div>

===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) "Hackathon" sessions where we begin to address the simpler targets and make detailed plans for future development and collaborations.

4) A conference dinner and other social events.

A full schedule will be posted here closer to the conference date.

===Registration===
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===

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.

===Travel===
Oxford is well served by public transport. From Europe, the Eurostar goes to London st Pancreas, 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===
We are grateful for support from EPSRC under grant EP/V06231X/1

===Attendees===

Photos of attendees from the [[OxDNA users and developers workshop 2019]] below:

[[Image:oxDNAworkshop.jpeg|440px]] [[Image:oxDNAworkshop_Jesus.jpeg|380px]] [[Image:oxDNAworkshop_dinner.jpeg|215px]]

__NOTOC__

OxDNA users and developers workshop 2024

2024-04-27T15:41:38Z

Louis:

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, 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 [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===
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"> [[Image:Beecroft-keble.jpg|700px]]
</div>

===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) "Hackathon" sessions where we begin to address the simpler targets and make detailed plans for future development and collaborations.

4) A conference dinner and other social events.

A full schedule will be posted here closer to the conference date.

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

<b> Apply fo 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===

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.

===Travel===
Oxford is well served by public transport. From Europe, the Eurostar goes to London st Pancreas, 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===
We are grateful for support from EPSRC under grant EP/V06231X/1

===Attendees===

Photos of attendees from the [[OxDNA users and developers workshop 2019]] below:

[[Image:oxDNAworkshop.jpeg|440px]] [[Image:oxDNAworkshop_Jesus.jpeg|380px]] [[Image:oxDNAworkshop_dinner.jpeg|215px]]

__NOTOC__

OxDNA users and developers workshop 2024

2024-04-27T12:00:29Z

Louis:

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, 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 [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===
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"> [[Image:Beecroft-keble.jpg|700px]]
</div>

===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) "Hackathon" sessions where we begin to address the simpler targets and make detailed plans for future development and collaborations.

4) A conference dinner and other social events.

A full schedule will be posted here closer to the conference date.

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

<b> Apply fo 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===

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.

===Travel===
Oxford is well served by trains and busses. 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]. More travel information can be found [https://www2.physics.ox.ac.uk/contacts/how-to-find-us 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 2019]] below:

[[Image:oxDNAworkshop.jpeg|440px]] [[Image:oxDNAworkshop_Jesus.jpeg|380px]] [[Image:oxDNAworkshop_dinner.jpeg|215px]]

__NOTOC__

OxDNA users and developers workshop 2024

2024-04-27T11:52:51Z

Louis:

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, 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 [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===
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"> [[Image:Beecroft-keble.jpg|700px]]
</div>

===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) "Hackathon" sessions where we begin to address the simpler targets and make detailed plans for future development and collaborations.

4) A conference dinner and other social events.

A full schedule will be posted here closer to the conference date.

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

<b> Sign up for the conference at this [https://docs.google.com/forms/d/1JBvnF6-0pFAMOme4hwuLISc7nkjpCZEmq7yTnQmt3fs/viewform? link]</b>

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

===Accommodation options===

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.

===Travel===
Oxford is well served by trains and busses. 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]. More travel information can be found [https://www2.physics.ox.ac.uk/contacts/how-to-find-us 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 2019]] below:

[[Image:oxDNAworkshop.jpeg|440px]] [[Image:oxDNAworkshop_Jesus.jpeg|380px]] [[Image:oxDNAworkshop_dinner.jpeg|215px]]

__NOTOC__

File:Radcam.jpeg

2024-04-27T11:48:23Z

Louis:

File:Skyline.jpeg

2024-04-27T11:48:11Z

Louis:

File:Beecroft-keble.jpg

2024-04-27T11:46:12Z

Louis:

OxDNA users and developers workshop 2024

2024-04-27T11:40:42Z

Louis: /* Location */

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, 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 [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===
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">
[[Image:Beecroft2.jpg|440px]] [[Image:Beecroft3.jpg|520px]] [[Image:Beecroft7.jpg|162px]]
</div>

===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) "Hackathon" sessions where we begin to address the simpler targets and make detailed plans for future development and collaborations.

4) A conference dinner and other social events.

A full schedule will be posted here closer to the conference date.

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

<b> Sign up for the conference at this [https://docs.google.com/forms/d/1JBvnF6-0pFAMOme4hwuLISc7nkjpCZEmq7yTnQmt3fs/viewform? link]</b>

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

===Accommodation options===

Bed and breakfast rooms at other colleges can be booked [http://conference-oxford.com/bb-self-catering here].

===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] or by [https://www.thetrainline.com/ train]. More travel information can be found [https://www2.physics.ox.ac.uk/contacts/how-to-find-us 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 2019]] below:

[[Image:oxDNAworkshop.jpeg|440px]] [[Image:oxDNAworkshop_Jesus.jpeg|380px]] [[Image:oxDNAworkshop_dinner.jpeg|215px]]

__NOTOC__

OxDNA users and developers workshop 2024

2024-04-25T21:27:45Z

Louis: /* Schedule */

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, 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 [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===
[https://www.physics.ox.ac.uk/ Department of Physics], University of Oxford ([https://maps.app.goo.gl/Q2vm7Cfisj1NGFus5 map]).

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

===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) "Hackathon" sessions where we begin to address the simpler targets and make detailed plans for future development and collaborations.

4) A conference dinner and other social events.

A full schedule will be posted here closer to the conference date.

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

<b> Sign up for the conference at this [https://docs.google.com/forms/d/1JBvnF6-0pFAMOme4hwuLISc7nkjpCZEmq7yTnQmt3fs/viewform? link]</b>

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

===Accommodation options===

Bed and breakfast rooms at other colleges can be booked [http://conference-oxford.com/bb-self-catering here].

===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] or by [https://www.thetrainline.com/ train]. More travel information can be found [https://www2.physics.ox.ac.uk/contacts/how-to-find-us 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 2019]] below:

[[Image:oxDNAworkshop.jpeg|440px]] [[Image:oxDNAworkshop_Jesus.jpeg|380px]] [[Image:oxDNAworkshop_dinner.jpeg|215px]]

__NOTOC__

OxDNA:About

2024-04-25T21:26:52Z

Louis: Created page with "OxDNA is a suite of programmes for coarse-grained simulations of DNA, RNA, and DNA/RNA hybrids."

OxDNA is a suite of programmes for coarse-grained simulations of DNA, RNA, and DNA/RNA hybrids.

OxDNA users and developers workshop 2024

2024-04-25T21:25:21Z

Louis:

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, 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 [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===
[https://www.physics.ox.ac.uk/ Department of Physics], University of Oxford ([https://maps.app.goo.gl/Q2vm7Cfisj1NGFus5 map]).

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

===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) "Hackathon" sessions where we begin to address the simpler targets and make detailed plans for future development and collaborations.

A full schedule will be posted here closer to the conference date.

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

<b> Sign up for the conference at this [https://docs.google.com/forms/d/1JBvnF6-0pFAMOme4hwuLISc7nkjpCZEmq7yTnQmt3fs/viewform? link]</b>

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

===Accommodation options===

Bed and breakfast rooms at other colleges can be booked [http://conference-oxford.com/bb-self-catering here].

===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] or by [https://www.thetrainline.com/ train]. More travel information can be found [https://www2.physics.ox.ac.uk/contacts/how-to-find-us 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 2019]] below:

[[Image:oxDNAworkshop.jpeg|440px]] [[Image:oxDNAworkshop_Jesus.jpeg|380px]] [[Image:oxDNAworkshop_dinner.jpeg|215px]]

__NOTOC__

OxDNA users and developers workshop 2024

2024-04-25T21:24:18Z

Louis:

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, 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 [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===
[https://www.physics.ox.ac.uk/ Department of Physics], University of Oxford ([https://maps.app.goo.gl/Q2vm7Cfisj1NGFus5 map]).

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

===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) "Hackathon" sessions where we begin to address the simpler targets and make detailed plans for future development and collaborations.

A full schedule will be posted here closer to the conference date.

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

<b> Sign up for the conference at this [https://docs.google.com/forms/d/1JBvnF6-0pFAMOme4hwuLISc7nkjpCZEmq7yTnQmt3fs/viewform? link]</b>

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

===Accommodation options===

Bed and breakfast rooms at other colleges can be booked [http://conference-oxford.com/bb-self-catering here].

===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] or by [https://www.thetrainline.com/ train]. More travel information can be found [https://www2.physics.ox.ac.uk/contacts/how-to-find-us 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 2019]] below:

[[Image:oxDNAworkshop.jpeg|440px]] [[Image:oxDNAworkshop_Jesus.jpeg|380px]] [[Image:oxDNAworkshop_dinner.jpeg|215px]]

__NOTOC__

OxDNA users and developers workshop 2024

2024-04-25T21:16:49Z

Louis:

We are planning to hold an oxDNA users and developers workshop in Oxford from <b>September 2-5 2024</b>.
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 [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===
[https://www.physics.ox.ac.uk/ Department of Physics], University of Oxford ([https://maps.app.goo.gl/Q2vm7Cfisj1NGFus5 map]).

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

===Schedule===

Attendees are welcome to give a short research presentations.

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

The programme will 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) "Hackathon" sessions where we begin to address the simpler targets and make detailed plans for future development and collaborations.

A full schedule will appear here closer to the conference date.

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

<b> Sign up at this [https://docs.google.com/forms/d/1JBvnF6-0pFAMOme4hwuLISc7nkjpCZEmq7yTnQmt3fs/viewform? link]</b>

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

===Accommodation options===

Bed and breakfast rooms at other colleges can be booked [http://conference-oxford.com/bb-self-catering here].

===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] or by [https://www.thetrainline.com/ train]. More travel information can be found [https://www2.physics.ox.ac.uk/contacts/how-to-find-us here].

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

===Attendees===

Attendees from the 2019 conference below:

[[Image:oxDNAworkshop.jpeg|440px]] [[Image:oxDNAworkshop_Jesus.jpeg|380px]] [[Image:oxDNAworkshop_dinner.jpeg|215px]]

__NOTOC__

OxDNA users and developers workshop 2024

2024-04-25T21:11:47Z

Louis: /* Sponsors */

We are planning to hold an oxDNA users and developers workshop in Oxford from September 2-5 2014.
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 [http://tacoxdna.sissa.it/], and user-friendly tools to improve oxDNA accessibility for non-expert users, see for example [https://sulcgroup.github.io/oxdna-viewer/ oxview]

===Location===
[https://www.physics.ox.ac.uk/ Department of Physics], University of Oxford ([https://maps.app.goo.gl/Q2vm7Cfisj1NGFus5 map]).

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

===Schedule===

Attendees are welcome to give a short research presentations.

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 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.

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

A [https://docs.google.com/forms/d/1JBvnF6-0pFAMOme4hwuLISc7nkjpCZEmq7yTnQmt3fs/viewform? sign up link]

You can email us at oxdnacommittee@gmail.com

===Accommodation options===

Bed and breakfast rooms at other colleges can be booked [http://conference-oxford.com/bb-self-catering here].

===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] or by [https://www.thetrainline.com/ train]. More travel information can be found [https://www2.physics.ox.ac.uk/contacts/how-to-find-us here].

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

===Attendees===

Attendees from the 2019 conference below:

[[Image:oxDNAworkshop.jpeg|440px]] [[Image:oxDNAworkshop_Jesus.jpeg|380px]] [[Image:oxDNAworkshop_dinner.jpeg|215px]]

__NOTOC__

OxDNA users and developers workshop 2024

2024-04-25T20:52:25Z

Louis:

We are planning to hold an oxDNA users and developers workshop in Oxford from September 2-5 2014.
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 [http://tacoxdna.sissa.it/], and user-friendly tools to improve oxDNA accessibility for non-expert users, see for example [https://sulcgroup.github.io/oxdna-viewer/ oxview]

===Location===
[https://www.physics.ox.ac.uk/ Department of Physics], University of Oxford ([https://maps.app.goo.gl/Q2vm7Cfisj1NGFus5 map]).

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

===Schedule===

Attendees are welcome to give a short research presentations.

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 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.

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

A [https://docs.google.com/forms/d/1JBvnF6-0pFAMOme4hwuLISc7nkjpCZEmq7yTnQmt3fs/viewform? sign up link]

You can email us at oxdnacommittee@gmail.com

===Accommodation options===

Bed and breakfast rooms at other colleges can be booked [http://conference-oxford.com/bb-self-catering here].

===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] or by [https://www.thetrainline.com/ train]. More travel information can be found [https://www2.physics.ox.ac.uk/contacts/how-to-find-us here].

===Sponsors===
We are grateful for support from EPSRC

===Attendees===

Attendees from the 2019 conference below:

[[Image:oxDNAworkshop.jpeg|440px]] [[Image:oxDNAworkshop_Jesus.jpeg|380px]] [[Image:oxDNAworkshop_dinner.jpeg|215px]]

__NOTOC__

OxDNA users and developers workshop 2024

2024-04-25T20:47:55Z

Louis:

We are planning to hold an oxDNA users and developers workshop in Oxford from September 2-5 2014.
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 [http://tacoxdna.sissa.it/], and user-friendly tools to improve oxDNA accessibility for non-expert users, see for example [https://sulcgroup.github.io/oxdna-viewer/ oxview]

===Location===
[https://www.physics.ox.ac.uk/ Department of Physics], University of Oxford ([https://maps.app.goo.gl/Q2vm7Cfisj1NGFus5 map]).

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

===Schedule===

Attendees are welcome to give a short research presentations.

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 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.

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

A [https://docs.google.com/forms/d/1JBvnF6-0pFAMOme4hwuLISc7nkjpCZEmq7yTnQmt3fs/viewform? sign up link]

You can email us at [oxdnacommittee@gmail.com]

===Accommodation options===

Bed and breakfast rooms at other colleges can be booked [http://conference-oxford.com/bb-self-catering here].

===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] or by [https://www.thetrainline.com/ train]. More travel information can be found [https://www2.physics.ox.ac.uk/contacts/how-to-find-us here].

===Sponsors===
We are grateful for support from EPSRC

===Attendees===

Attendees from the 2019 conference below:

[[Image:oxDNAworkshop.jpeg|440px]] [[Image:oxDNAworkshop_Jesus.jpeg|380px]] [[Image:oxDNAworkshop_dinner.jpeg|215px]]

__NOTOC__

OxDNA users and developers workshop 2024

2024-04-25T20:47:20Z

Louis:

We are planning to hold an oxDNA users and developers workshop in Oxford from September 2-5 2014.
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 [http://tacoxdna.sissa.it/], and user-friendly tools to improve oxDNA accessibility for non-expert users, see for example [https://sulcgroup.github.io/oxdna-viewer/ oxview]

===Location===
[https://www.physics.ox.ac.uk/ Department of Physics], University of Oxford ([https://maps.app.goo.gl/Q2vm7Cfisj1NGFus5 map]).

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

===Schedule===

Attendees are welcome to give a short research presentations.

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 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.

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

A [https://docs.google.com/forms/d/1JBvnF6-0pFAMOme4hwuLISc7nkjpCZEmq7yTnQmt3fs/viewform? sign up link]

You can email us at oxdnacommittee@gmail.com

===Accommodation options===

Bed and breakfast rooms at other colleges can be booked [http://conference-oxford.com/bb-self-catering here].

===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] or by [https://www.thetrainline.com/ train]. More travel information can be found [https://www2.physics.ox.ac.uk/contacts/how-to-find-us here].

===Sponsors===
We are grateful for support from EPSRC

===Attendees===

Attendees from the 2019 conference below:

[[Image:oxDNAworkshop.jpeg|440px]] [[Image:oxDNAworkshop_Jesus.jpeg|380px]] [[Image:oxDNAworkshop_dinner.jpeg|215px]]

__NOTOC__

Main Page

2024-04-25T13:25:18Z

Louis:

== oxDNA ==

oxDNA is a simulation code originally developed to implement the coarse-grained DNA model introduced by T. E. Ouldridge, J. P. K. Doye and A. A. Louis. It has been since reworked and it is now an extensible simulation+analysis framework. It natively supports simulations of DNA (oxDNA and oxDNA2) and RNA (oxRNA) on both CPUs and NVIDIA GPUs.

The code implements Monte Carlo and Molecular Dynamics. The developers are L. Rovigatti, F. Romano, P. Šulc, B. Snodin, F. Randisi and T. E. Ouldridge in the [http://physchem.ox.ac.uk/~doye/jon/ Doye] and [http://www-thphys.physics.ox.ac.uk/people/ArdLouis/ Louis] groups at the University of Oxford. Additionally, Molecular Dynamics simulations modeling DNA-linked nanoparticles have been implemented by J. Hendricks, T. Fochtman, and B. Walcutt in the [http://self-assembly.net/ Patitz] group at the University of Arkansas.

The oxDNA and oxRNA models are intended to provide a physical representation of the thermodynamic and mechanical properties of single- and double-stranded DNA and RNA, as well as the transition between the two. At the same time, the representation of DNA and RNA is sufficiently simple to allow access to assembly processes which occur on long timescales, beyond the reach of atomistic simulations. Basic examples include duplex formation from single strands, and the folding of a self-complementary single strand into a hairpin. These are the underlying processes of the fast-growing field of [http://en.wikipedia.org/wiki/DNA_nanotechnology DNA nanotechnology] and RNA nanotechnology, as well as many biophysical uses of DNA/RNA, allowing the model to be used to understand these fascinating systems.

There also exists an implementation of the oxDNA and oxDNA2 models for [http://lammps.sandia.gov/ LAMMPS] in the USER-CGDNA package, developed by [http://www.oliverhenrich.com/ Oliver Henrich] (with the help of Tom E. Ouldridge, F. Romano and L. Rovigatti). The package documentation can be found [https://lammps.sandia.gov/doc/Packages_details.html#pkg-user-cgdna here]. The code comes with any regular download from the central LAMMPS repository, and it is also available [https://github.com/ohenrich/cgdna here].

* [https://github.com/lorenzo-rovigatti/oxDNA/ Download]

* [https://lorenzo-rovigatti.github.io/oxDNA/install.html Installation]

* [[Features]]

* [[DNA model introduction]]

* [[RNA model introduction]]

* [https://lorenzo-rovigatti.github.io/oxDNA/ Documentation]

* [[Documentation|Old documentation]]

* [[:Category:Examples|Examples]]

* [[Tutorials]]

* [[Publications]]

* [[External Resources]]

* [[How To Write An Interaction]]

* [[Gallery of Journal Covers]]

* [[Online talks]]

* [[Screenshots|Screenshots and movies]]

* [[Gallery of studied systems]]

* [[License and Copyright]]

* [[Previous version]]

* [[Contact information]]

* [[oxDNA users and developers workshop 2019]]

* [[oxDNA users and developers workshop 2024]]

== News ==
* Code implementing [[DNA_model_introduction#oxDNA2|oxDNA2]], a new version of the oxDNA model, is now included in the latest release. See [https://doi.org/10.1063/1.4921957 ''J. Chem. Phys.'' '''142''', 234901 (2015)] for more information about the new model.
* Follow the latest updates about oxDNA on our twitter account: [https://twitter.com/ox_dna ox_dna]
* Youtube: More simulation movies can be found on the [https://www.youtube.com/channel/UCz3DCaoBsa9MvVSrVhyoU4A oxDNA] channel and video tutorials can be found on the [https://www.youtube.com/channel/UC4ClrQ8xMypSbDZG2QCehpA oxDNA tutorials] channel.
* The [http://sourceforge.net/p/oxdna/discussion/ Discussion forum] for the old repository of the oxDNA code at sourceforge.net may provide answers to some common questions.
* [[oxDNA users and developers workshop 2024]] Sept 2-5, 2024, Oxford.

== Acknowledgments ==

We thank our co-workers C. Matek, R. Harrison and W. Smith for having contributed bits of code and/or material for the examples and our webmasters Russell Jones and Greg Agacinski for maintaining the website.

Main Page

2024-04-25T13:24:35Z

Louis:

== oxDNA ==

oxDNA is a simulation code originally developed to implement the coarse-grained DNA model introduced by T. E. Ouldridge, J. P. K. Doye and A. A. Louis. It has been since reworked and it is now an extensible simulation+analysis framework. It natively supports simulations of DNA (oxDNA and oxDNA2) and RNA (oxRNA) on both CPUs and NVIDIA GPUs.

The code implements Monte Carlo and Molecular Dynamics. The developers are L. Rovigatti, F. Romano, P. Šulc, B. Snodin, F. Randisi and T. E. Ouldridge in the [http://physchem.ox.ac.uk/~doye/jon/ Doye] and [http://www-thphys.physics.ox.ac.uk/people/ArdLouis/ Louis] groups at the University of Oxford. Additionally, Molecular Dynamics simulations modeling DNA-linked nanoparticles have been implemented by J. Hendricks, T. Fochtman, and B. Walcutt in the [http://self-assembly.net/ Patitz] group at the University of Arkansas.

The oxDNA and oxRNA models are intended to provide a physical representation of the thermodynamic and mechanical properties of single- and double-stranded DNA and RNA, as well as the transition between the two. At the same time, the representation of DNA and RNA is sufficiently simple to allow access to assembly processes which occur on long timescales, beyond the reach of atomistic simulations. Basic examples include duplex formation from single strands, and the folding of a self-complementary single strand into a hairpin. These are the underlying processes of the fast-growing field of [http://en.wikipedia.org/wiki/DNA_nanotechnology DNA nanotechnology] and RNA nanotechnology, as well as many biophysical uses of DNA/RNA, allowing the model to be used to understand these fascinating systems.

There also exists an implementation of the oxDNA and oxDNA2 models for [http://lammps.sandia.gov/ LAMMPS] in the USER-CGDNA package, developed by [http://www.oliverhenrich.com/ Oliver Henrich] (with the help of Tom E. Ouldridge, F. Romano and L. Rovigatti). The package documentation can be found [https://lammps.sandia.gov/doc/Packages_details.html#pkg-user-cgdna here]. The code comes with any regular download from the central LAMMPS repository, and it is also available [https://github.com/ohenrich/cgdna here].

* [https://github.com/lorenzo-rovigatti/oxDNA/ Download]

* [https://lorenzo-rovigatti.github.io/oxDNA/install.html Installation]

* [[Features]]

* [[DNA model introduction]]

* [[RNA model introduction]]

* [https://lorenzo-rovigatti.github.io/oxDNA/ Documentation]

* [[Documentation|Old documentation]]

* [[:Category:Examples|Examples]]

* [[Tutorials]]

* [[Publications]]

* [[External Resources]]

* [[How To Write An Interaction]]

* [[Gallery of Journal Covers]]

* [[Online talks]]

* [[Screenshots|Screenshots and movies]]

* [[Gallery of studied systems]]

* [[License and Copyright]]

* [[Previous version]]

* [[Contact information]]

* [[oxDNA users and developers workshop 2019]]

* [[oxDNA users and developers workshop 2024]]

== News ==
* Code implementing [[DNA_model_introduction#oxDNA2|oxDNA2]], a new version of the oxDNA model, is now included in the latest release. See [https://doi.org/10.1063/1.4921957 ''J. Chem. Phys.'' '''142''', 234901 (2015)] for more information about the new model.
* Follow the latest updates about oxDNA on our twitter account: [https://twitter.com/ox_dna ox_dna]
* Youtube: More simulation movies can be found on the [https://www.youtube.com/channel/UCz3DCaoBsa9MvVSrVhyoU4A oxDNA] channel and video tutorials can be found on the [https://www.youtube.com/channel/UC4ClrQ8xMypSbDZG2QCehpA oxDNA tutorials] channel.
* The [http://sourceforge.net/p/oxdna/discussion/ Discussion forum] for the old repository of the oxDNA code at sourceforge.net may provide answers to some common questions.
* [[oxDNA users and developers workshop 2024]OxDNA users and developers conference Sept 2-5 2024]

== Acknowledgments ==

We thank our co-workers C. Matek, R. Harrison and W. Smith for having contributed bits of code and/or material for the examples and our webmasters Russell Jones and Greg Agacinski for maintaining the website.

OxDNA users and developers workshop 2024

2024-04-25T13:23:50Z

Louis: oxdna conference 2024

We are planning to hold an oxDNA users and developers workshop in Oxford from September 2-5 2014.
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 [http://tacoxdna.sissa.it/], and user-friendly tools to improve oxDNA accessibility for non-expert users, see for example [https://sulcgroup.github.io/oxdna-viewer/ oxview]

===Location===
[https://www.physics.ox.ac.uk/ Department of Physics], University of Oxford ([https://maps.app.goo.gl/Q2vm7Cfisj1NGFus5 map]).

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

===Schedule===

Attendees are welcome to give a short research presentations.

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 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.

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

A sign-up link will appear here soon.

===Accommodation options===

Bed and breakfast rooms at other colleges can be booked [http://conference-oxford.com/bb-self-catering here].

===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] or by [https://www.thetrainline.com/ train]. More travel information can be found [https://www2.physics.ox.ac.uk/contacts/how-to-find-us here].

===Sponsors===
We are grateful for support from EPSRC

===Attendees===

Attendees from the 2019 conference below:

[[Image:oxDNAworkshop.jpeg|440px]] [[Image:oxDNAworkshop_Jesus.jpeg|380px]] [[Image:oxDNAworkshop_dinner.jpeg|215px]]

__NOTOC__

OxDNA users and developers workshop 2024

2024-04-25T13:17:36Z

Louis:

We are planning to hold an oxDNA users and developers workshop in Oxford from September 2-5 2014.
The aim of the workshop is to bring together both developers and users of the oxDNA, oxRNA and oxNA 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 other simulation tools, see for example [http://tacoxdna.sissa.it/], and user-friendly tools to improve oxDNA accessibility for non-expert users, see for example [https://sulcgroup.github.io/oxdna-viewer/ oxview]

===Location===
[https://www.physics.ox.ac.uk/ Department of Physics], University of Oxford ([https://goo.gl/maps/U61yvrBi1Zn9VKBr7 map]).

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

===Schedule===

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.

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

A sign-up link will appear here soon.

===Accommodation options===

Bed and breakfast rooms at other colleges can be booked [http://conference-oxford.com/bb-self-catering here].

===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] or by train [https://www.thetrainline.com/]
More travel information can be found [https://www2.physics.ox.ac.uk/contacts/how-to-find-us here].

===Sponsors===
We are grateful for support from EPSRC

===Attendees===

Attendees from the 2019 conference below:

[[Image:oxDNAworkshop.jpeg|440px]] [[Image:oxDNAworkshop_Jesus.jpeg|380px]] [[Image:oxDNAworkshop_dinner.jpeg|215px]]

__NOTOC__

OxDNA users and developers workshop 2024

2024-04-25T13:06:03Z

Louis: 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..."

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 of DNA design and simulation tools, user-friendly tools to improve oxDNA accessibility for non-expert users.

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

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

===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
[http://doye.chem.ox.ac.uk/abstracts/oxDNA_programme.pdf 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 [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 other colleges can be booked [http://conference-oxford.com/bb-self-catering here].

===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].

===Sponsors===
We are grateful for support from the [https://innovation.ox.ac.uk/award-details/john-fell-fund/ 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

[[Image:oxDNAworkshop.jpeg|440px]] [[Image:oxDNAworkshop_Jesus.jpeg|380px]] [[Image:oxDNAworkshop_dinner.jpeg|215px]]

===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
__NOTOC__

Main Page

2024-04-25T13:05:03Z

Louis:

== oxDNA ==

oxDNA is a simulation code originally developed to implement the coarse-grained DNA model introduced by T. E. Ouldridge, J. P. K. Doye and A. A. Louis. It has been since reworked and it is now an extensible simulation+analysis framework. It natively supports simulations of DNA (oxDNA and oxDNA2) and RNA (oxRNA) on both CPUs and NVIDIA GPUs.

The code implements Monte Carlo and Molecular Dynamics. The developers are L. Rovigatti, F. Romano, P. Šulc, B. Snodin, F. Randisi and T. E. Ouldridge in the [http://physchem.ox.ac.uk/~doye/jon/ Doye] and [http://www-thphys.physics.ox.ac.uk/people/ArdLouis/ Louis] groups at the University of Oxford. Additionally, Molecular Dynamics simulations modeling DNA-linked nanoparticles have been implemented by J. Hendricks, T. Fochtman, and B. Walcutt in the [http://self-assembly.net/ Patitz] group at the University of Arkansas.

The oxDNA and oxRNA models are intended to provide a physical representation of the thermodynamic and mechanical properties of single- and double-stranded DNA and RNA, as well as the transition between the two. At the same time, the representation of DNA and RNA is sufficiently simple to allow access to assembly processes which occur on long timescales, beyond the reach of atomistic simulations. Basic examples include duplex formation from single strands, and the folding of a self-complementary single strand into a hairpin. These are the underlying processes of the fast-growing field of [http://en.wikipedia.org/wiki/DNA_nanotechnology DNA nanotechnology] and RNA nanotechnology, as well as many biophysical uses of DNA/RNA, allowing the model to be used to understand these fascinating systems.

There also exists an implementation of the oxDNA and oxDNA2 models for [http://lammps.sandia.gov/ LAMMPS] in the USER-CGDNA package, developed by [http://www.oliverhenrich.com/ Oliver Henrich] (with the help of Tom E. Ouldridge, F. Romano and L. Rovigatti). The package documentation can be found [https://lammps.sandia.gov/doc/Packages_details.html#pkg-user-cgdna here]. The code comes with any regular download from the central LAMMPS repository, and it is also available [https://github.com/ohenrich/cgdna here].

* [https://github.com/lorenzo-rovigatti/oxDNA/ Download]

* [https://lorenzo-rovigatti.github.io/oxDNA/install.html Installation]

* [[Features]]

* [[DNA model introduction]]

* [[RNA model introduction]]

* [https://lorenzo-rovigatti.github.io/oxDNA/ Documentation]

* [[Documentation|Old documentation]]

* [[:Category:Examples|Examples]]

* [[Tutorials]]

* [[Publications]]

* [[External Resources]]

* [[How To Write An Interaction]]

* [[Gallery of Journal Covers]]

* [[Online talks]]

* [[Screenshots|Screenshots and movies]]

* [[Gallery of studied systems]]

* [[License and Copyright]]

* [[Previous version]]

* [[Contact information]]

* [[oxDNA users and developers workshop 2024]]

* [[oxDNA users and developers workshop 2019]]

== News ==
* Code implementing [[DNA_model_introduction#oxDNA2|oxDNA2]], a new version of the oxDNA model, is now included in the latest release. See [https://doi.org/10.1063/1.4921957 ''J. Chem. Phys.'' '''142''', 234901 (2015)] for more information about the new model.
* Follow the latest updates about oxDNA on our twitter account: [https://twitter.com/ox_dna ox_dna]
* Youtube: More simulation movies can be found on the [https://www.youtube.com/channel/UCz3DCaoBsa9MvVSrVhyoU4A oxDNA] channel and video tutorials can be found on the [https://www.youtube.com/channel/UC4ClrQ8xMypSbDZG2QCehpA oxDNA tutorials] channel.
* The [http://sourceforge.net/p/oxdna/discussion/ Discussion forum] for the old repository of the oxDNA code at sourceforge.net may provide answers to some common questions.
* [[OxDNA users and developers conference]OxDNA users and developers conference Sept 2-5 2024]

== Acknowledgments ==

We thank our co-workers C. Matek, R. Harrison and W. Smith for having contributed bits of code and/or material for the examples and our webmasters Russell Jones and Greg Agacinski for maintaining the website.

OxDNA users and developers workshop

2024-04-25T13:01:11Z

Louis: Louis moved page OxDNA users and developers workshop to OxDNA users and developers workshop 2019: new

#REDIRECT [[OxDNA users and developers workshop 2019]]

OxDNA users and developers workshop 2019

2024-04-25T13:01:11Z

Louis: Louis moved page OxDNA users and developers workshop to OxDNA users and developers workshop 2019: new

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

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

===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
[http://doye.chem.ox.ac.uk/abstracts/oxDNA_programme.pdf 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 [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 other colleges can be booked [http://conference-oxford.com/bb-self-catering here].

===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].

===Sponsors===
We are grateful for support from the [https://innovation.ox.ac.uk/award-details/john-fell-fund/ 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

[[Image:oxDNAworkshop.jpeg|440px]] [[Image:oxDNAworkshop_Jesus.jpeg|380px]] [[Image:oxDNAworkshop_dinner.jpeg|215px]]

===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
__NOTOC__