[Dissemination-aoi] Dissemination Update - June 5, 2009

[Joy P. Ku]

Dissemination Update – a special one-month summary

May 11 – June 5, 2009



NIH Progress Report

*Wrote section on dissemination and training, and one of the highlights



BCR

*Simbios News story written on OpenMM Zephyr

*Editing of Summer issue



*To do this week:  Continue editing



OpenMM

* Publicized release of preview release 3

* Workshop update

- 20 attendees confirmed for the Developer part of the workshop.

- Sherm and Chris Bruns did a dry-run for the “HelloNaCl” exercise,
uncovered several issues resulting in suggestions:

                * Binaries for OpenMM, Linux-64 bit and Visual Studio 9 to
be made available

                * Exercises and long-term plan for C and Fortran
developers to be developed

                * Rework agenda to have one hands-on exercise in the
morning

                * Installation instructions for OpenMM need to be created
and posted



*To do this week:

- Follow up with items from dry-run

- Update agenda and circulate for approval

- Create and post installation instructions for OpenMM binaries

- Send out email to workshop participants telling them what to download in
preparation for workshop



MSMBuilder

* Tested MSMBuilder installation process on Linux – went smoothly with a
little additional instruction from Greg.  Drafted more detailed
installation directions and sent to Greg to review and update.

* Ran through first exercise for 2D potential for MSMBuilder – exercise
worked but wanted instructions on visualization



* To do this week:

                - Test MSMBuilder on Mac

- Come up with and test solution to run MSMBuilder on Windows (about ¼ of
participants are coming with a Windows laptop.  Current plan is to provide
a Linux virtual machine that they can use to install MSMBuilder)

                - Do a full dry run with Greg and Xuhui  (2nd full dry run
with larger audience scheduled for 6/16)

                - Update installation instructions so that email can be
sent out to workshop attendees on how to prepare for workshop





RNA Workshop

* RNA Society panel discussion held on May 27 – very successful.  Turnout
of 75-10.

* RNA workshop

                - One full dry run with Magda and Sam;  two dry runs with
Chris for Zephyr

                - Lots of testing of RNABuilder on Mac and Windows.  Now
have the final version ready to be made publicly available that can be
distributed to workshop attendees, along with a simple README file.

- Tested NAST/C2A installation and workshop examples on Windows.  Two bugs
found.  Magda and Randy updated code and re-posted today (Monday)



* To do this week:

                - Meet with Sam and Magda individually to review their
slides

                - Retest NAST/C2A installation and examples

                - Test new RNABuilder examples

                - Compile installation instructions for the three software
into one and email to participants

                - Draft of tutorial handout completed



Zephyr

* Two dry runs with Chris (mentioned earlier, as part of RNA Workshop) –
these slides and exercises will also be used for the MD workshop series

* Updated Zephyr User Manual.  That was packaged up and released today
with new version of Zephyr that runs on the Mac.

* Dry run of the mdrun part of the Zephyr workshop with Mark



* To do this week:

                - Publicize new release of Zephyr

- Send out email to workshop participants telling them what to download in
preparation for workshop





______________________________________________________



Joy P. Ku

Director of Dissemination

Simbios, Stanford University



(W) 650.736.8434

(F) 650.723.7461

Email:  joyku at stanford.edu

Website:  http://simbios.stanford.edu



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