2019 Introductory Workshop
2018 Introductory Workshop
We had a successful 1st virtual workshop. We are now distributing the videos (and accompanying slides) presented at the workshop. Please follow the following link to access the videos.
Sunday, May 31, 2020 – Wednesday, June 10, 2020
Scope. Over the 13 years that we have held this in-person introductory workshop we have covered the basic steps involved in solving a protein structure (ubiquitin) by NMR, giving the participants an opportunity to practice these steps in hands-on sessions led by the NMRFAM staff. Now in the 14th year and in the presence of a global pandemic, the nature of the workshop has changed. This year we will be presenting a virtual workshop concerning only the methods of assignment of NMR spectra of proteins. The workshop will still be hands-on with instructional videos introducing the assignment process for both backbone and side chains along with shorter video tutorials and practice materials for the participants to work through, followed by live Q&A sessions and demonstrations of more challenging assignment problems. The determination of the three-dimensional structure of the protein using NMR data will be offered in a similar virtual format at a later time.
The sessions for this workshop will be:
1 – Description of experimental data
2 – Introduction to NMRFAM-Sparky and peak picking
3 – Backbone assignments
4 – Sidechain assignments
5 – Automated peak picking (APES)
6 – Automated assignments using I–PINE and validation using PINE-Sparky
7 – Discussion of the BioMagResBank (BMRB) for deposition of data
8 – Introduction to Solid State NMR structure determination techniques
This workshop is intended to give participants a broad overview of the process of assigning the NMR spectra of a protein, so they can begin their own projects. Participants will be working on their own computers and will receive an NMRFAM software suite containing a complete set of tools for biomolecular NMR studies. This software provides easy access to external servers, websites, and video tutorials. This year we will be using the Moodle (moodle.com) online learning platform to provide access to all of the virtual workshop materials, including videos, lecture slides and links to live forums for Q&A. In addition, all of the lectures, data and software will be available for download from NMRFAM. Live question and answer sessions will be held, where participants will be able to interact directly with the workshop staff. As always, participants are invited to contact NMRFAM staff following the workshop with any questions or problems (nmrfam.wisc.edu/contacts/).
Format. The format of the virtual workshop will consist of access (via Moodle) to videos and slides describing the overall approach backbone and side chain assignment and then hands-on videos and tutorial materials so the participant can follow along with the instructor to perform the individual steps in both manual and automated assignment procedures. On the Moodle site there are forums associated with each session, where participants will be able to communicate with the workshop staff, and live Q&A sessions will be held using Google Meet to assist participants and demonstrate how to resolve more challenging assignment problems.
Schedule and Important Dates
Monday, May 25, 2020 – Last day to register for the workshop. We are setting the maximum number of participants to 25. The cost of this workshop is free. Our usual charges for the in-person workshop cover the costs of running the workshop, which don’t exist for a virtual one. Registration will be on first come, first serve basis. Registrants will need to create an account on the NMRFAM workshop Moodle site by May 25. Instructions as to how to create a Moodle account will be provided upon registration. Once the number of registrants, who have created Moodle accounts, reaches 25, account generation will be terminated. An email will be sent to participants, who have generated a Moodle account, describing what they need to download and install prior to the workshop which starts on May 31.
Sunday, May 31, 2020 – Wednesday, June 10, 2020. There will be plenty of time for participants to view the videos and work with the hands-on sessions.
Participant Requirements. Workshop participants are not expected to have prior experience with basic steps of NMR protein assignments. The workshop will cover the entire process and each session will build upon the previous sessions. Participants will be given the data necessary to complete each session. For example, processed data will be provided for the peak-picking session, and fully peak-picked data will be provided for the backbone and side-chain assignment sessions.
The workshop will utilize NMRFAM’s Integrative NMR package, which makes biomolecular NMR spectroscopy much more accessible by integrating software tools so that they interact efficiently in ways that support automation, result validation, and data visualization. Also included are links to web services, databases, and video tutorials. Participants will receive these tools pre-installed in a virtual machine that they will load onto their computer (see below). Integrative NMR includes NMRFAM-SPARKY (visual analysis of spectra and chemical structures), PyMOL (visualization of 3D molecular structures), PINE (protein chemical shift assignment), PECAN (secondary structure determination from chemical shifts), RNA-PAIRS (RNA assignment), and PONDEROSA-C/S (NMR-structure determination utilizing XPLOR-NIH/Ponderosa).
Integrative NMR is installed on a virtual machine (VM), an emulation of a particular computer system that can be installed and run on all flavors of other operating systems. We use a VM that runs the Linux operating system, Ubuntu 18.04 with the MATE desktop. To run this on your computer, you will need to install VM VirtualBox (Oracle), which is freely available at www.virtualbox.org. Oracle VM VirtualBox is a virtualization software package for x86 and AM64/Intel64-based computers. Supported host operating systems include Mac OS X, Windows XP, Windows Vista, Windows 7, Windows 8, and Windows 10 among others.
Computer Requirements: In order to install VirtualBox, you MUST have administrative privileges on your computer. It is recommended that the computer have at least 4 GB of memory. The memory and bit size are not strict requirements, but the speed will suffer. The computer should have ~10 GB of free disk space. It is recommended that you have a (preferably 2-button with scroll wheel) mouse for your computer. Two monitors for your computer OR a computer plus a phone or tablet will be helpful for following along on your own during tutorials or live Q&A sessions.
Registration.This year’s virtual workshop will be hosted on the Moodle learning platform, which will require each participant to generate an account at the NMRFAM assignment workshop Moodle site. (Registration is closed)
We hope you can participate in this popular workshop and become an NMRFAM user!
Please send registration form and questions to email@example.com