2019 Introductory Workshop
2018 Introductory Workshop
We will have a 15th year (virtual) workshop (May 24-June 11, 2021) based on the 2020 workshop videos. This year’s workshop will provide the 2020 videos (linked below) along with the recorded live Q&A videos that occurred during that during that workshop. We will have additional live sessions during this year’s workshop to answer any questions that may arise from last year’s video sessions.
We had a successful 1st virtual workshop in 2020. We are distributing the videos (and accompanying slides) presented at the workshop. Please follow the following link to access the videos. Please submit Registration form to Lai Bergeman before proceeding.
May 24 – June 11, 2021
Scope. Until last year, we have held an in-person introductory workshop in which we 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. Last year we held our 14th workshop, but because of the COVID-19 pandemic, that workshop was presented virtually. This year our 15th workshop will once again be virtual. Unlike our in-person workshops, which cover the full 3D structure determination of a protein by NMR, the virtual workshop concerns only the methods of assignment of NMR spectra of proteins. Another consequence of the pandemic is that this year’s workshop will be basically a repeat of last year’s workshop. The tutorial videos, which can be seen by clicking on the 2020 NMRFAM Virtual Introductory Structure Determination Workshop link above, will be supplemented with the more detailed 2020 “live” video sessions, which were recorded last year as part of the Workshop. All of these videos will be accessible to registrants of the Workshop.
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
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 recorded “live Q&A sessions” will be presented to assist participants and demonstrate how to resolve more challenging assignment problems. This year there will be live Q&A sessions that will augment the “live Q&A sessions” of last year.
Schedule and Important Dates
May 24, 2021 – Last day to register for the workshop. We are setting the maximum number of participants to 40. The cost of this workshop is free. Registration will be on first come, first serve basis. Registrants will need to create an account on the NMRFAM workshop Moodle site by May 24. Instructions as to how to create a Moodle account will be provided by email to registered participants by May 15. Once the number of registrants, who have created Moodle accounts, reaches 40, 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 June 1. During May 24 – May 28, all the videos will be available for viewing and practice.
June 1, 2021 – June 10, 2021. There will be plenty of time for participants to view the videos and work with the hands-on sessions. There will be several live sessions that will allow the participants to interact with the presenters. The live sessions will start at 9am CDT except on Thursdays when they will start at 11a CDT in order to not overlap with The ICMRBS: Emerging MR Webinars.
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.
The Virtual Machine does not work on the latest Apple M1-based computers. Apple M1 users must use POKY, which is the SPARKY extension from Woonghee Lee group (CU Denver). Instructions will be provided.
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. Register with Lai Bergeman (email@example.com).
We hope you can participate in this popular workshop and become an NMRFAM user!
Please send registration form and questions to firstname.lastname@example.org