NYSBC - New York Structural Biology Center


Training


New user training [monthly]:


New users are required to attend a group new user training session before use of the facility. We offer these 1-day training sessions the beginning of each month from 9am to 4:30pm. The morning session covers sample preparation (negative-staining and plunge freezing), and the afternoon session covers basic TEM use (loading samples and introduction to Leginon). New users may purchase a starter EM user kit from SEMC and are strongly encouraged to do some background reading before their first training session.
 
Following training, users may request time on the on the instruments in consultation with SEMC staff until they gain sufficient experience to receive sign off from staff to use the instruments independently.  Please note that each instrument requires individual training and sign off, which will be provided by SEMC staff on a one-on-one basis.  Separate training is required for 24 hour access; the initial sign off is only for use of equipment during normal business hours (9am to 6pm, Monday through Friday)
 
Please email EMG@NYSBC.org to inquire about future training session dates.

Appion Workshop Part 1:


A one-day Appion Workshop will be held on Tuesday, June 14th from 10:00AM to 4:00PM The Appion Part 1 Workshop provides hands-on training for the Appion single-particle data processing workflow. Appion is a "pipeline" for processing and analysis of EM images; it is integrated with Leginon data acquisition, but can also be used stand-alone after uploading images or particle stacks. Topics include analyzing the quality of your data collection, correcting the CTF, generating and cleaning up stacks, and generating 2D class averages. An Appion Part 2 Workshop will be offered in the future to provide training for making initial models and doing 3D reconstructions. If you are interested in attending an Appion Part 1 Workshop, please register at: https://www.surveymonkey.com/r/FZLPDXF.   The workshop is limited to 10 attendees.

Appion Workshop Part 2:


A one-day Appion Workshop will be held on July 26, 2016 from 10:00AM to 4:00PM. This Appion Part 2 Workshop is a follow-on to the Part 1 workshop and will focus on 3D initial models and refinement. If you are interested in attending an Appion Part 2 Workshop, please register at: https://www.surveymonkey.com/r/5NK7NGQ. The workshop is limited to 10 attendees.

Appion Workshop Part 3:


Tilt-series alignment is commonly performed by tracking fiducials in order to recover the three-dimensional structure and orientation of specimen in cryo-electron tomography, negative stain tomography, and tomography on plastic sections. However this approach is sometimes fraught with difficulty due to fiducial movement, fiducial aggregation, or the lack of fiducials in specimen such as FIB/SEM lamella.

In this workshop users will gain hand-on experience with a semi-automated implementation of Protomo into Appion. Protomo allows for fiducial-less alignment of tilt-series and refinement of specimen orientation on the grid through an iterative geometry refinement process. Appion-Protomo, which installs seamlessly with Appion, significantly reduces the effort and expertice required by the user to align fiducial-free tilt-series collected using any software package. All that is required is a stack of tilt images along with knowledge of their imaging conditions. Integrated within Appion-Protomo are pipelines for defocus estimation, CTF correction, and dose compensation, along with multiple reconstruction methods.

No previous experience in tilt-series alignment processing is required. Workshop attendees are encouraged to bring data in the form of tilt-series images or stacks for processing assistance.

Attedees are encouraged to sign up for the Dynamo workshop to learn how to extract and process subtomograms from their reconstructed tomograms.

Attendees should bring their own laptop in order to follow along during this hands-on workshop.

Register for the Appion Part 3 Workshop here: https://www.surveymonkey.com/r/SR2KWZT.

Dynamo Workshop:


This workshop will provide hands-on training in all practical aspects of sub-tomogram averaging using Dynamo. The new Dynamo catalogue system for organizing and centralizing tomograms will be featured along with new semi-automated picking procedures. All stages of the pipeline will be covered, including: tomogram visualization and archiving, particle picking, membrane picking, filament picking, averaging, refinement, and classification.

The workshop will begin on December 8 at noon with a SEMC@NYSBC Forum introducing Dynamo and continue all day December 9th.

No previous experience in sub-tomogram processing is required. Workshop attendees are encouraged to bring data, whether tomograms or sub-tomograms, for processing assistance at the end of the final day. Attendees should bring their own laptop in order to follow along during this hands-on workshop.

Register for the Dynamo Workshop here: https://www.surveymonkey.com/r/JHFDJ27.


Holey Gold Grid Workshop:


A workshop on making Holey Gold grids will be held on Thursday, August 25, 2016 from 1:00 to 3:00pm. This workshop will provide an overview of making holey gold films from holey carbon films supported on gold mesh. Holey gold films provide a stronger support film and reduce beam induced movement of the specimen. If you would like to attend this workshop, please register at: https://www.surveymonkey.com/r/YZQPWH3. The workshop is limited to 6 attendees.


For more information about the course, please email EMG@NYSBC.org


EM course [yearly]:

SEMC's "reverse classroom" style winter course is in session! Attendance has been high, and in the most recent class our students made ice cream with liquid nitrogen, one of the key components of sample preparation.

The course is based on an online video class taught by Grant Jensen.  Students watch these lectures prior to a formal 90 minute class that meets once per week for follow up materials and discussion.  Class dates and a detailed syllabus can be found on our website.

External Training and Courses

1st course on Cryo Electron Microscopy and 3 Dimensional Image Processing (CEM3DIP) of Macromolecular Assemblies and Cellular Tomography:
http://workshop.iisertvm.ac.in/cem3dip, IISER Thiruvananthapuram, India, July 2-13, 2016.

5th Dynamo Workshop on Subtomogram Averaging:
https://wiki.dynamo.biozentrum.unibas.ch/w/index.php/Dynamo Workshop 2016, University of Basel (Switzerland), August 17-19 2016.

NYC Structural Biology Meeting:
https://nysbdg.org, Mt. Sinai School of Medicine, August 4, 2016.

EMBO practical course on cryo-EM and 3D image processing www.embl.de/training/events/2016/CRY16-01/index.html EMBL in Heidelberg , August 28 - September 5, 2016.


To contact us for more information about one of our training courses, please email EMG@NYSBC.org

Please Note: Users of the resources at SEMC are requested to acknowlege use of the resources in publications as follows:

"Some of this work was performed at the Simons Electron Microscopy Center at the New York Structural Biology Center that is supported by a grant from the Simons Foundation (Grant Number: 349247) with additional support from: NIH S10 OD019994-01, the Agouron Institute (Grant Number: F00316), NIH S10 RR029300-01, NIH S10 RR017291-01, NYSTAR, and NIH C06 RR017528-01-CEM."