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2023

I2PC – Instruct course on Cryo-Electron Tomography Image Processing. Madrid, December 12 – 15, 2023

VENUE

The course will take place in person at CNB-CSIC 
December 12 – 15, 2023 from 09:00 to 18:00 CET
You do not need to install any special software to connect. A modern browser should be enough.

Overall aims and course outline

Cryo-electron Tomography is a rapidly growing technique that can visualize cell organelles and biological macromolecules in their cellular context. Image processing algorithms allow the identification of the macromolecules of interest in the electron tomograms. Then, by extracting small subtomograms around those locations and identifying those similar particles, we may average them and recognize their different conformations. This latter process is called subtomogram averaging and has allowed solving a growing number of macromolecules with a resolution between 20-5A.

The course aims at providing a comprehensive overview of the whole image processing pipeline in Electron Tomography (ET) from the movie alignment of the tilt series, 3D reconstruction of the tomogram, particle identification, and subtomogram averaging, all inside Scipion integration framework.  

With the experience gained in the organization of virtual and in-person courses, we plan to organize this course in an in-person modality. 20 people will be able to physically attend.

The course is aimed at researchers of all levels wanting to adopt electron microscopy as one of the tools at their disposal for elucidating biological structures.

Expected impact for young researchers

CryoET is one of the most promising structural techniques, and it bridges the gap between structural and molecular biology and cell biology. Ph.D. students, as well as post-docs, will undoubtedly benefit from approaching this technique. Knowing it will open new doors to new positions worldwide.

Prerequisites

  • You will need to bring a laptop with a modern browser
  • We will provide machines with the required software through Amazon Web Services.
  • We will provide launch and coffee breaks

Tutors: I2PC: Carlos Oscar Sorzano Sánchez, Jose-María Carazo, Pablo Conesa, Federico de Isidro,
David Herreros, Jorge Jiménez, Patricia Losana, Jose Luis Vilas, Borja Rodriguez,
CryoEM CNB-CSIC: Francisco Javier Chichón, Jose Javier Conesa.
Ramón y Cajal Researcher – Department of Information and Communication Engineering – University of Murcia: Antonio Martínez
Contacts: Lead contact:  Carlos Oscar Sorzano
E-mail: coss@cnb.csic.es
Administrative Contact: Blanca Benitez
E-mail: blanca@cnb.csic.es

Agenda

 Times are expressed in CET time Zone

DAY 1: 

From movies to tomograms

 9:30 – Welcome – (Jose Maria Carazo & Carlos Oscar Sorzano)
9:45 – Course introduction – (Jose Luis Vilas)
10:00 – Tomography in Scipion – (Jose Luis Vilas)
10:30 – Import Tilt Series, automatic alignment – (Federico de Isidro)
11:30 – 10 minutes break
11:40 – CTF estimation and correction –  (Federico de Isidro)
13:00 – Lunch break
14:00 – Tomogram reconstruction – (Federico de Isidro)
15:30 – 10 minutes break
15:40 – eTomo – (Grigory Sharov)
17:00 – AreTomo, ctfFind4 and novaCTF (Grigory Sharov)
17:30 – End of session

DAY 2: 

From tomograms to subtomograms- Picking and segmentation

9:30 – Non-directional picking with cryolo and SPA leap – (Borja Rodriguez)
11:10 – 10 minutes break
11:20 – Non-directional picking with cryolo and SPA leap – (Borja Rodriguez)
12:45 – Lunch break
13:45 – Tomogram denoising and membrane segmentation – (Antonio Martinez)
14:15 – Membrane picking with PySeg – (Jorge Jiménez)
15:00 – Dynamo – (Pablo Conesa)
16:00 – 10 minutes break
16:10 – Practice: Dynamo – (Pablo Conesa)
17:30 – End of session

DAY 3: 

Processing subtomograms

 9:30 –  Subtomogram averaging with RELION4 – (Patricia Losana)
11:30 – 10 minutes break
11:40 – Subtomogram Averaging with RELION4 – (Patricia Losana)
13:00 – Lunch Break
14:00 – Subtomogram Averaging with EMAN – (Jorge Jiménez)
15:00 – 10 minutes break 
15:10 – Subtomogram Averaging with EMAN – (Jorge Jiménez)
17:30 – End of session

DAY 4:  morning session

Tomogram Interpretation

 9:30 – Tomogram segmentation. Basic use of SuRVoS for cellular tomogram segmentation and basic analysis. 3D rendering using ChimeraUSFC with masked data – (Francisco Javier Chichón)
12:00/12:30 – End of coruse. Wrap Up.

 

Registration Fee

Fill your registration (Online registration closed)

 

This course is funded by Instruct – ERIC, an Integrated Structural Biology Infrastructure for Europe.

 

Scipion at facilities workshop. October 17th & 18th, 2023

Dates: 17th & 18th October 2023 ( 2 EU afternoons or 2 US ET mornings)
Venue: Remote (https://conectaha.csic.es/b/bla-i7j-g7z-klh)

Aim: The aim of this meeting is to get feedback and showcase how facilities are using Scipion and show what Scipion offers to a Cryo-em facility. There will be talks but also plenty of time for discussion.

Target Audience: Cryo-em facility staff wanting to do or already doing on-the-fly processing.

Conditions: The workshop will be remote. No programming skills are required. We will use in-house bigbluebutton conference system. 
Verify your browser works at https://demo.bigbluebutton.org/

Program:

San Francisco – 05:00 // Minneapolis – 07:00 // New York – 08:00 // São Paulo – 09:00 // Madrid – 14:00 // London – 13:00
Beijing – 20:00 // Tokyo – 21:00 // Sydney – 23:00

Tuesday 17th October – New developments/Solutions

14.00 (CEST) Welcome – Jose María
14.15-14:40 Introduction to Scipion – Pablo Conesa (CNB) 
14:40-15:20 Optimizing Cryo-EM facilities with SmartScope – Jonathan Bouvette (Princeton)
15:20-16:00 Scipion and Smart scope – Alberto García (CNB)
16:00-16:40 EMhub: a web platform for CryoEM centers management and on-the-fly data processing (Jose Miguel de la Rosa (St. Jude Children’s Research Hospital Memphis, TN, USA)
17:20-18:00 Streaming and Unattended Workflows for SPA Processing – Daniel Marchan (CNB)

Wednesday 18th October – Facilities real cases

14.00 (CEST) Data flow in cryo-EM facilities: LMB example – Grigory Sharov (LMB)
14.15-14:40 CM01 and processing pipeline at ESRF – Isai and Olof (ESRF)
14:40-15:20 Setup at CNB – Javier Chichón (CNB)
15:20-16:00 Facilities + Tomography + Scipion – Pablo Conesa (CNB)
16:00-17:45 Discussion and conclusions 
             – Data storage and transfer
             – IT support
             – Reporting
             – Automation: Grid screening, acquisition image processing
             – Others? 
17:45-18.00 “Group picture” + End

National Center for Biotechnology (CNB), Madrid, Spain
Madrid, October 17 – 18, 2023
How to find us: https://idospece.i2pc.margaro.eus/contact-us/

REGISTRATION

Registration will be free for all attendees.
Fill your application here

I2PC Seminar Series 2023

Following the tradition, I2PC (Instruct Image Processing Center) is organizing the forth edition of a seminar series on cryoEM and cryoET methods for image processing. The aim of the seminar series is to gather expert developers and users in a same framework where the algorithms can gain visibility and users can understand the applications and mechanisms of the presented algorithms.

The webinars will be online and free without registration of cost. You can join the session through next link:
https://conectaha.csic.es/b/bla-rkh-dqa-rpn

The contents and speakers will be:

7th September (Time:  9:00 AM New York, 15:00PM Madrid, 14:00PM London). Bernard Heymann – The implications and resolution of the Ewald sphere issue in cryoEM. National Cryo-EM Program, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc

21th September (Time: 9:00AM Los Angeles, 18:00PM Madrid, 17:00PM London). Petar Petrov – The laser phase plate in cryo-EM: new approaches to image acquisition and analysis. Holger Müller group at UC Berkeley.

5th October (Time: 9:00AM New York, 15:00PM Madrid, 14:00PM London). Christopher JF Cameron – Reliable protein identification in cryo-EM images by machine-learning consensus.  Hemant Tagare and Mark Gerstein groups at Yale University.

19th October (Time: 9:00AM New York, 15:00PM Madrid, 14:00PM London). Eduard Baquero – Structural study of a broadly neutralizing anti-HIV-1 antibody from a post-treatment controller. NanoImaging Facility Core Institut Pasteur


Instruct course on flexibility analysis and integrative modelling using Scipion. Madrid, June 19 – 23, 2023

Venue

National Center for Biotechnology (CNB), Madrid, Spain
Madrid, June 19 – 23, 2023
How to find us: https://i2pc.es/contact-us/

Overall aims and course outline

Cryo-Electron Microscopy has established itself as a mature technique to determine the three-dimensional structure of biological macromolecules. It is currently reaching atomic resolution and is capable of accessing the structure of conformationally heterogeneous samples, as well as macromolecular complexes. It is complementary to other structural techniques like X-ray crystallography and Nuclear Magnetic Resonance and at the moment it is the most rapidly growing technique in atomic structure depositions at public databases like the PDB.
The aim of the course is to introduce attendees to two techniques that are normally needed at the end of the Cryo-Electron Microscopy image processing pipeline: 1) understanding the possible continuous heterogeneity/flexibility of the sample, helping to obtain dynamical information in the form of conformational landscapes, and 2) interpreting the reconstructed map by means of an atomic model. The I2PC has a long tradition of organizing courses of image processing and atomic modelling, with Instruct courses that have been heavily oversubscribed and had to be repeated twice in the same year to be able to attend its demand.
We will use our software platform Scipion to present these two topics. Scipion is an integrative platform that allows interoperability among different software packages. In the domain of flexibility analysis, we include our own developments in Xmipp as well as tools coming from CryoDrgn, ProDy and HEMNMA. For the atomic modelling part, we include software like Coot, Chimera, Refmac, Phenix, and AlphaFold. In addition to simplifying the access to all these software packages in an integrated manner, Scipion adds a traceability and reproducibility layer so that any other researcher can understand the modelling workflow followed to reach a particular model.
This course is addressed to investigators at all levels.

Expected impact for young researchers

Atomic modelling of the CryoEM map is currently at the moment the natural next step once the map is reconstructed. Flexibility analysis is currently not so common, but the advantage of CryoEM is that it can capture the different conformations of the macromolecules under study. Both techniques are valuable assets in young researchers already with a background on image processing in CryoEM.

Contacts

Lead contact:
Carlos Oscar Sorzano
email. coss@cnb.csic.es

Administrative Contact:
Blanca Benitez
email: blanca@cnb.csic.es

Tutors

I2PC staff: David Herreros (DH), James Krieger (JK), Marcos Gragera (MG), Marta Martínez (MM), Roberto Marabini (RM), Daniel del Hoyo (DDH)
CNRS IMPMC-CNRS UMR 7590. Sorbonne Université: Remi Vuillemot (RV)

You can fill your registration here (Online registration closed)

Registration Fee

  • Academic Registration Fee Instruct countries: Predocs & Postdosc 50€
  • Academic Registration Fee Instruct countries: Others 100€
  • Academic Registration Fee Non Instruct countries: Predocs & Postdosc 100€
  • Academic Registration Fee Non Instruct countries: Others 150€
  • Industrial Registration Fee 300€
Program
Day 1: June 19, 2023

09:30: Introduction to Scipion and AWS
10:15: Introduction to macromolecular flexibility and Flexibility Hub
10:30: Flexibility approaches (theory): 
– Deformation field-based approach
– Density-based approach
11:00: Coffee break
11:30: Presentation of the dataset to be used during the practical session
11:45: Estimation of conformational landscapes
12:45: Flexibility consensus (theory)
13:30: Lunch
14:30: Flexibility consensus (practice)
15:15: Dimensionality reduction of estimated landscapes
16:00: Coffee break
16:30: Conformational landscape analysis tools
– Interactive landscape clustering and real-time inspection of conformations
– Best number of clusters analysis
18:00 – 18:30: End of the day
Day 2 June 20, 2023

09:30: Review from the previous day
09:45: Conformational landscape analysis tools (continuation)
– Interactive landscape annotation and real-time inspection of conformations (2D-based tools)
11:00: Coffee break
11:30: Conformational landscape analysis tools (continuation)
– Interactive landscape annotation and real-time inspection of conformations (3D-based and hybrid tools)
13:30: Lunch
14:30: Extracting conformational states from landscape selections:
Application of deformation fields to maps and structural models + strain/rotation analysis + motion statistics
15:00: Interactive local analysis of motions
15:30: Heterogeneity correction with ZART (theory)
16:00: Coffee break
16:30: Heterogeneity correction with ZART (practice)
17:15: Heterogeneity correction of different landscapes states with ZART
18:00 – 18:30: End of the day
Day 3 June 21, 2023

09:00: Review from the previous day
9:45: Introduction to atomic structure ensemble analysis, normal mode analysis, and ProDy
10:15: Ensemble analysis with ProDy ensemble construction, PCA and landscape projection, and motion analysis with NMWiz
11:00: Coffee break
11:30: Conformational landscapes from normal modes and molecular dynamics using ContinuousFlex (theory and practice)
13:30: Lunch
14:30: Introduction to model building in cryo-EM
  – How to get a first estimation of the model (homology, alphafold, modelangelo)
15:15: Presentation of the data used in the practical session
– Kahoot
15:45 min: Map preprocessing – I
  16:00: coffee break
16:30: Map preprocessing – II
17:00 : Getting a first estimate of the model
18:00-30: End of the day
Day 4 June 22, 2023

09:30 Structure analysis: Structure comparison
10:15: Rigid fitting of initial models
11:00: Coffee Break
11:30: Flexible fitting (coot) and validation (phenix)
13:30: lunch
14:30: Flexible fitting (coot) and validation (phenix) (cont)
15:30: kahoot
16:00: coffee break
16:30: Model building of the Beta sub-unit
18:00-30: end of the day
Day 5 June 23, 2023

09:30: Presentation of the course questionnaire
09:45: Building the model of the protein complex
10:30: kahoot.
11:00: Coffee Break
11:30: Submission of structures to EMDB. Understanding the validation report.
12:00: Structure analysis: Chain contacts
13:00: INSTRUCT short message and farewell
13:30: lunch and end of the day

Fill your registration here (Online registration closed)

This course is funded by Instruct – ERIC, an Integrated Structural Biology Infrastructure for Europe.

iNEXT Discovery – I2PC Course on Single Particle Analysis by CryoEM. Madrid, 27 – 29 March, 2023

Venue

National Center for Biotechnology (CNB), Madrid, Spain
Madrid, March 27 – 29, 2023
How to find us: https://i2pc.es/contact-us/

Overall aims and course outline

Cryo-Electron Microscopy has established as a mature technique to determine the three-dimensional structure of biological macromolecules. It is currently reaching atomic resolution and it is capable of accessing to the structure of conformationally heterogeneous samples, as well as macromolecular complexes. It is complementary to other structural techniques like X-ray crystallography and Nuclear Magnetic Resonance and at the moment it is the most rapidly growing technique in atomic structure depositions at public databases like PDB.

The aim of the course is to give an overall overview of the image processing in single particle analysis (SPA). The I2PC has a long tradition of organizing courses of image processing and atomic modelling, with Instruct courses that have been heavily oversubscribed and had to be repeated twice in the same year to be able to attend its demand.

With the experience gained in the organization of virtual and in-person courses, we plan to organize this course in an in-person modality. 20 people will be able to physically attend.

The course is aimed at researchers of all levels wanting to adopt electron microscopy as one of the tools at their disposal for elucidating biological structures.

Expected impact for young researchers

CryoEM is the most rapidly growing structural technique. PhD students as well as young post-docs will certainly benefit from approaching this technique. Knowing it will open new doors to new positions worldwide.

Contacts

Lead contact:  
Carlos Oscar Sorzano
email. coss@cnb.csic.es

Administrative Contact:
Blanca Benitez
email: blanca@cnb.csic.es

Tutors

Carlos Oscar Sorzano Sánchez (COSS), José-María Carazo (JMC), Marcos Gragera (MG), Carlos Perez Mata (CPM)

Program

Day 1: Data processing
9:30 Morning session:
– Movie alignment, Screening micrographs and CTF
– Particle picking and screening
13:00 Lunch Break
14:00 Afternoon session:
– Particle picking and screening
– 2D classification
17:00 End of day

Day 2:
9:30 Morning session
– Initial volume
– 3D classification
13:00 Lunch Break
14:00 Afternoon session
– 3D classification advanced (masking, classification with no alignment…)
– 3D reconstruction
17:00 End of day

Day 3:
9:30 Morning session
– Sharpening, local resolution and validation
13:00 Lunch Break
14:00 Afternoon session
– One-to-one troubleshooting meeting. NEW
17:00 End of day

REGISTRATION

Registration will be free for all attendees.
Fill  your application here.  (Registration is closed)

This course is organized by iNEXT Discovery (UE Proposal:  871037) and I2PC in collaboration with  Instruct – ERIC, an Integrated Structural Biology Infrastructure for Europe and CRIOMECORR Project


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