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Mon Mar 14, 2011 == NCMI Workshop on Single Particle Reconstruction, Validation and Analysis ==
=== March 14 - 17, 2011 ===
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Theme - Single particle reconstruction This page contains the workshop schedule, and will contain the PDFs of each of the presentations at the
workshop. Speakers are asked to upload their presentations sometime before the beginning of their talk
(preferably as far in advance as possible).
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||8:00 - 8:50||Registration||Outside PGH 200||
||8:50 - 9:10||Opening remarks/Introduction to Workshop||PGH200||Steve Ludtke and others||
||9:10 - 10:00||[[attachment:1_1_chiu_microscopy.pdf|Introduction to transmission electron microscopy]]||PGH200||Wah Chiu||
||10:00 - 10:50||[[attachment:1_2_henderson_image_processing.pdf|Image Processing Theory]]||PGH200||Richard Henderson||PGH200||
||11:00 - 11:20||Coffee Break||PGH200 Hall||
||11:20 - 12:30||[[attachment:1_3_ludtke_EMAN2.pdf|Tutorial 1 - Getting started with EMAN2, CTF & Class-averages]]||PGH232&200||Steve Ludtke||
||12:30 - 1:30||Lunch||Hall outside 200||
||1:30 - 3:00||Tutorial 1, contd - Initial models||PGH232&200||Steve Ludtke||
||3:00 - 3:20||Coffee Break||PGH200 Hall||
||3:20 - 5:00||Tutorial 1, contd - First refinement & other issues||PGH232&200||Steve Ludtke||
||5:00 - 6:00||[[attachment:1_4_cong_TriC-CCT.pdf|Research Lecture: Structural studies of TriC/CCT]]||PGH200||Yao Cong||
||6:00 - 9:00||Dinner - with participant short talks||PGH200||
The data and software required for participation in the tutorial sessions can be found at:
[[Workshop2011]].
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Tue Mar 15, 2011 Information on the location of the workshop and where to park is here: [[Ws2011/Location]]
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Theme - Helices & Heterogeneity The main workshop page is here: [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_114]]
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||9:00 - 10:00||[[attachment:2_1_egelman_IHRSR.pdf|IHRSR]]||PGH200||Ed Egelman||
||10:00 - 10:20||Coffee Break||PGH200 Hall||
||10:20 - 11:20||[[attachment:2_2_penczek_conformation.pdf|Identification of conformational states using resampling]]||PGH200||Pawel Penczek||
||11:30 - 12:30||[[attachment:2_3_goddard_chimera.pdf|Tutorial 2 - Chimera]]||PGH232&200||Tom Goddard||
||12:30 - 1:30||Lunch|| ||
||1:30 - 3:00||[[attachment:2_4_ludtke_EMAN2.pdf|Tutorial 3 - Evaluating refinements, heterogeneity, etc.]]||PGH232&200||Steve Ludtke||
||3:00 - 3:15||Coffee Break||PGH200 Hall||
||3:15 - 5:00||[[attachment:2_5_penczek_SPARX.pdf|Tutorial 4 - Introduction to identification of conformational states in SPARX]]||PGH232&200||Pawel Penczek||
||5:15 - 6:15||[[attachment:2_6_zhang_mmcpn.pdf|Research Talk - Multiple states of a chaperonin and a method for analyzing heterogeneous conformations in cryo-EM||
||6:30 - 9:00||Dinner||Library/Hilton||
'''Mon Mar 14, 2011'''
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Wed, Mar 16, 2011

Theme - Related methods

||'''8:50 - 9:15'''||[[attachment:3_1_murray_frealign.pdf|Quick morning tutorial session]]||'''PGH232&200'''||Stephen Murray||
||9:15 - 10:00||[[attachment:3_2_schmid_spt.pdf|Single Particle Tomography]]||PGH200||Mike Schmid||
||10:10 - 10:30||Coffee Break||PGH200 Hall||
||10:30 - 11:00||[[attachment:3_3_lawson_PDB.pdf|Single Particle Tomography]]||PGH200||Cathy Lawson||
Practicals (Computer classroom & Laptops in the lecture hall)
11:00 - 11:45 Greg Pinitilie
 Segger
11:45 - 12:45 Lunch
12:45 - 3:00 Multirefine
 EMAN2/Frealign
 Other topics
3:00 - 3:30 Break
3:30 - 5:00 Mike Schmid/Jesus Montoya
 Single particle tomography tutorial
 

5:10 - 6:10 Research Talk
 Irina Serysheva
 Structural studies of Calcium release channels
''Theme - Single particle reconstruction''
||8:00 - 8:50 ||Registration ||Outside PGH 200 || ||
||8:50 - 9:10 ||Opening remarks/Introduction to Workshop ||PGH200 ||Dr. Steve Ludtke ||
||9:10 - 10:00 ||[[attachment:1_1_chiu_microscopy.pdf|Cryo-EM Essentials]] ||PGH200 ||Dr. Wah Chiu ||
||10:00 - 10:50 ||[[attachment:1_2_henderson_image_processing.pdf|Image processing theory]] ||PGH200 ||Dr. Richard Henderson ||
||11:00 - 11:20 ||Coffee Break || || ||
||11:20 - 12:30 ||[[attachment:1_3_ludtke_EMAN2.pdf|Tutorial 1 - Getting started with EMAN2, CTF & class-averages]] ||PGH232&200 ||Dr. Steve Ludtke ||
||12:30 - 1:30 ||Lunch || || ||
||1:30 - 3:00 ||Tutorial 1, contd - Initial models ||PGH232&200 ||Dr. Steve Ludtke ||
||3:00 - 3:20 ||Coffee Break || || ||
||3:20 - 5:00 ||Tutorial 1, contd - First refinement & other issues ||PGH232&200 ||Dr. Steve Ludtke ||
||5:00 - 6:00 ||[[attachment:1_4_cong_TriC-CCT.pdf|Research Lecture: Structural studies of TriC/CCT]] ||PGH200 ||Dr. Yao Cong ||
||6:00 - 9:00 ||Dinner onsite - with participant short talks ||PGH200 || ||
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6:30 - Banquet at Fung’s Kitchen
 Bus leaves U of H at 6:30
'''Tue Mar 15, 2011'''
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Thu, Mar 17, 2011
Theme: Validation & Modeling
''Theme - Helices & Heterogeneity''
||9:00 - 10:00 ||[[attachment:2_1_egelman_IHRSR.pdf|Helical filaments, heterogeneity and polymorphisms]] ||PGH200 ||Dr. Edward Egelman ||
||10:00 - 10:20 ||Coffee Break || || ||
||10:20 - 11:20 ||[[attachment:2_2_penczek_conformation.pdf|Identification of conformational states using resampling]] ||PGH200 ||Dr. Pawel Penczek ||
||11:30 - 12:30 ||[[attachment:2_3_goddard_chimera.pdf|Tutorial 2 - Chimera]] ||PGH232&200 ||Tom Goddard ||
||12:30 - 1:30 ||Lunch || || ||
||1:30 - 3:00 ||[[attachment:2_4_ludtke_EMAN2.pdf|Tutorial 3 - Evaluating refinements, heterogeneity, etc.]] ||PGH232&200 ||Dr. Steve Ludtke ||
||3:00 - 3:15 ||Coffee Break || || ||
||3:15 - 5:00 ||[[attachment:2_5_penczek_SPARX.pdf|Tutorial 4 - Introduction to identification of conformational states in SPARX]] ||PGH232&200 ||Dr. Pawel Penczek ||
||5:15 - 6:15 ||[[attachment:2_6_zhang_mmcpn.pdf|Research Talk - Multiple states of a chaperonin and a method for analyzing heterogeneous conformations in cryo-EM]] ||PGH200 ||Dr. Junjie (George) Zhang ||
||6:30 - 9:00 ||Dinner ||UH Library || ||
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Morning Lectures (Main lecture hall)
9:00 - 10:00 Richard Henderson
 Validating maps with tilt data
 Resolution
10:00 - 10:30 Break
10:30 - 11:30 Gunnar Schroeder
 DireX
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Practicals (Computer classroom & Laptops in the lecture hall)
11:30 - 12:15 Ian Rees
 EMEN2 Tutorial and demo
12:15 - 1:00 Lunch
'''Wed, Mar 16, 2011'''
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1:00 - 2:30 Yao Cong
 Rosetta Introduction and Tutorial
2:30 - 3:00 Break
3:00 - 4:30 Matt Baker
 Gorgon Introduction and Tutorial
''Theme - Related methods''
||'''8:50 - 9:15''' ||[[attachment:3_1_murray_frealign.pdf|Tutorial 5 - Quick morning tutorial session]] ||'''PGH232&200''' ||Stephen Murray ||
||9:15 - 10:00 ||[[attachment:3_2_schmid_spt.pdf|Single particle tomography]] ||PGH200 ||Dr. Mike Schmid ||
||10:10 - 10:30 ||Coffee Break || || ||
||10:30 - 11:00 ||[[attachment:3_3_lawson_PDB.pdf|EMDatabank.org & Data Archival]] [[attachment:3_3_lawson_EMdepGuide.pdf|Tutorial/Guide]]||PGH200 ||Dr. Cathy Lawson ||
||11:00 - 11:45 ||[[attachment:3_4_pintilie_segger.pdf|Tutorial 6 - Segmentation with Segger]] ||PGH200&232 ||Dr. Greg Pintilie ||
||11:45 - 12:45 ||Lunch || || ||
||12:45 - 3:00 ||Tutorial 5 cont'd - Frealign, multirefine, etc. ||PGH200&232 || Stephen Murray & Dr. Steve Ludtke ||
||3:00 - 3:30 ||Coffee Break || || ||
||3:30 - 5:00 ||[[attachment:3_5_galaz_spt.pdf|Tutorial 7 - Single Particle Tomography in EMAN2 |&do=get]] ||PGH200&232 ||Jesus Galaz & Dr. John Flanagan ||
||5:10 - 6:10 ||[[attachment:3_6_serysheva_cachannels.pdf|Research Talk - Structural studies of Calcium release channels]] ||PGH200&232 ||Dr. Irina Serysheva ||
||7:00 - 9:00 ||Workshop Banquet '''Bus leaves U of H at 6:30 !''' ||[[http://www.fungskitchen.com|Fung’s Kitchen]]|| ||
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4:30 - 5:30 Workshop wrap-up, final issues '''Thu, Mar 17, 2011'''
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workshop ends ''Theme: Validation & Modeling''
||9:00 - 10:00 ||[[attachment:4_1_henderson_validation.pdf|Methods for Validation of Cryo-EM Maps]] ||PGH200 ||Dr. Richard Henderson ||
||10:00 - 10:30 ||Coffee Break || || ||
||10:30 - 11:30 ||[[attachment:4_2_schroeder_direx.pdf|Real-space Refinement of Atomic Models in DireX]] ||PGH200/232 ||Dr. Gunnar Schroeder ||
||11:30 - 12:15 ||[[attachment:4_3_rees_emen2.pdf|The EMEN2 Electronic Notebook and OODB]] ||PGH200/232 ||Ian Rees ||
||12:15 - 1:00 ||Lunch || || ||
||1:00 - 2:30 ||[[attachment:4_4_cong_rosetta.pdf|Introduction to Rosetta]] ||PGH200/232 ||Dr. Yao Cong ||
||2:30 - 3:00 ||Coffee Break || || ||
||3:00 - 4:30 ||[[attachment:4_5_baker_gorgon.pdf|Model Building and Analysis with Gorgon]] ||PGH200/232 ||Dr. Matt Baker ||
||4:30 - 5:30 ||Workshop wrap-up, final discussion || ||
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6:00 Speaker dinner '''''Workshop Ends'''''

''Note: Wah will host a dinner for any speakers who will be around Thurs evening''

NCMI Workshop on Single Particle Reconstruction, Validation and Analysis

March 14 - 17, 2011

This page contains the workshop schedule, and will contain the PDFs of each of the presentations at the workshop. Speakers are asked to upload their presentations sometime before the beginning of their talk (preferably as far in advance as possible).

The data and software required for participation in the tutorial sessions can be found at: Workshop2011.

Information on the location of the workshop and where to park is here: Ws2011/Location

The main workshop page is here: http://ncmi.bcm.edu/ncmi/events/workshops/workshops_114

Mon Mar 14, 2011

Theme - Single particle reconstruction

8:00 - 8:50

Registration

Outside PGH 200

8:50 - 9:10

Opening remarks/Introduction to Workshop

PGH200

Dr. Steve Ludtke

9:10 - 10:00

Cryo-EM Essentials

PGH200

Dr. Wah Chiu

10:00 - 10:50

Image processing theory

PGH200

Dr. Richard Henderson

11:00 - 11:20

Coffee Break

11:20 - 12:30

Tutorial 1 - Getting started with EMAN2, CTF & class-averages

PGH232&200

Dr. Steve Ludtke

12:30 - 1:30

Lunch

1:30 - 3:00

Tutorial 1, contd - Initial models

PGH232&200

Dr. Steve Ludtke

3:00 - 3:20

Coffee Break

3:20 - 5:00

Tutorial 1, contd - First refinement & other issues

PGH232&200

Dr. Steve Ludtke

5:00 - 6:00

Research Lecture: Structural studies of TriC/CCT

PGH200

Dr. Yao Cong

6:00 - 9:00

Dinner onsite - with participant short talks

PGH200

Tue Mar 15, 2011

Theme - Helices & Heterogeneity

9:00 - 10:00

Helical filaments, heterogeneity and polymorphisms

PGH200

Dr. Edward Egelman

10:00 - 10:20

Coffee Break

10:20 - 11:20

Identification of conformational states using resampling

PGH200

Dr. Pawel Penczek

11:30 - 12:30

Tutorial 2 - Chimera

PGH232&200

Tom Goddard

12:30 - 1:30

Lunch

1:30 - 3:00

Tutorial 3 - Evaluating refinements, heterogeneity, etc.

PGH232&200

Dr. Steve Ludtke

3:00 - 3:15

Coffee Break

3:15 - 5:00

Tutorial 4 - Introduction to identification of conformational states in SPARX

PGH232&200

Dr. Pawel Penczek

5:15 - 6:15

Research Talk - Multiple states of a chaperonin and a method for analyzing heterogeneous conformations in cryo-EM

PGH200

Dr. Junjie (George) Zhang

6:30 - 9:00

Dinner

UH Library

Wed, Mar 16, 2011

Theme - Related methods

8:50 - 9:15

Tutorial 5 - Quick morning tutorial session

PGH232&200

Stephen Murray

9:15 - 10:00

Single particle tomography

PGH200

Dr. Mike Schmid

10:10 - 10:30

Coffee Break

10:30 - 11:00

EMDatabank.org & Data Archival Tutorial/Guide

PGH200

Dr. Cathy Lawson

11:00 - 11:45

Tutorial 6 - Segmentation with Segger

PGH200&232

Dr. Greg Pintilie

11:45 - 12:45

Lunch

12:45 - 3:00

Tutorial 5 cont'd - Frealign, multirefine, etc.

PGH200&232

Stephen Murray & Dr. Steve Ludtke

3:00 - 3:30

Coffee Break

3:30 - 5:00

Tutorial 7 - Single Particle Tomography in EMAN2

PGH200&232

Jesus Galaz & Dr. John Flanagan

5:10 - 6:10

Research Talk - Structural studies of Calcium release channels

PGH200&232

Dr. Irina Serysheva

7:00 - 9:00

Workshop Banquet Bus leaves U of H at 6:30 !

Fung’s Kitchen

Thu, Mar 17, 2011

Theme: Validation & Modeling

9:00 - 10:00

Methods for Validation of Cryo-EM Maps

PGH200

Dr. Richard Henderson

10:00 - 10:30

Coffee Break

10:30 - 11:30

Real-space Refinement of Atomic Models in DireX

PGH200/232

Dr. Gunnar Schroeder

11:30 - 12:15

The EMEN2 Electronic Notebook and OODB

PGH200/232

Ian Rees

12:15 - 1:00

Lunch

1:00 - 2:30

Introduction to Rosetta

PGH200/232

Dr. Yao Cong

2:30 - 3:00

Coffee Break

3:00 - 4:30

Model Building and Analysis with Gorgon

PGH200/232

Dr. Matt Baker

4:30 - 5:30

Workshop wrap-up, final discussion

Workshop Ends

Note: Wah will host a dinner for any speakers who will be around Thurs evening

Ws2011/Agenda (last edited 2011-04-10 05:04:52 by SteveLudtke)