|
Size: 9236
Comment:
|
Size: 13807
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 130: | Line 130: |
''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_83|CryoEM Training Workshop: June 8, 2007]] ''' '''Presentations''' * [[attachment:Cryo_Transfer.mov||&do=get]] - Cryo Transfer movie - Cruciano, Angela; Rees, Ian * [[attachment:Chiu handout 1 07-06-08.ppt||&do=get]] - Day 1 Lecture- Overview of Cryo EM - Wah Chiu * [[attachment:MDS Alignment.ppt||&do=get]] - MDS alignment - Cruciano, Angela ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_66|Workshop on Single Particle Reconstruction and Visualization: Mar. 14, 2007]] ''' '''Presentations''' * [[attachment:houston_march07.ppt||&do=get]] - EMdep: Deposition EM maps - Kim Henrick * [[attachment:Chiu_EMAN Contrast theory_07_03-15.pdf]] - Image Contrast Theory - Wah Chiu * [[attachment:2007-EMAN-Workshop-Wen-Jiang.pdf]] - Icosahedral Reconstruction - Jiang, Wen * [[attachment:EMANworkshop-Ferrin.pdf||&do=get]] - Visualization tools for complex biological structures - Tom Ferrin * [[attachment:chimera-eman-2007.pdf]] - Chimera Tutorial - Tom Goddard * [[attachment:ianrees_emen2_mar8.pdf]] - EMEN2: An Extensible, Collaborative, Electronic Lab Notebook - Rees, Ian * [[attachment:EMAN-workshop07-AIRS.ppt||&do=get]] - VIsualizing and Analyzing CryoEM Density Maps with AIRS - Matthew Baker * [[attachment:EMAN_Wkshp_MFS_Handout.ppt||&do=get]] - Aligning and Averaging 3-D Subvolumes from Electron Cryo-Tomograms - Schmid, Michael * [[attachment:Fourier Transforms.ppt||&do=get]] - Fourier Transforms, Filtering and Convolution - Marsh, Mike * [[attachment:updated_Wrks_EMAN_07.pdf||&do=get]] - updated Image similariry measures and such - Pawel A. Penczek * [[attachment:PmvVision.pdf]] - A Brief Introduction to PMV-VIsion - Zhao, Yong; Sanner, Michel * [[attachment:EMAN_CM_Modeller.ppt||&do=get]] - Introduction to comparative modeling with MODELLER (final version) - Webb, Ben and Topf, Maya * [[attachment:EMAN_Modeller_hands_on.ppt||&do=get]] - MODELLER hands-on session (final version) - Webb, Ben and Topf, Maya * [[attachment:EMANDemo1.pdf]] - EMAN Practical Session Slides - Ludtke, Steven * [[attachment:python_intro.pdf]] - Introduction to Python - Ludtke, Steven * [[attachment:talk1-intro.pdf]] - Workshop Welcome and Single Particle Reconstruction Overview - Ludtke, Steven * [[attachment:talk2-ctf.pdf]] - CTF Correction, Resolution Measurement & Model Bias - Ludtke, Steven ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_64|CryoEM Workshop: Oct. 17, 2006]] ''' '''Presentations''' * [[attachment:2006Oct18CryoEMCourseCCDs.ppt||&do=get]] - Introduction To Using CCD Cameras In cryo-EM - Booth, Christopher * [[attachment:CHIU Handout CryoEM Rice 06-10-18.ppt||&do=get]] - CryoEM Lecture for Biophysics Course and Workshop on Oct 18 2006 - Wah Chiu * [[attachment:Cryo TEM from specimen prep to the microscope_Gatan Presentation_LAM1.pdf]] - Cryo TEM from specimen prep to the microscope - Linda Melanson * [[attachment:CryoEM_Imaging_NCMI_20061018.pdf||&do=get]] - Imaging in Cryo-electron microscopy - Brink, Jaap * [[attachment:Frederik.pdf]] - CryoEM of supsension - Professor Peter Frederik ---- ''' [[http://ncmi.bcm.edu/ncmi/events/workshops/workshops_60|Introduction to Programming for Scientists Lecture Series: Jun. 12, 2006]] ''' '''Presentations''' * [[attachment:lecture1.pdf]] - Lecture 1 - Simple Datatypes - Steve Ludtke * [[attachment:lecture2.pdf]] - Lecture 2 - Lists, Tuples and Dictionaries - Steve Ludtke * [[attachment:lecture3.pdf ]] - Lecture 3 - if, while, for - Steve Ludtke * [[attachment:lecture4.pdf]] - Lecture 4 - Review of homework and File I/O - Steve Ludtke * [[attachment:pycrust-20060629-1132.py||&do=get]] - Examples from review - Steve Ludtke * [[attachment:lecture6-examples.ppt||&do=get]] - Lecture 6 notes * [[attachment:test2.py||&do=get]] - Scrabble program from Lecture 6 * [[attachment:test.py||&do=get]] - Box file scaling example from lecture 6 * [[attachment:pycrust-20060706-1134.py||&do=get]] - Partial interactive session from lecture 6 - Steve Ludtke * [[attachment:pycrust-20060710-1112.py||&do=get]] - Demo session from lecture 7 - Steve Ludtke * [[attachment:lecture7-stdlib.pdf]] - Lecture 7 - Standard Library - Steve Ludtke * [[attachment:lecture8-numbers.pdf]] - Lecture 8 - Numbers and CPUs - Steve Ludtke * [[attachment:lecture9-external.pdf]] - Lecture 9 - External Packages - Steve Ludtke * [[attachment:lecture10-eman.pdf]] - Lecture 10 - EMAN & Chimera - Steve Ludtke ---- |
NCMI Workshops: Presentations and Videos Archive
Presentations
wah-introduction.pdf - Introduction to the Workshop and NCMI
ludtke-overview.pdf - Workshop Overview - Steve Ludtke
mcmullanintro.pdf - Electron Microscopes & Imaging Artifacts - Greg McMullan
penczek-alignment.pdf - 2D Alignment Theory - Pawel Penczek
ludtke-minitalks.pdf - CTF, Refinement, other topics - Steve Ludtke
baldwin-orientation.pdf - Orientation and Symmetry - Phil Baldwin
scheres-heterogeneity.pdf - Methods for Heterogeneity Analysis - Sjors Scheres
mcmullanDetector.pdf - Direct Detector Technology - Greg McMullan
pintilie.pdf - Chimera & Segger - Greg Pintilie
baker-model-building.pdf - Model Building - Matt Baker
lawson-challenges.pdf - EMDB Challenges - Cathy Lawson
Tutorials
EMAN2-12_Tutorial2_heterogeneity.pdf
- Please note that e2refine_split has been improved significantly since 2.12. Suggest an update if using this method.
Cryo-EM Workshop at the National University of Singapore: July 9 - July 13, 2012
Presentations
emviz.pdf - Map Visualization with Chimera - Tom Goddard
CHIU CryoEM lecture NUS workshop 2012.pdf - CryoEM Basics - Wah Chiu
Model_bias.pdf - Model Bias- Mini Lecture Quantitative - Steve Ludtke
Particle_Eval.pdf - Particle Analysis (mini-lecture) - Steve Ludtke
EMAN2_Intro.pdf - EMAN2 Introduction - Steve Ludtke
Single_Particle_Intro.pdf - Introduction to Single Particle Analysis - Steve Ludtke
Lu Gan NUS cryo-ET lecture.pdf - Cryo-ET Basics - Lu Gan
Slides_for_workshop3_handout_red.pdf - Single Particle Tomography slides/handout - Michael Schmid et al
Flagella01-07-10-2012_red.pdf - Trypanosome Flagella - Schmid, M, Koyfman AY, Gheiratmand L, Fu CJ, Khant HA, Huang D, He CY, Chiu W
CHIU CryoEM Modeling NUS-reduced.pdf - CHIU Modeling Lecture - Wah Chiu
Modeling of Cryo-EM map Workshop: Jan 14 - Jan 17, 2010
Presentations
modeling2010_tao.pdf - Geometric Algorithms for De Novo Modeling - Abeysinghe, Sasakthi; Schuhl, Steven; Abrams, Austin; Ju, Tao; Baker, Matthew; Chiu, Wah
PDB_Items_for_EM.ppt - PDB Items for EM (EMDB Schema) - Abeysinghe, Sasakthi; Schuhl, Steven; Abrams, Austin; Ju, Tao; Baker, Matthew; Chiu, Wah
HoustonWorkshopJan2010-v4.ppt - EM Maps and Models in EMDB/PDB - Abeysinghe, Sasakthi; Schuhl, Steven; Abrams, Austin; Ju, Tao; Baker, Matthew; Chiu, Wah
xray-validation-for-em.ppt - Applied common sense: The why, what and how of validation - Kleywegt, Gerard J.
Baker-workshop2010.pdf - De Novo Modeling with Cryo-EM Density Maps - Baker, Matthew
2010-01-16 NCMI Baylor Workshop 90min Sali.pdf - Integrative structure determination at pseudo-atomic resolution - Andrej Sali
2010 Jan Mesoscale CryoEM Workshop.pdf - MESOSCALE MODELING OF MACROMOLECULAR MACHINES - Michael Levitt
EMdepoInstructions2010.doc - EM Depo Instructions - Lawson, Cathy
Schulten1.pdf - Molecular Modeling Flexible Fitting 1: Introduction to Molecular Dynamics - Schulten, Klaus
Schulten2.pdf - Molecular Modeling Flexible Fitting 2: Introduction to Method - Schulten, Klaus
Schulten3.pdf - Molecular Modeling Flexible Fitting 3: Application to Ribosome - Schulten, Klaus
EMD5127-3iyd.ppt - Deposition example EMD-5127-PDB-3iyd - Lawson, Cathy
EMdepoTutorial2010.doc - EM Deposition Tutorial - Lawson, Cathy
talk-houston_jan10-schroeder.pdf - Structure Refinement at Low Resolution - Schroeder, Gunnar
Structural & Computational Biomedical Informatics and Cryo-EM (UK): June 8 - June 12, 2009
Presentations
workflow_tutorial_final.pdf - EMAN2 Workflow Tutorial (Revised) - Steve Ludtke
Workshop_1.pdf - Introduction to Single Particle Reconsruction and EMAN2 - lecture notes - Steve Ludtke
Presentations
Ludtke_1.pdf - Introduction to Single Particle Reconsruction and EMAN2 - Steve Ludtke
workflow_tutorial.pdf - EMAN2 Workflow Tutorial - David Woolford
Python_1.pdf - Introduction to Python - Steve Ludtke
berman-NCMI-dec08.ppt - What the Protein Data Bank teaches us about structural biology - Berman, Helen M.
Wrks_EMAN2_08.pdf - Introduction - Penczek, Pawel
2008-EMAN-Wen-Jiang.pdf - Near-atomic resolution 3-D reconstruction of viruses - Jiang, Wen
2008-12-11 NCMI Baylor Workshop 60min.pdf - Integrating Diverse Data for Structure Determination of Macromolecular Assemblies - Andrej Sali
EMAN/Single Particle Tutorial: June 11, 2008
Presentations
Talk1.pdf - Introduction to Single Particle Reconstruction in EMAN1 - Steve Ludtke
Talk2-ctf.pdf - Introduction to Fourier Transforms and CTF Correction - Steve Ludtke
Demo1.pdf - Demo session containing walkthrough for EMAN1 DVD - Steve Ludtke
fits.pdf - FFT's Part 1 (more detailed lecture) - Steve Ludtke
ffts2.pdf - FFT's Part 2 (more detailed lecture) - Steve Ludtke
Grand challenges for Nanomedicine and Nanobiology: Aug 27, 2007
Presentations
ACS poster.ppt - Single-walled Carbon Nanotubes in the Intact Organism:Near-IR Imaging and Biocompatibility Studies in Drosophila - Beckingham, Kathleen
collaboration.ppt - Surfaces/nanopatterns presenting biomolecules and signaling molecules - Cai, Chengzhi
Suh.ppt - Reengineering Adeno-Associated Virus - Suh, Junghae
cutaneous nanotoxicology.shs - Cutaneous Nanotoxicology - Wilkerson, Michael
CHIU Centers 07-08-27.pdf - Chiu's NIH Centers at Baylor College of Medicine - Chiu, Wah
Introduction remark.ppt - Introduction Remarks - Chiu, Wah
Wah Chiu action plan.ppt - Action Plan - Chiu, Wah
Blaney.ppt - Dan Duncan Cancer Center - Blaney, Susan
Aigner HOUSTONTALK807.ppt - NIH Nanomedicine Roadmap - Aigner, Thomas
Judy CBEN.ppt - NSF Nanotechnology - Judy Raper
Larry GCNN-LAN-082707 (final).ppt - NCI Nanomedicine Alliance - Nagahara, Larry
Lee 82707.ppt - NCI Nanomedicine and nano-technology - Lee, Jerry
Karen.ppt - Recommendations: Leadership and Organization - Ethun, Karen
Achieving FDA approval for novel new nanomaterials.ppt - Recommendations: Achieving FDA approval for novel nanomaterials - Sevick, Eva M.
Baylor.ppt - Nanotechnology Center for Mechanics - Michael Sheetz
Clinical problems for nanotechnology.ppt - Defining the right clinical problems for nanotechnology - Oghalai, John
Nano discussion.ppt - Challenges for Clinical Applications of Nanotechnology - Eissa, N. Tony
Cell biology.ppt - Recomendations: Cell Biology and Nanoscience - Sifers, Richard N.
nanomed-computation.ppt - Recomendations: Computation and Informatics - Baker, Matthew
CryoEM Structure Mining: June 17, 2007
Presentations
CHIU CryoEM Structure mining 070617.ppt - Introduction to cryoEM - Wah Chiu
CryoEM Training Workshop: June 8, 2007
Presentations
Cryo_Transfer.mov - Cryo Transfer movie - Cruciano, Angela; Rees, Ian
Chiu handout 1 07-06-08.ppt - Day 1 Lecture- Overview of Cryo EM - Wah Chiu
MDS Alignment.ppt - MDS alignment - Cruciano, Angela
Workshop on Single Particle Reconstruction and Visualization: Mar. 14, 2007
Presentations
houston_march07.ppt - EMdep: Deposition EM maps - Kim Henrick
Chiu_EMAN Contrast theory_07_03-15.pdf - Image Contrast Theory - Wah Chiu
2007-EMAN-Workshop-Wen-Jiang.pdf - Icosahedral Reconstruction - Jiang, Wen
EMANworkshop-Ferrin.pdf - Visualization tools for complex biological structures - Tom Ferrin
chimera-eman-2007.pdf - Chimera Tutorial - Tom Goddard
ianrees_emen2_mar8.pdf - EMEN2: An Extensible, Collaborative, Electronic Lab Notebook - Rees, Ian
EMAN-workshop07-AIRS.ppt - VIsualizing and Analyzing CryoEM Density Maps with AIRS - Matthew Baker
EMAN_Wkshp_MFS_Handout.ppt - Aligning and Averaging 3-D Subvolumes from Electron Cryo-Tomograms - Schmid, Michael
Fourier Transforms.ppt - Fourier Transforms, Filtering and Convolution - Marsh, Mike
updated_Wrks_EMAN_07.pdf - updated Image similariry measures and such - Pawel A. Penczek
PmvVision.pdf - A Brief Introduction to PMV-VIsion - Zhao, Yong; Sanner, Michel
EMAN_CM_Modeller.ppt - Introduction to comparative modeling with MODELLER (final version) - Webb, Ben and Topf, Maya
EMAN_Modeller_hands_on.ppt - MODELLER hands-on session (final version) - Webb, Ben and Topf, Maya
EMANDemo1.pdf - EMAN Practical Session Slides - Ludtke, Steven
python_intro.pdf - Introduction to Python - Ludtke, Steven
talk1-intro.pdf - Workshop Welcome and Single Particle Reconstruction Overview - Ludtke, Steven
talk2-ctf.pdf - CTF Correction, Resolution Measurement & Model Bias - Ludtke, Steven
CryoEM Workshop: Oct. 17, 2006
Presentations
2006Oct18CryoEMCourseCCDs.ppt - Introduction To Using CCD Cameras In cryo-EM - Booth, Christopher
CHIU Handout CryoEM Rice 06-10-18.ppt - CryoEM Lecture for Biophysics Course and Workshop on Oct 18 2006 - Wah Chiu
Cryo TEM from specimen prep to the microscope_Gatan Presentation_LAM1.pdf - Cryo TEM from specimen prep to the microscope - Linda Melanson
CryoEM_Imaging_NCMI_20061018.pdf - Imaging in Cryo-electron microscopy - Brink, Jaap
Frederik.pdf - CryoEM of supsension - Professor Peter Frederik
Introduction to Programming for Scientists Lecture Series: Jun. 12, 2006
Presentations
lecture1.pdf - Lecture 1 - Simple Datatypes - Steve Ludtke
lecture2.pdf - Lecture 2 - Lists, Tuples and Dictionaries - Steve Ludtke
lecture3.pdf - Lecture 3 - if, while, for - Steve Ludtke
lecture4.pdf - Lecture 4 - Review of homework and File I/O - Steve Ludtke
pycrust-20060629-1132.py - Examples from review - Steve Ludtke
lecture6-examples.ppt - Lecture 6 notes
test2.py - Scrabble program from Lecture 6
test.py - Box file scaling example from lecture 6
pycrust-20060706-1134.py - Partial interactive session from lecture 6 - Steve Ludtke
pycrust-20060710-1112.py - Demo session from lecture 7 - Steve Ludtke
lecture7-stdlib.pdf - Lecture 7 - Standard Library - Steve Ludtke
lecture8-numbers.pdf - Lecture 8 - Numbers and CPUs - Steve Ludtke
lecture9-external.pdf - Lecture 9 - External Packages - Steve Ludtke
lecture10-eman.pdf - Lecture 10 - EMAN & Chimera - Steve Ludtke