| 42 | | [http://www.cgl.ucsf.edu/chimera/data/cosmos-jul2013/brain.html Multiscale brain visualization] for COSMOS science program high school students. |
| 43 | | Used 3-d LCD glasses, and leap motion and space navigator navigation devices in the RBVI Visualization Vault to show 20 students from Davis, California |
| 44 | | light microscopy of whole human brain, traced neurons, rat cortex electron microscopy, neural synapse tomography, acetylcholine receptor synapse ion channel, |
| 45 | | and snake neurotoxin. 45 minutes. 30 hours preparation. Organized by Toby Allen and Sarah Driver from UC Davis and Scooter Morris from UCSF. |
| 46 | | - Tom Goddard, Scooter Morris |
| | 48 | |
| | 49 | [http://www.cgl.ucsf.edu/chimera/data/cosmos-jul2013/brain.html Multiscale brain visualization] for COSMOS science program high school students. Used 3-d LCD glasses, and leap motion and space navigator navigation devices in the RBVI Visualization Vault to show 20 students from Davis, California light microscopy of whole human brain, traced neurons, rat cortex electron microscopy, neural synapse tomography, acetylcholine receptor synapse ion channel, and snake neurotoxin. 45 minutes. 30 hours preparation. Organized by Toby Allen and Sarah Driver from UC Davis and Scooter Morris from UCSF. |
| | 50 | |
| | 51 | * Tom Goddard, Scooter Morris |
| 75 | | UCSF BP204,"Macromolecular Interactions" class: 35-minute presentation followed by 45 mins of the students |
| 76 | | (about 15 of them) doing a Chimera tutorial on their own laptops. The presentation included 5 mins on history |
| 77 | | of Computer Graphics Lab, 30 mins of Chimera demonstration: basic usage, finding H-bonds, morphing, viewing |
| 78 | | sequences, showing attribute values, building multimers, stereo. Prep time 10 hours including updating and |
| 79 | | rehearsing the presentation, updating and preparing handouts. |
| 80 | | - Elaine Meng, Eric Pettersen |
| | 84 | |
| | 85 | UCSF BP204,"Macromolecular Interactions" class: 35-minute presentation followed by 45 mins of the students (about 15 of them) doing a Chimera tutorial on their own laptops. The presentation included 5 mins on history of Computer Graphics Lab, 30 mins of Chimera demonstration: basic usage, finding H-bonds, morphing, viewing sequences, showing attribute values, building multimers, stereo. Prep time 10 hours including updating and rehearsing the presentation, updating and preparing handouts. |
| | 86 | |
| | 87 | * Elaine Meng, Eric Pettersen |
| 83 | | Training at UCSF on Pythoscape and sequence similarity networks for two members of the Fetrow group |
| 84 | | (from Wake Forest University). Prep time 16 hours. |
| 85 | | - Patsy Babbitt, Gemma Holliday, Jeff Yunes, Susan Mashiyama, Rebecca Davidson, Jack Yu |
| | 90 | |
| | 91 | Training at UCSF on Pythoscape and sequence similarity networks for two members of the Fetrow group (from Wake Forest University). Prep time 16 hours. |
| | 92 | |
| | 93 | * Patsy Babbitt, Gemma Holliday, Jeff Yunes, Susan Mashiyama, Rebecca Davidson, Jack Yu |
| 88 | | EMBL-Australia Masterclass on Protein Sequence Analysis, Garvan Institute, Sydney, Australia. 24 attendees. |
| 89 | | 2 sessions on Cytoscape, 40 hours prep time. |
| 90 | | 2 sessions on Chimera, 12 hours prep time. |
| 91 | | Plenary talk on networks and structures, 14 hours prep time. |
| 92 | | Identifying and understanding protein-protein interactions and residues involved in intermolecular contacts |
| 93 | | using Cytoscape and structureViz/Chimera. Using Chimera for sequence-structure analysis and creating animations. |
| 94 | | - Scooter Morris |
| | 96 | |
| | 97 | EMBL-Australia Masterclass on Protein Sequence Analysis, Garvan Institute, Sydney, Australia. 24 attendees. 2 sessions on Cytoscape, 40 hours prep time. 2 sessions on Chimera, 12 hours prep time. Plenary talk on networks and structures, 14 hours prep time. Identifying and understanding protein-protein interactions and residues involved in intermolecular contacts using Cytoscape and structureViz/Chimera. Using Chimera for sequence-structure analysis and creating animations. |
| | 98 | |
| | 99 | * Scooter Morris |
| 97 | | Cytoscape workshop sponsored by the Systems Biology Institute in Melbourne, Australia. 14 attendees, 10 hours prep time. |
| 98 | | (1) Introductory tutorial on the analysis and visualization of biological networks; |
| 99 | | (2) Hands-on tutorial introduction to Cytoscape; |
| 100 | | (3) Demonstration and hands-on use cases of Cytoscape, with numerous example use cases showing what is possible. |
| 101 | | (4) Master class: Bring your own data, cancer pathway data, proteomics data, mass spectrometry pull downs, etc. The Master Class will also include demos of Cytoscape features in development, and Cytoscape scripting. |
| 102 | | - Scooter Morris |
| | 102 | |
| | 103 | Cytoscape workshop sponsored by the Systems Biology Institute in Melbourne, Australia. 14 attendees, 10 hours prep time. (1) Introductory tutorial on the analysis and visualization of biological networks; (2) Hands-on tutorial introduction to Cytoscape; (3) Demonstration and hands-on use cases of Cytoscape, with numerous example use cases showing what is possible. (4) Master class: Bring your own data, cancer pathway data, proteomics data, mass spectrometry pull downs, etc. The Master Class will also include demos of Cytoscape features in development, and Cytoscape scripting. |
| | 104 | |
| | 105 | * Scooter Morris |
| 105 | | Chimera demo for Biochemistry students from the University of San Francisco. Arranged by instructor Willie Melaugh. |
| 106 | | 12 attendees, prep time 3 hours. 30-minute demo using stereo graphics, space navigator input device to show a Drexel nanomachine and |
| 107 | | [http://www.cgl.ucsf.edu/chimera/data/cosmos-jul2013/brain.html brain imaging] at multiple levels of resolution ranging from whole |
| 108 | | brain to atomic detail of the nicotinic acetylcholine receptor. |
| 109 | | - Tom Goddard |
| | 108 | |
| | 109 | Chimera demo for Biochemistry students from the University of San Francisco. Arranged by instructor Willie Melaugh. 12 attendees, prep time 3 hours. 30-minute demo using stereo graphics, space navigator input device to show a Drexel nanomachine and [http://www.cgl.ucsf.edu/chimera/data/cosmos-jul2013/brain.html brain imaging] at multiple levels of resolution ranging from whole brain to atomic detail of the nicotinic acetylcholine receptor. |
| | 110 | |
| | 111 | * Tom Goddard |
| 112 | | Meetings with staff at the European Bioinformatics Institute (EMBL-EBI Hinxton Outstation, Cambridge, UK) including demonstrations |
| 113 | | of the SFLD; sequence similarity networks and Pythoscape; troubleshooting issues and discussing future collaborations. |
| 114 | | 12 hours prep time, ~60 hours of meetings. 25-50 attendees. |
| 115 | | - Gemma Holliday, Patsy Babbitt |
| | 114 | |
| | 115 | Meetings with staff at the European Bioinformatics Institute (EMBL-EBI Hinxton Outstation, Cambridge, UK) including demonstrations of the SFLD; sequence similarity networks and Pythoscape; troubleshooting issues and discussing future collaborations. 12 hours prep time, ~60 hours of meetings. 25-50 attendees. |
| | 116 | |
| | 117 | * Gemma Holliday, Patsy Babbitt |
| 118 | | Visualization demo for UCSF student recruitment tours. Showed differential gear nano machine, stereo glasses, space navigator, |
| 119 | | dendritic cells in collagen, oculus rift goggles collagen visualization. Arranged by Rebecca Brown. Two half hour demonstrations |
| 120 | | each with 4 students. 6 hours preparation and delivery. |
| 121 | | - Tom Goddard |
| | 120 | |
| | 121 | Visualization demo for UCSF student recruitment tours. Showed differential gear nano machine, stereo glasses, space navigator, dendritic cells in collagen, oculus rift goggles collagen visualization. Arranged by Rebecca Brown. Two half hour demonstrations each with 4 students. 6 hours preparation and delivery. |
| | 122 | |
| | 123 | * Tom Goddard |
| 124 | | Visualization demo for UCSF student recruitment tours. Showed differential gear nano machine, stereo glasses, space navigator, |
| 125 | | dendritic cells in collagen, oculus rift goggles collagen visualization. Arranged by Rebecca Brown. 30 minute demonstration |
| 126 | | 3 students. Discussion with another group of 5 students about virus structure and cell motion. 3 hours preparation and delivery. |
| 127 | | - Tom Goddard |
| | 126 | |
| | 127 | Visualization demo for UCSF student recruitment tours. Showed differential gear nano machine, stereo glasses, space navigator, dendritic cells in collagen, oculus rift goggles collagen visualization. Arranged by Rebecca Brown. 30 minute demonstration 3 students. Discussion with another group of 5 students about virus structure and cell motion. 3 hours preparation and delivery. |
| | 128 | |
| | 129 | * Tom Goddard |
| 130 | | Showed human brain planetarium dome video at the Biophysical Society Annual meeting in San Francisco attended by 7000 researchers. |
| 131 | | Video was shown to a few hundred visitors per day. The [http://www.youtube.com/watch?v=RE2XMzInX_o video] showed imaging data and molecular structures from the human brain, |
| 132 | | was made with RBVI Chimera software, and took about 50 hours to produce. |
| 133 | | - Tom Goddard, Matt Dougherty |
| | 132 | |
| | 133 | Showed human brain planetarium dome video at the Biophysical Society Annual meeting in San Francisco attended by 7000 researchers. Video was shown to a few hundred visitors per day. The [http://www.youtube.com/watch?v=RE2XMzInX_o video] showed imaging data and molecular structures from the human brain, was made with RBVI Chimera software, and took about 50 hours to produce. |
| | 134 | |
| | 135 | * Tom Goddard, Matt Dougherty |
| 136 | | Showed virus, brain, cell and rna videos in a portable 6 meter planetarium dome that we setup at UCSF in Genentech Hall. |
| 137 | | The RBVI hosted this event and created two of the dome videos on HIV RNA and human brain imaging and molecules. |
| 138 | | About 150 researchers viewed the videos presented many times over 3 hours in the afternoon. 30 hours preparation. |
| 139 | | - Matt Dougherty, Tom Goddard, Al Conde, Tom Ferrin |
| | 138 | |
| | 139 | Showed virus, brain, cell and rna videos in a portable 6 meter planetarium dome that we setup at UCSF in Genentech Hall. The RBVI hosted this event and created two of the dome videos on HIV RNA and human brain imaging and molecules. About 150 researchers viewed the videos presented many times over 3 hours in the afternoon. 30 hours preparation. |
| | 140 | |
| | 141 | * Matt Dougherty, Tom Goddard, Al Conde, Tom Ferrin |
| 142 | | Introduction to Chimera 90 minute hands-on tutorial for a workshop at the International Institute of Macromolecular Analysis and Nanomedicine Innovation in Taiwan. |
| 143 | | Presented via video conference (GoToMeeting.com). 20 students, 8 hours preparation. Organized by Shang-Rung Wu of Natial Cheng Kung University, Tainan, Taiwan. |
| 144 | | - Tom Goddard |
| | 144 | |
| | 145 | Introduction to Chimera 90 minute hands-on tutorial for a workshop at the International Institute of Macromolecular Analysis and Nanomedicine Innovation in Taiwan. Presented via video conference (GoToMeeting .com). 20 students, 8 hours preparation. Organized by Shang-Rung Wu of Natial Cheng Kung University, Tainan, Taiwan. |
| | 146 | |
| | 147 | * Tom Goddard |
| | 148 | |
| | 149 | March 10-11 2014 |
| | 150 | |
| | 151 | Taught a two-day course to teach participants to develop Apps for the Cytoscape 3.x series. As part of the course, covered the app development process as well as the key aspects of the Cytoscape API necessary to manipulate Cytoscape tables, networks, and user interface. Also worked through how to set up development environments on multiple platforms, and develop an initial Cytoscape App. The second day of this course provided time for each participant to interact with the instructor and other participants to plan and develop their own Cytoscape app. 20 students 30 hours preparation. |
| | 152 | |
| | 153 | * Scooter Morris |
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