Activities

iCn3D / VIZomics Activities

• 2016 NCBI Codeathon (Organizers: Ben Busby)
  • Visualizations of SNPs and Protein Interaction Data:
    Jiyao Wang, Eric Weitz, Peter Meric, Rajeeva Lochan Musunuri, Elise Flynn, and Ben Busby
    
    
• 2016 ISMB Codeathon (Organizers: Ben Busby and Philippe Youkharibache)
  • 2D Interaction Schematic:
    Qiangling Li, Spencer Bliven, Eli Draizen, Jose Duarte, Keiichiro Oto, Tim Schaefer, Jiyao Wang, and Philippe Youkharibache
    
    
  • Use MMTF in iCn3D:
    Jiyao Wang, and Alexander S. Rose
    
    
• 2020 ISMB Codeathon (Organizers: Ravinder Abrol, Philippe Youkharibache, and Allissa Dillman)
  • iCn3D in Jupyter Notebook:
    Jiyao Wang, Ben Busby, Nicholas Johnson, Francesco Tabaro, David Enoma, Jiyao Wang, Guangfeng Song, and Yuchen Ge
    
    
  • Differential analysis of viral protein sequence variants interactions with host proteins:
    Philippe Youkharibache, Adriaan Ludl, Mingzhang Yang, Yuchen Ge, Yuk Kei Wan, Ariel Aptekmann, Awtum Brashear, Xavier Watkins, Tom Madej, and Jiyao Wang
    
    
  • ExoDATA:
    Raul Cachau, Giulia Babbi, Matthew Sinnott, Todd Smith, and Francesco Tabaro
    
    
• 2020 NCBI Codeathon
  • Variation Analysis and Visualization of SARS-CoV-2 sequences in GenBank:
    Brad Holmes, Jiyao Wang, Vichet Hem, Eric Cox, Kurtis Haro, and Carl Leubsdorf, Jr.
    
    
• 2020 STRIDES Codeathon (Organizer: Allissa Dillman)
  • View SNPs in 3D, Dynamic Symmetry Calculation:
    Jiyao Wang, Rachel Dunn, Sridhar Acharya Malkaram, Chin-Hsien Tai, Thomas Madej, and David Enoma
    
    
• 2021 ISMB Codeathon (Organizers: Ravinder Abrol, Philippe Youkharibache, and Allissa Dillman)
  • 2D Cartoons:
    Jiyao Wang, Li Chuin Chong, Kevin Yang, Sarah Zhao, Zhiyu Cheng, and Jack Lin
    
    
  • ProteoMaps:
    Philippe Youkharibache, Matteo Manfredi, Chiragkumar Patel, Stephanie Byrum, and Raul Cachau
    
    
  • SARS2 antibody interface analysis:
    Marcus Mendes, Mahita Jarjapu, Henry Webel, and David Bell
    
    
  • Molecular Sentry:
    Todd Smith, Sandra Porter, Elzbieta Gralinska, Sachendra Kumar, Giovanni Madeo, Luis Jaimes Santiago, and Sheela Vemu
    
    
• 2022 Antibody Engineers Codeathon (Organizers: Sandra Porter, Todd Smith, and Allissa Dillman)
  • Antibody Engineers – iCn3D:
    Todd Smith, Jiyao Wang, Ami Johanson, Chetna Patel, David Menshew, Kate Johnston, Madhavan Narayanan, Khalid Tantawi, Nik Tsotakos, Selena Lu, and Christain John Ventura
    
    
  • Break an Antibody:
    Margaret Bryans, Andrew Givone, Hetal Doshi, Savita, David Menshew, Feather Ives, and Annie
    
    
  • Anti-SARS vs variants:
    Sandra Porter, Arshdeep Kaur, Ben Bekey, Uwe Hilgert, Erica Lannan, and Michelle Stieber
    
    
• 2022 ISMB Codeathon (Organizers: Ravinder Abrol, Philippe Youkharibache, Allissa Dillman, and Alexa Salsbury)
  • Annotations in iCn3D:
    Jiyao Wang, Raphael Trevizani, Sachendra Kumar, and Li Chuin Chong
    
    
  • Differential analysis of residue interactions of a SNP based on side chain prediction:
    Zachery Mielko, Kailash Adhikari, David Bell, Jiyao Wang, Marina Herrera Sarrias, and Ravinder Abrol
    
    
  • Visualizing the effect of SNPs extracted from genomic data on protein structure using iCn3D:
    Bonface Onyango, Manoj M Wagle, Michael Sierk, and Pranavathiyani G
    
    
  • Standardization of Ig datasets using universal numbering system and auto generating Bridged 1D maps:
    Umesh Khaniya, Chirag Patel, Caesar Tawfeeq, Siddhi Jani, Sujitkumar, Prasanthkumar, and Philippe Youkharibache
    
    
  • ImmunoZoo – Making iCn3D accessible for many audiences:
    Sandra Porter, Todd Smith, Sheela Vemu, Carsten Fortmann-Grote, Yagoub Adam, Shikha Kathrani, and Jack Lin
    
    
  • Analysis of multiple structures for automatic capture of conformational changes:
    Tom Madej, David Bell, Chase Freschlin, Gabby Vent, and Lianna Khachikyan
    
    
• 2022 NCBI Workshop, Exploring 3D Molecular Structures with iCn3D: (Organizers: Alexa Salsbury, Rana Morris, Jiyao Wang, Aron Marchler-Bauer)
  
  
• 2022 BioMolViz Workshop, Modeling Program Training (iCn3D, Jmol, PyMOL, UCSF Chimera): (Organizer: Kristen (KP) Procko; Featured Presenters: Henry Jakubowski, Jiyao Wang; Workshop Facilitators: Josh T. Beckham, Shane Austin, Daniel Dries, Pamela Mertz)
  
  
• 2023 BOSC CollaborationFest, Show isoforms and exons as tracks in iCn3D: Jiyao Wang
  
  
• 2023 NCBI Workshop, Exploring 3D Molecular Structures with iCn3D: (Organizers: Alexa Salsbury, Rana Morris, Jiyao Wang, Aron Marchler-Bauer)
  
  
• 2023 DiscoveryBMB Workshop, Basics of the iCn3D program, a user-friendly tool for biomolecular modeling: (Organizers: Kristen Procko, Henry Jakubowski, Josh T. Beckham, Daniel Dries, Shane Austin, Pamela Mertz)
  
  
• 2024 BOSC CollaborationFest
  • Displaying Protein-Ligand Interactions in iCn3D: Jiyao Wang, Ravinder Abrol, Philippe Youkharibache
    
    
  • Combining JBrowse2 and iCn3D: Colin Diesh, Jiyao Wang, Francois Belleau, Philippe Youkharibache, Ravi Abrol
    
    
• 2025 BOSC CollaborationFest
  • Integrate iCn3D viewer with Jalview on MSA display: Philippe Youkharibache, James Procter, Jiyao Wang
    
    
• 2025 ISMB Expo
  • ViZomics.org: Open Science using iCn3D Immersive Visualization: Chris Henn, Philippe Youkharibache, Allissa Dillman
    
    
• 2025 ELIXIR BioHackathon Europe
  • BioHackEU_MolViewSPec: David Sehnal, Philippe Youkharibache, Adam Midlik, Jiyao Wang, Chris Henn, Ravi Abrol, Mahin momin, Marc Baaden, Elyse Cheng