Data Visualization
EMSL pushes the boundaries of scientific discovery by creating a broad range of visualizations for experimental results—including modeling of molecular interactions, ab initio simulation, and visual and statistical integration of disparate data types.
Research application
The Data Transformations Integrated Research Platform supports EMSL’s visualization resources, which are vital in advanced data analytics, simulation, and integration.
These tools support our expertise across all Integrated Research Platforms, but are especially useful in
- Biomolecular Pathways Integrated Research Platform: Robust statistical analysis and visualization of organic matter function and composition.
- Rhizosphere Function Integrated Research Platform: Visualizations for spatially resolved genotypic and phenotypic traits.
- Biogeochemical Transformations Integrated Research Platform: Computational chemistry tools and models across scales.
Available Resources
Tips for success
To best use these visualization capabilities, it is recommended you speak with the integrated research platform lead for specific guidelines applicable to your project.
- Reach out to your EMSL science point of contact at the beginning of your project. By engaging early, data can be analyzed as expeditiously as possible.
- Visualization, analysis, and collaboration throughout the life of the project will help guide ultimate analysis.
Contributing Teams and Resources
EMSL develops and deploys capabilities for the user program by conducting original research independently or in partnership with others and by adapting/advancing science and technologies developed outside of EMSL. In some instances, EMSL directly deploys mature capabilities developed by others where there is value for the EMSL user community. The following grants/activities, PI’s and teams contributed to the development of this capability:
- Ryan Hafen, https://trelliscope.org/
- David Degnan, Environmental Molecular Sciences Laboratory, https://shinyproxy.emsl.pnnl.gov/app/pspecter
- Ljiljana Paša-Tolić (HuBMAP PI), David Degnan (developer), https://github.com/PNNL-HubMAP-Proteoform-Suite/IsoMatchMS
- Lisa Bramer, Project 51146, Environmental Molecular Sciences Laboratory and Microbes in Transition LDRD (90001 – N56672) https://shinyproxy.emsl.pnnl.gov/app/freda
- Lisa Bramer (PI) and David Degnan (developer), Project 51146 Environmental and Molecular Sciences Laboratory, https://map.emsl.pnnl.gov/app/mode-classic (GUI for Trelliscope displays, under development/updates)
Related Publications
Hafen, Ryan, et al. "Trelliscope: A system for detailed visualization in the deep analysis of large complex data." 2013 IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV). IEEE, 2013. DOI: 10.1109/LDAV.2013.6675164.
Degnan, David J., et al. "PSpecteR: A User-Friendly and Interactive Application for Visualizing Top-Down and Bottom-Up Proteomics Data in R." Journal of Proteome Research 20.4 (2021): 2014-2020.
Degnan, David J., et al. "IsoMatchMS: Open-Source Software for Automated Annotation and Visualization of High Resolution MALDI-MS Spectra." Journal of the American Society for Mass Spectrometry 34.9 (2023): 2061-2064.
Bramer, Lisa M., et al. "ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data." PLoS computational biology 16.3 (2020): e1007654.