Welcome to the Johnson Lab at UCSF, home of the Mesoscope Project
started working as a QB3@UCSF Faculty Fellow in January 2012 and the lab is looking to recruit new members.
If we had a scope that could "see" living cells in atomic detail, a scope that could distinguish a few select molecules at a time from billions of neighbors:
•what would these molecules look like?
•what molecules would they interact with and what macromolecular structures might they form?
•how would these building blocks fit and work together to enable life?
•can we trust what we "see"?
The mesoscope project aims to generate a database and associated file types that enable biologists, physicists, computational biologists, animation experts, and others to contribute to modeling, analyzing, and visualizing our molecular world, from atoms to cells.
(Note the banner image metaphor at the top of this page implies that our knowledge of biology is relatively sparse and "blurry" on the mesoscale, which is the range of magnification (10–7 to 10–8m) that exists between atoms and cells.
The Johnson Lab focuses primarily on developing algorithms to enable scientists to generate, simulate, and visualize molecular models of cells, namely a software called autoPACK/cellPACK
and continues to work with Ludovic Autin to develop ePMV
in extended collaboration with Arthur Olson's lab
at Scripps. This summer we have engaged in a google summer of code project called sigViz
with other UCSF and Gladstone researchers to generate cell signaling network flux simulators.
The Johnson lab also develops outreach software that enables scientists and illustrators to interoperate the computational tools of science and art and works closely on these fronts with Tom Ferrin's Computer Graphics Lab (CGL
) at UCSF as a Resource for Biocomputing, and Visualization, and Informatics (RBVI
) collaborator, and with the Molecular Graphics Lab (MGL
) at The Scripps Research Institute as a former National Biomedical Computational Resource (NBCR
) member and current collaborator.
Please visit the Projects
tab on this site for more details.