Recent Announcements

  • Megan Riel-Mehan featured in USCF Science in Focus article Megan's work with Lillian Fritz-Laylin, Dyche Mullins, and Tom Goddard is briefly described in a UCSF Science in Focus articlehttps://www.ucsf.edu/news/2016/11/404936 ...
    Posted Nov 22, 2016, 11:56 AM by Graham Johnson
  • HHMI illustration brought back to life Some of Johnson's old DNA repair images have been brought back by HHMI to illustrate HHMI Investigator Paul Modrich's 2015 Nobel Prize in Chemistry:https://www.hhmi.org ...
    Posted Oct 27, 2015, 6:36 PM by Graham Johnson
  • Best Blender Animation Ever (uses ePMV too!) Chris Hammang, a Biomedical Animator at Garvan Institute of Medical Research and CSIRO has created many stunning animations while simultaneously taming the savage beast I know as the open-source ...
    Posted Feb 23, 2015, 7:22 PM by Graham Johnson
  • Immune Defense kickstarter 16 days I've worked on many prototypes and have provided consultation on many iterations of Immune Attack and Immune Defense over the years.  The project inventor and leader Melanie Stegman is ...
    Posted Jan 15, 2015, 8:10 PM by Graham Johnson
  • Happy Holidays Have a joyous winter break and enjoy this card that Mesoscope student intern Thao P. Do created in collaboration with Graham Johnson for the UCSF Chimera 2014 Holiday card as ...
    Posted Dec 17, 2014, 3:16 PM by Graham Johnson
Showing posts 1 - 5 of 16. View more »
Welcome to the Johnson Lab at UCSF, home of the Mesoscope Project.

Graham Johnson started working as a QB3@UCSF Faculty Fellow in January 2012 and the lab is looking to recruit new members.

For the public:
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?
•how would they move?
•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.
For researchers:
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.

Main project autoPACK: