Welcome to the new home of cellPACK.

Overview: cellPACK is a biological software tool designed to assemble large scale models from molecular building-blocks. cellPACK integrates structural biology and systems biology data with packing algorithms (figure 1) to assemble comprehensive 3D models of cell-scale structures in molecular detail (figure 2).

Why: To combine data from all branches of biology into comprehensive mesoscale models for hypothesis generation, experimentation, communication, & education.

Who: Researchers, scientific illustrators, animators, educators, students, curious minds.

Try: By January 19, 2015 the Use tab will allow you to explore data that goes into several available recipes (HIV, Blood Plasma, Synaptic Vesicles, etc.). These temporary View pages will also display background information, images, and 3D models output by cellPACK. The deeper functionalities of cellPACK are currently a bit trickier to use and require some effort to install and learn.  We are working on a user-friendly online and mobile interfaces for constructing recipes and for viewing, analyzing, and building models. Until that is available, you can view models in UCSF Chimera, or the intrepid can use cellPACK from within 3D animation software via our free cellPACK uPy interface plugins– details here.

Where: The cellPACK system is and open-source project with core developers in Graham Johnson's Mesoscope Lab at the University of California, San Francisco (QB3@UCSF) and in Art Olson's Molecular Graphics Lab at The Scripps Research Institute. Graham and Ludovic Autin are the primary core programmers who work with a growing list of contributors.

cellPACK news

  • phys.org article: Science at cusp of 'transformational' grasp of life via cell modeling, researchers say A review published by Arthur Olson in the Journal of Molecular Biology highlights advances towards 3D models of whole cells.http://phys.org/news/2016-10-science-cusp-grasp-life ...
    Posted Oct 25, 2016, 10:24 AM by Graham Johnson
  • UC San Diego and TSRI Launch New Consortium to Create ‘Virtual Cell’ Drawing on complementary strengths, the University of California, San Diego and The Scripps Research Institute have formed a new consortium with a big mission: to map cells in space and ...
    Posted Oct 21, 2015, 5:36 PM by Graham Johnson
  • PSI & Nature's Structural Biology Knowledgebase features cellPACK The Structural Biology Knowledgebase (SBKB), a collaboration between the Protein Structure Initiative and Nature Publishing Group, wrote an article entitled Molecular Portraits of the Cell to describe how "The cellPACK ...
    Posted Mar 17, 2015, 8:49 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, 3:09 PM by Graham Johnson
  • Science magazine Editors' Choice Our cellPACK article in Nature Methods was selected for the Science magazine Editor's Choice article... this week in other journals December 12, 2014. http://www.sciencemag.org/content/346 ...
    Posted Dec 11, 2014, 5:49 PM by Graham Johnson
Showing posts 1 - 5 of 7. View more »

Figure 1. autoPACK is a software program that packs objects into volumes with zero overlaps.



Figure 2. cellPACK is a software program that extends autoPACK with biologically relevant packing algorithms and a database of molecular recipes to construct models of whole cells or viruses like HIV shown here.