In diverse fields spanning developmental biology, tissue engineering, and cancer, dynamical interactions between large multicellular populations and the microenvironment shape the emergent behaviors of the larger systems, often in surprising ways. While mathematical models can help to understand these systems, 3-D simulation studies often require solving for the dynamics of 105 or more cells, along with several diffusing growth substrates and signaling factors. Such simulations are challenging, generally requiring either complex parallelization on supercomputers, or restriction to smaller systems of 103 or 104 cells in 2-D or very small 3-D domains. Moreover, largely incompatible data formats have impeded the development of robust tools for 3-D visualization and data analysis, further slowing systematic investigations. We will discuss our work to address these problems with parallelized open source codes designed for desktop computers or single HPC compute nodes. We will introduce PhysiCell: an agent-based model that simulates cell cycling, apoptosis, necrosis, volume changes, and biomechanics-based movement in 3-D systems of 105 to 106 cells. We will introduce BioFVM: a finite volume solver for diffusive transport in large 3-D tissues (5+ diffusing substrates on 106 or more voxels: 5-10 mm3 at 20 �m resolution). We will discuss MultiCellDS: a draft data standard for cell phenotype and multicellular simulation data. And we will discuss our efforts to connect these tools to simulate breast cancer and colon cancer metastases in the liver. It is our hope that this work will help seed an ecosystem of compatible computational tools and experimental data. At the close of the talk, we will open the floor to discussion on how these tools can be adapted to meet the needs of the stem cell modeling community. See mbi2015.MathCancer.org for more information.