<p> Computational tools provide the automation and power that enable detailed modeling and analysis of many biomolecular phenomena of interest. Open source programs and automated tools empower researchers and provide opportunities for improvement to existing software. In the past few years, I have developed several open-source scientific software packages for the purposes of automating difficult or menial tasks pertaining to computational biophysics. These software packages involve the analysis of molecular dynamics simulations, Brownian dynamics simulations, electrostatics, pocket volume measurement, solvent fragment mapping, binding site characterization, milestoning theory, and allosteric network communications. In addition to allowing my research group and me to approach biomedical challenges that would otherwise be intractable, I hope and intend that these tools will be useful to the computational and theoretical biophysics research community.</p>