The Best Practices and Tools for Secure Scientific Software Development slide decks include components for evaluating design practices to create secure software, appropriate software processes for managing secure software, threat modeling, and quality assurance testing using both static and dynamic analysis tools. The goal of these slide decks is to enable the reader to analyze the security of scientific software using threat models such as DREAD and STRIDE. Threat models aid in identifying risks that often cost an organization thousands of dollars when patching vulnerabilities stemming from unsecured code. Readers from various domains are introduced to best practices for developing secure scientific software and are given hands-on techniques for penetration testing tools to mitigate threats such as loss of business and sensitive information that arise from potential vulnerabilities. The information contained herein will enable the reader to develop secure and trustworthy scientific software.