Evaluation of MolCog Software and NUPACK Integration
Jameel Kelley · 2022
Molecular engineers currently lack toolsets specifically built for a selection of their needs and processes. This gap creates a non-insignificant amount of overhead work during tasks that are vital to their research and design. The MolCog tool/framework aims to address a gap in simultaneous three-dimensional viewing and editing of molecular structures on both desktops and in Head-Mounted Displays (HMDs). However, the framework needs additional features built upon it to minimize task overhead and introduction of errors for molecular engineers. Improving this pipeline creates a shorter feedback loop and a better spatial understanding of how things integrate into the environment. Specifically, the integration of a tool named NUPACK into this platform allows for analysis of DNA staples in the usage of DNA origami. For this creative component, NUPACK was integrated into MolCog (Part 1) and tested against the traditional suite of tools that molecular engineers use to analyze DNA structures (Part 2). The evaluation analyzed 48 participants in a between-subjects study on their performance, errors, and understanding of molecular concepts before and after the condition of integrated and non-integrated software. Results showed that the 3D integrated software suite (MolCog) showed some promise in improving productivity over a using the 2D aspect of the non-integrated software suite caDNAno + Excel + NUPACK. Additionally, some results seemed to show that the 3D representation in MolCog was more effective at teaching certain concepts, but not all. Additionally, using MolCog editing and analyzing DNA origami is not preferred for a better user experience yet. Overall, results suggest that future software creators in this field could create powerful tools that assist with productivity, learning certain concepts, and reducing specific categories of errors.