The innovation evaluates the feasibility of developing a tablet-based suite of applications that allow students to interrogate relationships between molecular sequences, molecular structures, and their biological functions. One of the most difficult concepts for students to understand is why certain mutations affect the function of a protein and others do not. Students are better able to understand this relationship when they compare molecular structures from different allelic forms of a protein, locate the mutation site, and identify structural changes that occur as a consequence of a mutation. Few students have the opportunity to carry out these kinds of investigations because they lack suitable software tools and their teachers lack both experience and relevant instructional materials. These problems will be addressed by creating a tool kit to support molecular investigations. The tool kit will be designed for tablet-based computers and will contain an application for viewing and manipulating structures, an interactive digital lab manual that supports bioinformatics investigations related to genetic disease, an instructor guide, and a data set with superimposed and annotated structures.
The broader impact/commercial potential of this project relates to the potential in this suite of tools for interesting students in careers related to science, technology, engineering, or math (STEM) and in increasing student understanding of the connections between genetics, proteins, and protein function. The ease of interacting with molecular objects through touch with tablet-based computers and the availability of instructional materials that guide students through the process of discovery will lower the barriers to learning about protein structure and genetics and make student-driven investigations possible for a wider group of students in both high school and college courses. The instructor guide will assist instructors in implementing these materials by describing example work-flows and providing guidance in using different types of applications to achieve learning outcomes by helping students carry out these new types of laboratory investigations. The technology developed through this project will generate business opportunities through licensing fees and by providing opportunities to develop additional molecular investigations and learning materials.
The overarching goal of this Small Business Innovation Research (SBIR) Phase I project was to determine the feasibility of developing a tablet-based suite of applications that would allow students to interrogate relationships between molecular sequences, molecular structures, and their biological functions. In the project description, this suite was described as a tool kit that would function on tablet computers and support molecular investigations. The proposed components of the toolkit were: an application for viewing and manipulating structures, an interactive digital lab manual to support bioinformatics investigations related to genetic disease, an instructor guide, and a data set of molecular structures. During this phase I SBIR project, Digital World Biology (DWB) addressed these goals by developing prototype versions of two mobile applications (Molecule World™ and the Molecule World DNA Binding Lab) and making them available in the iTunes App store. Through a customer discovery process, DWB interviewed over 370 potential customers, and tested hypotheses to learn more about their challenges in teaching molecular concepts and perceived benefits that might be obtained by working with DWB’s applications. Molecule World supports viewing and manipulating large biological and smaller chemical structures from three major public databases (MMDB, PubChem, and the PDB). Search tools in the app allow users to search and download structures from all three databases. Visualization options include three rendering modes: ball and stick, space fill, and tube drawings, and five coloring modes. Atoms can be colored by element type. Amino acid and nucleotide residues can be colored by charge, identity, or hydrophobicity. Protein and nucleic acid chains and chemical groups can be colored by molecule. V2.0 also includes rainbow coloring to show the location of residues within a chain. An adaptive color key allows users to connect the colors used with the chemical and physical properties of the residues and atoms. An image capture function allows users to save and share photos in order to document their work. More research remains to be done, but this app constitutes a solid minimal viable product and is being demonstrated to teachers and used to gain feedback. Additional features such as the ability to select and hide specific residues and components of a structure are being implemented and will be available in version 2.0 when it’s released in the next two months. The Molecule World DNA Binding Lab (MW DNA Lab) is the first prototype of the interactive lab and digital toolkit. The MW DNA Lab uses the rendering engine and display properties of Molecule World to support a classroom investigation into the structure of DNA and the interactions between DNA and other molecules. It contains a data set of structures ranging from examples of DNA molecules and nucleotide subunits to 40 unidentified structures for student investigations. Student instructions are presented in a scrollable window that allows students to work on the project and view the instructions at the same time. A worksheet and glossary can be downloaded within the app or from the DWB website. Instructors can obtain answer keys and power point slides by setting up educator accounts at the DWB website. During this project, DWB established procedures for tracking work and managing software development, version control, and bug reporting. The company has built a culture of communication with both developers and stakeholders. Since the end of the grant period, DWB has continued to develop and enhance both applications and released updated versions of both apps in the iTunes App store during September and October. The broader impact of this work is that these applications and follow-on products will make it possible for a wider group of students and researchers to work with and investigate molecular structures and use molecular models as a tool for discovery and understanding.
