Developing and applying computational resources for biochemistry education

Abstract

Biochemistry is about structure and function, but it is also about data and this is where computers come in. From my time as a graduate student and post doc, whenever I encountered data I thought, "I can work this up by hand, but I think a computer could do a better job." Since that time, I have been working at the interface of biochemistry and computers, by attracting talented students and collaborating with colleagues with complementary skills. This has resulted in several exciting projects: a simulation of 2D electrophoresis and tandem mass spectrometry, the human visualization project, and two different programs that enable biochemists to search protein structures for enzyme active sites: ProMOL (promol.org) and Moltimate (moltimate.appspot.com). The human side of software development for education involved finding the right students and colleagues, communicating effectively across disciplines, building and managing effective teams and the importance of serendipity throughout the process. K E Y W O R D S computational biology, genomics proteomics bioinformatics, integration of research into undergraduate teaching, molecular visualization, using simulation and internet resources for teaching

Research on the Path of Aiding Integrating Excellent Traditional Chinese Culture into Biochemistry Teaching Curriculum with the Artificial Intelligence Technologies

“…Cause the teaching of biochemistry mostly involves interdisciplinary themes, it is really a difficult subject for both teachers and students [2,3]. Previously, research on the reform of biochemistry teaching mainly focused on online teaching [4], distance education [5], PBL(Problem based learning), TBL(Team Based Learning) or CBL(Case Study Based Learning) teaching model research [6][7][8], the construction of a framework for cultivating students' biochemical literacy [9], or the development of computing resources in biochemistry education and applications [10]. There was a lack of exploration of the path of combining humanities education and subject education.…”

PDB‐101: Educational resources supporting molecular explorations through biology and medicine

“…The PDB resource is essential to multiple communities: It provides a permanent and expertly curated resource for structural biologists to archive and disseminate their work, provides mechanisms to ensure reproducibility in the structural biology literature, and makes biomolecular structures freely and easily available to a wide community of researchers across scientific disciplines 1 . PDB data are also broadly used in science, technology, engineering, and mathematics (STEM)‐related education, including textbook illustrations, coursework, and learning activities 2–11 . Images of 3D PDB structures are frequently used to tell scientific stories in mainstream news media, starting with the familiar double helix of DNA to more recent examples of CRISPR and coronavirus 12…”

Supporting Computational Apprenticeship Through Educational and Software Infrastructure: A Case Study in a Mathematical Oncology Research Lab

“…Similarly, the traditional educational divisions between engineering, computational, physical science, and biological curricula have impeded communication between these silos and raised barriers both to the use of simulations by biologists and the effective understanding of biological needs and design of tools for biological applications by engineers [ 5 , 43 ]. There has been an ongoing effort to incorporate quantitative or computational content into undergraduate biology courses [ 1 , 4 , 9 , 14 , 42 , 53 ]. Similarly, there are several reports of reforms to provide greater life sciences disciplinary content to engineering students [ 18 , 24 , 52 ].…”