Relative quantification is a popular analysis in gene expression studies using quantitative real-time PCR (qPCR). However, the calculation steps using the major algorithms for this analysis are rather complicated. In this study, we developed an easy-to-use spreadsheet-based method for relative quantification. The inputs from end-users are the…

Dimensionality reduction techniques are essential in analyzing large 'omics' datasets in biochemistry and molecular biology. Principal component analysis, t-distributed stochastic neighbor embedding, and uniform manifold approximation and projection are commonly used for data visualization. However, these methods can be challenging for students…

The Java software jBar consists of a graphical user interface that allows the user to customize and assemble an included script for R. The scripted R pipeline calculates means and standard errors/deviations for replicates of numerical bivariate data and generates presentations in the form of bar graphs. A two-sided Student's t test is carried out…

Viewing and manipulating three-dimensional (3D) structures in molecular graphics software are essential tasks for researchers and students to understand the functions of molecules. Currently, the way to manipulate a 3D molecular object is mainly based on mouse-and-keyboard control that is usually difficult and tedious to learn. While gesture-based…

Understanding of proteins and other biological macromolecules must be based on an appreciation of their 3-dimensional shape and the fine details of their structure. Conveying these details in a clear and stimulating fashion can present challenges using conventional approaches and 2-dimensional monitors and projectors. Here we describe a method for…

DockoMatic 2.0 is a powerful open source software program (downloadable from sourceforge.net) that allows users to utilize a readily accessible computational tool to explore biomolecules and their interactions. This manuscript describes a practical tutorial for use in the undergraduate curriculum that introduces students to macromolecular…

Research shows that computer animations are especially helpful in fields such as chemistry and in this mixed-methods study, we investigate the educational effectiveness of Bio-Organic Reaction Animations (BioORA), a 3-D software, in four undergraduate biochemistry classes at different universities. Statistically significant findings indicate that…

Real-time PCR (quantitative PCR or qPCR) has become the preferred method for validating results obtained from assays which measure gene expression profiles. The process uses reverse transcription polymerase chain reaction (RT-PCR), coupled with fluorescent chemistry, to measure variations in transcriptome levels between samples. The four most…

In proteomics, complex mixtures of proteins are separated (usually by chromatography or electrophoresis) and identified by mass spectrometry. We have created 2DE Tandem MS, a computer program designed for use in the biochemistry, proteomics, or bioinformatics classroom. It contains two simulations--2D electrophoresis and tandem mass spectrometry.…

A learning module for molecular level analysis of protein structure and ligand/drug interaction through the visualization of X-ray diffraction is presented. Using DeepView as molecular model visualization software, students learn about the general concepts of protein structure. This Biochemistry classroom exercise is designed to be carried out by…

As biochemists, one of our most captivating teaching tools is the use of molecular visualization. It is a compelling medium that can be used to communicate structural information much more effectively with interactive animations than with static figures. We have conducted a survey to begin a systematic evaluation of the current classroom usage of…

We developed the three-dimensional visualization software, Tonal Interface to MacroMolecules or TIMMol, for studying atomic coordinates of protein structures. Key features include audio tones indicating x, y, z location, identification of the cursor location in one-dimensional and three-dimensional space, textual output that can be easily linked…

This article discusses the challenges that bioinformatics education is facing and describes a bioinformatics course that is successfully taught at the California State Polytechnic University, Pomona, to the fourth year undergraduate students in biological sciences, chemistry, and computer science. Information on lecture and computer practice…

Bioinformatics is one of the fastest growing scientific areas over the last decade. It focuses on the use of informatics tools for the organization and analysis of biological data. An example of their importance is the availability nowadays of dozens of software programs for genomic and proteomic studies. Thus, there is a growing field (private…

The biochemistry lecture is often the place where students receive the greatest exposure to the structural nature of biomolecules. The use of molecular visualization software and web-based animated tutorials has enhanced the way instructors teach this important area of structural biology. Using the software and tutorials in class is an excellent…