Writing code in Java and Perl, students produce user-friendly software that works on all platforms. Projects include spot finding, gridding, ratio measurements, clustering, and interactive visualization of data.
Produce test chips with different spot concentrations of targets and use known probe ratios to determine limits of methodology. Probe color reversal and positive and negative controls features will be included on all chips.
Reading the literature, we discovered that experimental design of some time-course experiments are prone to alterations in outcome due to unintentional variations. We will utilize mathematical methods to calculate the optimal design for future experiments.
Students will optimize student-friendly proteomics protocols. Areas of interest include crystalization, Y2H plasmid construction, and GFP and RFP fusion gene creation.
Protein structure is critical to its function. We need to develop expertise in appropriate classroom and laboratory use in 3D visualization methods. We have funding to establish a small lab equipped with CrystalEyes goggles for active viewing. Students will work with the software to create tutorials and samples of what can be learned through interactive and immersion viewing of protein structures.
NCBI has a wonderful collection of bioinformatics tools but we have developed a prototype perl script that facilitates the identification of evolutionarily conserved domains in proteins. Rather than searching known motifs or global sequences, our program allows the user to uncover conserved domains based on a sliding scale of sequence comparisons.