We propose to design and implement MGX as a software application that will run on multiple computing platforms, including Microsoft Windows, Mac OS, Linux and Sun Solaris. We anticipate two general types of MGX users—student and instructor. The instructor, who will serve as the administrator of the software, will be able to configure MGX for class assignments. The student will use MGX to complete these assignments. Both types of user will interact with MGX in a graphical computing environment. Shown in Figure 1 is a Statechart, a form of design representation providing a top-level behavioral description of MGX. A curved arrow connector indicates the default entry point, which is VGL (an arbitrary choice). The three VBLs—VGL, GeneX, and Protex are shown as separate states of the MGX system. Arrows indicate the transition paths among those states.

The MGX user will be able to access each VBL on its own as a separate application—in stand-alone mode, and together as part of one application—in integrated mode. The functionalities of MGX in integrated mode and of Protex in stand-alone mode were discussed by the MGX Team (in 2004). The stand-alone functionalities of VGL and GeneX were discussed by the VGL Team (in 2002) and the GeneX Team (in 2003), respectively. MGX in integrated mode will display a zoo holding hypothetical creatures. The user will be able to cross (mate) these creatures by accessing VGL in integrated mode. MGX VGL will display the resulting progeny, and will sort those progeny according to gender (male and female) and phenotype (appearance).

To interpret the information held in the DNA sequence of a parent or one of its offspring, the user will access MGX GeneX, which will generate sequences of DNA corresponding to the genes (alleles) from a pair of homologous chromosomes. MGX GeneX will scan each DNA sequence for its promoter and terminator, and will graphically display the steps of gene expression, including the transcription, splicing and translation of a gene from a nucleotide sequence into a protein. The user will also be able to modify a creature by editing its DNA sequence.

To visualize protein folding and post-transactional modifications, the user will accesss MGX Protex, which will generate two linear polypeptide sequences taken from a pair of homologous chromosomes. MGX Protex will display the folded structure and associated function (color) of proteins, which depend on the properties of the amino acids present in their polypeptide chains. The user will be able to alter the appearance of a creature by changing the sequence of the amino acids in these chains.