Along with the completion of many genome sequencing with the living systems function in terms of all levels of biological information, and then to develop information technology for applying such systemic information to medicine and biology.
Needs: It is vital to develop information technology with which we can easily
represent and simulate the structurally complex dynamic causal interactions
and processes of various biological objects, e.g. genomic DNA, mRNA, proteins,
functional proteins, molecular transactions.
In order for software tools to be accepted by users in biology/medicine for
biopathway representation and simulation, the following two matters should be
resolved, at least:
(1) Remove issues that are irrelevant to biological importance.
(2) Allow users to represent biopathways intuitively and understand/manage easily
the details of representation and simulation mechanism.
Cell Illustrator is a software tool for representing and simulating interactions
and processes in biopathways.
It is based on the technology [1,2] and the XML-based visualization technique
so that would satisfy (1) and (2).
Usually, a biopathway information is conceptually described as a figure together
with the explanation
about the relations between biological objects of concern and the measured/observed
data proving
their qualitative/quantitative relations. These information can be easily represented
and simulated with Cell Illustrator.
(1) The notion of hybrid object net [2] and the biopathway design/representation
principle [1] are employed as its basic architecture for simulation mechanism.
The hybrid object net is an "object-oriented" extension of Petri net
[3] that can express explicitly the relationship between
objects taking continuous values and discrete values with any control functions
while keeping the characteristics of discrete Petri net soundly.
(2) A tool based on XML for visualizing and animating biopathway simulation
results produced from the simulation mechanism of Cell Illustrator is also
being developed. Its aim is to help intuitive understanding/managing of biopathway
simulations and designs.
Some representation and simulation examples of typical biopathways are given
at Biopathway Files which cover the basic aspects in biopathways:
- Switching mechanism of lambda phage
- Circadiam rhythm of Drosophila melanogaster
- lac operon and glycolytic pathway of E. coli
- Apoptosis induced by Fas ligand
- Cell cycle
Furthermore, with the tool currently being developed, we will exhibit a full
series of animated simulations of the lambda phage gene regulatory network shown
in [4] that is represented and simulated with Cell Illustrator .
The software and representation/simulation examples are freely available under
the copyright of Human Genome Center, Institute of Medical Science, University
of Tokyo.
We are very pleased to collaborate for modelling your biopathways with Cell Illustrator.
Please email to support@genomicobject.net for contact.
See PUBLICATIONS.