Please go to simulator tab, if you want more information about the installation and running of CellDesigner.
Step 1: Import a model from pantherdb
Go to “Database” from the main menu in CellDesigner and click on “Import model from pantherdb.org”, it redirects to the panther database. Here it has an options like import/cancel , by clicking on import it will lead to view the model as shown in figure 1.
Figure 1: Importing model from Pantherdb.
The imported model can be visualized using CellDesigner:
Figure 2: VIsualizing the imported model.
Step 2: Simulate the model
To run the simulation on the model which is imported from the pantherdb, one has to create a mathematical equation for the model. The mathematical equations can be edited by the user according to the reactant and product of the model. These equations are edited by clicking the reactions from the list menu, and then by double clicking on the math options. It will redirect to a popup window named as reaction. By clicking the edit from the popup window it will redirect to another popup named as KineticLaw there user can edit the math equation depends on the kinetic law which is shown in figure 3.
Figure 3: Editing mathematical equation.
Step 3: Using pantherdb database to understand more about the model.
It searches for protein families, molecular functions, biological process and pathways. It generates the information about the genes, that belong to a given protein family and sub family and analyze the lists of genes, proteins, based on family, molecular function, biological process, cellular component or pathway.
For example take the same model which has been imported using pantherdb, and checks for the lists of genes and proteins based on family, molecular function, biological process, cellular component or pathway and find the phylogenetic analysis of the genes.
Step 4: Search by keyword
Select the type of search from the “Keyword search”, and type the query in the query box and it will redirects to the corresponding page.
“Sequence search” searches against a library of family and subfamily HMMs, and gives the subfamily which is best match for the query sequence. By clicking on the subfamily it will redirects to the subfamily details.
Figure 4: Searching
For example select pathways and give ATP synthesis in query box. It will redirects to the page which has detailed information about pathway like pathway name, the components, subfamilies, and associated sequences included in the model.
Figure 5: Viewing the Pathway details.
Go to “convert list” tab and select genes from the list, it will redirects to the genes with information like Gene name, panther family and subfamily, GO molecular function, GO biological process, GO cellular component, PANTHER protein class, pathway and species.
Figure 6: Gene details.
By clicking on each gene it will redirect to the information like PANTHER gene information and PANTHER classification. According to gene information it will gives the Gene ID, Protein ID, Gene Name, Symbol, Organism and alternate IDs of the gene. Panther classification gives details like panther family, sub family, GO molecular function, GO biological process, GO cellular component, PANTHER protein class, and pathway categories. This page also has information about ORTHOLOGS.
Figure 7: PANTHER Information.
Tree viewer explores the phylogenetic relationships among different genes within the family. There are four types of nodes present in the phylogenetic trees. User can view the multiple sequence alignment by clicking on MSA and view the attributes by clicking on grid.
Orange circles: Gene duplication nodes.
Green circles: Speciation nodes.
Blue diamond’s: Subfamily nodes. It is easy to distinguish between different families.
Figure 8: Tree Representation .
This experiment uses: CellDesigner, www.celldesigner.org.