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Construct/import and visualize biological interaction maps built using kinetic/logical formalism
A map of biological interactions of a/set of biological process(es) of research interest represents the participating biomolecules (such as DNA, proteins and small molecules) and their influences on each other. For e.g. energy metabolism, MAPK signaling cascade. Holistic study of such maps helps identify key proteins and provide mechanistic insights into emergent properties of biological systems.
Cell-in-Silico offers a user-friendly environment to construct biological interaction maps based on researcher’s knowledge and literature evidences. The interaction maps are shown as hypergraphs with distinct shapes for representing different types of biomolecules and interactions.
Search and import interaction maps from public databases expressed in SBML format directly from Reactome, BioModels and Panther DB
Apart from allowing construction of interaction maps, Cell-in-Silico also allows searching and importing of interaction maps existing in major public databases, namely, Reactome, BioModels and Panther DB.
Define logical rules for protein activation/inhibition
Cell-in-Silico allows the creation of logical rules (such as AND, OR) to encode the activation/inhibition of various signaling proteins by their upstream signaling molecules.
Integrate maps to generate (w)holistic maps
Sometimes, the available maps of individual pathways are not sufficient to cover the research scope, and several maps need to be studied simultaneously to understand the biology. To address such cases, Cell-in-Silico provides a facility to merge interaction maps in a consistent fashion to make a larger map. This feature is also useful in a collaborative environment where groups are working on individual pathways, which can be merged to get the bigger picture.
Categorize map into pathways and processes
Cell-in-Silico offers categorization of interaction maps into classical modules such as biological pathways and processes for easy visualization and analysis.
Annotate genes/proteins with public data and user-supplied PubMed references
It is often necessary to gather more information about the genes/proteins participating in a network than just knowing their interacting partners. Cell-in-Silico collates detailed annotation of each gene/protein participating in a map from public databases like NCBI and UniProt, and presents them in an easy-to-view form on its integrated interface. It further allows user to add PubMed references to supplement participation of genes/proteins to a pathway/process.
Identify highly connected proteins in the map
Cell-in-Silico allows categorization of genes/proteins based on the number of interactions they have in the map. This information is a key in identifying the proteins that play key roles in the network as a step towards drug target identification.
Customized visualization of maps
Cell-in-Silico offers customizable ways to visualize interaction maps. For e.g. user can selectively visualize only those biomolecules and interactions that participate in a particular pathway/process, or, that belonging to a particular organelle and participate in a particular pathway/process.
Overlay gene expression data on maps and study effect on pathways/processes
Overlaying gene expression data on maps helps visualize differentially expressed genes and pathways in the context of interaction map, thus enabling interpretation of holistic picture. Cell-in-Silico offers three visualizations of overlaid maps, viz, network view: showing the genes in the context of interaction map, pathway view: showing the genes organized with respect to the pathways they participate in, and, process view: showing the genes organized with respect to the processes they participate in. The latter two views are helpful in identifying the differentially expressed genes in each pathway and process respectively.
Report generation and export
Cell-in-Silico provides an option to generate customizable report containing the details of the model, images of interaction maps and the graphs and tables pertaining to the gene expression data analysis. The report can be previewed, or, can be exported in two convenient formats, PDF and HTML.
SBML and SBGN standards for Systems Biology are adopted
Cell-in-Silico supports import of models in all SBML levels including the recently announced level 3 version 1, and, export to level 2 version 1 or higher. Cell-in-Silico has also adopted the SBGN graphical notations to represent biomolecules and interactions among them. Such adoption would facilitate consistent representation, interoperability and exchange of Systems Biology models.
© 2013 Persistent Systems Ltd.