NRNB sponsors a variety of competitions for the communities around network biology tools. These competitions range from app development to bug bounties. Check out ongoing competitions and the results of past competitions below. Also feel free to suggest a competition.
Provide a “wizard” user interface for simple styles based on common data-driven visualizations to:
Use Oracle JavaFX packager for Cytoscape installers, which package the required version of Java with the application, thus cutting down on the amount of headscratching by users.
Implement edges with multiple sources and targets to allow for programmatic representation of more complex interactions. For example, they could be used to represent Gene-Protein-Reaction relationships without necessitating the introduction of Enzyme subunits.
1st - Srikanth B. - TieDIE Subnetworks
The TieDIE algorithm computes a subnetwork of gene and protein interactions that connect genomic perturbations to gene expression changes characteristic of cancer subtypes. The pathways derived using the TieDIE app(algorithm) predict interlinking genes(linker nodes, yellow ones in animation) that may correspond to essential components of cancer signaling and may provide a mechanistic explanation of tumor behavior and suggest subtype-specific drug targets.
Subnetworks were generated on a GBM pathway by tuning the size parameter(from a lesser value to desirable size of subnetwork). The idea of the animation of subnetworks using CyAnimator is that it helps biologists for a closer and intuitive inspection of the events.
2nd - Adam T. - The Cell Ontology
I parsed the Cell Type Ontology using the is_a relation for edges, animated the transitions between a few different layouts, and set it to a reggae beat.
3rd - Mohammed F. - Heuristic to Travelling Salesman Problem
CySpanningTree app has a feature that creates Hamiltonian cycle using pre-order traversal. Pre-order traversal on a minimum spanning tree is one of the heuristic solutions for Travelling Salesman Problem. This video created using CyAnimator shows how the app traverses on minimum spanning tree to create a cycle.
Automatically import node annotations. By default, node annotations like gene ID, gene symbol, UniProt ID, GO terms, PFAM IDs, PDB IDs, ProSite ID, would automatically be imported. (The MyGene.info web service has a pretty comprehensive list of annotations). By default, all linkouts should work.
The first feature I'd like to add to Cytoscape is a drop event handler so that tables, graphs, images and annotations can be dragged in from the desktop.