Cytoscape WikiThe Conference: Biological Networks: Reconstruction, Analysis and Modelling, 5 & 6 May 2009
General Theme: The conference's overarching theme was to have industry obtain new ideas from academics in systems biology.
Geographic Scope: The speakers were from the UK, Switzerland, Germany, and France; the attendees were overwhelmingly from the UK
Types of Talks: The conference had three primary groups of talks:
Reconstructing Networks: The talks focused on obtaining networks from data sources like gene expression profiles and protein interaction networks.
Analysing Networks: The talks focused on how one can drill a complicated network down into more meaningful constituents
Modelling Networks: The talks focused on creating models from a given network
The Audience: The audience was mostly made up of postdocs or heads of research groups in pharmaceutical companies in the UK like Pfizer and Glaxo Smith Kline. This conference seemed to be beyond the scope of business managers in industry who wish to learn a bit about systems biology.
The Audience's Interest in Cytoscape:
- Most of the audience heard of Cytoscape—again, these were scientists in the pharmaceuticals industry.
At least one forth of the audience was fairly comfortable with Cytoscape. They knew about importing networks from databases, visualizing networks with the VizMapper, and doing some kind of processing with plugins like MCode. My talk did not offer much new information to these people.
- Most people were not aware of the organizational structure of Cytoscape.
- Many people did not know there was an entire consortium that managed Cytoscape.
Few people did not know the role of the core development team. Moreover, many did not see much of a distinction between the core and plugins. They were not aware that the core development team isn't technically responsible for plugins.
- Maybe our website should include more about how it's organized. For example, the "About Cytoscape" paragraph could include a few words about the consortium.
- It seems many people were interested in contributing to Cytoscape. Perhaps our website should include a "Get Involved" tab at the top, then put the "Dev Team" page somewhere under that tab.
- Because these people were from pharmaceutical companies, a lot of people were interested in analyzing pathways. I briefly mentioned Cytoscape's Pathway Commons plugin, which generated a lot of interest.
- One individual asked if Cytoscape had richer visualization capacities for pathways, like displaying formal biochemical reactions, on the network. (This could be done as a plugin, where a node could represent a reaction, and if one clicks on the node, one can get a window that displays the chemical reaction.)
- Another asked if existing Pathway Commons data can be overlayed on top of a network.
- One particular individual came to the conference just to get ideas about how to process networks down to get interesting subnetworks. It seems quite a few people were facing large hairballs of networks and wanted to know how get something interesting out of that.
- Thanks to the solid documentation of Cytoscape, we have ample supply of how-tos on this. Maybe Cytoscape's processing capabilities should be more apparent.
- It seems many people were not aware of the Help Desk, and questions are answered there quite consistently.