Cytoscape Retreat 2007

Amsterdam; the Netherlands - November 6th - 9th, 2007

This is a preliminary set-up for the retreat 2007. Consider it a kind of RFC for the coming month or so; any suggestions changes are welcome! The only date that's pretty much fixed is the symposium date; than is the only time a big conference room is available. In the current scenario (CytoRetreat2007Planning : due in a few days) a first announcement will be sent at the beginning of april; so that should be the end of RFC status.

The 5th Annual Cytoscape Retreat will be held November 6th - 9th, 2006 (Tue-Fri) at the [http://www.amc.nl/ Academic Medical Center] of the University of Amsterdam in the Netherlands. [http://maps.google.com/maps?f=q&hl=en&q=Academisch+Medisch+Centrum,+Amsterdam,+North+Holland,+Netherlands&ie=UTF8&sll=52.373922,4.958954&sspn=0.178998,0.466919&z=11&ll=52.32275,4.957581&spn=0.179205,0.692139&om=1&iwloc=addr map]

Cytoscape is a bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. Additional features are available as plugins. Examples of features added in this way are network and molecular profiling analyses, new layouts, additional file format support and connection with external databases. Cytoscape is written in Java and the code is completely open source. The software architecture enables adaptation of Cytoscape functionality to the specific needs of molecular biologists and bioinformaticians. This is obvious from the range of research groups in a wide variety of fields that use Cytoscape to facilitate publications in high-profile scientific journals (See figure 1 for some examples).

Cytoscape is jointly developed by the groups of Benno Schwikowski (Pasteur Institute, Paris), Trey Ideker (University of California San Diego), Chris Sander (Memorial Sloan-Kettering Cancer Center), Lee Hood (Institute of Systems Biology, Seattle), and Annette Adler (Agilent Technologies, Santa Clara, CA). This year the retreat will be co-hosted by two new contributor groups of Tom Ferrin (UCSF Computer Graphics Laboratory) and Bruce Conklin (Gladstone/UCSF, GenMAPP). These groups have dedicated themselves to maintaining and further developing Cytoscape and providing support to the user community.

The Cytoscape community organizes a retreat each year to establish a roadmap for Cytoscape development. Until now these were held in the USA. At last year’s retreat the possibility of organizing the next retreat in Europe was raised and the Cytoscape team was enthusiastic. The Human Genetics Department of the AMC has accepted the challenge of organizing the meeting.

The goal of the retreat is threefold:

• 1: Involve the large user community in Europe in Cytoscape development; create a Cytoscape bridgehead in the Netherlands
• 2: Gather user feedback and use it to plan future development.
• 3: Establish a development roadmap for the next year

We want to reach these goals in a retreat spanning four days. The first and last day are mainly intended for the Cytoscape core development team and other developers who write their own Cytoscape plugins. The second and third days are aimed at a wide audience of molecular biologists and bioinformaticians in the Netherlands, Europe and internationally and to attract them we will invite several high profile speakers.

The meeting will be partly informal and technically focused with all major Cytoscape team members gathered together to set new directions for Cytoscape, plan new features and collaboratively work on code. Cytoscape-related presentations by invitees are welcome. Social activities around the meeting are also scheduled. This is a great chance to influence the development direction of Cytoscape.

On the other hand the public symposium will offer an excellent scientific program capable of attracting participants independently of the rest of the retreat activities.

Preliminary Schedule

Registration

To be done

Location

To be done

Hotel Suggestions

To be done

Travel

To be done

Example Trip Planner

To be done

Amsterdam tourism

To be done