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Name of Collaboratory :

 

Alliance for Cellular Signaling (AfCS)

 
 

Logo :

   
 
 

URL :

  http://www.afcs.org/  
 

Collaboratory Status :

 
Completed   Start Date : 1999 End Date : 2009 Info Last Updated : Wed, Dec 8 2010 1:01am PST
 
 

Primary Collaboratory Function :

  Distributed Research Center  
 

Secondary Collaboratory Functions :

   
 

Domain(s) :

  cellular signaling (cell biology, chemistry, biochemistry, bioinformatics, cellular engineering)  
 

Brief Description of the Collaboratory :

 

The overall goal of the Alliance for Cellular Signaling was to understand as completely as possible the relationships between sets of inputs and outputs in signaling cells that vary both temporally and spatially. The same goal, stated from a slightly different perspective, was to understand fully how cells interpret signals in a context-dependent manner. This work involved the identification of many of the proteins that comprise the various signaling systems, the assessment of time-dependent information flow through the systems in both normal and pathological states, and finally the reduction of the mass of detailed data into a set of interacting theoretical models that describe cellular signaling. All primary research results from experiments previously performed by the Alliance for Cellular Signaling, including B-lymphocyte and RAW 264.7 ligand screens and yeast two-hybrid data are archived on their Website.

AfCS research was conducted in nine cooperating labs. Three of these labs were housed in the UT Southwestern Medical Center (Cell Preparation and Analysis, Protein Chemistry, and Antibody) and the other six were housed at UC San Francisco Veterans Administration Medical Center (Macrophage Biology), Stanford (Microscopy), Cal Tech (Molecular Biology), Vanderbilt University (Lipidomics), UC San Diego Super Computing Center (Data management, analysis, and Bioinformatics), and University of California, Berkeley (Data Modeling and Network Analysis).

AfCS participants were categorized into: steering committee, external advisory committee, macrophage committee, laboratory directors, data analysis group, membership and editorial committee, and bridging project investigators (with project title).

They had a project management plan, organization chart, administrative management plan, annual meetings, three newsletters per year.

AfCS, working with Nature Publishing group, also coordinated the construction of an ambitious Signalling Gateway, an online resource for the cell signalling community. A major part of the gateway will be approximately 3,000 molecule pages. Each Molecule page is intended to be a complete and current literature review about one protein molecule relevant to cell signalling. Together, they would form the most comprehensive database of signalling information to date. (The gateway later became a collaboration between UCSD and the Nature Publishing Group, and is a successor to this collaboratory.)

*******************PREVIOUSLY*******************

The Alliance for Cellular Signaling (AfCS) goal was to create a complete model cell, accounting for the cell signalling behavior of a cell. The project originally focused on two mouse cells, B Lymphocyte and Myocyte. However, in 2003, AfCS made the decision to switch to the RAW 264.7 macrophage cell line.

Work was centered around identification of all the proteins that comprise the various signaling systems, the assessment of time-dependent information flow through the systems in both normal and pathological states, and the reduction of the mass of detailed data into a set of interacting theoretical models that describe cellular signaling.

AfCS bench research was conducted in seven cooperating labs. Three of these labs were housed in the UT Southwestern Medical Center (Cell Preparation, Protein, and Antibody) and the other four were housed at UC San Francisco Veterans Hospital (Signaling Assays), Stanford (Microscopy), Cal Tech (Molecular Biology) Vanderbilt University, and UC San Diego Super Computing Center (Bioinformatics). Participants were categorized according to funding stipulations as participating investigators, AfCS employees, or alliance members.

AfCS, working with Nature Publishing group, also coordinated the construction of an ambitious Signalling Gateway, an online resource for the cell signalling community. A major part of the gateway will be approximately 3,000 molecule pages. Each Molecule page is intended to be a complete and current literature review about one protein molecule relevant to cell signalling. Together, they would form the most comprehensive database of signalling information to date.

 
 

Access to Instruments :

  2-D gel analysis, mass spectrometry, and advanced confocal, epifluorescence, and total internal reflection microscopy (none for remote operation)  
 

Access to Information Resources :

  Alliance Labs' data (online database of results and analysis conducted by participating labs), reports
 
 

Access to People as Resources :

  Expert consultation from other participating specialists  
 

Funding Agency or Sponsor :

 
Agouron Research Institute
Aventis Pharmaceuticals
Eli Lilly and Company
Johnson and Johnson
Merck Genome Research Institute, The
United States Department of Health and Human Services
National Institutes of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
National Institute of Allergy and Infectious Diseases (NIAID)
National Cancer Institute (NCI)
Novartis Pharma AG
University of Texas Southwestern Medical Center at Dallas
 
 
 

Notes on Funding Agencies/Sponsors:

 
 
 
Organizations with Funded Participants:
 
Organization name:
Approx # of participants:
Description of organization's role(s):
Boston University
Data analysis group
California Institute of Technology (Caltech)
Molecular Biology Laboratory; Data analysis group
Duke University
Membership and editorial committee
Harvard University
Steering committee member; Data analysis group
University of California, San Diego (UCSD)
Data analysis group
   San Diego Supercomputer Center (SDSC)
Data management, analysis, and Bioinformatics Laboratory
San Francisco Veterans Administration Medical Center
Macrophage Biology Laboratory
Stanford University
Microscopy Laboratory; Data analysis group
University of California, Berkeley
Data Modeling and Network Analysis
University of California, San Francisco (UCSF)
Macrophage committee; data analysis group
University of Texas Southwestern Medical Center at Dallas
Antibody Laboratory; Protein Chemistry; Cell Preparation and Analysis Laboratory; Data analysis group
Vanderbilt University
Lipidomics Laboratory
 
Organizations Otherwise Associated:
 
Organization name:
Approx # of participants:
Description of organization's role(s):
Babraham Institute
Macrophage Committee
Institute for Systems Biology
Macrophage Committee
University of British Columbia
Macrophage Committee
University of Michigan
University of Washington
Macrophage Committee
   UW School of Medicine
Macrophage Committee
 
TOTAL PARTICIPANTS:
 

Notes on Participants/Organizations:
Core lab participants: 25 Ph.D.s, 40 technicians, & 8 programmers in 8 functional laboratories @ 6 sites
Also advisory boards, and 700 Alliance members

   
     
 
 

Communications Technology Used :

  Polycom ViewStations, website, email lists, electronic message boards, electronically distributed newslettters  
 

Technical Capabilities :

  Management of technical resources
Access control/login facilities
Support for transition between synch and asynch
Directory of services/experts/resources, Awareness of people's activities
Asynchronous object sharing
Index/metadata, General search capability, Centrally controlled knowledge base, Vetted knowledge based of multiple authors, Common file space, Data stream capture, Email/attachments
Asynchronous conversation
Threaded discussion, Audio capture and replay, Video capture and replay, Web forms, Email
Synchronous object sharing
Data conferencing, Application sharing
Synchronous conversation
Audio, Video
 
  Key Articles :  

Abbott, A. (2002). Alliance for cellular signaling: Into unknown territory Nature, 420, 600 - 601.

Li, J., Ning, Y., Hedley, W., Saunders, B., Chen, Y., Tindill, N., Hannay, T. & Subramanian, S. (2002). The Molecule Pages database Nature, 420, 716-717.

R. Taussig, R. Ranganathan, E. M. Ross and A. G. Gilman (2002). Overview of the Alliance for Cellular Signaling Nature, 420, 703 - 706.

 
 

Project-reported performance data :

   
  Images of the Collaboratory:  
Organizational Chart
 
 
         
    
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