R4L and Wellcome: Pushing Forward the Repository Agenda
EPS Insights 9 June 2005:
To date, however, much of the content contained within repositories is journal articles, technical reports, e-books or conference reports. Experimental data is, however, being shared through e-science projects such as the Cell Signaling Gateway (run by Nature and the Alliance for Cellular Signaling), and FlyBase (a database of genetic and molecular data for the Drosophila fly with contributions from researchers at Indiana, UC Berkeley, Harvard and Cambridge universities).
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In pursuit of systems
Nature 5 May 2005:
It is an explicit aim of both the Kyoto Encyclopedia of Genes and Genomes and the Alliance for Cellular Signaling to construct a fully functioning computer model of a cell.
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International alliances for quantitative modeling in systems biology
Molecular Systems Biology 29 March 2005:
AfCS is a major US initiative lead by Nobel-prize winner Alfred Gilman and funded by NIH, so that participants are primarily US researchers, and major funding was secured upon the launch of the alliance.
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Setback forces rethink for cell signalling alliance Nature 29 May 2003:
Scientists at the meeting said they now plan to use a macrophage cell line, which is suitable for RNA-interference studies and function normally in culture.
doi:10.1038/423472a
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The People's Biology The Scientist 24 February 2003:
Biology Cellular signaling alliance puts a socialist spin on systems biology
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L'AfCS: vous saurez tout...tout...tout...sur la cellule Médecine/Sciences 1 February 2003:
The AfCS: you will know everything...everything...everything... about the cell.
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Alliance for cellular signaling: Into Unknown Territory Nature 12 December 2002:
The Alliance for Cellular Signaling is exploring new frontiers, both in fundamental scientific terms and in the way in which research in cell biology is conducted. Alison Abbott reports.
doi:10.1038/420600a
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Alliance for Cellular Signaling Supplement Nature 12 December 2002:

• Overview of the Alliance for Cellular Signaling
  The Alliance for Cellular Signaling is a large-scale collaboration designed to answer global questions about signalling networks. Pathways will be studied intensively in two cells - B lymphocytes (the cells of the immune system) and cardiac myocytes - to facilitate quantitative modelling. One goal is to catalyse complementary research in individual laboratories; to facilitate this, all alliance data are freely available for use by the entire research community.
  doi:10.1038/nature01304
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• Unravelling the signal-transduction network in B lymphocytes
  The Alliance for Cellular Signaling has chosen the mouse B lymphocyte as a model system to understand basic principles that govern cellular signalling. Progress to that end has focused initially on establishing a reproducible experimental cell system and characterizing essential signalling responses. Although unravelling this complex network will take years, findings revealed in the interim will prove immensely useful to the scientific community at large.
  doi:10.1038/nature01305
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• Navigating the signalling network in mouse cardiac myocytes
  Cardiac myocytes have a complex network of signals that regulates their essential role in the rhythmic pumping of the heart. This network is an appealing model system in which to study the basic principles underlying cellular signalling mechanisms. Progress in this effort has come through the establishment of standardized myocyte isolation and culture procedures and characterization of important signalling responses.
  doi:10.1038/nature01306
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• The Molecule Pages database
  The Alliance for Cellular Signaling (AfCS)-Nature Molecule Pages will be a comprehensive database of key facts about more than 3,000 proteins involved in cell signalling. Each entry will be created by invited experts and be peer-reviewed. Alongside the large-scale experiments being conducted by the AfCS scientists, the wealth of information contained in this database offers the potential of accelerating the pace of discovery in signal transduction research.
  doi:10.1038/nature01307
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Cellular Signaling Gateway to Debut on Nature Website December 14 Online 11 December 2002:
A new website launching on December 14 is an advance in data accessibility and a milestone in scientific publishing, say its founders. The Alliance for Cellular Signaling and the Nature Publishing Group are launching a Web portal called the Signaling Gateway. Through this portal, the ongoing work of the Alliance -- a major research consortium begun in 2001 through an initiative of the National Institutes of Health -- and cell signaling news, updates, and reviews, will be available to anyone.
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Signalling help Nature Cell Biology 1 December 2002:
At the heart of this collaboration is the development of a comprehensive and free online resource, the Molecule Pages (MPs), a relational database of all significant published qualitative and quantitative information on signalling molecules...A first version of the MP database, embedded in a new web-resource called the Signalling Gateway, will be launched this month.
doi:10.1038/ncb1202-e273
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The future of the electronic scientific literature Nature 6 September 2002:
Take the Alliance for Cellular Signaling (AfCS), a 10-year, multimillion-dollar, multidisciplinary project run by a consortium of 20 US institutions. It is taking a systems view of proteins involved in signalling, and integrating large amounts of data into models that will piece together how cellular signalling functions as a whole in the cell. Here, authors would be required to input information, for example, on the protocols, tissues, cell types, specific concentration factors used and the experimental outcomes. Inputs would be chosen from menus of strictly defined terms and ranges, corresponding to predefined knowledge representations and vocabularies for cell signalling.
doi:10.1038/35092665
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What is the point of a database? Nature Structural Biology 1 July 2002:
In many ways these Molecule Pages will form more of an encyclopedia than a conventional database; therefore, guaranteeing the accuracy of their content becomes critically important. The AfCS molecule pages will be updated regularly, authored by leading researchers and subjected to a form of peer review. Producing these pages thus constitutes a form of publishing. Indeed Nature is collaborating with the AfCS to help reviewing and distributing these resources.
doi:10.1038/nsb0702-495
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Alfred Gilman Nature Medicine 1 August 2001:
At the age of 10, Alfred Gilman wanted to go to the moon; on a visit to New York's Hayden Planetarium with his parents, he signed up to be an astronaut. Fifty years later, Gilman is preparing to take on a different, yet equally astronomical task. Instead of traveling to outer space, he is heading up a research program to detail the workings of cellular space.
doi:10.1038/90898
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Cell signalling Nature 19 April 2001:
Alliance signals a fresh type of scientific research endeavour as the post-genomic face of 'big biology' gets under way. Diane Gershon investigates.
doi:10.1038/35108003
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Alfred Goodman Gilman: Please Check EGO at Door Molecular Interventions 1 April 2001:
Alfred Goodman Gilman was born in the same year (1941) that his father and Louis Goodman published the first edition of The Pharmacological Basis of Therapeutics. Pharmacology has thus always been part of his life, and in his own career he has focused primarily on cell signaling. For the past twenty years, he has chaired the Department of Pharmacology at UT Southwestern, and his long list of accomplishments includes a Nobel Prize (1994) for his work on G proteins. In 1998, Gilman embarked on his most ambitious program of research yet, bringing dozens of leading investigators from the cell signaling community to Dallas in order to plan out a ten-year project aiming "to understand as completely as possible the relationships between sets of inputs and outputs in signaling cells." Now directing the full-fledged, federally funded Alliance for Cellular Signaling, Gilman stresses that a solid database for constructing a "virtual cell" will depend on extensive collaboration from the entire signaling community. (For a complete Program Summary, and to register for membership in the Alliance, consult www.cellularsignaling.org.) The luminaries that were invited to the Dallas planning meeting, in fact, were greeted at the door with a note from Gilman exhorting them:
Please Check EGO at Door.
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Working in Alliances, Collaborations, and Consortia The Scientist 19 March 2001:
Gilman's model is creating job opportunities for life scientists, noting that it will probably have the most benefit for those interested in an academic-industry experience. "I would categorize these labs as a hybrid between an academic and a biotech situation," says Gilman. "There is a certain level of industrial throughput that we need to do." In that sense, the labs are more equivalent in function to industry. But, Gilman adds, that the alliance will also develop assays and competencies, a more academic feature. Additionally, the labs are in academic settings, with Ph.D. laboratory members also holding faculty appointments.
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Wanted: Applicants for NIGMS Grants The Scientist 8 January 2001:
In recent years NIH/NIGMS has pushed further. This past September the organization announced a series of collaborative "glue grants" to "large groups of scientists pursuing some of the biggest unsolved problems in biomedicine today," according to a published announcement. One example is NIGMS' $5 million grant for the first of five years to a consortium of basic scientists called the Alliance for Cellular Signaling (AFCS). The team will study aspects of cellular communications in two mouse cell types: cardiomyocytes (heart muscle cells that can beat in a dish) and B-cells (immune cells accustomed to "roving" around the bloodstream to carry out diverse functions). A key task will be to map out the vast numbers of signals transmitted between these two cell types, including a special class of liaison molecules known as G proteins. "We hope to create a piece of a virtual cell," said Alfred G. Gilman, pharmacologist at the University of Texas Southwestern Medical Center who is le! ading the AFCS effort. The cell signaling project, coupled with completed mouse sequencing data, will enable AFCS to inventory the genetic "stew" responsible for cardiomyocyte and B-cell functionality. Ultimately, this information will be useful to drug developers testing new compounds "in silico"--using a computer alone.
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Cell Signaling Alliance Gets Under Way The Scientist 16 October 2000:
Nobel laureate invites researchers worldwide
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NIH 'glues' cell biologists together Nature Medicine 1 October 2000:
American research into cell signaling is to benefit from the latest, large-scale National Institutes of Health (NIH) funding initiative. The National Institute of General Medical Sciences (NIGMS) has announced that its first 'glue grant'-a new type of grant designed to fund projects requiring cooperation between investigators at multiple institutions-will provide an estimated $25 million over a period of five years to the Alliance for Cell Signaling, an effort to produce a detailed map of the signal transduction pathways in two types of cells, cardiomyocytes and B cells.
doi:10.1038/80380
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Glue Grant' Boosts Cell Signaling Consortium Science 15 September 2000:
The National Institute of General Medical Sciences (NIGMS) is using a novel funding approach to bind together researchers in cutting-edge fields at many institutions, allowing them to transcend their individual areas of expertise. NIGMS has awarded $5 million a year for 5 years to a group of scientists studying cellular signaling. To speed their findings into the public domain and make them available for use in drug testing, members of the project have agreed to post new results in a public database and forgo some patent and authorship claims.
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Alliance of US labs plans to build map of cell signalling pathways Nature 18 November 1999:
A prominent US cell biologist is seeking funds for a multi-laboratory, multidisciplinary initiative intended to map how molecules in a cell interact with each other in response to various signals.
doi:10.1038/46111
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