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).
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.
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.
forces rethink for cell signalling alliance Nature 29
Scientists at the meeting said they now plan to use a macrophage cell
line, which is suitable for RNA-interference studies and function normally
People's Biology The Scientist 24 February 2003:
Biology Cellular signaling alliance puts a socialist spin on systems biology
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.
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.
Alliance for Cellular Signaling Supplement Nature
12 December 2002:
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.
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.
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
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.
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.
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
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.
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.
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.
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.
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.
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.
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.
Signaling Alliance Gets Under Way The Scientist 16 October
Nobel laureate invites researchers worldwide
'glues' cell biologists together Nature Medicine 1 October
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.
Grant' Boosts Cell Signaling Consortium Science 15 September
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.
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.