Physiome Project
The Physiome Project is a worldwide effort to define the physiome through the development of databases and models which will facilitate the understanding of the integrative function of cells, organs, and organisms. The Project is focused on compiling and providing a central repository of databases, linking experimental information and computational models from many laboratories into a single, self-consistent framework. This coalescence of research effort will promote comprehensive databases and an integrative, analytical approach to the study of medicine and physiology.
Arabidopsis 2010
Functional Genomics and the Virtual Plant: A blueprint for understanding how plants are built and how to improve them
GOALS: Create a wiring diagram of a plant through its entire life cycle: from germinating seed to production of the next generation of seeds in mature flowers.
E-Cell.org - Japan
E-Cell Project is an international research project aiming to model and reconstruct biological phenomena in silico, and developing necessary theoretical supports, technologies and software platforms to allow precise whole cell simulation.
Computational Biology, Model Based Reasoning - Ross King at Aberystwyth (Wales)
Their aim is to do innovative research in both computer science and biological science by developing computing and artificial intelligence techniques for application to important biological problems. An essential component in this multidisciplinary field is their close collaboration with the biotechnology and pharmaceutical industries, and with other key research groups.
Reprogramming Plant Develpoment - Jim Haseloff Lab in Cambridge
Their lab is interested in cellular development of the model plant, Arabidopsis thaliana. Their aim is to better understand and manipulate intercellular interactions that regulate patterning in this relatively simple biological system. They use a combination of genetic and microscopy techniques in their work, and have adopted 3D computer visualisation techniques for looking at plant development.
Snapdragon Development - Enrico Coen & Andrew Bangham
The Dutch Silicon Cell Project
The long-term goal of the Silicon Cell (SiC) Consortium is the computation of Life at the cellular level on the basis of the complete genomic, transcriptomic, proteomic, metabolomic and cell-physiomic information that will become available in the forthcoming years. Completing this ambition will take more than a decade. This application concentrates on three major challenges, i.e. networks, space and time, and deals with systematic handling of the relevant data and results.
C.Elegans & Cell-O-Sim - Markus Gumble at German Cancer Research Centre Heidelberg
This group works in the field of cell simulation, cell lineage analysis, and genetic network simulation.
Plant Cell Imaging (3D Microscopy) - Carnegie Washington
The plant cell imaging web pages at the Carnegie Institution. We are using fluorescent molecular tags combined with laser scanning confocal microscopy (LSCM) to visualize live plant cells.
Biological Modeling and Visualization using L-Systems - Calgary Prof. Przemyslaw Prusinkiewicz
Software Tools for Systems Biology - Seattle
Detailed Modeling of Growth of C.elegans - Armand M. Leroi, Imperial College
For the past few years we have been studying the evolution of body size in nematodes. We aim to understand both evolutionary and developmental mechanisms; to do this we use a range of tools from gene knockouts to mathematical models. Most of our work is on the nematode Caenorhabditis elegans, but we also use a whole zoo of relatives (at least 50 spp.) all of which are small (0.5 - 3.0mm long) and easy to grow in the lab. Below, is a brief summary of some of our projects.
Arabidopsis Thaliana Embryogenesis - Daniel Vernon Lab
The main interest of The Vernon Lab is understanding the molecular mechanisms underlying plant embryogenesis. Embryogenesis is perhaps the least-understood period of plant development, yet this is the time when the plant develops from a single cell into an organized, complex multicellular organism. The complicated web of events that occur during embryogenesis must be controlled at the genetic level. To investigate the genetic and molecular mechanisms involved in plant embryogenesis, we work with a small weed, Arabidopsis thaliana. Arabidopsis has become "the fruit fly of plant biology" because of its popularity as a model system for plant developmental biologists, and there is currently a large effort underway to characterize its genome. We are doing developmental genetics: using mutants with defective development as tools to identify genes and understand how development normally operates. We are investigating mutants that are defective in genes required for proper embryonic cell organization,differentiation, and morphogenesis. Our goals are to analyze mutant phenotypes and clone the genes that are disrupted. This requires a multidisciplinary strategy that combines molecular, biochemical,and genetic techniques.
One mutant we are studying, twin1, displays numerous defects in morphogenesis and frequently produces twin embryos due to de-differentiation of cells in the suspensor. Other mutants, the round embryo (rem) mutants, are defective in early embryonic cell organization and morphogenesis. Characterization of these developmental mutants, and cloning of the defective genes, will lead to a better understanding of the molecular mechanisms underlying plant embryogenesis.
Much of our research is carried out by Whitman undergraduates: see our Team Weed and Research links for examples and more information on students and their research.