Cells

• Genomics
  • TRND

    TRND is an integrated workflow wherein user-supplied gene expression data generates transcriptional regulatory networks and derives their biological implications. TRND uses a built-in database of experimentally validated gene-transcription factor regulatory interactions and a non-linear dynamical systems analysis package for discovering transitions in cell behavior supported by a transcription-translation-post-translation process network.

  • TRND Results

    TRND Results is a database of Transcriptional Regulatory Network data.

  • SRND (in development)

    SRND is a bioinformatics software for discovering splicing regulatory networks (SRNs).

  • Geogen

    Geogen is an interactive database of transcriptional regulatory information for Geobacter species.

  • MicroArray Tools

    MATools is a software for microarray dataset manipulation.

  • CellX

    CellX is a database and platform for cooperative research on a particular cell type. Presently, transcriptional regulatory networks (TRNs) are available for a representative set of cell types of relevance to the NIH mission. These TRNs are intended to serve as a basis of user working groups who expand, curate, and use them as training-set TRNs that are transformed via bioinformatics, cell modeling, and gene expression and proteomic data to a TRN tailored for a particular cell line.

• Cell Modeling
  • Karyote

    Karyote is an integrated set of modules for building and simulating ordinary differential equation models of single cells and arrays of interacting cells. Karyote is hierarchical so that models can accommodate intracellular compartments for arrays of interacting cells. It allows automatic integration of simpler models to create more complete ones and has a set of example models.

  • Electrometabolomics

    Electrometabolomics is like Karyote, but augmented to account for electrophysiological effects.

SimNanoWorld

• NewtonianNanoWorld (in development)

  NewtonianNanoWorld is an all-atom model of viruses, ribosomes and other bionanosystems that solves the molecular dynamics problem with great efficiency for supramillion-atom systems.

• QuantumNanoWorld (in development)

  QuantumNanoWorld simulates quantum phenomena in systems such as nanoparticles (of magnetic, superconducting or catalytic materials), graphene, molecular wires, and quantum dots.

• Poisson-Boltzmann Electrostatics (in development)

  Poisson-Boltzmann Electrostatics solves the electrostatics problem for supramillion atom biological and other systems

Outreach

• The Self-Organizing Planet

  The objective of the Self-Organizing Planet project is to develop an appreciation of the great richness of structures and patterns that have emerged spontaneously on our planet over its approximately 4.5 billion years of existence. We seek to delineate the chemical and physical processes underlying this emergence. This site facilitates the participation of visitors in this quest. It contains material for both casual observers and professional researchers.