Software

 

eons

EONS

www.synapticmodeling.com

EONS (Elementary objects of the Nervous System) is the perfect modeling platform to study the dynamic interactions between synaptic elements in a friendly manner. There are no complicated equations to write: all the elementary models are predefined using state of the art models.
EONS consists of a graphical modeling platform containing the major elements that comprise a glutamatergic synapse (both pre- and post-synaptically). These elements parameters as well as the underlying synaptic geometry can be modified. EONS is a parametric model of a generic glutamatergic synapse that takes into account pre-synaptic mechanisms, such as calcium buffering and diffusion, neurotransmitter release, diffusion and uptake in the cleft, and postsynaptic elements, such as ionotropic AMPA and NMDA receptors, their distribution and synaptic geometry, as well as metabotropic glutamate receptors.

Pathline

Pathline

www.pathline.org

Pathline is a visualization tool for comparative functional genomics that supports analysis of three types of biological data at once: functional data such as gene activity measurements; pathway data that presents a series of reactions within a cellular process; and phylogenetic data describing ancestral relationships between species.

The design of Pathline includes two new visual encoding techniques. The first is an encoding of a linearized metabolic pathway representation that provides appropriate topological information and supports the comparison of quantitative data along the pathway. The second is a curvemap, a matrix layout of temporal expression data for enhanced perception of trends in gene and cell activity levels across multiple species.

MulteeSum

MulteeSum

www.multeesum.org

MulteeSum is a visualization system that supports inspection and curation of data sets showing gene expression over time, in conjunction with the spatial location of the cells where the genes are expressed -- it is the first tool to support comparisons across multiple such datasets. MulteeSum is part of a general and flexible framework that allows biologists to explore the results of computations that mix spatial information, gene expression measurements over time, and data from multiple species or organisms. MulteeSum was developed to support the research activities of biologists studying developing Drosophila embryos.

MizBee

MizBee

www.mizbee.org

MizBee is a multiscale synteny browser for exploring conservation relationships in comparative genomics data. Using side-by-side linked views, MizBee enables efficient data browsing across a range of scales, from the genome to the gene. The design of MizBee is grounded in perceptual principles, and includes several techniques such as edge bundling and layering to enhance visual cues about conservation relationships related to proximity, size, similarity, and orientation.

ImageVis3D

ImageVis3D

www.imagevis3d.org

ImageVis3D is a new volume rendering program developed by the NIH/NIGMS Center for Integrative Biomedical Computing (CIBC). The main design goals of ImageVis3D are: simplicity, scalability, and interactivity. Simplicity is achieved with a new user interface that gives an unprecedented level of flexibility. Scalability and interactivity mean that users can interactively explore terabyte-sized data sets on hardware ranging from mobile devices to high-end graphics workstations. Finally, the open source nature as well as the strict component-by-component design allow developers not only to extend ImageVis3D itself but also reuse parts of it, such as the rendering core. This rendering core for instance is planned to replace the volume rendering subsystems in many applications at the SCI Institute and with our collaborators.

SCIRun

SCIRun

www.scirun.org

SCIRun is a problem solving environment or "computational workbench" in which a user selects software modules that can be connected in a visual programing environment to create a high level workflow for experimentation. Each module exposes all the available parameters necessary for scientists to adjust the outcome of their simulation or visualization. The networks in SCIRun are flexible enough to enable duplication of networks and creation of new modules.

Many SCIRun users find this software particularly useful for their bioelectric field research. Their topics of investigation include cardiac electro-mechanical simulation, ECG and EEG forward and inverse calculations, modeling of deep brain stimulation, electromyography calculation, and determination of the electrical conductivity of anisotropic heart tissue. Users have also made use of SCIRun for the visualization of breast tumor brachytherapy, computer aided surgery, teaching, and a number of non-biomedical applications.