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Tool is being actively developed, with new features being added.

Invis

Invis is the first visual analysis tool to facilitate exploration of in vitro selection sequence spaces. invis introduces a novel configuration of coordinated views that enables simultaneous inspection of global projections of sequence data alongside local regions of selected dimensions and sequence clusters. It allows scientists to isolate related sequences for further data analysis, compare sequence populations over varying conditions, filter sequences based on their similarities, and visualize likely pathways of genetic evolution. User feedback indicates that invis enables effective exploration of in vitro RNA selection sequences.

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Institution: Stanford University, Cloudera & Mt. Sinai Medical School

COMBat

The prototype tool COMBat allows users to construct a new matrix on the fly by selecting subsets of items of interest, or filtering out uninteresting ones, and it provides various additional interaction techniques.


The visual analysis approach employs a matrix-based visualization technique to explore relations between annotation terms in biological data sets. Its flexible framework provides various ways to form combinations of data elements, which results in a co-occurrence matrix. Each cell in this matrix stores a list of items associated with the combination of the corresponding row and column element. By re-arranging the rows and columns of this matrix, and color-coding the cell contents, patterns become visible.

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Institution: HAN University of Applied Sciences, Eindhoven University of Technology, Center for the Biology of Disease (VIB), Leuven

ZigCell3D

ZigCell3D is a virtual 3D whiteboard approach to chemical reaction modelling. It aims to provide a realtime interactive environment, where complex biophysics research is turned into a creative and game-like 3D environment. The complete system entails modelling, simulation and visualisation as part of a unified framework.

The core visualisation is based on a multi-core parallel C/C++ ray tracing engine, that builds a complete 3D iso-surface model of the cell, its organelles and molecules down to the atomic level using PDB files. The simulator itself is based on coarse-grained Brownian motion of the individual molecules, which is visualised in detail in a tightly coupled manner. Using a virtual fluorescence microscope the virtual simulation environment can be benchmarked against real life experimental data.

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Institution: ETH Zurich, ScienceVisuals Sarl

This work was supported in part by a grant from the Swiss Commission for Technology and Innovation (CTI), Project 12532.1 PFLS-LS. Heinz Koeppl acknowledges funding from Swiss National Science Foundation, grant no. PP00P2_128503.

MoClo Planner

MoClo Planner is an interactive visualization system for collaborative bio-design, utilizing a multi-touch interactive surface. The system integrates the information gathering, design, and specification of complex synthetic biological constructs using the Modular Cloning (MoClo) assembly method. Modular Cloning is a hierarchical DNA construction method that allows for the assembly of multi-part constructs from a library of biological parts in a one-pot reaction. This cutting-edge method facilitates and expedites the assembly of complex biological designs.

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Institution: Agilent Technologies, Wellesley College, Boston University

MoClo Planner is a result of a participatory and user-centered design process, which included close collaboration with domain experts. Using multi-touch interactions and a rich graphical interface, the system accelerates the MoClo learning process, and reduces design time and errors. This tool was developed in collaboration with Nahum Seifeselassie, Casey Grote, and Taili Feng, Natalie Kuldell, and the BU and MIT iGEM teams. This work was partially funded by NSF grant number IIS-1149530 and by Agilent Technologies. 

VisNEST

VisNET is a visualization system for the analysis of simulated network models. It comprises of four distinct visualization designs that support the inspection of different model aspects. 

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Institution: Jülich Aachen Research Alliance (JARA)

A prototype of the VisNEST  application has been implemented and used by domain experts to simultaneously visualize 32 vision-related areas of the macaque brain. The system has been designed in close collaboration with neuroscientists. It follows a multiple-view approach in order to integrate a variety of data modalities, e.g. geometrical information, raw simulation input, and derived, aggregate information. The system enables users to interactively browse brain areas, identify areas of interest and interactively analyze these in more detail. Initial user feedback on the utility of VisNEST is positive. Yet, the collaborative development process strongly encourages continuous improvement based on user feedback. A key aspect that has recently been targeted by comments is the depiction of graph information. The current design is very much based on the initial requirement to leave node positions fixed.

HumMod Browser

HumMod Browser is a multi-scale exploratory visualization tool that allows physiologists to explore human physiology simulation data with more than 6000 attributes. The HumMod Browser produced can give physiologists flexible control over the visualization displayed for quick understanding of complicated simulation results. The visualization is constructed through the metaphorical bubble interface to allow dynamic view controls and the data relationships and context informaiton unfold as physiologists querying groups of connected bubbles within the hierarchical or causal relationships. HumMod Browser contributions to the interaction design provide multi-scale coordinated interactive exploration for a new type of physiological modeling data.

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Institution: University of Maryland, Baltimore County, University of Mississippi Medical Center

This work is partially supported by the National Science Foundation under grant numbers DBI-1260795, IIS-1341254, EPS-0903234, and HL-51971.

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