Four of the Best Free Tools for Molecular DataViz

Visualizing the interactions between DNA, RNA, and proteins and their biosynthesis, as well as the regulation of these interactions is not an easy task.

As a researcher in molecular biology, how you can make your data showing macroscopically the microscopic events happening in the cells?

Well, data visualization (or DataViz) is there for you.

Genomics and molecular data can be hard to interpret when you collect raw data. To interpret and highlight results you should organize data. For example, it can be organized in a graph or a scheme. Data visualization can be a second step to present results and to point out the results. It may help the interpretation of the results and to communicate about your research.

So, here is a top 5 of the web-based free tools you can use to illustrate your molecular data easily.

XiNet

Online tool • For cross-linking and mass-spectrometry • Made in UK • Free

XiNet is a DataViz tool that allows displaying cross-linking and mass spectrometry results. It generates cross-link network materialized in the form of node-link diagrams.

You can see how it shows on these figures extracted from an article of the Molecular and Cellular Proteomics Journal.

XiNET allows visualizing positional information, such as linkage sites and linked peptides, at the residue scale.

You can see it in this second example the representation of the RNA polymerase II – TFIIF complex. It is a XiNET illustration from an article in the EMBO Journal.

It also displays all types of cross-linking reaction product and additional sequence information like protein domains.

RCSB Protein Data Bank

Online tool • For protein visualization • Made in USA • Free

This tool is powered by the Protein Data Bank (PDB) archive information about the 3D shapes of proteins, nucleic acids, and other complex assemblies.

On RCSB’s website, you can deposit and search for protein structure illustrations. You can find different visualization options such as the “3D structure viewers” or the “ligand explorer”.

You have the possibility to enter the PDB identification name and display the illustration you want with a specific viewer. Here is the example of the Human Deoxyhaemoglobin ( 4HHB) viewed with the JSmol viewer.

CellVIEW

Online tool • For multiscale large dataset • Made in Austria • Free

source: Eurographics workshop on visual computing for biology and medicine

CellVIEW is a tool that enables to illustrate multi-scale rendering of large datasets. It is implemented in a “free-to-use game engine” as they describe it on Autopack.org. Which makes the latest and best graphics techniques more accessible to the end-users.

CellVIEW allows visualizing biomolecular datasets on the atomic level, as you can see the HIV virus surrounded by blood plasma just above.

According to Mathieu Le Muzic, a researcher in computer graphics at the TU Wien in Austria, “cellVIEW will become a critical tool for cellPACK users who wish to explore multi-scale modeling extremes”. CellPACK is a well known powerful modeling tool. With cellVIEW, you can load files generated by cellPACK and visualize entire organisms at the atomic level, with the state-of-the-art graphics techniques.

Paraview

Online tool • For large data scale • Made in the USA, France • Free (advanced paid features)

Paraview is a data analysis and visualization application. As described on its website, Paraview can be run on supercomputers to analyze datasets of petascale as well as on laptops for smaller data.

Here is a visualization of blood cells with Paraview:

There is also a video feature using Paraview cinema. Here is the example of in situ MPAS-Ocean image-based visualization:

Their aim is to create an open, flexible, and intuitive user interface that is the most user-friendly possible while processing large data sets.