Open source

LayerCake is a tool designed to assist in the exploration of the genetic variability of the population of viruses at multiple time points and in multiple individuals, a task that necessitates considering large amounts of sequence data and the quality issues inherent in obtaining such data in a practical manner. This design affords the examination of the amount of variability and mutation at each position in the genome for many populations of viruses. This design contains novel visualization techniques that support this specific class of analysis while addressing the issues of data aggregation, confidence visualization, and interaction support that arise when making use of large amounts of sequence data with variable uncertainty. These techniques generalize to a wide class of visualization problems where confidence is not known a priori, and aggregation in multiple directions is necessary.

The time series alignment analysis tool Tiala allows one to align multiple time series experiments and to visually explore the aligned expression profiles. A two- and three-dimensional visualization strategy was implemented that is especially designed to enhance the display of multiple aligned time series expression profiles.

Tiala is available as a part of the microarray data analysis software Mayday. Mayday itself is open source software distributed under the terms of the GNU General Public License. It is available from http://it.inf.uni-tuebingen.de/?page_id=248.

This is a novel and effective method for visualizing probabilistic tractograms within their anatomical context. This illustrative rendering technique, called fiber stippling, is inspired by visualization standards as found in anatomical textbooks. These illustrations typically show slice-based projections of fiber pathways and are typically hand-drawn. Applying the automatized technique to diffusion tractography, it is possible to demonstrate its expressiveness and intuitive usability as well as a more objective way to present white-matter structure in the human brain.

FluoRender is an interactive tool for neurobiologists to visualize confocal microscopy data in their research. Multiple channels, detailed three-dimensional structures, and time-dependent sequences are the three major features of confocal microscopy data. With these features and usability in mind, we designed and engineered our system, which is now a free package for public download. We present the visualization pipeline and main features of our system for 3D/4D multi-channel confocal data visualization. Our system supports different input formats commonly seen for confocal microscopy. By minimizing pre-processing and optimizing data reading codes, it can read 3D/4D data with minimal latency. It has easy-to-use parameters for volume rendering effects, which are adjusted with real-time speed. It uses several image post-processing methods for detail enhancement, which are applied after volumetric data are rendered, and thus their adjustments are real-time even for 4D sequences. For multi-channel data, our system supports three different blending modes and channel grouping. Users can easily change all the settings and emphasize the most important features.

By applying gradient vector flow analysis to the MSA data, it is possible to extract and visually emphasize conservations and other patterns that are relevant during the MSA exploration process. In contrast to the traditional visual representation of MSAs, which exploits color-coded tables, the proposed visual metaphor allows us to provide an overview of large MSAs as well as to highlight global patterns, outliers, and data distributions.

PresentaBALL is a presentation framework which uses established web technology standards to provide a freely configurable browser-based interface into the extensive modeling and visualization capabilities of the Biochemical Algorithms Library (BALL). This allows easy yet powerful dissemination of structure based research results at conferences or trade fairs, the preparation of lectures, or the development of massive open online courses (MOOCs)

The web interface is embedded into BALL's graphical frontend BALLView, and provides complete, interactive access to the loaded molecular data.

PresentaBALL enables researchers in biology with basic knowledge in HTML, JavaScript, or Python to easily setup academic tutorials, demonstrations, or scientific presentations and lectures with 3D structure content and interactive workflows. Owing to its flexible design, other modern forms of teaching and presentation, such as massive open online courses (MOOC) can also use PresentaBALL as their core component.

PresentaBALL is licensed under the GNU Public License (GPL) and will be made available in BALL/BALLView, starting with the upcoming release.

rNAV (for rna NAVigator) is a tool for the visual exploration and analysis of bacterial sRNA-mediated regulatory networks. rNAV has been designed to help bioinformaticians and biologists to identify, from lists of thousands of predictions, pertinent and reasonable sRNA target candidates for carrying out experimental validations.

We now propose an automatic mRNAs extraction from a simple genbank or embl genome file. Moreover, rNAV now features an automatic annotation enrichement plugin powered by DAVID statistical enrichement tool.
rNAV algorithms can be gathered into pipelines which can then be saved and reused over several sessions. To support exploration awareness, rNAV also provides an exploration tree view that allows to navigate through the steps of the analysis but also to select the sub-networks to visualize and compare. These comparisons are facilitated by the integration of multiple and fully linked views.

This framework had been used to analyse various real biological data including several mycoplasma strains.

Some key features :

• Automatic functional annotation with DAVID[1] webservice (Database for Annotation, Visualization and Integrated Discovery)
• Annotation clustering : cluster redudant annotations
• Simultaneous visual analysis of annotations AND positions of several targets with enhanced neighbors tool.
• Visual analysis of sRNA regulatory networks at genome scale
• Automatic mRNA extraction from genome files (genbank or embl) with user defined region
• Integration of two interactions prediction tools : ssearch and IntaRNA[2]
• Position clustering : cluster targets from their interaction positions
• Multiple and fully linked view
• Exploration tree view
• Labels can display many input information like P-value, Similarity or interaction energy