Tag: Exploring

HYPERSPACE – Exploring Parameter Spaces in Systems Biology

HYPERSPACE

:: DESCRIPTION

HYPERSPACE is a matlab package to sample high-dimensional parameter spaces in dynamical systems models of regulatory circuits in cell and developmental biology.

::DEVELOPER

Andreas Wagner Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Matlab

:: DOWNLOAD

 HYPERSPACE

:: MORE INFORMATION

Citation:

Zamora-Sillero, E., Hafner, M., Ibig, A., Stelling, J., Wagner, A.
Efficient characterization of high-dimensional parameter spaces for systems biology.
BMC Systems Biology 2011, 5:142 doi:10.1186/1752-0509-5-142

VESPA 1.1.1 – Visual Analytics Platform for Exploring Proteogenomics data

VESPA 1.1.1

:: DESCRIPTION

VESPA (Visual Exploration and Statistics to Promote Annotation) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates.

::DEVELOPER

Computational Biology & Bioinformatics, Pacific Northwest National Laboratory

:: SCREENSHOTS

VESPA

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 VESPA

:: MORE INFORMATION

Citation

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.
Peterson ES, McCue LA, Schrimpe-Rutledge AC, Jensen JL, Walker H, Kobold MA, Webb SR, Payne SH, Ansong C, Adkins JN, Cannon WR, Webb-Robertson BJ.
BMC Genomics. 2012 Apr 5;13:131. doi: 10.1186/1471-2164-13-131.

NaviCell – Web Tool for Exploring large maps of Molecular Interactions

NaviCell

:: DESCRIPTION

NaviCell is a web tool for exploring large maps of molecular interactions created in CellDesigner. The tool is characterized by a unique combination of three essential features: efficient map navigation based on Google maps engine, semantic zooming for viewing different levels of details on the map and an integrated blog for collecting the community curation feedbacks.

::DEVELOPER

NaviCell Team

:: SCREENSHOTS

:: REQUIREMENTS

  • any web browser
:: DOWNLOAD

  no (only web service)

:: MORE INFORMATION

Citation

BMC Syst Biol. 2013 Oct 7;7:100. doi: 10.1186/1752-0509-7-100.
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps.
Kuperstein I1, Cohen DP, Pook S, Viara E, Calzone L, Barillot E, Zinovyev A.

VIPER 1.01 – Exploring and Cleaning Inheritance Inconsistencies within Pedigree/Genotype Data

VIPER 1.01

:: DESCRIPTION

VIPER  (Visual Pedigree Explorer) combines an improved ResSpecies algorithm for genotype inheritance checking and inference with a novel space-efficient visualisation of pedigree structure in a desktop tool for exploring then cleaning data errors in pedigree/genotype datasets.

::DEVELOPER

Roslin Bioinformatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • Java

:: DOWNLOAD

 VIPER

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012;13 Suppl 8:S5. doi: 10.1186/1471-2105-13-S8-S5. Epub 2012 May 18.
VIPER: a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees.
Paterson T, Graham M, Kennedy J, Law A.

Semantic Body Browser 1.6.2 – Graphically Exploring an Organism’s Body

Semantic Body Browser 1.6.2

:: DESCRIPTION

The Semantic Body Browser (SBB) is a web application for intuitively exploring the body of an organism from the organ to the sub-cellular level and visualising expression profiles by means of semantically annotated illustrations. It is used to comprehend biological and medical data related to the different body structures while relying on the strong pattern recognition capabilities of human users.

::DEVELOPER

SBB team

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 Semantic Body Browser

:: MORE INFORMATION

Citation

Semantic Body Browser: Graphical exploration of an organism and spatially resolved expression data visualisation.
Lekschas F, Stachelscheid H, Seltmann S, Kurtz A.
Bioinformatics. 2014 Oct 24. pii: btu707.

GenomeBrowse 3.0.0 – Free Genome Browser for Exploring Sequencing Pile-up

GenomeBrowse 3.0.0

:: DESCRIPTION

GenomeBrowse raises the bar on the experience of exploring and finding key insights into your genomic data. Every component has been designed and optimized to give you a user-experience beyond imagination.

::DEVELOPER

Golden Helix, Inc

:: SCREENSHOTS

::REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 GenomeBrowse

:: MORE INFORMATION

PICA Browser 0.9 – Integrating and Exploring Multiple Connected Datasets

PICA Browser 0.9

:: DESCRIPTION

The PICA Browser tool is a cross-platform Java application for visually exploring a soft clustering produced by integrating data from multiple connected views. The application highlights the contributions of each view and the frequency of appearance of the clusters (i.e. reliability), with the aim of providing insight into the provenance of the cluster relationships in the model. Parallel Integration Clustering Algorithm (PICA) is a new data integration approach for performing multi-view clustering in domains where two or more related datasets are available.

::DEVELOPER

the Machine Learning Group (MLG)

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /Mac OsX
  • Java

:: DOWNLOAD

 PICA Browser

:: MORE INFORMATION

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