HBN – Integration of Relational and Hierarchical Network Information for Protein Function Prediction

HBN

:: DESCRIPTION

HBN is a software of hierarchical binomial neighborhood (HBN) method for Protein Function Prediction

::DEVELOPER

Eric D. Kolaczyk

:: SCREENSHOTS

n/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Matlab

:: DOWNLOAD

 HBN

:: MORE INFORMATION

Citation

Jiang, X., Nariai, N., Steffen, M., Kasif, S., and Kolaczyk, E.D. (2007).
Integration of Relational and Hierarchical Network Information for Protein Function Prediction.
BMC Bioinformatics, 9:350.

Situs 3.1r2 – Integration of Multi-Resolution Structures

Situs 3.1r2

:: DESCRIPTION

Situs is a program package for the modeling of atomic resolution structures into low-resolution density maps e.g. from electron microscopy, tomography, or small angle X-ray scattering.

::DEVELOPER

Willy Wriggers

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Situs

:: MORE INFORMATION

Citation

Willy Wriggers.
Using Situs for the Integration of Multi-Resolution Structures.
Biophysical Reviews, 2010, Vol. 2, pp. 21-27.

DynaMIT 1.1.5 – Dynamic Motif Integration Toolkit

DynaMIT 1.1.5

:: DESCRIPTION

DynaMIT is a flexible platform for sequence and structure motifs integration, providing the means to execute multiple motif search tools, integrate their output and display the obtained results in a plethora of different ways.

::DEVELOPER

Laboratory of Translational Genomics , CIBIO

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Python

:: DOWNLOAD

 DynaMIT

:: MORE INFORMATION

Citation

DynaMIT: the dynamic motif integration toolkit.
Dassi E, Quattrone A.
Nucleic Acids Res. 2015 Aug 7. pii: gkv807

RABIT – Regression Analysis with Background InTegration

RABIT

:: DESCRIPTION

RABIT is a very efficient feature selection algorithm. It was applied to find tumor associated regulators in diverse cancer types.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RABIT

:: MORE INFORMATION

Citation

Inference of transcriptional regulation in cancers.
Jiang P, Freedman ML, Liu JS, Liu XS.
Proc Natl Acad Sci U S A. 2015 Jun 23;112(25):7731-6. doi: 10.1073/pnas.1424272112.

Pathview 1.24.0 – R package for Pathway based Data Integration and Visualization

Pathview 1.24.0

:: DESCRIPTION

Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs.

::DEVELOPER

Weijun Luo <luo_weijun at yahoo dot com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 Pathview

:: MORE INFORMATION

Citation

Pathview: an R/Bioconductor package for pathway-based data integration and visualization.
Luo W, Brouwer C.
Bioinformatics. 2013 Jul 15;29(14):1830-1. doi: 10.1093/bioinformatics/btt285.

Mobyle 1.5.5 – Integration of Bioinformatics Software and Databanks

Mobyle 1.5.5

:: DESCRIPTION

Mobyle is a framework and web portal specifically aimed at the integration of bioinformatics software and databanks., Mobyle provides a flexible and usable Web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce analyses and to combine tools using a hierarchical typing system. Mobyle offers invocation of services distributed over remote Mobyle servers, thus enabling a federated network of curated bioinformatics portals without the user having to learn complex concepts or to install sophisticated software.

Mobyle Online

::DEVELOPER

 Mobyle Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Mobyle

:: MORE INFORMATION

Citation:

Bioinformatics. 2009 Nov 15;25(22):3005-11. Epub 2009 Aug 17.
Mobyle: a new full web bioinformatics framework.
Néron B, Ménager H, Maufrais C, Joly N, Maupetit J, Letort S, Carrere S, Tuffery P, Letondal C.

SePIA – RNA Sequence Processing, Integration, and Analysis

SePIA

:: DESCRIPTION

SePIA is a comprehensive RNA Sequencing workflow standardizing Processing, Integration, and Analysis of large-scale sequencing data. It provides a systematic, pipeline architecture to manage, individually analyze, and integrate both small-RNA and RNA data.

::DEVELOPER

Hautaniemi Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SePIA

:: MORE INFORMATION

Citation

SePIA: RNA and small RNA sequence processing, integration, and analysis.
Icay K, Chen P, Cervera A, Rantanen V, Lehtonen R, Hautaniemi S.
BioData Min. 2016 May 20;9:20. doi: 10.1186/s13040-016-0099-z

mixOmics 5.2.0 – Omics Data Integration Project

mixOmics 5.2.0

:: DESCRIPTION

mixOmics analyses highly dimensional data sets: regularized Canonical Correlation Analysis (‘rCCA’) and sparse Partial Least Squares variants (‘sPLS’) to unravel relationships between two heterogeneous data sets of size (n times p) and (n times q) where the p and q variables are measured on the same samples or individuals n.

::DEVELOPER

mixOmics team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 mixOmics

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Dec 6;13:325. doi: 10.1186/1471-2105-13-325.
A novel approach for biomarker selection and the integration of repeated measures experiments from two assays.
Liquet B1, Lê Cao KA, Hocini H, Thiébaut R.

QUILTS 2.0 – Proteogenomic Data Integration tool

QUILTS 2.0

:: DESCRIPTION

QUILTS is a tools for creating sample specific protein sequence databased. It uses genomic and transcriptomic information to create comprehensive sample specific protein database that supports the identification of novel proteins, resulting from single nucleotide variants, splice variants and fusion genes.

::DEVELOPER

Laboratory of Computational Proteomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Mol Cell Proteomics. 2015 Dec 2. pii: mcp.M115.056226.
An analysis of the sensitivity of proteogenomic mapping of somatic mutations and novel splicing events in cancer.
Ruggles KV et al.

MOSFLM 7.2.1 / iMOSFLM 7.2.1 – Integration of Macromolecular Diffraction Data

MOSFLM 7.2.1 / iMOSFLM 7.2.1

:: DESCRIPTION

Mosflm is a program for integrating single crystal diffraction data from area detectors. It is assumed that the experiment was conducted using the Arndt-Wonacott oscillation method, and also that monochromatic radiation was used.

iMOSFLM is a graphical user interface to the diffraction data-integration program MOSFLM. It is designed to simplify data processing by dividing the process into a series of steps, which are normally carried out sequentially. Each step has its own display pane, allowing control over parameters that influence that step and providing graphical feedback to the user.

:: DEVELOPER

Harry Powell

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 MOSFLMiMOSFLM

:: MORE INFORMATION

Citation:

Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):48-57. Epub 2005 Dec 14.
The integration of macromolecular diffraction data.
Leslie AG.

Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):271-81. Epub 2011 Mar 18.
iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM.
Battye TG, Kontogiannis L, Johnson O, Powell HR, Leslie AG.