LR_PPI – large-scale Prediction of Human protein-protein interaction

LR_PPI

:: DESCRIPTION

LR_PPI is a web server for large-scale prediction of human protein-protein interaction from amino acid sequence based on latent topic feature

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

J Proteome Res. 2010 Oct 1;9(10):4992-5001. doi: 10.1021/pr100618t.
Large-scale prediction of human protein-protein interactions from amino acid sequence based on latent topic features.
Pan XY1, Zhang YN, Shen HB.

NAViGaTOR 3.0 – Visualize and Analyze Protein-protein Interaction Networks.

NAViGaTOR 3.0

:: DESCRIPTION

NAViGaTOR (Network Analysis, Visualization, & Graphing TORonto ) is a software package for visualizing and analyzing protein-protein interaction networks.NAViGaTOR can query OPHID / I2D – online databases of interaction data – and display networks in 2D or 3D. To improve scalability and performance, NAViGaTOR combines Java with OpenGL to provide a 2D/3D visualization system on multiple hardware platforms. NAViGaTOR also provides analytical capabilities and supports standard import and export formats such as GO and the Proteomics Standards Initiative (PSI).

::DEVELOPER

Jurisica Lab of the Ontario Cancer Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 NAViGaTOR

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Dec 15;25(24):3327-9. doi: 10.1093/bioinformatics/btp595. Epub 2009 Oct 16.
NAViGaTOR: Network Analysis, Visualization and Graphing Toronto.
Brown KR1, Otasek D, Ali M, McGuffin MJ, Xie W, Devani B, Toch IL, Jurisica I.

Djebbari, A., Ali, M., Otasek, D., Kotlyar. M., Fortney, K., Wong, S., Hrvojic, A. and Jurisica, I.
NAViGaTOR: Scalable and Interactive Navigation and Analysis of Large Graphs.
Internet Mathematics, 7(4):314-347, 2011

mirConnX – Analysis of mRNA and microRNA (miRNA) Gene Regulatory Networks

mirConnX

:: DESCRIPTION

mirConnX is a user-friendly web interface for inferring, displaying and parsing mRNA and microRNA (miRNA) gene regulatory networks. mirConnX combines sequence information, and computational predictions with gene expression data analysis to create a disease-specific, genome-wide regulatory network.

::DEVELOPER

Benos Lab

 SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W416-23. doi: 10.1093/nar/gkr276. Epub 2011 May 10.
mirConnX: condition-specific mRNA-microRNA network integrator.
Huang GT, Athanassiou C, Benos PV.

sLDA – Sparse Linear Discriminant Analysis

sLDA

:: DESCRIPTION

sLDA (Sparse Linear Discriminant Analysis) is a software for testing the significance of Gene Pathways when signal is relatively weak. Also included is general code for running two-group L1 penalized linear discriminant analysis.

::DEVELOPER

Michael Wu’s Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • R
:: DOWNLOAD

 sLDA

:: MORE INFORMATION

Citation

Wu, M.C., Zhang, L., Wang, Z., Christiani, D.C., Lin, X. (2009).
Sparse linear discriminant analysis for simultaneous gene set/pathway significance test and gene selection“.
Bioinformatics, 25,1145-1151.

ALSYSTA 1.07 Beta – Analysis of different Aspects of Biological Systems

ALSYSTA 1.07 Beta

:: DESCRIPTION

ALSYSTA (BioSystAnSe) is a software suite that includes a series of tools for the analysis of different aspects of biological systems, such as the expression phenotype and the metabolic flux profiles of cells, as well as various tools to search web based databases.

::DEVELOPER

The Bioinformatics & Metabolic Engineering Laboratory, Massachusetts Institute of Technology

:: SCREENSHOTS

ALSYSTA

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 ALSYSTA

:: MORE INFORMATION

GenSSI 2.0 – Structural Identifiability Analysis of Biological Models

GenSSI 2.0

:: DESCRIPTION

GenSSI (Generating Series for testing Structural Identifiability) is a software which enables non-expert users to carry out  structural identifiability analysis of biological models analysis.

::DEVELOPER

(Bio)Process Engineering group, IIM-CSIC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux /MacOsX
  • Matlab

:: DOWNLOAD

 GenSSI

:: MORE INFORMATION

Citation:

Chis, O., Banga, J.R., Balsa-Canto, E. (2011).
GenSSI: a software toolbox for structural identifiability analysis of biological models,
Bioinformatics, doi: 10.1093/bioinformatics/btr431.

CRNreals v2 – Distinguishability Analysis of Biochemical Reaction Networks

CRNreals v2

:: DESCRIPTION

CRNreals is a toolbox for distinguishability and identifiability analysis of biochemical reaction networks.

::DEVELOPER

(Bio)Process Engineering group, IIM-CSIC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Matlab

:: DOWNLOAD

 CRNreals

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Jun 1;28(11):1549-50. doi: 10.1093/bioinformatics/bts171. Epub 2012 Apr 6.
CRNreals: a toolbox for distinguishability and identifiability analysis of biochemical reaction networks.
Szederkényi G1, Banga JR, Alonso AA.

DOTcvpSB 2010_E4 – Matlab Toolbox for Dynamic Optimization in Systems Biology

DOTcvpSB 2010_E4

:: DESCRIPTION

DOTcvpSB is a software toolbox which uses the CVP approach for handling continuous and mixed integer DO problems. DOTcvpSB has been successfully applied to several problems in systems biology and bioprocess engineering. The toolbox is written in MATLAB and provides an easy to use environment while maintaining a quite good performance. DOTcvpSB is designed for the Windows operating systems. The toolbox also contains a function for importing SBML models.

::DEVELOPER

(Bio)Process Engineering group, IIM-CSIC

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Matlab

:: DOWNLOAD

 DOTcvpSB

:: MORE INFORMATION

Citation:

T. Hirmajer, E. Balsa-Canto and J. R. Banga:
DOTcvpSB, a software toolbox for dynamic optimization in systems biology.
BMC Bioinformatics 2009, 10:199

AMIGO2 R2019b – Advanced Modelling and Identification using Global Optimization

AMIGO2 R2019b

:: DESCRIPTION

AMIGO is a multi-platform (Windows and Linux) toolbox which covers all the steps of the iterative identification procedure: local and global sensitivity analysis, local and global ranking of parameters, parameter estimation, identifiability analysis and optimal experimental design.

::DEVELOPER

(Bio)Process Engineering group, IIM-CSIC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux /MacOsX
  • Matlab

:: DOWNLOAD

 AMIGO

:: MORE INFORMATION

Citation:

AMIGO2, a toolbox for dynamic modeling, optimization and control in systems biology.
Balsa-Canto E, Henriques D, Gabor A, Banga JR.
Bioinformatics. 2016 Jul 4. pii: btw411.

Bioinformatics (2011)doi: 10.1093/bioinformatics/btr370 First published online: June 17, 2011
AMIGO, a toolbox for Advanced Model Identification in systems biology using Global Optimization
Eva Balsa-Canto and Julio R. Banga

SensSB 20120926 – Development and Sensitivity Analysis of Systems Biology Models

SensSB 20120926

:: DESCRIPTION

SensSB (Sensitivity Analysis for Systems Biology) is an easy to use, MATLAB-based software toolbox, which integrates several local and global sensitivity methods that can be applied to a wide variety of biological models.

::DEVELOPER

(Bio)Process Engineering group, IIM-CSIC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Matlab

:: DOWNLOAD

SensSB

:: MORE INFORMATION

Citation:

M. Rodriguez-Fernandez and J. R. Banga (2010)
SensSB: a software toolbox for the development and sensitivity analysis of systems biology models.
Bioinformatics 26(13):1675-1676