Lynx v3.0 – Integrated Systems Biology Platform

Lynx v3.0

:: DESCRIPTION

Lynx is a database and knowledge extraction engine for integrative medicine

::DEVELOPER

Somaye Hashemifar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation:

Sulakhe D, Xie B, Taylor A, D’Souza M, Balasubramanian S, Hashemifar S, White S, Dave UJ, Agam G, Xu J, Wang S, Gilliam TC, Maltsev N.
Lynx: a knowledge base and an analytical workbench for integrative medicine.
Nucleic Acids Res. 2016 Jan 4;44(D1):D882-7. doi: 10.1093/nar/gkv1257. Epub 2015 Nov 20. PMID: 26590263; PMCID: PMC4702889.

GenomeVIP v1.2.1 – Cloud based Genome Variant Investigation Platform

GenomeVIP v1.2.1

:: DESCRIPTION

GenomeVIP is a web application platform for performing variant discovery on Amazon’s Web Service (AWS) cloud or on local high-performance computing clusters.

::DEVELOPER

Ding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

GenomeVIP

:: MORE INFORMATION

Citation

Mashl RJ, Scott AD, Huang KL, Wyczalkowski MA, Yoon CJ, Niu B, DeNardo E, Yellapantula VD, Handsaker RE, Chen K, Koboldt DC, Ye K, Feny? D, Raphael BJ, Wendl MC, Ding L.
GenomeVIP: a cloud platform for genomic variant discovery and interpretation.
Genome Res. 2017 Aug;27(8):1450-1459. doi: 10.1101/gr.211656.116. Epub 2017 May 18. PMID: 28522612; PMCID: PMC5538560.

Icy 2.2.0.0 – Open Community Platform for Bioimage Informatics

Icy 2.2.0.0

:: DESCRIPTION

Icy provides the software resources to visualize, annotate and quantify bioimaging data.

:: DEVELOPER

the Quantitative Image Analysis Unit at Institut Pasteur

:: SCREENSHOTS

Icy

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

 Icy

:: MORE INFORMATION

Citation

de Chaumont, F. et al. (2012)
Icy: an open bioimage informatics platform for extended reproducible research,
Nature Methods, 9, pp. 690-696

OpenSPIM 20150427 – Open-access Light-sheet Microscopy Platform

OpenSPIM 20150427

:: DESCRIPTION

OpenSPIM is an Open Access platform for applying and enhancing Selective Plane Illumination Microscopy (SPIM).

::DEVELOPER

OpenSPIM team

:: SCREENSHOTS

OpenSPIM

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 OpenSPIM

:: MORE INFORMATION

Citation

Nat Methods. 2013 Jul;10(7):598-9. doi: 10.1038/nmeth.2507. Epub 2013 Jun 9.
OpenSPIM: an open-access light-sheet microscopy platform.
Pitrone PG, Schindelin J, Stuyvenberg L, Preibisch S, Weber M, Eliceiri KW, Huisken J, Tomancak P.

VSDMIP pre-2.0 – Automated Structure & Ligand-based Virtual Screening Platform

VSDMIP pre-2.0

:: DESCRIPTION

VSDMIP (Virtual Screening Data Management on an Integrated Platform)  is divided in two parts: programs which actually do things (local packages) and program which translate those things to the database (cluster packages and cartridge).

::DEVELOPER

Unidad de Bioinformatica CBMSO

:: SCREENSHOTS

VSDMIP

:: REQUIREMENTS

  • Linux / WIndows
  • Python
  • PyMOL

:: DOWNLOAD

    VSDMIP

:: MORE INFORMATION

Citation

VSDMIP 1.5: an automated structure- and ligand-based virtual screening platform with a PyMOL graphical user interface.
Cabrera áC, Gil-Redondo R, Perona A, Gago F, Morreale A.
J Comput Aided Mol Des. 2011 Sep;25(9):813-24. doi: 10.1007/s10822-011-9465-6.

Cytoscape 3.8.2 – Platform for Complex-Network Analysis & Visualization

Cytoscape 3.8.2

:: DESCRIPTION

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.

Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization.

::DEVELOPER

Cytoscape Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

Cytoscape

:: MORE INFORMATION

Citation:

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T.
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Genome Research 2003 Nov; 13(11):2498-504

Seqcrawler 0.6.2 – Biological Data Indexing and Browsing Platform

Seqcrawler 0.6.2

:: DESCRIPTION

Seqcrawler provides a complete open source search and store solution for labs or platforms needing to manage large amount of data/meta-data with a flexible and customizable web interface.

::DEVELOPER

Seqcrawler team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

 Seqcrawler

:: MORE INFORMATION

Citation

Seqcrawler: biological data indexing and browsing platform.
Sallou O, Bretaudeau A, Roult A.
BMC Bioinformatics. 2012 Jul 24;13:175. doi: 10.1186/1471-2105-13-175.

WebLab 1.2 – Multifunctional Bioinformatics Analysis Platform

WebLab 1.2

:: DESCRIPTION

WebLab is a multifunctional bioinformatics analysis platform integrating diversified tools with unified, user-friendly web interface. However, WebLab is not a mere bioinformatics toolbox, we also offer powerful data management function, group strategy and knowledge sharing mechanism, which will bring considerable advance of efficiency for both wet bench and in silico scientists working in biomedicine community.

::DEVELOPER

Gao Lab, Peking University.

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 WebLab

:: MORE INFORMATION

Citation

Liu, X., Wu, J., Wang, J., Liu, X., Zhao, S., Li, Z., Kong, L., Gu, X., Luo, J. and Gao, G. (2009)
WebLab: a data-centric, knowledge-sharing bioinformatic platform.
Nucleic Acids Res.2009) doi: 10.1093/nar/gkp428

Cytobank – Analytics Platform for Community Cytometry Data Analysis

Cytobank

:: DESCRIPTION

Cytobank is a platform that allows researchers to annotate, analyze, and share results along with the underlying single-cell data.

::DEVELOPER

Cytobank Inc.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Curr Top Microbiol Immunol. 2014;377:127-57. doi: 10.1007/82_2014_364.
Cytobank: providing an analytics platform for community cytometry data analysis and collaboration.
Chen TJ1, Kotecha N.

BiGG Models 1.6 – A Platform for integrating, standardizing and sharing Genome-scale Models

BiGG Models 1.6

:: DESCRIPTION

BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions.

::DEVELOPER

the Systems Biology Research Group at theUniversity of California, San Diego.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web server
  • Python

:: DOWNLOAD

  BiGG Models

:: MORE INFORMATION

Citation:

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.
King ZA, Lu J, Dräger A, Miller P, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, Lewis NE.
Nucleic Acids Res. 2015 Oct 17. pii: gkv1049.