Table 1.
Summary of visualization programs for multidimensional data that can be applied to user-provided datasets. For each tool reviewed, we evaluated a number of features organized by the various categories: General Information, Licensing. PoC = Proof of Concept.
| Category | Item |
Freely available |
Commercial |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Name of the platform | cBioPortal | iGPSe | Igloo-Plot | tranSMART | G-DOC Plu | Data-cube-based model supporting heterogeneous data | Papilio | Caleydo Domino | Qlucore Omics Explorer | Oracle Health Sciences Translational Research Center | OmicsOffice® powered by TIBCO Spotfire | |
| General information | PMID or article reference | 22588877 | 25000928 | 24444495 | 25717408 | 27130330 | 25248201 | (Steenwijk et al. 2010) [8] | 26356916 | NA | NA | NA |
| Initial release year | 2012 | 2014 | 2014 | 2012 | 2016 | 2014 | 2010 | 2014 | 2007 | 2011 | 1996 | |
| URL | cbioportal.org | osumo.org/ #process | metagenomics.atc. tcs.com/IglooPlot | transmart foundation.org | gdoc.george town.edu | NA | NA | caleydo.org/ tools/domino | qlucore.com | oracle.com/us/ industries/ health-sciences/ hs-cohort- explorerds- 1672120.pdf | cambridge soft.com/ ensemble/ spotfire/ OmicsOffice/ | |
| Reference | github.com/cBioPortal/ cbioportal | osumo.org | metagenomics. atc.tcs.com/ IglooPlot/walk through.html | wiki.transmart foundation.org | NA | NA | NA | github.com/ Caleydo/org. caleydo.view. domino | qlucore.com/ documentation | oracle.com/ us/industries/ health-sciences/ hs-cohort -explorerds- 1672120.pdf | scistore. cambridgesoft.com/ ScistoreProduct Page.aspx ?ItemID=8541 | |
| Data housing | MySQL | apache server | Internal memory from loaded data | any Relational Database Management System (e.g. Oracle, PostgreSQL) | Oracle | Internal c ++ data structures from data | SQLite | Internal memory from loaded data | Internal memory from loaded data | SAS Cloud or on premis (MySQL) | Cloud or on premis (Oracle or SQL) | |
| Principle frontend and/or backend programming languages | Java and Spring in backend, Javascript with libraries such as D3 and JQuery in front end | Javascript, d3.js, R | perkTk | Grails, Java | Groovy & Grails, Adobe Flex, JavaScript | C ++, using a framework based on opengl and qt4 | C ++ | Java, OpenGL/JOGL | C ++ | Oracle ADF/Java EE on the front end, with hooks into Oracle BI. The backend is Oracle stack data and middle tiers so Oracle DB, Oracle BIFS, Oracle Weblogic in a Java 2EE environment | .NET/C# with code in Iron Python, R, and in some cases C/C ++ | |
| Current status | In use | PoC | In use | In use | In use | PoC | PoC | In use | In use | In use | In use | |
| Dedicated domain | Exploration of largescale cancer genomics sets | Integrative genomics based cancer patient stratification | General visualization of multidimensional datasets | Hypothesis generation, hypothesis validation, and cohort discovery in translational research | Integrative analysis of various data types to uncover disease mechanisms | Exploration of heterogeneous data in clinical cohorts | Exploration of heterogeneous data in clinical cohorts | General visualization of multidimensional datasets | Visualization, exploration, and analysis of bioinformatics data | Data agregation, integration, data cleaning for clinical cohort studies | Start to end genomics data analysis | |
| Licensing | Software availability | Opensource (GNU Affero General Public License, version 3) | Open source | Open source | Open source | Open source | NA | NA | Open-source (BSD License) | Fee-based | Fee-based | Fee-based |
| Client-side interface | Web browser | Web browser | Stand-alone for linux or windows | Web browser | Web browser | Stand-alone stand-alone (Trolltech Qt interface) | Web browser or standalone | Stand-alone | Web browser | Stand-alone | ||
| User mailing list or support | Yes | No | No | Yes | Yes | No | No | No | Yes | Yes | Yes | |