Tag: Databases

Molgenis 9.1.0 – Generate Databases for Life Science Experiments

Molgenis 9.1.0

:: DESCRIPTION

MOLGENIS ( MOLecular GENetics Information Systems) is an collaborative open source project on a mission to generate great software infrastructure for life science research. Each app in the MOLGENIS family comes with rich data management interface and plug-in integration of analysis tools in R, Java and web services. The MOLGENIS platform allows you to automatically generate rich database software to your specifications, including web user interfaces to manage and query your data, various database back ends to store your data, and programmatic interfaces to the R language and web services. You tell MOLGENIS what to generate using an data model and user interface model described in XML; at the push of a button MOLGENIS translates this model into SQL, Java and R program files. Also documentation is generated. While the standard generated MOLGENIS is sufficient for most data management needs, MOLGENIS also allows you to plug in handwritten software components that build on the auto-generated software platform.

::DEVELOPER

Molgenis team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Molgenis 

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S12.
The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.
Swertz MA, Dijkstra M, Adamusiak T, van der Velde JK, Kanterakis A, Roos ET, Lops J, Thorisson GA, Arends D, Byelas G, Muilu J, Brookes AJ, de Brock EO, Jansen RC, Parkinson H.

Make2D-DB II 3.10.2 – Gel Electrophoresis 2D-PAGE Databases

Make2D-DB II 3.10.2

:: DESCRIPTION

Make2D-DB II is an environment to create, convert, publish, interconnect and keep up-to-date two-dimensional gel electrophoresis (2D-PAGE) databases.  It converts data from various formats into a relational format. The tool offers the possibility to automatically update data related to numerous external data resources in a highly consistent manner. It is also possible with this tool to dynamically interconnect several remote databases or projects to form a virtual global database accessible from one single entry point.

::DEVELOPER

The SIB Swiss Institute of Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Make2D-DB II 

:: MORE INFORMATION

Citation

Mostaguir K, Hoogland C, Binz PA, Appel RD.
The Make 2D-DB II package: conversion of federated two-dimensional gel electrophoresis databases into a relational format and interconnection of distributed databases.
Proteomics. 2003 Aug;3(8):1441-4.

DisGeNET 6.0 / DisGeNET2R 0.99.0 – Query and Analyze a Network representation of human Gene-disease databases

DisGeNET 6.0 / DisGeNET2R 0.99.0

:: DESCRIPTION

DisGeNET is a plugin for Cytoscape to query and analyze a network representation of human gene-disease databases. For this purpose, we have developed a new gene-disease database integrating data from several public sources. DisGeNET allows user-friendly access to our database, which includes queries restricted to (i) the original data source, (ii) the association type, (iii) the disorder class of interest and (iv) specific diseases, respectively genes. It represents gene-disease associations in terms of bipartite graphs and additionally provides gene centric and disease centric views of the data. It assists the user in the interpretation and exploration of human complex diseases with respect to their genetic origin by a variety of built-in functions. Moreover, DisGeNET permits multicoloring of nodes (genes/diseases) according to their disease classes for expedient visualization

DisGeNET2R contains a series of functions to retrieve and expand gene-disease, and variant-disease data, and to perform mappings of several biomedical vocabularies.

::DEVELOPER

The Integrative Biomedical Informatics group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Java / R
  • Cytoscape

:: DOWNLOAD

  DisGeNET / DisGeNET2R

:: MORE INFORMATION

Citation

The DisGeNET knowledge platform for disease genomics: 2019 update.
Piñero J, Ramírez-Anguita JM, Saüch-Pitarch J, Ronzano F, Centeno E, Sanz F, Furlong LI.
Nucleic Acids Res. 2019 Nov 4. pii: gkz1021. doi: 10.1093/nar/gkz1021.

Anna Bauer-Mehren; Michael Rautschka; Ferran Sanz; Laura I. Furlong:
DisGeNET – a Cytoscape plugin to visualize, integrate, search and analyze gene-disease networks.
Bioinformatics, Vol. 26, No. 22. (15 November 2010), pp. 2924-2926.

Exit mobile version