Tag: Environment

VLDP – Analysing Protein Structures in their Environment

VLDP

:: DESCRIPTION

VLDP ( Voronoi Laguerre Delaunay Protein) webserver is designed to determine protein contacts, accessibility and residue volume using Laguerre diagram.

::DEVELOPER

the DSIMB bioinformatic group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

VLDP web server: a powerful geometric tool for analysing protein structures in their environment.
Esque J, Léonard S, de Brevern AG, Oguey C.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W373-8. doi: 10.1093/nar/gkt509.

GEB – Genome Environment Browser

GEB

:: DESCRIPTION

GEB is a Java application developed to provide a dynamic graphical interface to visualise the distribution of genome features and chromosome-wide experimental data in high resolution.

::DEVELOPER

the Bioinformatics Support Service, Centre for Bioinformatics, Imperial College London, UK and the MRC Clinical Sciences Centre, London, UK

:: SCREENSHOTS

GEB

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Java
  • MySQL 

:: DOWNLOAD

 GEB

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2008 Nov 27;9:501. doi: 10.1186/1471-2105-9-501.
Genome Environment Browser (GEB): a dynamic browser for visualising high-throughput experimental data in the context of genome features.
Huntley D, Tang YA, Nesterova TB, Butcher S, Brockdorff N.

FLAME – Flexible Large-scale Agent Modelling Environment

FLAME

:: DESCRIPTION

FLAME is a generic agent-based modelling system which can be used to development applications in many areas.

::DEVELOPER

FLAME Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

 FLAME

:: MORE INFORMATION

Citation

Brief Bioinform. 2010 May;11(3):334-47. doi: 10.1093/bib/bbp073. Epub 2010 Feb 1.
High performance cellular level agent-based simulation with FLAME for the GPU.
Richmond P, Walker D, Coakley S, Romano D.

TAMEE 1.1 – Tissue Array Management and Evaluation Environment

TAMEE 1.1

:: DESCRIPTION

TAMEE is a web-based database application for the management and analysis of data resulting from the production and experimental use of TMAs. In addition to production and experimental parameters images generated during the different stages of the TMA workflow are stored. Parameter values are based on structured classifications to ensure consistent database content which is the basis to yield biologically meaningful results in subsequent data analysis. Therefore existing public classifications are used and new controlled vocabularies have been defined in the context of the application. Tissue cores in the images of stained tissue sections are automatically located and extracted and can be automatically evaluated with a set of predefined analysis algorithms. Additional algorithms for the evaluation of tissue cores can be added to the application via a plug-in interface. Downstream analysis of the results is facilitated via a set of standard queries. More complex queries can be formulated with the help of a flexible query generator.

::DEVELOPER

Genomics & Bioinformatics Graz, Graz University of Technology

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  •  MySQL

:: DOWNLOAD

 TAMEE

:: MORE INFORMATION

Citation

Thallinger GG, Baumgartner K, Pirklbauer M, Uray M, Pauritsch E, Mehes G, Buck CR, Zatloukal K, Trajanoski Z.
TAMEE: data management and analysis for tissue microarrays.
BMC Bioinformatics. 2007. 8:81.

MDLab – Molecular Dynamics Simulation Prototyping Environment

MDLab

:: DESCRIPTION

MDLab (MDL) is a user-friendly environment for prototyping molecular dynamics simulation protocols and numerical methods, built with the scripting language Python. Our goal is to provide developers of propagator scheme and force computation algorithms with (1) mathematical syntax which enables them to develop these methods using array and matrix operations, and (2) a set of domain-specific libraries which enable testing and debugging of these methods using real biological systems.

::DEVELOPER

Izaguirre Lab at Notre Dame

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MDLab

:: MORE INFORMATION

Citation

T. Cickovski, S. Chatterjee, A. Wenger, C. Sweet and J. A. Izaguirre.
MDLab: A Molecular Dynamics Simulation Prototyping Environment.
J Comput Chem. 2010 May;31(7):1345-56.