Tag: Integrating

FRETraj v0.2.6 – Integrating Single-molecule Spectroscopy with Molecular Dynamics

FRETraj v0.2.6

:: DESCRIPTION

FRETraj is a Python module for predicting FRET efficiencies by calculating multiple accessible-contact volumes (multi-ACV) to estimate donor and acceptor dye dynamics.

::DEVELOPER

FRETraj team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows
  • Python
  • PyMOL

:: DOWNLOAD

FRETraj

:: MORE INFORMATION

Citation

Steffen FD, Sigel RKO, Börner R.
FRETraj: Integrating single-molecule spectroscopy with molecular dynamics.
Bioinformatics. 2021 Sep 3:btab615. doi: 10.1093/bioinformatics/btab615. Epub ahead of print. PMID: 34478493.

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.

MAIA 0.5 – Integrating Genome Assemblies

MAIA 0.5

:: DESCRIPTION

MAIA (Multiple Assembly IntegrAtion) is an algorithm to integrate multiple genome assemblies. For example, assemblies originating from:
– Different runs of a de novo assembler
– Assemblies of different data types
– Comparative assemblies

::DEVELOPER

The Delft Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Matlab
  • MUMmer package
  • GAIMC toolbox

:: DOWNLOAD

  MAIA

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 15;26(18):i433-9.
Integrating genome assemblies with MAIA.
Nijkamp J, Winterbach W, van den Broek M, Daran JM, Reinders M, de Ridder D.

PICA Browser 0.9 – Integrating and Exploring Multiple Connected Datasets

PICA Browser 0.9

:: DESCRIPTION

The PICA Browser tool is a cross-platform Java application for visually exploring a soft clustering produced by integrating data from multiple connected views. The application highlights the contributions of each view and the frequency of appearance of the clusters (i.e. reliability), with the aim of providing insight into the provenance of the cluster relationships in the model. Parallel Integration Clustering Algorithm (PICA) is a new data integration approach for performing multi-view clustering in domains where two or more related datasets are available.

::DEVELOPER

the Machine Learning Group (MLG)

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /Mac OsX
  • Java

:: DOWNLOAD

 PICA Browser

:: MORE INFORMATION