Tag: Evaluation

MetaboQC 1.0 – Evaluation of peak picking quality in LC-MS Metabolomics data

MetaboQC 1.0

:: DESCRIPTION

MetaboQC program is based on the analysis of discrepancies between replicate samples. It suggests the optimal parameters of peak-picking procedure and detects local discrepancies of the chromatogram alignment.

::DEVELOPER

Department of Plant Sciences,WIS

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MetaboQC

:: MORE INFORMATION

Citation

Brodsky, L., Moussaieff, A., Shahaf, N., Aharoni, A. and Rogachev, I. (2010)
Evaluation of peak picking quality in LC-MS Metabolomics data.
Analytical Chemistry, 82 :9177-9187.

PSCE 1.01 – Pairwise Sequence Comparison / Evaluation

PSCE 1.01

:: DESCRIPTION

PSCE (Pairwise Sequence Comparison Evaluation) is a Pairwise Sequence Comparison Tools.

::DEVELOPER

Computational Genomics Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PSCE

:: MORE INFORMATION

Citation:

Green RE, Brenner SE. 2002.
Bootstrapping and normalization for enhanced evaluations of pairwise sequence comparison.
IEEE 9:1834-47.

FERN 1.4 – Stochastic Simulation & Evaluation of Reaction Networks

FERN 1.4

:: DESCRIPTION

FERN (Framework for Evaluation of Reaction Networks) is an extensible and comprehensive framework for efficient simulations and analysis of chemical reaction networks written in Java. It includes state of the art algorithms for stochastic simulation and a powerful visualization system based on gnuplot and Cytoscape.FERN is subdivided into three layers for network representation, simulation and visualization of the simulation results each of which can be easily extended. It provides efficient and accurate state-of-the-art stochastic simulation algorithms for well-mixed chemical systems and a powerful observer system, which makes it possible to track and control the simulation progress on every level.

::DEVELOPER

Institut für Informatik, Ludwig-Maximilians-Universität München

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

FERN

:: MORE INFORMATION

Citation

Florian Erhard, Caroline C. Friedel, Ralf Zimmer.
FERN – a Java framework for stochastic simulation and evaluation of reaction networks.
BMC Bioinformatics, vol 9, no. 1, pp. 356, 2008.

ProCope 1.2 – Protein Complex Prediction and Evaluation

ProCope 1.2

:: DESCRIPTION

ProCope is a software package which provides easy access to different methods used for the prediction and evaluation of protein complexes from purification data experiments. Methods can be accessed via a graphical user interface, command line tools and a Java API. Using ProCope, existing algorithms can be applied quickly and reproducibly on new experimental results, individual steps of the different algorithms can be combined in new and innovative ways and new methods can be implemented and integrated in the existing prediction framework.

::DEVELOPER

Institut für Informatik, Ludwig-Maximilians-Universität München

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

ProCope

:: MORE INFORMATION

Citation

Jan Krumsiek, Caroline C. Friedel, Ralf Zimmer.
ProCope–protein complex prediction and evaluation.
Bioinformatics, vol 24, no. 18, pp. 2115–2116, Sep 2008.