Databases and Tools

IPB researchers are continually developing a number of resources, tools and databases for plant, bio- and chemoinformatics research. They are available for order and online use.

Computational Mass Spectrometry

XCMS

LC/MS and GC/MS Data Analysis

CAMERA

Collection of annotation related methods for mass spectrometry data

MassBank

Tandem MS Reference Database

MetFamily

For the identification of regulated metabolite families.

Rdisop

Molecular formula calculations

MetShot

High throughput prioritized acquisition and processing of tandem mass spectra

MetFrag

In‐silico Metabolite identifikation

Bioinformatics

PaCeQuant

A tool for high-throughput quantification of pavement cell shape. PaCeQuant is included in the MiToBo package for Fiji/ImageJ.

Golden Mutagenesis

Rapid design of primers for amino acid exchanges and saturation mutagenesis by Golden Gate cloning.

cisHighlight

Highlight cis Elements in Promoter Sequences

RootDetection

Detects root strands in photographs and measures their lengths.

CytoskeletonAnalyzer2D

For the quantification of cytoskeleton structural patterns in microscopy images with texture measures.

Protein Models

Protein structures based on both de-novo molecular dynamics and homology modelling.

FlagScreen

Calibration of aequorin‐based calcium measurements