Bioinformatics Laboratory Medical Bioinformatics and e-Bioscience

Department of Clinical Epidemiology, Biostatistics and Bioinformatics

Academic Medical Center

University of Amsterdam

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Software
As part of research collaborations we developed several software applications, which are listed below. For some of these applications the source code is available. Please acknowledge our group and refer to the associated publication if you use our software or databases as part of your research

Web applications

• Human Transcriptome Map (HTMseq)
  • The Human Transcriptome Map visualizes the expression of genes along the genome and is used as a tool to identify candidate genes for specific diseases or to gain fundamental insight in the higher-order organization of the genome. Caron et al (2001) Science, Versteeg et al (2003) Genome Research.
    
• ViMac
  • ViMAc generates user-specified (genome-wide) metabolic maps to explore gene expression data. To enhance the interpretation of these maps information such as sub-cellular localization is included. ViMAc can be used to analyse human or yeast expression data obtained with DNA microarrays or SAGE. Luyf et al (2002) Bioinformatics.
• δρ-WEB
  • This application enables you to determine the genomic dissimilarity delta* (the average dinucleotide relative abundance difference) between an input sequence and any published prokaryotic genome sequence. The determination of genomic dissimilarities allows the identification of alien DNA or pathogenic islands. Van Passel et al (2005) Bioinformatics.
• Compare prokaryotic genomic islands
  • This application allows you to compare different prokaryotic genomic islands (GIs, which are larger than 10 kbp) with each other, and assess composition similarities between these islands. Within a prokaryotic genome sequence this type of analysis facilitates the detection of GIs that may have been acquired from a (compositionally) similar donor. Van Passel et al (2005) BMC Genomics.

Versions of the Peroxisome Knowledge Base

The Peroxisome Knowledge Base (PxKB) is a curated repository about the peroxisome that integrates biomedical knowledge (e.g., pathways, discorders) about this cellular organelle. PxKB is based on semantic web technologies.

• Peroxisome knowledge base (V1.0)
  • Willemsen et al (2008) Bioinformatics.
• Peroxisome Knowledge base (v1.5) (Februari 2010)

Web services

• Statistical analysis of proteomics data (to be added)

Workflows

• to be added

Source code	Description	Pubmed
Usage	USAGE: a web-based approach for the analysis of SAGE data	van Kampen et al (2000) Bioinformatics
Vimac	Visualization of microarray data in the context of metabolic pathways.	Luyf et al (2002) Bioinformatics
Ridgeogrammer	A workflow-based tool that can detect significantly enriched windows of (genomic) features in a (DNA) sequence	Inda et al (2008) BMC Research Notes