Difference: SoftwareBioLab (r20 vs. r19)

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)
  • ViMac 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.
  • ??-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.
  • C2CardsHuman
    • This application provides users with clear and compact overviews of the current opinion of each of five metabolic pathway databases (EHMN, Homo sapiens Recon 1, HumanCyc, KEGG and Reactome) without having to search them all. Stobbe et al (2013) BMC Systems Biology.
  • NBIC Galaxy Server
    • We contributed several proteomics tools to the NBIC Galaxy server. See NPC: Proteomics Tools in the tools menu. Boekel et al (2014) Nature Biotechnology.


Versions of R packages the Peroxisome Knowledge Base


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.


Web services
  • Statistical analysis of proteomics data (to be added)


Workflows


Source code Description Pubmed
Usage Galaxy tools USAGE: a web-based approach NBIC Galaxy Module Repository for the analysis of SAGE data van Kampen et al (2000) Bioinformatics Boekel et al (2014) Nature Biotechnology
Vimac metabo-conv Visualization of microarray data Application to upload human in the context of metabolic pathways. pathway data from KEGG, Reactome, HumanCyc, and WikiPathways to a data warehouse 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
metabo-conv Usage Application USAGE: to upload human metabolic pathway data from KEGG, Reactome, HumanCyc, and WikiPathways to a web-based approach for the analysis of SAGE data warehouse   van Kampen et al (2000) Bioinformatics
Vimac Visualization of microarray data in the context of metabolic pathways. Luyf et al (2002) Bioinformatics

 
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