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 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.
  • 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 (2015) Nature Biotechnology.


R packages


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.


Workflows


Source code Description Pubmed
WREP Workflow for REPertoire sequencing van Schaik et al (2016), in prep
Progress Job monitoring system with smartwatch integration 2016
Galaxy tools NBIC Galaxy Module Repository Boekel et al (2015) Nature Biotechnology
metabo-conv Application to upload human metabolic pathway data from KEGG, Reactome, HumanCyc, and WikiPathways to a data warehouse  
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
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
Topic revision: r22 - 14 Sep 2016, BarberaVanSchaik
 

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