bioKepler

bioKepler is a Kepler module of scientific workflow components to execute a set of bioinformatics tools using distributed execution patterns.
Once customized, these components are executed on distributed platforms available in PL-GRID NG infrastructure.
bioKepler is funded by NSF DBI-1062565 under CI Reuse and Advances in Bioinformatics programs.

Ready to use Virtual Research Environment is available on the PSNC cloud resources,
including a Kepler engine and all bioinformatics tools and applications used as building components for in bioKepler.

 

Main Features

A graphical user interface and a run­-time engine that can execute workflows either from within the graphical interface or from a command line.

Workflows can leverage the compu­tational power of grid technologies , as well as take advantage of Kepler’s native support for parallel processing.

BioKepler ships with a searchable library containing over 400 ready-to-use processing components (‘actors’), general purpose or domain specific that can be easily customized, connected and then run from to perform an analysis and automate data management.

Virtual Research Environment – virtual machine including a BioKepler engine and all bioinformatics tools and applications installed.

Example BioKepler domain specific actors:

2bwt-builder,DynamicTrim.pl, RNA_parse.pl SOAPdenovo31mer, blast_rRNA.pl, blastall, bowtie, bowtie-build, bowtie2-build, breakdancer-max, bwa_align bwa_index, cd-hit cd-hit-454, cd-hit-est, clustalw, clustalx, cuffdiff, cytoscape, faa_stat.pl, fastq2fasta.py, fraggene_scan.pl, fraggene_scan_parse.pl, hmm_rRNA.pl, hmmsearch.pl, hmmsearch_parse.pl, kegg.pl, kegg_parse.pl, metagene.pl, mother, muscle orf_2_tbl.pl, orf_finder, qc_filter.pl, qc_filter_fastq.pl, qiime rasmol, rpsblast.pl, rpsblast_parse.pl, samtools, soap, ssake, tRNAscan-SE.pl, tophat, uchime, velvetg, velveth

Only 4 steps to use the bioKepler services

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1. Register to PL-GRID

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2. Apply to biology services: documentation

3. Download X2GO and login to the remote desktop

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4. Run Kepler and enjoy

Documentation

PL-Grid NG

bioKepler services in PL-GRID NG documentation

Please refer to the bioKepler for the detailed documentation on the bioKepler itself.

bioKepler is a module that is distributed on top of the core Kepler scientific workflow system. Please refer to the Kepler collaboration website for more information on Kepler in general.