What's New?

August, 2011
  • Individual BioExtract Server workflow steps now have editable names and descriptions, so you can customize your workflows. We added simple names and descriptions to existing workflows, but users can provide their own as well.
July, 2011
June, 2011
  • There is a new public workflow showcasing BioMart tools. The 'BioMart SNP' workflow retrieves known SNPs located on the human chromosome 8 between positions 148200 and 148800. It then proposes Primers and Restriction enzymes that can be used within the same region. The same workflow can be used for any other region in the Human genome.
May, 2011
  • bioextract.org is now hosted on a new server at The University of South Dakota.
April, 2011
  • BioMart tools are now available in the Tools menu.
  • Help documents have been revised and updated.
  • There is a new FAQ linked on the help page.
March, 2011
    New in Version 2.3.05
  • Workflow graphs are now drawn with smaller nodes, allowing more of a workflow to be visible at once. The numeric labels on the workflow nodes correspond to the steps listed in the left pane.
  • Clicking on a workflow graph node and selecting "More Info..." displays an option to download all of the workflow step's output files in a single zip file.
January, 2011
  • There is a new workflow demonstration video available on the help page. The video describes how to create a simple workflow with the blastn and clustalw tools.
  • Users may now share data extracts with other group members in the same way they share tools and workflows. This feature is available on the Groups tab.
November 10, 2010
  • We present the mRNA Markup workflow as a realistic workflow example created within the BioExtract Server. Using NCBI BLAST+, MuSeqBox , and Linux shell scripting, an input transcript set is partitioned in many ways, including into contaminants (sequencing artifacts), potential chimeras, likely full-length protein-coding mRNAs, and potentially novel transcripts for further analysis with other programs. more information
  • There is no constraint on the number of records returned from data source queries. In the past, results from a query were limited to 5,000 records but this restriction has been eliminated. The number of records that can be saved to a data extract or download has been expanded to 25,000.
  • Researchers may share data extracts. Data extracts that have been saved by researchers may be added to research groups allowing them to be shared with collaborators in the same manner that tools and workflow may be shared.
  • There is a new “look and feel” to the workflow graphics. An algorithm has been applied to the workflow graphical display to minimize the number of overlapping edges. New graphical node functionality has been added to the workflow graphs allowing for the workflow graph to be expanded and providing easier access to the input/output information.
  • There is a new CpGAT Maize workflow. PlantGDB's Comprehensive plant Gene Annotation Tool (CpGAT) workflow allows users to annotate any genomic region using any combination of transcript and protein datasets. The pipeline uses EVM (EVidence Modeler) to evaluate transcript- and ab initio-derived exons, and incorporates PASA to derive UTR regions and alternative splice variants. The pipeline outputs a GFF3-formatted file of gene structures.

    How it works: The user chooses a genome region to annotate, and then selects transcript datasets (same species and/or related species) and/or protein datasets (related species) based on taxonomic similarity to the genome of interest. The user selects a splice-site model as close as possible representing the species of interest. more information

Roadmap

  • March 17, 2011: Allow download of all tool outputs as a single zip archive
  • March 2011: Updated workflow overview graphics
  • April 2011: BioMart will be added as a new data source
  • May 2011: Upgrade bioextract.org server hardware
  • June 2011: Workflow update allowing names and descriptions to be assigned to individual workflow steps