Design and Process Bioinformatics Workflows without Scripting

PipeWorks® is an intuitive software package that allows researchers to visually design and process powerful workflows. These workflows are easy to generate and edit, and can be easily shared among colleagues, without the need for tedious scripting.

The PipeWorks® Client provides easy access to a range of search and analysis tools, stored input objects and databases. Workflows can also be saved, shared, and modified, even automated, without advanced programming skills. By dragging the appropriate search tools to the workflow space and connecting them with filters and analysis tools, complex analyses can be launched from your desktop computer. Visual indicators display workflow status and projected completion time at each step.

  • Stitch together pipelines of sequence searches, data filters, and analysis tools, all without Perl or Python scripting
  • Utilize DeCypher's accelerated sequence comparison methods within your workflows to process huge data sets without a computer cluster
  • Create workflows that can be saved, shared and modified by other users
  • Can only be used on Windows-based DeCypher systems.
  • Install the PipeWorks® client software on your laptop for remote execution and status checks.



Intuitive Visual Interface Streamlines Workflow Design

The PipeWorks® Client interface provides easy access to a range of search and analysis tools, stored input objects and databases. Just drag the appropriate search tools to the workflow space, connect them with filters and analysis tools, and launch your workflow. Visual indicators display workflow status and projected completion time at each step.


PipeWorks Structure


PipeWorks’ data and workflow sharing enable more effective research collaboration, and the visual workflow streamlines the design of analyses for your entire team. In comparison to command line bioinformatics applications, PipeWorks is much easier to learn and use on a daily basis.

Advanced Pipeline Development for Bioinformaticists


Build once, deploy to many, and maximize productivity

  • Design and deploy workflows that can be updated and executed without your involvement, freeing you from many repetitive tasks.
  • Researchers can add new input sequences, experiment with search parameters and databases, schedule their own workflows, and retrieve & analyze their own results without bioinformatics support.

Extend workflows with custom scripts or 3rd party applications

  • Incorporate EMBOSS tools like Pepinfo for hydrophobicity plots and residue histograms
  • Additional tools include CpGplot, DotMatcher, CompSeq, Prophecy, ShowSeq and OddComp
  • PipeWorks’ Script Executor Tool enables you to incorporate Perl or Python scripts into any workflow.
  • The Generic Wrapper helps you share custom tools with all PipeWorks™ users
  • The PipeWorks® API helps you define XML inputs, outputs and data translators that are required to extend workflows with your own code

Additional features of this package include:

  • The ability to install PipeWorks® on any PC computer in your lab, and your laptop for remote execution and status checks of DeCypher® jobs.
  • Support for 5 users is included with each CodeQuest® system.

Example Workflows

The following sample workflows are included in PipeWorks®. Once conceptualized, many workflows can be assembled in under 10 minutes using the drag-and-drop interface.

Please click on the images for full-sized screen shots.

Connect Sequential Searches for More Powerful Annotation

Sequential SearchesIn this workflow, adding a filter step enables you to route results data based upon percent identity, e-value, bitscore, gap percentage or score count. At each search step, you can view multiple results to help optimize your workflows.

  1. Input sequences are processed with Tera-BLAST.
  2. Sequences that generate no hits—or score below your filter threshold—are compared to Swiss-Prot using Smith-Waterman (S-W).
  3. Sequences that are not confidently identified by BLAST or S-W are routed to an HMM search that attempts to link them to particular superfamilies or protein families.

Automate and Schedule Repetitive Tasks

  • Database UpdaterPipeWorks’ Database Updater workflow downloads database sources from one or more FTP sites, then formats them for local searching.
  • Workflows can also employ the File Grabber to retrieve a remote set of query sequences.
  • All workflows can be scheduled by date or frequency.

Merge Results, Embed Perl Scripts

Merge Results

You can also merge multiple sets of extracted sequences to serve as the input for additional operations. You can also embed custom Perl and Python scripts into workflows.

Search, Filter and Analyze

  1. Search & Analyze WorkflowUse Tera-BLASTP to compare new protein sequences to a custom protein databas.
  2. Filter the results by e-value.
  3. High-confidence hits are processed by the EMBOSS tool Pepinfo (a). Pepinfo’s hydrophobicity plots and residue histograms will be displayed for each hit.
  4. Results that score below the filter threshold (b) are routed to a more sensitive Smith-Waterman search

Build Hidden Markov Models to Expand Protein Families

  1. HMM WorkflowGenerate a multiple sequence alignment from a protein family using ClustalW.
  2. Build a hidden Markov model (HMM) for searching UniProt

The unique combination of PipeWorks® and CodeQuest® enables you to process high-throughput EST and protein annotation workflows, as well as HMM-heavy metagenomics projects. Your entire lab can design and process workflows on a resource-friendly desktop system to advance their genomics projects or drug discovery efforts.