UPDATE: Taverna Workflows at the University of Chicago and Beyond
Reusable Workflows Poised to Speed Investigations, Empower Researchers
In September 2009 a team at the University of Chicago was hard at work developing new resources that would help basic researchers conduct experiments more efficiently. Using Taverna, the group created reusable workflows to support in silico research and to ensure that experiments can be consistently reproduced. To date, 14 reusable workflows have been developed and are publicly accessible on caGrid. These workflows also mark continued efforts by the caBIG® community to contribute to research efforts in disease areas outside of cancer.
"Although every researcher approaches problems in a unique way, Taverna provides flexible, customizable, and sharable workflows that can be used to formalize the way that investigations are conducted," explains Baris Suzek, Associate Team Lead (Bioinformatics) and Research Instructor at Georgetown University, where Taverna is currently being evaluated for use at the Georgetown In Silico Research Center of Excellence.
He continued, "Since Taverna allows users to create and save workflow, there is no longer a worry about losing vital information if, for example, staff changes during the investigation."
Research Need Drives Development
Ravi Madduri, project manager at the Argonne National Lab and Computation Institute Fellow at the University of Chicago, is quick to point out that Taverna was developed as a direct response to needs outlined by researchers.
"As technologists, we are the enablers of science, but we are not creating new science. We need to remember that tools should never dictate the process; science should always dictate the tools," explained Madduri. "To be successful, we knew we needed to really understand the problems researchers face and provide tools that can help."
From Hypothesis to Reality
As a result of Madduri's thoughtful approach, the tools developed by his team are beginning to move from the drawing board to the bench.
"Taverna takes what used to be a weeks-long process and shortens it to a day; the workbench acts as a one-stop shop, supplying our team with a library of analytical routines that they can pull from to assemble workflows that best suit our research," explained Alex Rodriquez of the Initiative in Biomedical Informatics (iBi), who plans to use the tool to build workflows that will identify genetic variations (CNVs and SNPs) associated with bipolar disorder and schizophrenia.
New Frontiers: In Silico Science and Cardiovascular Research
Madduri and his team are also working closely with the In Silico Research Centers for Excellence to develop workflows and promote the impact and value of in silico research methods.
For example, at the Georgetown University in silico center, reusable workflows could aid researchers working to identify new drugs that will target specific genes. Suzek explains, "We use workflows to narrow down which drugs deserve further exploration. Using a system like Taverna creates reproducible results from workflows to support such in silico research."
And, researchers at the National Heart, Lung and Blood Institute and the Initiative in Biomedical Informatics (iBi) at the University of Chicago, are investigating the use of Taverna workflows to speed cardiovascular disease research and manage next-generation sequencing data.
For more information on TAVERNA, please visit the following resources:
- caGrid Workflow: TAVERNA
- caBIG® in Action: Speeding research with data analysis workflows
- How to Create caGrid Workflow Using Taverna 2
- Bringing caBIG® Services Together Using TAVERNA
- Wei Tan, Ravi Madduri, Kiran Keshav, Baris E. Suzek, Scott Oster, Ian Foster, "Orchestrating caGrid Services in Taverna," icws, pp.14-20, 2008 IEEE International Conference on Web Services, 2008
