Tag Archives: myexperiment

Tip of the week: The Taverna Project for workflows

We’re on the road this week doing workshops, so I needed to have this tip prepared well ahead of time. To make it easy on myself, I’m going to simply point you to a recent informative webinar on Taverna, that was hosted by Bitesize Bio (and check out their other upcoming webinars).

The image I used as the screen shot made me laugh. It was a graphical illustration of what you might need to do to analyze a piece of sequence data that you might obtain. You have to leap around to all kinds of sites and tools and they all stand nearly independent of each other, and if you wanted to do it with another sequence later you’d have to face the same series of events. Workflow tools are now being developed to streamline, automate, and simplify this process.

Taverna is an application that supports bioinformatics workflows (and other types of workflows as well, actually).  It combines with the MyExperiment social networking aspects, and the BioCatalogue collection of web services. You can create complex and effective workflows, share them with others, and store them for re-use.

If you are considering using workflows to at least partially automate some of the processes you need to accomplish, you should know about Taverna. And this webinar is a nice introduction to the basics and philosophy around it.

It was just over 30 minutes if I remember correctly. And you can hear my question at the end–I asked if the version numbers of software tools or data sets is stored with the analysis. The short answer: no, it’s up to you to do that. [This is something that concerns me a lot about workflow tools and I try to press for this all the time.]

Currently I use Galaxy for the workflows I need. But recently it was announced that there’s a way to use eGalaxy with Taverna to generate workflows that can run in Galaxy–but I haven’t explored this at all yet.

Quick links:

Taverna Webinar at BiteSizeBio: http://bitesizebio.com/webinars/the-taverna-project/

Taverna application: http://www.taverna.org.uk

Tip of the Week: BioExtract Server

The BioExtract Server is a tool that allows the researcher to search and access data, analyze that data and then store the data and create workflows from the analysis. In that respect it’s very similar to Galaxy. BioExtract was developed by two groups (Brendel and Lushbough) at Iowa State and University of South Dakota, respectively.

Today’s tip in a quick introduction to BioExtract. If you have used Galaxy before*, you will immediately notice differences in execution, usability and community. Both have workflows. I like Galaxy’s implementation of histories better and Bioextract does seem to focus on comparative genomics more. Both BioExtract and Galaxy are (or will be) part of MyExperiment, a site to find, use and share workflows and other “research objects.”

In today’s tip I am giving a basic intro, they have a good tip on how to do workflows, which I don’t go into, here (more help here).

*(Disclosure: OpenHelix does training and outreach for Galaxy)