Tag Archives: workflows

"Frictionless connection of bioinformatics tools"

Video Tip of the Week: GenomeSpace Orientation

"Frictionless connection of bioinformatics tools"

“Frictionless connection of bioinformatics tools”

The GenomeSpace site has been highlighted before in our “tips of the week”. We appreciated this site that pulled together a lot of different useful types of data sources and analysis strategies. On their site they describe their ethos as “Frictionless connection of bioinformatics tools”. Since that time (2012), it’s continued to grow and provide new features. So I was delighted to see that there was a new orientation video that they offered, and that is this week’s Video Tip of the Week.

Currently there are 20 tools connnected in GenomeSpace, many more than when we first looked. These include mining, visualizing, and workflow tools. This intro video focuses on a couple of them, GenePattern for demonstrating workflow, and Cytoscape for visualization. But you can see how the others would help support many types of genomics analyses.

This overview talks about their “recipes” concept, with step-by-step analysis protocols, which can be found here: http://recipes.genomespace.org . And there’s a demo of the recipe resource. There are some “official” recipes from their team, but they definitely want to have people contributing their own as well. Towards the end of the video they describe how to do that (~28min).

The one used to illustrate the features of the recipes includes a narrative description, but also the specific steps that would be employed. This has the GenePattern and Cytoscape steps examples that they use in the demo.

About half-way through, the demo of the analysis starts (~14min). It’s a helpful walk-through of how to use the recipes effectively to reproduce an analysis. Sara Garamszegi, our guide here, completes the pieces of the work that need to be done with GenePattern, and then shows how to pull out the file you generate from GenomeSpace for Cytoscape to use on your desktop.

There’s also a separate video of the question/answer section, so if you had some unresolved issues you might check if they were covered, or you can hear about how others might be considering using the tools. I often learn as much from the questions as from the formal presentation pieces. They have transcribed the issues in their video info section as well so you could just quickly scan them.

Follow them on Twitter for more like this, and you can also follow their YouTube channel:

Quick link:

GenomeSpace: http://www.genomespace.org/

References:

Qu, K., Garamszegi, S., Wu, F., Thorvaldsdottir, H., Liefeld, T., Ocana, M., Borges-Rivera, D., Pochet, N., Robinson, J., Demchak, B., Hull, T., Ben-Artzi, G., Blankenberg, D., Barber, G., Lee, B., Kuhn, R., Nekrutenko, A., Segal, E., Ideker, T., Reich, M., Regev, A., Chang, H., & Mesirov, J. (2016). Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace Nature Methods, 13 (3), 245-247 DOI: 10.1038/nmeth.3732

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)