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:
— GenomeSpace Team (@genomespace) March 11, 2016
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