Video Tip of the Week: Helium plant pedigree software, because “Plants are weird.”

A lot of people find our blog by searching for “pedigree” tools. We’ve covered them in the past, and we’ve got some training on the Madeline 2.0 web tools that we like. We have groused about the fact that some pedigree tools do not accommodate same-sex families. Largely focused on human relationships, there are a variety of options.

Another branch of this type of software is animal colony management software. This can be used to track animals in breeding situations. We’ve highlighted The Jackson Lab’s Mouse Colony Management Software, and we see a lot people going over to take a look. But there are other types of breeding software out there too.

Plant pedigrees are a special challenge, though. Although I did begin to look into that software at one point, I hadn’t looked again for a while. So when I saw the announcement about an upcoming talk at the  Bio-IT World conference, I thought it was time to look again. Helium was new to me, and I admit I laughed out loud at my first introduction to it:

BioVis 2013: Poster: Evaluation of Helium: Visualization of Large Scale Plant Pedigrees from VGTCommunity on Vimeo.

“Ok, so, plants are weird….” Best poster intro I’ve heard.

But really, the potential complexity of plant breeding pedigrees is much more daunting than even tricky human pedigrees. Their paper on the Helium efforts (linked below) describes some of those aspects in more detail:

Firstly, the named entities in plant pedigrees may, but not always, represent a population of genetically identical individuals, not a single plant. While it is relatively simple to grow many plants from seed, potentially many decades after production, in humans and animals this is understandably not the norm. The generation of these genetically identical (homozygous) varieties is possible through doubled haploidy, inbreeding, or crossing of pairs of inbred lines to achieve what is termed an F1 hybrid. Successive inbreeding by self-pollination of these F1 generation plants leads to individual plants that are close to homozygous across all alleles.

There are no standards for plant pedigrees yet, I learned from this paper. Zoiks! Well, I guess that gives them free rein to design something that users want. The folks on the Helium project got a bunch of potential users, asked them what they needed, what worked, what didn’t work, and they are building a nice looking tool with the specs they got. Their paper goes on to describe their paper prototyping, the feedback, and other interactions they got further downstream in the process. It’s a nice example of how to get some direction from the likely end users.

Another video offers a bit longer view on their software, but there’s no audio (below). The most detailed video is the one attached to their paper in the supplemental files, but I can’t embed it. Go over there to download and watch that, with captions about what’s happening.

I wasn’t able to find any downloadable software yet to kick the tires myself. And because of the blizzard I’m worried I won’t have power for the next few days to check it out. But from what I can see and read in the paper, it looks promising and I’m eager to try it out at some point. Looking forward to Jessie Kennedy’s talk.

Quick link:

Helium project page: http://ics.hutton.ac.uk/helium/

Best intro video version, with explanation captions: http://www.biomedcentral.com/1471-2105/15/259/additional

This is the item that caught my eye, via email. I’m going to be at Bio-IT World, so I’m hoping to be able to see this presented live.

Dr. Jessie Kennedy to Deliver Keynote Presentation on Visualization Tools Designed for Biologists at 2015 Bio-IT World Conference, as part of the Data Visualization and Exploration Tools Track.

Jessie KennedyKeynote Presentation: Pedigree Visualization in Genomics
Jessie Kennedy, Ph.D., Professor & Director, Institute for Informatics and Digital Innovation, Edinburgh Napier University Most visualizations that display pedigree structure for genetic research have been designed to deal with human family trees. Animal and plant breeders study the inheritance of genetic markers in pedigrees to identify regions of the genome that contain genes controlling traits of economic benefit and, ultimately, to improve the quality of animal and plant breeding programs. However, due to the size and nature of plant and animal pedigree structures, human pedigree visualizations tools are unsuitable for use in studying animal and plant genotype data. We discuss two visualization tools, VIPER (designed for cleaning genotyping errors in animal pedigree genotype datasets) and Helium (designed to visualize the transmission of alleles encoding traits and characteristics of agricultural importance in a plant pedigree-based framework), and show how they support the work of biologists.

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Reference:

Shaw P.D., Martin Graham, Jessie Kennedy, Iain Milne & David F Marshall (2014). Helium: visualization of large scale plant pedigrees, BMC Bioinformatics, 15 (1) 259. DOI: http://dx.doi.org/10.1186/1471-2105-15-259

Note: OpenHelix is a part of Cambridge Healthtech Institute.