Tag Archives: plant

expVIP example

Video Tip of the Week: expVIP, an Expression, Visualization, and Integration Platform

As I mentioned last week, I am watching a lot of farmers on twitter talk about this year’s North American growing season. To get a taste of that yourself, have a look at #Plant16 + wheat as a search. This is where the rubber of tractor tires and plant genomics hits the…well…rows. And just coincidentally I saw a story about this new plant genomics research tool–actually in the farming media.

It’s kind of nice to see plant bioinformatics get some recognition beyond the bioinformatics nerd community. The piece “New online tool helps predict gene expression in food crops” did a pretty good job of talking about the features of the expVIP tool, and I was eager to have a look.

expVIP stands for expression Visualization and Integration Platform. expVIP exampleAlthough the emphasis here is plant data, it can be used for any species. A good summary of their project is taken from their paper (linked below):

expVIP takes an input of RNA-seq reads (from single or multiple studies), quantifies expression per gene using the fast pseudoaligner kallisto (Bray et al., 2015) and creates a database containing the expression and sample information.

And it can handle polyploid species–try that on some of the tools aimed at human genomics! They illustrate this with some wheat samples from a number of different studies. And then they use the metadata about the studies, such as tissues and treatment conditions, to show how it works with some great sorting and filtering options. They created a version of this for you to interact with on the web: Wheat Expression Browser. But you can create your own data collections with their tools, aimed at your species or topics of interest.

This week’s Video Tip of the Week is their sample of how this Wheat Expression Browser works. Although you see the wheat data here, it’s just an example of how it can work with any species you’d like to examine.

I followed along and tried what they were showing in the video, and I found it to be a really slick and impressive way to explore the data. The dynamic filtering and sorting was really nice. You can customise the filtering/sorting/etc for the visualizations with the metadata that’s useful to your research. So you could set the tissue types, or treatment conditions, or whatever you want–and filter around to look at the expression with those. They go on to show that their strategies to compare genes in different situations seemed to reflect known biology in disease and abiotic stress conditions.

So their pipeline for gene matching, as well as the tools to explore and visualize RNA-Seq data, offer a great way to look at data that you might generate yourself or you could mine from existing submitted data–but that might not be well organized and available in a handy database just yet.

Quick links:

Wheat expression browser: www.wheat-expression.com

expVIP at GitHub: https://github.com/homonecloco/expvip-web

Reference:

Philippa Borrill, Ricardo Ramirez-Gonzalez, & Cristobal Uauy (2016). expVIP: a customisable RNA-seq data analysis and visualisation platform Plant Physiology, 170, 2172-2186 : 10.​1104/​pp.​15.​01667

Feeding the World – Everywhere I Turn the Page (update)

This past weekend I spent a bunch of time cleaning my office.

Some people are triggered to renew & reorganize by the start of a new year, or the transition from winter into spring. For me, it is the beginning of a new school year that triggers my ‘get organized’ impulses. Even when I was a kid and should have HATED ‘back to school’, I loved getting organized, packing my supplies, and preparing for a new year. So even though the weather still says the dog days of summer, I cleaned my desk top of extra files & tackled one or two of my reading piles (do they breed & multiply at night?) with sincerity.

The first set of articles that I read were from the July 29th issue of Nature, which includes a special feature of articles under the title of “Can Science Feed The World?” I didn’t log into my subscription before reading the articles, so I believe full access to Nature Features is free, but I could be wrong. The editorial “How to feed a hungry world” summarizes the articles in the special issue and interested me enough to keep reading the other articles. In “Food: The growing Problem” I learned a lot of things, including that some of my default assumptions about the reasons for food shortages may not be valid. I also learned that the world’s agricultural research budget is a fraction (just 5%) of its disease research budget – that doesn’t sound like enough to me (though I’m not sure where to find more money for it…)

I liked the writing style of the “Food: Inside the hothouses of industry” it was interesting & easy to read. The author also made me aware of a switch in philosophy of major seed developers such as Monsanto, Pioneer Hi-Bred and Syngenta. I knew that they had been developing all sorts of expression systems and genetic modifications that allowed their plants to be resistant to their pest- and herbicides. I didn’t notice that they had switched towards developing strains more resistant to environmental conditions. This makes global sense to me, but does seem to need a modified business plan – I’ll be interested to see how this progresses.

Having participated in a few soybean nodule harvests myself (which I found full of manual labor with no guaranty of a mother load of knowledge, or even nodules) the article on root research, “Food: An underground revolution” was great news & an interesting read. I can see why roots aren’t the easiest thing to study, but would have thought there was a lot of research already accomplished. Even as an amateur gardener I can see plant prognosis is directly correlated with root structure. “Food: the global farm” was also an interesting read. I applaud Brazil’s efforts & successes.

I next was turning the pages of the Science July 23rd issue & noticed an editorial entitle “Escalating Threat of Wheat Rusts“. It paints a somewhat scary picture, especially with the levels of research funding reported in the Nature article. Several years ago now I attended an SBIR writing conference & in the hotel bar I heard a grant reviewer talking to a researcher. She pointed out that every major disease with NIH funding also probably had funding from the USDA & although the USDA’s budget was MUCH smaller than NIH’s, so was the number of their grant applicants. These articles make me wonder if that is still true, or whether plant research is coming to the forefront again.

Update, 8/24/19: I just received my copy of “Hybrid – The History & Science of Plant Breeding” by Noel Kingsbury, which I bought based on the review in Science by Alan Bennett & am anxious to begin it. I’ll let you know what I think as I progress through it.

Gramene Announces Scholarships for Groups Underrepresented in Science to Learn How to Use Bioinformatics and Genomics Resources

Cold Spring Harbor Laboratory, Oregon State University and Cornell University, creators of the Gramene Resource for Comparative Plant Genomics, partner with OpenHelix to offer online training on genomic resources to encourage diversity in science.

Bellevue, WA (PRWEB) April 22, 2010 — The creators of the Gramene Resource for Comparative Grass Genomics and OpenHelixannounce the availability of scholarships to colleges and universities serving underrepresented minorities for full access to over 85 online tutorial suites on bioinformatics and genomics resources. The program is partially funded by the National Science Foundation (NSF).

“An ongoing goal for Gramene, our institutions, and the NSF, has been to provide opportunities for advancement and training to underrepresented groups in science,” said Dr. Doreen Ware, of Cold Spring Harbor Laboratory and Principal Investigator of Gramene, “So we are excited to be able to offer individual and institution scholarships to an extensive and valuable catalog of online training on genomics resources.”

…we are excited to be able to offer individual and institution scholarships to an extensive and valuable catalog of online training on genomics resources.

Recipients will have access to the OpenHelix catalog of tutorial suites on a wide range of bioinformatics and genomics resources, including Gramene, PlantGDB, NCBI tools such as Entrez Gene, BLAST and PubMed and many more. A full catalog of tutorial suites is available at http://www.openhelix.com/cgi/tutorials.cgi.

Each tutorial suite includes a 45-60 minute, online, self-run, narrated introductory tutorial on how to use a specific resource. The tutorial suite also includes PowerPoint slides, slide handouts and exercises which can be used as reference material or to build classroom content.

“The study of genomics has affected just about every area of life sciences, so learning how to access and interpret genomic data is critical to research success,” said Scott Lathe, Chief Executive Officer of OpenHelix, “With the convenience and broad accessibility of online training, we hope these scholarships will help in leveling access to this important training and further the potential and ongoing careers of the recipients.”

Institutions can apply for a scholarship for access to the tutorials at http://www.openhelix.com/cgi/scholarships.cgi. The scholarships are available to to minority serving colleges and universities. Underrepresented in science means those racial and ethnic populations that are underrepresented in biology research relative to their numbers in the general population. Individual scholarships are available to U.S undergraduates, graduate students, post-doctoral students, faculty and staff. Application deadline is June 30, 2010 and a limited number of scholarships are available.

About Gramene
Extensive research over the past two decades has shown significant conservation of gene order within large segments of linkage groups in agriculturally important grasses such as rice, maize, sorghum, barley, oats, wheat, and rye. Grass genomes are substantially colinear at both large and short scales, opening the possibility of using syntenic relationships to rapidly isolate and characterize homologues in maize, wheat, barley and sorghum.

As an information resource, Gramene’s purpose is to provide added value to data sets available within the public sector to facilitate researchers’ ability to understand plant genomes and take advantage of genomic sequence known in one species for identifying and understanding corresponding genes, pathways and phenotypes in other plant species.

Current work is being supported by the NSF Plant Genome Research Resource grant award #0703908.

About OpenHelix
OpenHelix, LLC, (www.openhelix.com) provides the genomics knowledge you need when you need it. OpenHelix provides a bioinformatics and genomics search and training portal, giving researchers one place to find and learn how to use resources and databases on the web. More efficient use of the most relevant resources means quicker and more effective research.

International Conference on Biodiversity Informatics

arabidopsisI’m always interested in the range of tools available in bioinformatics.  I mean, I know why we have so many built around human and other model organisms.  But I love to hear about other types of projects around biology that need and use computational tools.  I’m kind of a fan of the underserved species.  In fact, I think there is so much room there for exciting applications and discoveries that it may actually be more interesting than some of the human navel-gazing stuff :)

So when I was looking around at the Agricultural Biodiversity Blog I came across the conference announcement for the International Conference on Biodiversity Informatics.  I’m intrigued.

http://www.e-biosphere09.org/ But I don’t see the metagenomics folks.  Huh.

Another thing I had come across on the Agro Biodiversity site was a plant pedigree.  I’ve recently become interested in that flood-tolerant rice project, and they were discussing the pedigree of that rice.  Plant pedigrees…cool.  We are just about to release a training on a pedigree tool and I have been thinking about the strengths and limitations of various tools (because that’s what we do, as Jennifer illustrates here) and I realized that plant pedigrees are a new wrinkle entirely.  The temporal difference in the parents–and even the possible species range of differences–really got me thinking.  But check out their pedigree for that rice (large image, reminds me of a Gene Ontology diagram).  Wicked neat.  Reminded me of my favorite diagram on mouse pedigrees.  The software for this comes from this project that I had stumbled upon separately: Generation Challenge Program.

So much to learn.

EDIT: as I was still percolating on this I remembered my dismay about the representations of synthetic organisms in phylogenies and databases.  I wonder what their pedigrees will look like….

Pinot noir genome, for your holiday contemplation

As you raise a glass this holiday season, you can think about the complexities of the pinot noir genome release.

Pinot Noir Genome Sequence Could Help Cut Costs of Wine Production

….As part of the sequencing study Velasco and colleagues identified a number of genes that are related to disease-resistance, of which 289 contain one or more SNPs.

The study found that the grape plant has a relatively small genome for a crop plant, with more than two million SNPs and 28,585 genes…. Continue reading