Brainstorming ideas

After a visit to Cornell visiting with Plant Pathology & Plant-Microbe Biology dept, Pseudomonas syringae groups, and SGN and also a breakfast with Tim Hubbard when he was in Berkeley I had a few ideas.

  • We need to be able to put the power of annotation in the hands of more people.  Community assisted annotation at the level of just function, linking to articles, and general curation should be accessible ala-wikipedia.
  • For genome annotation though, there is a more specialized need to be able to incorporate data from different sources. Git-like repository for genome annotation (in GFF) which can be served up to Gbrowse. Edits can be saved to ones own branch.  (all of this assumes the same reference genome assembly which is about the level I’m comfortable worrying about — tho some of the genome projector type tools would seem to make it easy to lift annotation from one assembly to the other).
  • Would probably necessitate a GenomeAnnotationDiff tool.  This might be already accomplished by tools that the Yandell lab has produced described in publication by Eilbeck et al.
  • Gene page with community annotation tools at SGN are ready to go and they have VMs to avoid having to install all the software. I even saw a cool QTL on the fly calculation.  The challenges I see in our data is always linking the data from one context to another how we make this useful. Will have to try and do a transformation of some of the different data we have here.
  • The SGN approach is to use aspects of Chado for the schema that deals with ontologies/controlled vocabularies but to also have domain specific databases for annotation and related info rather than the giant “everything is a feature” that is the Chado-way and doesn’t seem to scale.
  • It is about time to try out hadoop/MapReduce on our big datasets and to also earnestly start running the automated the all-vs-all ortholog prediction scripts on our genomes, there are just too many times it seems important to have an updated dataset – something to deploy on new hardware environment this summer.
  • No one has figured out how to interface with NCBI/GenBank/EMBL to deal with the updating of genomes in a sensible — basically all the really complicated systems are essentially keeping the bulk of the data in their own domain-specific databases and at some appointed times feeding that data back in, but often this is a huge process and only works where there is a real effort from both NCBI/GenBank/EMBL and the group.  E.g. Ensembl has the CCDS and RefSeq projects that can take the output from Ensembl and feed that back into the system.
    What would a comparative reannotation of X fungal genomes system be able to do with the data?

On the Plant Path & fungal side of discussions

  • Looking at multiple genotypes of both the host and pathogen seem like a really smart way to start to explore the effects of mutations. With so many more tools now in both systems it seems like this would be next logical arraying of experimental designs.
  • I really need to get some movies made of Bd (Chytrid) zoospores swimming around, would make for better introductions to talks, I had to settle for showing oomycete zoospores which are cool but not the same.
  • There needs to be new/better tools for population genetics for systems where the populations are clearly not in Hardy-Weinberg equilibrium such as newly introduced pathogens
  • Closeup pictures of fungi are really cool especially through the boroscope

Montana catchup

Great time in Montana.

First got to visit with Todd and Audrey and Chaco at their place in Paradise Valley near Livingston. We did some hiking in Pine Creek and dinner at the perfect cafe to greet your arrival in Montana, Pine Creek Cafe. The Buffalo Sloppy Joes were spicy and great to wash down with Todd’s favorite: Miller Lite. 

Paradise Valley from 28 Cutthroat

The morning of the second day was spent enjoying the View from the front porch of the house and checking out their amazing home. We did a swing through town (Livingston) to pick up supplies and get a necessary coffee infusion.  

Then we headed out to West Boulder Meadows for some more hiking in the Beartooth wilderness in the Gallatin National Forest.  The forest had burned two years ago and there was ample evidence of that as well as regrowth. A great day with lots of pictures including the happy couple & dog, me posing in front of the Brokaw’s ranch a view of the Crazies Mtn range on the road back.

Beartooth entrance

 We made it back to Livingston, had stopped off in town to see Mark’s burger joint before heading to Pizza night where we met up with some friends. The day ended back in Paradise Valley with some shots during the magic hour just before sunset.  We shot lots of pictures of the sunset and the cloud formations and enjoyed the last rays on the mountains.  The Yellowstone river was also high because of the snowmelt from the recent 85F+ days.

Monday I headed to Bozeman to visit with Robb, who overlapped at Duke for his Postdoc and my graduate work.  I got to meet his lab and spend some time getting ready to teach a tutorial and give a seminar at Montana State. I took some time to walk around and check out the downtown as well as had some meals with students and faculty there.  Was a fun visit, I learned about the microbial and metagenomic research going on in Yellowstone, met students working on some interesting projects (I now a lot more about viruses in hot springs than I did before!), and some more connections to how labs are using genomes and comparisons in many different biological systems.

By the end I was exhausted and ready for my own bed at home, but enjoyed the visits with everyone immensely.  Thanks to Robb for organizing and inviting me out and Todd and Audrey for showing me around their slice of the valley.

Mushroom farm trip

Per Lisa‘s request – here is a quick description of mushroom farm trip in October.

There are several indoor mushroom farms in the US. We got to visit a farm outside of Watsonville – Monterey area 1.5 hours south of the SF Bay area. The class was able to visit because John knows one of the research scientists, Steve, who works for Monterey Mushroom farms. We had to wear hair nets for health code reasons, although ignore the fact that the mushrooms grow in a pile of compost (which IS heated to a suitable temperature to kill most of the nasties).

The compost piles are actually quite amazing as they have a delicate system of monitoring the temperature and moisture content of the piles. They are frequently turns to insure good air mixture and are watered with a collection of nitrogen rich liquids (can you imagine where that might come from… such lovely smells…)

Primarily the farms grow Agaricus bisporus (bi-sporus because it produce two spore chains instead of four like most Agaricus). Tom Volk of course has more to say about these mushrooms. They also grow Pleurotus ostreatus or oyster mushrooms.

The white and brown A.bisporus are the same species. It may only be a few genes having to do with lacasse The brown ones you see at the store are often called Crimini but they are the same species as the white button mushrooms that go on your pizza or in your mushroom soup. Portabello mushrooms are just Crimini which has been allowed to grow larger. They typically prune the mushrooms around one they will want to make a Portabello and allow it to grow longer. Mushrooms can be re-picked up to three times before the soil has to be thrown out. If the pickers are careful sometimes a bin can be up to five times, but each time there is a picking there can be problems with mites and infections so often by the 3rd time the size and health of the fruiting bodies are reduced.

Apparently one of the large growing rooms, which has a stack of 5 – 6 tall boxes, 6 of these stacks in a row, and ~50 rows (I think) can generate $100k a month in mushroom sales. I think it works so well because a) they have a lot of good workers who do the picking b) they understand the science of the compost so well, c) they are one of the largest west coast distributors so they have contracts with a lot of places.

Steve also showed us a new hybrid mushroom they had made via crossing a wild strain with the monoculture strain that is grown. They had to do a lot of crosses to breed in the particular traits they wanted from the wild strain. The actually don’t have a lot of genetic resources, but maybe genome projects will come for Agaricus…

One problem with the monoculture is they can get infected with mites that can attack the Agaricus and reduce the production. They use a variety of techniques including an oil that is typically used to combat nematodes. It smells like rotten garlic, but it works. The hybrids may also provide additional resistance naturally.

The evening finished with some freshly picked portabello mushrooms fried up in my omelet. Definitely a different flavor when they are fresh.