Higher Seq

Illumina introduces the HiSeq 2500

The Hiseq 2000, which can be upgraded to this machine, is already a data fire hose. This upgrade promises an option to turn data out even faster, 120GB in a day! Also longer reads (but at a lower density?) are going to be possible. Its quickly getting to the point (if its not already there) where library prep is going to be the limiting step for data generation, especially if one is dealing with non-standard libraries or with multiplexing.  From an analysis perspective this will mean new challenges and opportunities.

Seed Hunter: a documentary

Seed Hunter, a 2008* documentary about the search for germplasm, is worth checking out. It takes you on a hunt for wild chick peas in remote Tajikistan and has a little bit on wheat breeding. There is some good footage of some very marginal farms, a hint of what could come.

I found the narration very extreme, so be warned that 1) some things are not as bad as it make them seem and 2) although breeding is going to be absolutely crucial to feeding people its not a stand alone magic bullet.

The documentary makes it appear that collection trip only yielded a chick peas at a single site, whether or not thats the actual case it made me think about ownership issues surrounding germplasm. A small increase in yield of any major crop can quickly add up to millions of dollars of value. If it is the case that ultra valuable chick pea land races, collected at single village, will change chick pea production globally shouldn’t the village or farmers who grew and protected them for generations get something? What about wild relatives? If countries can make money from germplasm there would be incentive to protect and/or collect them. Leave a comment and let me know what you think!

You can order the DVD from the official site, or you maybe be able to rent it or get it at a library. Its also broken into parts on youtube.

*new to me

Screen

Its recently come to my attention that not everybody who does bio-infomatics knows about a useful tool called “screen”. It is a useful tool for anyone who uses ssh. It allows you to close your terminal and still have processes running. This is very useful if you are using a laptop for example. You can check in on the process from anywhere afterwards.
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Sunflower Germplasm – Google Earth

There are over 5000 accessions of Helianthus (Sunflowers) in the gene banks of the USDA. Using data available from GRIN, a simple perl script* and google earth we can look at the distribution of all the collections on the globe. You can toggle species on and off. Clicking an accession gives you more information. You can take a look for yourself just download this kml file* change the .txt to .kml and open it (should open with google earth).

*Wordpress security features are preventing me from uploading things with their proper extensions, I will work this out in the future.

Introducing: Sunflower

Thousands of years ago in the eastern United States people started a process that continues to this day. Seeds from wild sunflowers, Helianthus annuus, were harvested for their oil and protein. This ritual of collection resulted in conscious and unconscious selection and sunflowers which were more useful to humans. Sunflowers have made some changes. Here you can see a wild flower head on top of a head of a maturing modern cultivar. The difference in head and seed size is drastic. Now sunflowers are an extremely important source of fat and calories in over 70 countries. Researchers and plant breeders continue to improve sunflowers, although now it is done in a very conscious manner.

Drought and hunger

via The Economist

Right now the horn of Africa is experiencing its worst drought in 60 years. Whether climate change or La Nina are responsible is not yet clear. The resulting food shortage is affecting millions. Staple foods have more than tripled in price. Thousands are fleeing. A massive influx of food aid is needed immediately.

Whether this crisis could have been avoided we will never know. Working towards food security for this planet’s inhabitants is one of the most complicated problems we are faced with as a society. It will require efforts from many disciplines. Better crop technologies will be paramount to this process. The science of improving our crop plants, as well as various satellite issues, will be the focus of this weblog.