DrelCore | Computational Systems Biology - Centre of Excellence

CIF dictionary structure

This applet can parse CIF dictionaries and display them as a tree. Also any methods are parsed and converted to their equivalent python form. The applet jar files are signed so you may be able to access your local filesystem to parse other CIF dictionaries if you agree to accept the certificates. Try it! If you want the evalutator go here


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Unfortunately being an applet it doesn't retain state and may not be able to access your filesystem. Sun offers a way of making this applet a fully functioning application on your desktop with Java Web Start. Try launching it:

Under Linux you may have to tell your browser to associate the extension .jnlp (Java Network Launch Protocol - an XML document) with the javaws client executable found - for example - in the JDK or JRE distribution on your machine viz: /usr/local/java/jdk1.5.0_02/bin/javaws.

Info on CIF dictionaries

  • CIF dictionaries have an implicit tree structure, if fact two, one via the parent_id values and one via the _category.attribute_id "dot" notation. It it not evident what this means.
  • Obviously the python/jython tree structure is more structured that the CIF dictionary that was used. It's not evident if this is the "correct" tree structure envisaged by the dictionary author(s). This parent/child structure has to be translated into an object/instance - method/attribute structure of a computing environment. There is not much guidance.
News

Centre Researcher Sota Fujii part of Rhizanthella Team

Western Australia's Mysterious Underground Orchid Revealed

Highslide JS
[click image for slideshow]
View of the Rhizanthella gardneri capitulum with its shoot emerging from the deeply buried bulb.
Close up of the individual flowers in a dark Rhizanthella gardneri capitulum.
Close up of the individual flowers in a white Rhizanthella gardneri capitulum.
partially closed Rhizanthella gardneri capitulums right after their discovery.
fully open Rhizanthella gardneri capitulum at the base of a Melaleuca uncinata trunk.
purification of genomic DNA from Rhizanthella gardneri
Another view of the Rhizanthella gardneri capitulum with its shoot emerging from the deeply buried bulb
Rhizanthella gardneri plastid genome. Exons are displayed as blue arrows, introns as lines joining exons. tRNAs as black triangles, rRNAs in red. inverted repeats as yellow arrows and fragments or pseudogenes in orange. Ψ: pseudogenes. frag: fragment.

Rhizanthella gardneri is a cute, quirky and critically endangered orchid that lives all its life underground. It even blooms underground, making it virtually unique amongst plants. Last year, using radioactive tracers, scientists at The University of Western Australia showed that the orchid gets all its nutrients by parasitising fungi associated with the roots of broom bush, a woody shrub of the WA outback. Now, with less than 50 individuals left in the wild, Plant Energy Biology scientists have made a timely and remarkable discovery about its genome.

Read our story in Cosmos magazine
Link to the UWA media release

Publication:

Delannoy E, Fujii S, Colas des Francs C, Brundrett M and Small ID (2011) "Rampant Gene Loss in the Underground Orchid Rhizanthella gardneri Highlights Evolutionary Constraints on Plastid Genomes" Molecular Biology and Evolution (in press) online

Centre Researcher Sota Fujii awarded by the JSPS 独立行政法人日本学術振興会

Sota Fujii Awarded:

Plant Energy Biology Research Associate Dr Sota Fujii is off to a terrific start in 2011. Following on from his recent publication (Full Text) in the Proceedings of the National Academy of Sciences (PNAS), he has won both a Japanese research award and a fellowship to continue his valuable work in plant genetics.

Dr Fujii was selected from 300 agricultural scientists for the position of "Super Postdoctoral Fellow" by the Japan Society for the Promotion of Science (JSPS). The fellowship is funded by the Japanese Ministry of Education, Science, Sports and Culture.

I will do my best to use this precious money from Japanese Taxpayers to contribute to the advancement of life science at global level, like my hero Dr. Barbara McClintock,

pledged Dr Fujii.

Dr Fujii's research on restorer to fertility genes in plants has also earned him a Inoue Research Award for Young Scientists. This prize for early career scientists highlights the great work being done by this promising young researcher.


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