sticking this here for now...

doc/Grant/GRANT_APP.txt

+
+
+looks like the dates for this grant which is an R01 research grant are:
+
+Cycle 1: Feb 5th
+Cycle 2: June 5th
+Cycle 3: Oct 5th
+
+but I don't know what the cycles are.....
+
+
+
+On page called PHS 398 Research Plan there are the following sections:
+
+
+
+Specific Aims
+-------------
+
+To produce a genome viewer with a display speed comparable to current high speed
+computer games such as car racing programs.
+
+To show that such a viewer will significantly increase the effectiveness of
+curation and annotation of genomes with particular reference to the display of:
+
+	   - variation in its many forms
+
+	   - the huge volume of data produced by new sequencing technology
+
+To use the substantially faster performance to investigate new ways to show
+sequence data to improve and speed up annotation.
+
+
+
+Background and Significance
+---------------------------
+
+Current genome viewers are either quite low performance because they are
+web-based or even when coded in efficient languages such as C or C++ are some
+way behind gaming software because they do not make use of the graphics hardware
+to be found on even modest desktop machines. This is a problem becuase of two
+different but related developments:
+
+	- the amount of alignment data in the form of nuclotide and peptide
+	matches is increasing extremely rapidly meaning that current browsers
+	are becoming unwieldy.  This problem will increase many-fold when the
+	full flow of the new sequencing technologies goes into production and
+	enters the annotation process.
+
+	- The improvement in throughput of sequencing technologies is making it
+	possible to compare variation between and within species but this
+	requires the display of much larger amounts of data.
+
+Exploiting the graphics hardware traditionally requires use of esoteric software
+toolkits mostly only available to gaming enthusiasts, recently however a number
+of Open Source toolkits have emerged (e.g. Clutter) which provide more straight
+forward access to the hardware. They provide well supported and portable
+toolkits which largely shield the programmer from the intricacies of the
+hardware.
+
+
+
+Preliminary Studies
+-------------------
+
+An analysis of three common open source conventional toolkits for writing
+graphical applications shows that their performance while good cannot
+realistically be significantly improved (USE ROYS ASSESSMENT OF FOOCANVAS,
+GOOCANVAS AND THE OTHER ONE...). Generally to get good reactivity means drawing
+a large number of features up front so that subsequent scrolling/panning/zooming
+works well. This means a sometimes substantial delay because the drawing calls
+cause a bottleneck and also uses substantial amounts of memory. Features simply
+cannot be drawn fast enough on the fly to avoid this.
+
+Gaming software takes a different approach and objects must be drawn in real
+time _as_ the user scrolls/pans/zooms. This is possible because the game
+software makes good use of the graphics hardware. Where such hardware assistance
+is either disabled or is not available gaming programs are not much faster than
+normal graphics programs.
+
+
+
+Research Design and Methods
+---------------------------
+
+The research will be conducted in the following phases:
+
+
+1) Software/hardware performance, reliability, usability assessment
+
+A set of standard drawing tests will be designed and used for assessment.  This
+will include testing several different flavours of hardware to ensure that the
+software is stable and its performance dependable.
+
+
+2) Prototype viewers
+
+Different viewing modes wil be implemented as prototypes to assess with the help
+of annotators their use and speed.
+
+
+
+3) Viewer development
+
+The most useful prototype(s) will be taken forward for development to the level
+where it can be used in the Sanger Institues annoation system.
+
+
+
+