1.1 --- a/grant.txt Tue Apr 21 05:38:52 2009 -0700 1.2 +++ b/grant.txt Tue Apr 21 05:50:39 2009 -0700 1.3 @@ -236,7 +236,6 @@ 1.4 1.5 1.6 1.7 -\newpage 1.8 == The approach: Preliminary Studies == 1.9 \begin{wrapfigure}{L}{0.35\textwidth}\centering 1.10 %%\includegraphics[scale=.27]{singlegene_SS_corr_top_1_2365_jet.eps}\includegraphics[scale=.27]{singlegene_SS_corr_top_2_242_jet.eps}\includegraphics[scale=.27]{singlegene_SS_corr_top_3_654_jet.eps} 1.11 @@ -451,7 +450,6 @@ 1.12 1.13 1.14 1.15 -\newpage 1.16 == The approach: what we plan to do == 1.17 1.18 1.19 @@ -535,20 +533,20 @@ 1.20 1.21 === Aim 1 === 1.22 1.23 -* October-November 2009: develop an automated mechanism for segmenting the cortical voxels into layers 1.24 -* November 2009 (milestone): a preliminary automated mechanism for segmenting the cortical voxels into layers 1.25 -* October 2009-April 2010: develop scoring methods and to test them in various supervised learning frameworks. Also test out various dimensionality reduction schemes in combination with supervised learning. create or extend supervised learning frameworks which use multivariate versions of the best scoring methods. 1.26 -* January 2010 (milestone): submit a publication on single marker genes for cortical areas 1.27 +* September-November 2009: Develop an automated mechanism for segmenting the cortical voxels into layers 1.28 +* November 2009 (milestone): Have completed construction of a flatmapped, cortical dataset with information for each layer 1.29 +* October 2009-April 2010: Develop scoring methods and to test them in various supervised learning frameworks. Also test out various dimensionality reduction schemes in combination with supervised learning. create or extend supervised learning frameworks which use multivariate versions of the best scoring methods. 1.30 +* January 2010 (milestone): Submit a publication on single marker genes for cortical areas 1.31 * February-July 2010: Continue to develop scoring methods and supervised learning frameworks. Explore the best way to integrate radial profiles with supervised learning. Explore the best way to make supervised learning techniques robust against incorrect labels (i.e. when the areas drawn on the input cortical map are slightly off). Quantitatively compare the performance of different supervised learning techniques. Validate marker genes found in the ABA dataset by checking against other gene expression datasets. Create documentation and unit tests for software toolbox for Aim 1. Respond to user bug reports for Aim 1 software toolbox. 1.32 -* June 2010 (milestone): submit a paper describing a method fulfilling Aim 1. Release toolbox. 1.33 -* July 2010 (milestone): submit a paper describing combinations of marker genes for each cortical area, and a small number of marker genes that can, in combination, define most of the areas at once 1.34 +* June 2010 (milestone): Submit a paper describing a method fulfilling Aim 1. Release toolbox. 1.35 +* July 2010 (milestone): Submit a paper describing combinations of marker genes for each cortical area, and a small number of marker genes that can, in combination, define most of the areas at once 1.36 1.37 === Aim 2 === 1.38 * April-March 2011: Explore dimensionality reduction algorithms for Aim 2. Explore standard hierarchial clustering algorithms, used in combination with dimensionality reduction, for Aim 2. Explore co-clustering algorithms. Think about how radial profile information can be used for Aim 2. Adapt clustering algorithms to use radial profile information. Quantitatively compare the performance of different dimensionality reduction and clustering techniques. Quantitatively compare the value of different flatmapping methods and ways of representing radial profiles. 1.39 -* March 2011 (milestone): submit a paper describing a method fulfilling Aim 2. Release toolbox. 1.40 -* February-May 2011: Using the methods developed for Aim 2, explore the genomic anatomy of the cortex. Read the literature and talk to people to learn about research related to unexpected and interesting discoveries. Create documentation and unit tests for software toolbox for Aim 2. Respond to user bug reports for Aim 1 software toolbox. 1.41 -* May 2011 (milestone): submit a paper on the genomic anatomy of the cortex, using the methods developed in Aim 2 1.42 -* May-August 2011: revisit Aim 1 to see if what was learned during Aim 2 can improve the methods for Aim 1. 1.43 +* March 2011 (milestone): Submit a paper describing a method fulfilling Aim 2. Release toolbox. 1.44 +* February-May 2011: Using the methods developed for Aim 2, explore the genomic anatomy of the cortex. If new ways of organizing the cortex into areas are discovered, read the literature and talk to people to learn about research related to interpreting our results. Create documentation and unit tests for software toolbox for Aim 2. Respond to user bug reports for Aim 2 software toolbox. 1.45 +* May 2011 (milestone): Submit a paper on the genomic anatomy of the cortex, using the methods developed in Aim 2 1.46 +* May-August 2011: Revisit Aim 1 to see if what was learned during Aim 2 can improve the methods for Aim 1. Follow up on responses to our papers. Possibly submit another paper. 1.47 1.48 \newpage 1.49