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--- projects [2015/08/11 20:42] – jarek
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-====== Proposed Projects for Fall 2014 ======
+====== Proposed Projects for Fall 2015 ======
 \\
-===Genome-wide identification of plant micro RNAs===
+=====Data visualization in Skydive=====
+**Supervisor: Jarek Gryz**
+Skydive is a prototype system designed for database visualization using a concept of the so called
+data pyramid. The system is composed of three modules (DB - Database Module, D2I -
+Data-to-Image module, and VC - Visualizaton Client). Each is designed to use a different type
+of computer memory. The DB module uses disk to store and manage the raw data, and materialized
+data pyramids. The D2I module works with a small subset of the aggregated dataset,
+and stores data in main memory (RAM). The VC module uses the graphic card’s capabilities to
+perform more advanced operations – such as zooming, scaling, panning, and rotation – over the
+graphical representation of the data.
+Currently the system support three presentation models implemented within the Visualization
+Component, namely:
+• a 2D heat-map;
+• a 2.5 D heat-map by 3D barchart; and
+• a 2.5 D terrain (by mesh and UV-mapping).
+The goal of the project is to implement two additional ways of data visualization as well as
+extend some of existing ones, that is:
+. Implement and test functions for data pyramid-based visualization of time series.
+. Implement functions for visualization based on cross-product of data pyramids.
+. Add support for specular and normal maps for 2.5 D terrain presentation model.
+Required Background: CSE 3421, Java programming course, (C programming course a plus)
+\\
+=====Genome-wide identification of plant micro RNAs=====
@@ Line 11: / Line 45: @@
 Working with the support of a PhD student, your project will involve:
 ) Prediction of micro RNA (miRNA) targets on the basis of complementary sequence matches
 ) Correlation of miRNA and mRNA expression changes to identify genes that are regulated by miRNAs
 ) Conducting pathway analysis to determine which biological processes are controlled by miRNAs
 ) Construction of a miRNA/target interaction network to visualize predictions
 This work will contribute to a scientific manuscript on miRNA-mediated gene regulation in pokeweed during response to JA.
 Requirements:
 ) Pre-requisites as per EECS Calendar
 ) Facility with script-writing/modification (in Perl or Python)
 ) Preference for students with knowledge of statistics and familiarity with R programming
 ) Able to begin in September 2015
 Learning outcomes:
 ) Manipulate and analyze quantitative biological data
 ) Develop and test hypotheses by modifying existing software and writing new script
 ) Manage a CentOS computer server to store and facilitate ongoing research
 No knowledge of biology is required.
 For more information, please see:
  Hudak Lab website- http://hudak.lab.yorku.ca/
 RNA sequencing- http://www.illumina.com/applications/sequencing/rna.html
 miRNAs- http://en.wikipedia.org/wiki/MicroRNA
 \\
+=====Dynamic Interface Detection and Control Project=====
-===Dynamic Interface Detection and Control Project===
 **Supervisor: Michael Jenkin**