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--- projects [2015/08/11 15:25] – jarek
+++ projects [2015/08/17 12:02] – jarek
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-====== Proposed Projects for Fall 2014 ======
+====== Proposed Projects for Fall 2015 ======
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-===Dynamic Interface Detection and Control Project===
+=====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=====
+**Supervisor: Katalin Hudak**
+The Hudak Lab in the Biology Department has an opening for a fourth-year Honours student to assist with a bioinformatics project. We study the pokeweed plant, Phytolacca americana, which displays broad-spectrum virus resistance. To evaluate pokeweed gene expression, we recently sequenced the plant’s mRNA and small RNA transcriptomes under jasmonic acid (JA) treatment. JA is a plant hormone that mediates defence against pathogens and insect herbivores. We are interested in learning how pokeweed gene expression is regulated by miRNAs during biotic stress.  Please note: no previous knowledge of biology is required.
+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=====
 **Supervisor: Michael Jenkin**
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-====== Hunting for Bugs in Logging: applying JPF to log4j ======
+====== JPF in a Jar ======
 **Supervisor:** Franck van Breugel
 Description:
-Java PathFinder (JPF) is a tool that can detect bugs in Java code.
+JPF, which is short for Java PathFinder, is an open source
-The Java library Apache log4j allows developers to control which log
+tool that has been developed at NASA's Ames Research Center.
-statements are output.  In the past, Dickey et al. [1] have attempted
+The aim of JPF is to find bugs in Java code.  Instead of
-to detect bugs in log4j by means of JPF with very limited succes.
+using testing to find those bugs, JPF uses model checking.
+The facts that JPF is downloaded hundreds of times per month
+and that some of the key papers on JPF have been cited more
+than a thousand times reflect the popularity of JPF. In
+fact it is the most popular model checker for Java.
+A study done by Cambridge University in 2014 found that the
+global cost of debugging code has risen to $312 billion annually.
+Furthermore, on average software developers spend 50% of their
+programming time with finding and fixing bugs.  As a consequence,
+advocating the use tools, such as JPF, may have significant impact.
+Installing JPF is far from trivial.  The tool itself has been
+implemented in Java.  Therefore, it should, in theory, be
+feasible to encapsulate JPF in a Java archive (jar) file.
+This would make it significantly simplifying the installation
+process of JPF and, therefore, make the tool more easily
+accessible to its potential users.
-Recently, in collaboration with Shafiei (NASA) we have developed
+The aim of this project is to attempt to put JPF in a jar.
-an extension of JPF called jpf-nhandler.  The aim of this project
+Since JPF relies on a number of configuration files, so-called
-is to apply this extension to log4j.
+Java properties files, incorporating these properly into the
+jar is one of the challenges.  Setting JPF's classpath is
+another challenge.  Since JPF changes almost on a daily basis,
+our modifications to JPF should ideally be limited to only a
+few classes, yet another challenge.
-[1] David A. Dickey, B. Sinem Dorter, J. Michael German, Benjamin D. Madore, Mark W. Piper, Gabriel L. Zenarosa. "Evaluating Java PathFinder on Log4J."  2011.
+In this project you may collaborate with graduate students
+of the DisCoVeri group (discoveri.eecs.yorku.ca) and
+computer scientists of NASA.  For more information, feel
+free to send email to franck@cse.yorku.ca.
 **Required Background:** General CSE408x prerequisites