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--- projects [2014/08/26 12:52] – jarek
+++ projects [2015/08/11 21:00] – jarek
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-====== Proposed Projects for Fall 2014 ======
+====== Proposed Projects for Fall 2015 ======
+\\
+===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**
+Contrary to most industries, fine chemical manufacturing is dominated by batch production methods. Increasing economic, environmental and safety pressures are motivating a turn towards continuous synthesis. Rather than making products in one big flask, continuous synthesis involves performing chemical reactions by flowing reagents through a tube. Working in this way provides more control over the reaction parameters leading to increases in product quality, and process efficiency and safety. The flow chemistry industry for fine chemical production is a relatively new but burgeoning field with a projected market capacity of billions of dollars by 2018.
+Extraction of the reaction mixture for purification and/or further processing is an important step in chemical manufacturing. This is a relatively straightforward operation in batch production, but offers several challenges for flowing processes. In order to facilitate continuous liquid extraction we require a sophisticated control system. This project involves designing, constructing and evaluating a pertinent practical problem in the field.
+A key step in the process takes place in a clear tube that is mounted vertically. The tube contains two fluids with a boundary between them. During the process material flows into and out of the tube from the top and the bottom. Chemical reactions take place within this tube and It is essential that the position of the boundary be monitored as its position in the tube is used to control the flow of materials into the tube.
+One way of solving this problem is to float a marker at the boundary between the two liquids and to monitor this boundary using a video camera. Although this approach solves the problem, it requires the introduction of a specific float within the tube. Can we build a system that monitors the boundary without resorting to the use of an artificial float?
+Specific goals of the project include:
+- Develop a computer vision system that can detect and monitor the interface between two miscible fluids of different density.
+- Evaluate the performance of the system over a range of different (and typical) fluids
+- Explore the use of different illuminant/filter choices to simplify the task for specific fluid combinations.
+The successful candidate(s) will have the experience of working with a diverse group of scientists and engineers toward the design and implementation of an automated liquid extraction device with applications across many industries. Upon successful prototyping, you will be able to interact with professionals in high-throughput manufacturing and system integration. Based on project success, you may be invited to join the MACOS(TM) team for implementation and process validation, which may involve opportunities in graduate school. You will have the opportunity to interact with the broad audience of MACOS(TM) technology including governmental regulatory agencies and industrial partners. This project will give you a great opportunity to apply your engineering expertise and gain experience in process implementation and technology transfer.
+For further information please contact,
+Michael Jenkin (jenkin@cse.yorku.ca) or Michal Organ (organ@yorku.ca)
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 ====== DDoS Attack using Google-bots ======
-Project Outline:
+**Supervisor**: Ntalija Vlajic
+**Recommended Background**: CSE 3213 or CSE 3214, CSE 3482
 Not long ago, botnets - networks of compromised computers - were seen as
 the most effective (if not the only) means of conducting Distributed Denial
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 to an actual (real-world) target/victim site.
-Recommended Background: CSE 3213 or CSE 3214, CSE 3482
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-======Hybrid 2D/3D User Interfaces for 3D Rotation ======
-**Supervisor:** Wolfgang Stuerzlinger
-**Required Background:** General 408X prerequisites, 3D Computer Graphics (3431) completed or equivalent, C/C++ coding experience or (if using Unity 4) Javascript C# coding experience
-This project implements and evaluates a new method for 3D Rotation where the user uses both a 2D and 3D user interface to complete the task. The fundamental idea is to use the 3D interface for large-scale manipulation, but the 2D interface for precise adjustments. The project will use a Leap Motion or similar technology for 3D tracking.
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-====== Immersive Virtual Reality Kitchen Planner ======
-**Supervisor:** Wolfgang Stuerzlinger
-**Required Background:** General 408X prerequisites, 3D Computer Graphics (3431) completed or equivalent, 4431 desired, Javascript or C# coding experience
-This project implements a kitchen planner application for an immersive virtual reality system. The implementation will be based on Unity 4.
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-======3D Interaction in Immersive Virtual Reality======
-**Supervisor:** Wolfgang Stuerzlinger
-**Required Background:** General 408X prerequisites, 3D Computer Graphics (3431) completed or equivalent, 4431 desired, Javascript or C# coding experience
-This project implements and tests various 3D Navigation and 3D Interaction methods in an immersive virtual reality system. The target is to enable the user to roam freely in a large environment while still being able to interact with the environment. The implementation will be based on Unity 4.
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-======Reliably tracking horizontal eye movements======
-**Supervisor:** Wolfgang Stuerzlinger
-**Required Background:** General 408X prerequisites, C++/C# coding experience. Ideally CSE3451, CSE4422 or CSE4452.
-**Description:** The Intel Perceptual Computing SDK includes support for head tracking and facial analysis. The project will use the Creative Interactive Gesture Camera, a depth camera designed to work with the SDK. Based on these technologies, the project implements an eye tracking system that detects the horizontal eye position and consequently, if the user is looking at the left, center, or right portion of the screen. Based on this, the project will implement a simple media browsing browsing system, e.g., for TV channels, music, or videos.
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 ======Model-based Design and Development of Embedded Systems with Code Generation Tools======