projects
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projects [2013/01/02 21:58] – bil | projects [2015/08/11 20:42] – jarek | ||
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- | ====== | + | ====== |
- | (Listed in order received.) | + | \\ |
+ | ===Genome-wide identification of plant micro RNAs=== | ||
+ | |||
+ | |||
+ | **Supervisor: | ||
+ | |||
+ | |||
+ | 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. | ||
+ | |||
+ | Working with the support of a PhD student, your project will involve: | ||
+ | 1) Prediction of micro RNA (miRNA) targets on the basis of complementary sequence matches | ||
+ | 2) Correlation of miRNA and mRNA expression changes to identify genes that are regulated by miRNAs | ||
+ | 3) Conducting pathway analysis to determine which biological processes are controlled by miRNAs | ||
+ | 4) Construction of a miRNA/ | ||
+ | This work will contribute to a scientific manuscript on miRNA-mediated gene regulation in pokeweed during response to JA. | ||
+ | |||
+ | Requirements: | ||
+ | 1) Pre-requisites as per EECS Calendar | ||
+ | 2) Facility with script-writing/ | ||
+ | 3) Preference for students with knowledge of statistics and familiarity with R programming | ||
+ | 4) Able to begin in September 2015 | ||
+ | |||
+ | Learning outcomes: | ||
+ | 1) Manipulate and analyze quantitative biological data | ||
+ | 2) Develop and test hypotheses by modifying existing software and writing new script | ||
+ | 3) Manage a CentOS computer server to store and facilitate ongoing research | ||
+ | |||
+ | No knowledge of biology is required. | ||
+ | For more information, | ||
+ | Hudak Lab website- http:// | ||
+ | RNA sequencing- http:// | ||
+ | miRNAs- http:// | ||
+ | |||
+ | \\ | ||
+ | |||
+ | |||
+ | ===Dynamic Interface Detection and Control Project=== | ||
+ | |||
+ | **Supervisor: | ||
+ | |||
+ | |||
+ | 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/ | ||
+ | |||
+ | 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, | ||
+ | |||
+ | For further information please contact, | ||
+ | |||
+ | Michael Jenkin (jenkin@cse.yorku.ca) or Michal Organ (organ@yorku.ca) | ||
+ | |||
+ | \\ | ||
+ | ====== DDoS Attack using Google-bots ====== | ||
+ | |||
+ | **Supervisor**: | ||
+ | |||
+ | **Recommended Background**: | ||
+ | |||
+ | Not long ago, botnets - networks of compromised computers - were seen as | ||
+ | the most effective (if not the only) means of conducting Distributed Denial | ||
+ | of Service (DDoS) attacks. However, with the growing popularity and prevalence | ||
+ | of application-layer over other types of DDoS attacks, the DDoS execution | ||
+ | landscape is becoming increasingly more diverse. An especially interesting | ||
+ | new trend is the execution of application-layer DDoS attacks by means of | ||
+ | skillfully manipulated Web-crawlers, | ||
+ | The goal of this project is to design, implement and test a real-world | ||
+ | framework consisting of the following: a) the attacker' | ||
+ | domain specially designed to attract Google-bots and then manipulate them | ||
+ | into generating attack traffic towards the target/ | ||
+ | victim' | ||
+ | component, the project will also look into the statistical/ | ||
+ | estimation of the framework' | ||
+ | to an actual (real-world) target/ | ||
+ | |||
+ | |||
+ | |||
+ | |||
+ | \\ | ||
====== Attentive Sensing for Better Two-Way Communication in Remote Learning Environments ====== | ====== Attentive Sensing for Better Two-Way Communication in Remote Learning Environments ====== | ||
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- Implement algorithms for detecting hand-raises based upon this investigation | - Implement algorithms for detecting hand-raises based upon this investigation | ||
- Evaluate these algorithms in a real-classroom setting, using proprietary attentive sensing technology | - Evaluate these algorithms in a real-classroom setting, using proprietary attentive sensing technology | ||
+ | |||
+ | |||
+ | ====== Attentive Sensing for Sport Video Recording Markets ====== | ||
+ | |||
+ | **Supervisor**: | ||
+ | |||
+ | **Required Background**: | ||
+ | |||
+ | |||
+ | The goal of this project is to modify York University’s patented attentive sensor technology to the sport video recording market. | ||
+ | |||
+ | The general problem is to use attentive sensing technology (www.elderlab.yorku.ca) to visually detect and track multiple moving agents (e.g., skiers, riders, horses) and to select specific agents for active high-resolution smooth pursuit. | ||
+ | |||
+ | The student will work with senior graduate students, postdoctoral fellows and research scientists to help modify the attentive sensing technology to operate in these domains. | ||
+ | |||
+ | 1. | ||
+ | 2. | ||
+ | 3. | ||
+ | |||
+ | ------------ | ||
- | ====== Continuation of a Path Diagram to Syntax Application ====== | ||
- | **Supervisor**: Jeff Edmonds | + | \\ |
+ | ====== Hunting for Bugs in Logging: applying JPF to log4j ====== | ||
- | **Required Background**: General CSE408x prerequisites | + | **Supervisor:** Franck van Breugel |
- | **Recommended Background**: Java software development | + | Description: |
+ | Java PathFinder (JPF) is a tool that can detect bugs in Java code. | ||
+ | The Java library Apache log4j allows developers to control which log | ||
+ | statements are output. | ||
+ | to detect bugs in log4j by means of JPF with very limited succes. | ||
- | Structural equation modeling | + | Recently, in collaboration with Shafiei |
+ | an extension of JPF called jpf-nhandler. The aim of this project | ||
+ | is to apply this extension to log4j. | ||
- | The software required is an application that allows researchers to define their hypothesized models visually and will output the correct syntax for the analytical software of their choosing. | + | [1] David A. Dickey, B. Sinem Dorter, J. Michael German, Benjamin D. Madore, Mark W. Piper, Gabriel L. Zenarosa. " |
- | To date a promising functional application has been developed in JAVA by a Computer Science student as a 4080 project. The existing software allows the user to draw a path diagram and outputs code for the R package sem. There are a number of improvements to be made (refinements and additions to graphical user interface) and then the application needs to be extended to output syntax appropriate for additional software applications (openMX, MPlus and EQS). Though this project may not begin at “the first stages” of the software lifecycle, this scenario is likely common in the software development market. In addition, the student will be working with a primary “client” who is far less technically advanced, which is also reflective of real-world situations. | + | **Required Background: |
+ | \\ | ||
+ | ------------ | ||
+ | \\ | ||
- | More details {{: | ||
- | ====== YUsend Thermal Vacuum (TVAC) Test Manager ====== | ||
- | **Supervisor**: | ||
- | **Required Background**: | ||
- | **Description** The YUsend (York University Space Engineering Nanosatellite Demonstration) Lab has procured a Windows XP-based industrial computer and temperature acquisition card (as well as other hardware) for performing TVAC testing of nanosatellites in the CSIL Lab (PSE 003). A “TVAC Test Manager” application written using LabView' | ||
- | Specific tasks include: 1. Writing temperature acquisition card (OMEGA Engineering CIO-DAS-Temp) drivers for LabView - should be written in Visual C++ or similar and compiled into SubVI format. 2. Write LabView VI's (“Virtual Instrument”) to perform (a) Test set-up activities - checkout of sensor and lamps, assigning neumonics to temperature sensors, setting of alarm conditions for sensors and lamps (b) Acquire and monitor temperature data and control lamp voltage during test, raise operator alarms for temperature or IR lamp anomalous conditions as required © Store temperature and control data for subsequent analysis and reporting. 3. (Optional) Interface the Test Manager with an orbital simulation tool which would be used to compute IR lamp inputs based on a simulation of the nanosatellite' | + | ====== Mining Software Repositories Data====== |
+ | **Supervisor: | ||
+ | **Required Background: | ||
+ | **Short Description: | ||
- | ====== Numerical Methods ====== | + | \\ |
+ | ------------------ | ||
+ | \\ | ||
- | **Supervisor**: | ||
- | **Required Background**: | ||
- | of Fortran, C or similar language. | ||
- | **Description**: | + | ======Model-based Design |
- | polynomial equations, | + | |
- | ====== Enabling SaaS access to an experimental AI planner ====== | + | **Supervisor: |
- | **Supervisor**: Sotirios Liaskos | + | **Required Background:** At least a B+ in Embedded Systems |
+ | such as Arduino. | ||
- | **Required Background**: Good knowledge of Unix tools / Python, Perl or Awk. Comfort with algorithms and programming. Essential: 2031 -- Software Tools. Desired: | + | **Project Description: |
- | 3402 -- Functional & Logic Programming, | + | |
- | 3101 -- Design and Analysis of Algorithms, | + | |
- | 4302 -- Compilers and Interpreters. | + | |
- | **Description**: | + | Model-based design with code generation tools can be used for simulation, rapid prototyping, and hardware-in-the-loop testing of embedded systems. This project explores model-based design and development of embedded systems on various hardware platforms with code generation tools. The selected student will develop and test embedded systems using model-based design and code generation tools such as MathWorks MATLAB /Simulink Coder. |
- | The components are various Unix executables and LISP programs that need to interact in complex ways. The components may be residing in different servers in different universities. Currently integration is performed manually, at the expense of usability. Thus, we aim at constructing a module that: (a) integrates involved components to deliver output in one call, (b) exports a unique web interface (preferably following WSDL/SOAP) to be easily accessed by custom front-end tools by anyone, anywhere, (c ) offers a simple front-end for human users. | + | \\ |
+ | ------------------ | ||
+ | \\ | ||
- | Learning objectives: | + | ======C2000 Concerto Microcontrollers====== |
- | * Understand the technologies and process involved in turning native code into a web-service (" | + | |
- | * Study a state-of-the-art AI planner and understand its workings. | + | |
- | * Exercise scripting skills. | + | |
+ | **Supervisor: | ||
- | ====== Predicting Angular Error in Rigid Registration ====== | + | **Required Background: |
+ | strong C programming skills, solid knowledge of microcontrollers | ||
- | **Supervisor**: Burton Ma | + | **Description: |
+ | two cores on a single-chip with on-chip low latency interprocessor communication between the two cores: a C28x 32-bit control core for | ||
+ | real-time control with faster/more loops and small sampling window; | ||
+ | and an ARM 32-bit Cortex-M3 host core for communications and general purpose. The selected student will evaluate the capabilities of the | ||
+ | C2000 Concerto family of microcontrollers through testing and investigating open source software for real-time control applications | ||
+ | that runs on C2000 Concerto Microcontrollers. | ||
- | **Description**: | + | \\ |
- | navigation. Several (seemingly) different approaches for predicting | + | ------------------ |
- | distance errors in registration are known, but for some surgical | + | \\ |
- | procedures, the angular error in registration is more important. | + | |
- | This project will validate an approach for predicting angular | + | |
- | error in registration; | + | |
- | simulated and actual registration data for testing purposes. | + | |
- | ====== | + | ======Real-Time Bidding Platform====== |
- | **Supervisor**: Burton Ma | + | **Supervisor:** Jia Xu |
- | **Description**: Tracked pointers are the most common tools used in surgical | + | **Required Background:** At least a B+ in Operating System Fundamentals |
- | navigation systems. A typical pointer has a tracked target on one | + | (CSE3221), strong Ubuntu/ |
- | end and a sharp or ball tip on the other end. Finding the location | + | |
- | of the tip relative to the target is a calibration problem. One | + | |
- | solution to the calibration problem involves pivoting the pointer | + | |
- | about the tip while tracking the target; if the tip is kept | + | |
- | stationary, then the target moves on the surface of a sphere. | + | |
- | Fitting the tracking data to the surface of a sphere yields the | + | |
- | location of the tip as the sphere center. Unfortunately, the | + | |
- | calibrated tip position obtained using such a spherical calibration | + | |
- | has high variance. This project will investigate how much variance | + | |
- | there is in the calibrated tip position, and methods for reducing | + | |
- | the variance of the calibrated tip position. | + | |
+ | **Description: | ||
- | ====== A privacy safeguard framework for sharing photos on Facebook ====== | + | \\ |
+ | ------------------ | ||
+ | \\ | ||
- | **Supervisor**: Uyen Trang Nguyen | + | ======Circuit and Board Design for a Pulsed Ground Penetrating Radar====== |
- | + | ||
+ | **Supervisor:**Sebastian Magierowski | ||
- | **Description**: | + | **Description:** The project requires |
- | One of the major privacy concerns in Online Social Networks is photo sharing. | + | |
- | **Required | + | **Required |
- | **Desired prerequisite**: | + | \\ |
+ | ------------------ | ||
+ | \\ | ||
+ | More project proposals may be added here in the first week of the winter term. | ||
+ | \\ | ||
+ | ------------------ | ||
+ | \\ | ||
+ | \\ |
projects.txt · Last modified: 2016/01/13 20:05 by stevenc