projects
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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: | ||
+ | |||
+ | 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: | ||
+ | |||
+ | 1. Implement and test functions for data pyramid-based visualization of time series. | ||
+ | |||
+ | 2. Implement functions for visualization based on cross-product of data pyramids. | ||
+ | |||
+ | 3. 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: | ||
- | 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. | 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: | 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 | 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 | 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 | 3) Conducting pathway analysis to determine which biological processes are controlled by miRNAs | ||
+ | |||
4) Construction of a miRNA/ | 4) Construction of a miRNA/ | ||
This work will contribute to a scientific manuscript on miRNA-mediated gene regulation in pokeweed during response to JA. | This work will contribute to a scientific manuscript on miRNA-mediated gene regulation in pokeweed during response to JA. | ||
Requirements: | Requirements: | ||
+ | |||
1) Pre-requisites as per EECS Calendar | 1) Pre-requisites as per EECS Calendar | ||
+ | |||
2) Facility with script-writing/ | 2) Facility with script-writing/ | ||
+ | |||
3) Preference for students with knowledge of statistics and familiarity with R programming | 3) Preference for students with knowledge of statistics and familiarity with R programming | ||
+ | |||
4) Able to begin in September 2015 | 4) Able to begin in September 2015 | ||
Learning outcomes: | Learning outcomes: | ||
+ | |||
1) Manipulate and analyze quantitative biological data | 1) Manipulate and analyze quantitative biological data | ||
+ | |||
2) Develop and test hypotheses by modifying existing software and writing new script | 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 | 3) Manage a CentOS computer server to store and facilitate ongoing research | ||
No knowledge of biology is required. | No knowledge of biology is required. | ||
+ | |||
For more information, | For more information, | ||
Hudak Lab website- http:// | Hudak Lab website- http:// | ||
+ | |||
RNA sequencing- http:// | RNA sequencing- http:// | ||
+ | |||
miRNAs- http:// | miRNAs- http:// | ||
- | + | \\ | |
- | + | =====Dynamic Interface Detection and Control Project===== | |
- | + | ||
- | ===Dynamic Interface Detection and Control Project=== | + | |
**Supervisor: | **Supervisor: | ||
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\\ | \\ | ||
- | ====== | + | ====== JPF in a Jar ====== |
**Supervisor: | **Supervisor: | ||
Description: | Description: | ||
- | Java PathFinder | + | JPF, which is short for Java PathFinder, is an open source |
- | The Java library Apache log4j allows developers | + | tool that has been developed at NASA's Ames Research Center. |
- | statements are output. | + | 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, | ||
+ | programming time with finding and fixing bugs. | ||
+ | advocating | ||
+ | |||
+ | Installing JPF is far from trivial. | ||
+ | implemented in Java. Therefore, it should, in theory, be | ||
+ | feasible | ||
+ | This would make it significantly simplifying the installation | ||
+ | process | ||
+ | accessible to its potential users. | ||
- | Recently, in collaboration with Shafiei (NASA) we have developed | + | The aim of this project |
- | an extension of JPF called jpf-nhandler. | + | Since JPF relies on a number of configuration files, so-called |
- | is to apply this extension | + | Java properties files, incorporating these properly into the |
+ | jar is one of the challenges. | ||
+ | another challenge. | ||
+ | our modifications | ||
+ | few classes, yet another challenge. | ||
- | [1] David A. Dickey, B. Sinem Dorter, J. Michael German, Benjamin D. Madore, Mark W. Piper, Gabriel L. Zenarosa. " | + | 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: | **Required Background: |
projects.txt · Last modified: 2016/01/13 20:05 by stevenc