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Hom Lab Continuous Culture Device.

About the Project

The Hom lab is looking for a computer science student who is proficient in python. The student will be expected to design a python GUI using a common library such as PyQT or Tkinter that will be used to control a continuous culture device for the evolution of microbial cultures. The interface will be used to control basic input settings as well as plot critical information provided by nutrient sensors (glucose, pH, carbon dioxide, nitrite, etc.). The student will work closely with a PhD student to complete the following:
• Interface with laboratory nutrient sensors to retrieve nutritional information
• Create a local SQL database to deposit the nutrient data
• Write a custom python script to retrieve nutrient information from the database to act as inputs into a preexisting control protocol
• Design a graphical interface (preferably with PyQT) to query nutrient data and plot the data in real-time
• Students with an interest in html and webhosting are encouraged to design a webpage for remote monitoring of nutritional data

Project Summary

09/05/2019

Desktop/Server Application

Contact Information

Erik Hom

erik@olemiss.edu


Hom Lab Genomic Data Analyzer

About the Project

The Hom lab is looking for a computer science student that can help stream line workflows to analyze genomic data on the cluster resources at the Mississippi Center for Supercomputing Research. The student will be expected to become proficient with running and scripting batch jobs in collaboration with a biology graduate student currently performing these analyses. The goals will be to:
• create an integrated pipeline/workflow (of scripts) for the component analyses currently being implemented into a form that can be published, managed, and distributed on GitHub for both collaborators and community members
• help document the workflow with instructions on how to execute the workflow (that will include analysis results)
Students should be proficient in UNIX and BASH shell scripting; familiarity with PBS queue system is a plus (but can work with MCSR staff to get up to speed). Python and/or Perl are also a plus as data cleaning is a normal part of the sort of bioinformatic analyses we do. This is a great opportunity to learn how informatics skills can be applied to working with genomic sequencing data.

Project Summary

09/05/2019

Research

Contact Information

Erik Hom

erik@olemiss.edu


Hom Lab AIDA Image Processing

About the Project

The Hom lab is looking for a computer science or imaging-oriented engineer to help further develop AIDA image processing package: https://github.com/erikhom/aida. Several CS students have previously helped modernize the code and how we’d like to move things forward even more. E.g., we now have the code “translated” into Python 3. The student should be proficient in Python and will work closely with Dr. Hom and another CS Honors Student to complete the following:
• Fine tune the GUI developed for the package
• Implement the FFTW package (the Fastest Fourier Transfer in the West) in the new python 3 version of the code
• Help code new algorithmic changes as directed by Dr. Hom
• As a plus, there are opportunities to: (i) try implementing a GPU version of the AIDA package, or (ii) try integrating the AIDA package with the popular ImageJ platform for wider use in the biology community

Project Summary

09/05/2019

Research

Contact Information

Erik Hom

erik@olemiss.edu


Pharmacy graduate student evaluation

About the Project

Brief description: The project involves automation and revision of the annual evaluation of graduate student abilities in the department of pharmacy administration.

Background: For over 15 years, the Department of Pharmacy Administration has been using the “Abilities Transcript” (AT) process to evaluate student progress on each of the seven abilities (scholarly/professional communication, research, analysis, scholarly/professional citizenship, ethics, theoretical reasoning, and self-reflection) declared by the department as outcomes of its Master of Science and Doctor of Philosophy programs. The Abilities Transcript, as a formative and summative evaluation, encourages the personal and professional growth of each graduate student. Currently, this is a paper-based form that is filled out by each graduate student in May before meeting with their advisor and completing the required signatures. The form is in much need of a revision, digitization, and improvement.
Goals: The AT form is currently being revised by the department's faculty. As part of the project, we need an online system that accomplishes some or all the following goals -
1. The form should be open throughout the year for continuous input and should send notices to students and faculty as reminders for participation
2. The system should allow the advisor to compare student self-rating to peer ratings from faculty and other graduate students
3. The system should allow the advisor to check the historical performance of the student to track progress
4. The completed AT should have the option to be exported into a custom PDF to be included in the student's CV
5. Some pre-defined metrics from the AT form must be automatically be exported to the department chair for the purposes of the annual report

Project Summary

09/04/2019

Desktop/Server Application

Contact Information

Sujith Ramachandran

sramacha@olemiss.edu


Library Patron Detection in Images

About the Project

The project would involve working with a very large dataset of library photographs
(approximately 200,000 images) to determine how many library patrons
are visible in each image.

Project Summary

08/29/2019

Research

Contact Information

Alex Watson

apwatson@olemiss.edu


Shared Context

About the Project

I am developing online instructional materials such as the textbook Exploring
Languages with Interpreters and Functional Programming (ELIFP), which is for
use in courses such as CSci 450 and CSci 555.
I create and maintain the content of these materials in plain text source files
encoded in a dialect of Markdown, a minimalistic markup language. I then
convert the Markdown documents to other document formats—HTML, LaTeX,
and PDF—using the Pandoc “universal document converter” tools. In the future,
I plan to add support for EPUB ebooks and possibly Word (.docx) documents.
Pandoc consists of:
• frontend reader programs that parse a source document in some supported
format and create an “equivalent” format-independent abstract syntax tree
(AST)
The best supported source format is probably Pandoc-Flavored Markdown.
• backend writer programs that take an AST and generate the “equivalent”
document in some supported target format according to the provided
template
The best supported target format is probably HTML.
• optional filter programs that can transform one AST to another as it passes
from a reader to a writer
Note: Send an email to set up an appointment. I am not in my office much.

Project Summary

08/28/2019

Desktop/Server Application

Contact Information

H. Conrad Cunningham

hcc@cs.olemiss.edu


Embedded Interactive Questions Project

About the Project

Filters can be written in Haskell (as is Pandoc itself), Lua (using a highly
efficient embedded interpreter), Python, and other languages.
The builtin Pandoc processing can be customized by supplying “user-defined”
filters and templates. In my normal workflow, I do not currently use any custom
filters or templates.
I carry out my writing and document processing on the MacOS platform, using a
text editor (e.g. Emacs) and calling the pandoc tools from the “Unix” command
line or via Bash scripts.
Embedded Interactive Questions Project
I want to be able to embed definitions of interactive, multiple-choice questions
within the Pandoc-Flavored Markdown source document. Each question must
include the question text, an optional hint, and the possible choices for the
answer. The choices must be marked as correct or incorrect and optionally
marked with feedback on why they are correct or incorrect.
The Final Project description (Exam DSL) in my Python-based, Fall 2018, CSci
556 class describes the concept for the questions. Assignment #4 (Exam DSL)
in my Haskell-based, Fall 2018, CSci 450 class is based on similar ideas.
In the HTML target document, I want to render each interactive question
appropriately in HTML/JavaScript/CSS to ask the question, give a hint if
requested, take the reader’s answer, and give the reader feedback on the selected
answer.
I see this project as likely involving steps such as the following:
• Customizing the Pandoc-Flavored Markdown source format to enable such
questions to be specified within a larger document
This likely can be done using Pandoc-Flavored Markdown’s fenced_divs
and bracketed_spans extensions. It might also be useful to use the
separate PP macro preprocessor to give a more convenient syntax.
• Adding a Pandoc filter and/or custom template for HTML to generate the
needed code in the target output
Pandoc ASTs are essentially JSON structures. Filters are programs that
read this representation and create a new JSON structure that is modified
appropriately.
• Coding the HTML5, JavaScript, and CSS needed to display and ask the
question interactively in a Web browser
Each question in the source must generate appropriate code in the target
document.
Note: Send an email to set up an appointment. I am not in my office much.

Project Summary

08/28/2019

Website

Contact Information

H. Conrad Cunningham

hcc@cs.olemiss.edu


Accessibility Analyzer Project (Revisited)

About the Project

I wish to make my online instructional materials accessible to persons with a wide
range of abilities and disabilities. This is needed to comply with legal expectations
such as the Americans with Disabilities Act of 1990, the Rehabilitation Act
of 1973, and other laws, court rulings, and international conventions. See my
[Accessibility Resources page](https://john.cs.olemiss.edu/~hcc/Accessibility_R
esources3.html] for more background on accessibility.
In 2018 and early 2019, I worked with undergraduate researcher Hao Zhou to
develop a set of Pandoc-based tools we called the Broadly Accessible Documents
Analyzer and Specification Language (BADASL, pronounced like “bedazzle”).
It was motivated by the WebAIM Wave tool. The core of BADASL is an
accessibility analyzer implemented as a Pandoc filter. It “walks” the document’s
AST checking for various issues that would make the document less accessible
and generates an appropriate report.
Zhou implemented the BADASL Accessibility Analyzer in Haskell.
This project has the following requirements:
• Redevelop the BADASL Accessibility Analyzer filter in either Lua or
Python 3
• Extend the capability to check additional accessibility issues
• Optionally redevelop the BADASL Specification Language filter in the
same language
Note: Send an email to set up an appointment. I am not in my office much.

Project Summary

08/28/2019

Desktop/Server Application

Contact Information

H. Conrad Cunningham

hcc@cs.olemiss.edu


Mississippi Today Mobile App

About the Project

Mississippi Today is a nonprofit newsroom specializing in investigative and enterprise reporting. Launched in 2016, Mississippi Today has grown to be one of the largest newsrooms in the state, publishing online only with added value content such as a podcast, niche newsletters and both virtual and in-person events.

As our readership grows, we continue to receive great interest in debuting a smartphone app for our site. The biggest asset to launching an app that we cannot achieve through our mobile-friendly site is the ability to send push notifications.

Mississippi Today’s website was developed by the Institute for Nonprofit News’ Labs team. The INN Labs developers designed a custom child theme for Mississippi Today using the Largo parent theme. The site is responsive and optimized for news.

A Mississippi Today mobile news app needs to have a user-focused approach to delivering daily and enterprise news. When opted in, users will receive push notifications delivered at the editors’ discretion, so a user-friendly backend is crucial. Users will also use the app to quickly access news by category/section with a design that complements our mobile site. The app should also include ways to easily share and save stories.

Project Summary

08/28/2019

Mobile App

Contact Information

Debora Rae Wenger

drwenger@olemiss.edu

(662) 915-7912


StatsViz - An open visual analysis tool

About the Project

The Hi5 lab frequently sponsors honors, senior, and capstone projects in Computer Science, Biology, Neuroscience, and Electrical Engineering. These experiences are intended to expose students to real-world job and research experiences. As such, these are challenging. In order to participate, you must apply and interview for a specific project. To apply, e-mail your resumé or CV to Dr. Jones. In your email, please specify which project you are interested in and why you are interested in it. Applying and interviewing does not guarantee that you will be assigned to one of these projects. All students doing projects in the lab are required to complete the CITI Human Subjects Research training program (even if your project does not directly study humans).
(Project)
StatsViz is a tool developed as a part of a Computer Science Senior Project. This tool is used to generate plots commonly needed by the Hi5 Lab. Additional features are needed. You will be expanding the capabilities of this existing tool.

Project Summary

08/28/2019

Research

Contact Information

Dr. Adam Jones

jajone13@olemiss.edu


SLAM Tracking Verification in Virtual Reality

About the Project

The Hi5 lab frequently sponsors honors, senior, and capstone projects in Computer Science, Biology, Neuroscience, and Electrical Engineering. These experiences are intended to expose students to real-world job and research experiences. As such, these are challenging. In order to participate, you must apply and interview for a specific project. To apply, e-mail your resumé or CV to Dr. Jones. In your email, please specify which project you are interested in and why you are interested in it. Applying and interviewing does not guarantee that you will be assigned to one of these projects. All students doing projects in the lab are required to complete the CITI Human Subjects Research training program (even if your project does not directly study humans).
(Project)
Simultaneous Localization and Mapping (SLAM) is a tracking method that utilized video to tracking a camera's position in the real-world. You will be using SLAM tracking in Unity3D and verifying its performance.

Project Summary

08/28/2019

Research

Contact Information

Dr. Adam Jones

jajone13@olemiss.edu


Spatial Behavior in Virtual Reality (multiple projects available)

About the Project

The Hi5 lab frequently sponsors honors, senior, and capstone projects in Computer Science, Biology, Neuroscience, and Electrical Engineering. These experiences are intended to expose students to real-world job and research experiences. As such, these are challenging. In order to participate, you must apply and interview for a specific project. To apply, e-mail your resumé or CV to Dr. Jones. In your email, please specify which project you are interested in and why you are interested in it. Applying and interviewing does not guarantee that you will be assigned to one of these projects. All students doing projects in the lab are required to complete the CITI Human Subjects Research training program (even if your project does not directly study humans).
(Project)
People move and respond differently in virtual reality as compared to the real-world. This project examines how people perceived and act in 3D space in virtual reality.

Project Summary

08/28/2019

Research

Contact Information

Dr. Adam Jones

jajone13@olemiss.edu


ABET course repository/organizer

About the Project

The idea is to help the Department with the upcoming ABET accreditation. Create a tool to give professors a better way to arrange the required course materials (assignments and grades) for ABET and away for the ABET inspectors to access the data.

Project Summary

08/28/2019

Website

Contact Information

Dr. Tim Holston

tlholsto@olemiss.edu


Honors College URL shorten-er

About the Project

I’m looking to roll my own URL shorten-er clone (think bit.ly) to aid our recruiting and admissions efforts at the Honors College. We have begun using keywords attached to our primary url as redirects to various internal/external resources (e.g. honors.olemiss.edu/boysstate, honors.olemiss.edu/password). Currently, these redirects are done via an Apache mod_rewrite directive, which is incredibly fast and reliable, but requires root privilege to set up and doesn’t provide easy stat tracking.
Preferred components for project (but flexible):
PHP
PHP framework (Laravel, Lumen, SlimPHP)
Redis > relational DB
Foundation > Bootstrap (for staff/admin side)
Javascript libraries for stats info gathering/display

Project Summary

08/28/2019

Research

Contact Information

Scotty Polston

spolston@olemiss.edu

(662) 915-7294


IREP Graduating Student Survey Questions

About the Project

For IREP (Institutional Research Effect/Planning)

IREP needs a much better way to deal with the updates to the graduating student survey questions each year.

Right now,
IT gives me an excel file.
Camille then emails this to chairs & assessment contacts for their revisions.
Then each of these folks either ignores the email or emails provides changes to their section.
Camille then finds all of the emails and complies these into one excel file to send back to IT.
There are often errors - that is the chairs don’t make the changes in a way that is consistent with the instructions (e.g., questions too long, don’t choose an appropriate action, it’s hard to find all of relevant emails)

I have the feeling that the IT processes aren’t easy either. David Winters does those, so we would want to involve him if someone picks this as a project.

Project Summary

08/28/2019

Desktop/Server Application

Contact Information

Kate Kellum

kkellum@olemiss.edu