Tag Archives: computer programming
Research Opportunity: Modern PDF annotation software for Windows 8
Contact Name: Setthivoine You
Contact Email: syou[at]aa.washington.edu
Department: Aeronautics & Astronautics
Description:
The project involves developing an application for the modern Windows 8 interface. The application is designed to interact with pdf files in the same intuitive way we interact with paper: annotate, sign, etc. For good ergonomics, artistic and design experience is also a plus.
Requirements:
Programming experience in modern Windows 8 environment, and experience with PDF protocols. Artistic and design experience.
Research Opportunity: Bioengineering with the Yeast Gene Regulatory Network 2.0
Contact Name: Samuel Danziger
Contact Email: sam.danziger[at]seattlebiomed.org
Department: Seattle Biomed
Description:
We have a developed a predictive environment and gene regulatory influence network (EGRIN) for S. Cerevisiae. This network uses publicly available and in-house gene expression data from microarrays to predict genetic regulation and cellular responses. We intend to expand it to a stochastically robust EGRIN 2.0 that we will use to engineer yeast to produce economically relevant compounds in peroxisomes.
10-week Project #1: Write a framework for generating multiple EGRINs so that the EGRIN 2.0 can be generated with additional processor time. This project would involving using the gene biclustering program cMonkey in [R] or python and interacting with a Sun Grid Engine cluster. There would be plenty of opportunity to improve the cMonkey algorithm.
Requirements:
Familiarity with the [R] statistical programming language or Python.
Familiarity with Unix shell scripting and cluster computing using the Sun Grid Engine (SGE) or similar system.
Research Opportunity: Malaria Resistance in Mixed Infection
Contact Name: Sam Danziger
Contact Email: sam.danziger[at]seattlebiomed.org
Department: Seattle Biomed
Description:
We have completed a pilot study using protein arrays with children in Papua New Guinea to study mixed infection of P. Falciparum and P. Vivax malaria causing parasites. These experiments have allowed us to identify combinations of antigens that correlate with resistance to malaria fever. We hope the follow-up studies will ultimately lead to a malaria vaccine, especially one that works in areas with multiple parasites.
10-week Project #1: The data involves 224 children in Papua New Guinea who were each tested for serum response to 4441 antigen polypeptides. Each of these children was either suffering from malaria fever, or had developed a malaria resistance. For this project, the student would expand a deep learning module written in [R] to detect relevant antigen combinations encoded in the hidden layer(s) and improve the classifier. There would be plenty of opportunity to compare results with known (dynamic) malaria surface adhesion molecules.
10-week Project #2: Seven other centers around the globe have used the same array for similar studies. This project would involve retrieving and curating the data from published studies (as well as through contacts with the company that prints/analyzes the arrays) and formulating research questions to explore with the combined data set. There would be plenty of opportunity to apply / develop / expand machine learning and analysis techniques developed in the original study.
Requirements:
Familiarity with [R] statistical programming language or similar programming language.
Research Opportunity: Scientific Programmer
Contact Name: Thomas Sibley
Contact Email: trsibley[at]uw.edu
Department: Microbiology
Description:
The Mullins Lab (http://mullinslab.microbiol.washington.edu) seeks a part-time student intern to assist with development of Viroverse, a scientific web application used for HIV research. The lab uses Viroverse to manage clinical, experimental, and analytical data for a number of ongoing projects.
You’ll be working with the primary software engineer to tackle a range of tasks depending on your interests as well as your areas and levels of experience. The goals of this internship are 1) to improve the application in identified areas and 2) for you to learn and gain experience from an in-production web service, working with real research data from wet-labs and clinics. To gather feedback about changes and usage, you’ll interact directly with the scientists using the application day-to-day.
To ensure a useful and productive experience for everyone, nearly all work will need to be done in South Lake Union at the Rosen Building (960 Republican St).
To apply, please email your CV to Thomas Sibley with a brief description of your experience and interests, as well as a code sample (need not be Perl).
Requirements:
Object-oriented, modern Perl should be a language you’ve used before, and at least a few of the following keywords should interest you and describe your experience if you apply for the internship:
* Modern Perl
– Catalyst
– Moose
– PSGI
* Javascript
* SQL / PostgreSQL
* Database quality control / reconciliation
* git
* Devops
* Full stack development
* Root-cause analysis
* Security vulnerability discovery and resolution
* Profiling and performance tuning
* UI / UX design
Familiarity with basic molecular biology concepts (PCR, sequencing, etc) and bioinformatics will be helpful but is not necessary.
Research Opportunity: Exon Array for Disease Classification
Contact Name: Samuel Danziger
Contact Email: sam.danziger[at]seattlebiomed.org
Department: Seattle Biomed
Description:
We are exploring exon arrays on serum response cells to detect alternative splicing events that act as disease biomarkers and possibly give clues to the mechanism of disease progression. We are currently applying this technology to investigate ALS (i.e. Lou-Gehrig Disease) in mice and Alzheimer’s Disease in humans. We expect these techniques to transition from exon arrays to RNA-seq as the technology progresses. The idea is to train a discriminating classifier to predict ALS on the basis of features derived from the exon array. We have currently used the FIRMA algorithm to predict alternative splicing events and an ensemble of classifiers to make predictions. Techniques developed in this project are also applied to HIV related data sets.
10-week Project #1: For this project, the student would expand a deep learning module written in [R] (or other language) with an eye to using the hidden layer(s) to improve the classifier and possibly identify gene network pathways. There would be plenty of opportunity to apply / develop / expand machine learning and analysis techniques for both disease classification and biomarker discovery.
Requirements:
Experience with [R] statistical programming language.
Research Opportunity: Educational Outreach Real-time Strategy Immune Response Game
Contact Name: Samuel Danziger
Contact Email: sam.danziger[at]seattlebiomed.org
Department: Seattle Biomed
Description:
Immunology is complicated and stuff has strange names, and this makes it very hard for students of all ages to learn immunology. However, many video games and fantasy worlds are similarly complex and strange, but many school children can tell you about them in painstaking detail. Fortunately, the immune system is a perfect fit for a real time strategy (RTS) game with macrophages killing invaders and dendritic cells gathering resources to build yet more powerful invader-killing cells. We’ve spec’ed out level progression and basic game mechanics, and are hoping to get an alpha version of the game together so we can shop around for financial backing (currently unfunded, enthusiast beware.).
Requirements:
Basic programming skills.
Proficiency or willingness to learn Unity or similar game development platform.
Research Opportunity: Brain Imaging Biomarkers of Neurodegeneration and Injury
Contact Name: Donna Cross
Contact Email: dcross[at]uw.edu
Department: Radiology
Description:
My lab uses brain imaging modalities such as MRI and PET to investigate neurodegenerative processes and the physiological consequence of brain injury in animal models as well as human subjects. We currently have several projects in these areas that might be suitable for undergraduate research. Potential student benefits include technical skills and knowledge of imaging sciences.
Requirements:
Student applicants should be comfortable with analytical computing environments. Background and/or interests in basic statistics, computer programming, animal behavioral research and tissue processing would be beneficial. 10-15 hours/week commitment
Research Opportunity: Search for New Physics with ATLAS at the LHC
Contact Name: Shih-Chieh Hsu
Contact Email: schsu[at]uw.edu
Department: Physics/EE
Description:
My group is searching for new physics beyond the Standard Model to address big questions remained after the Higgs discovery. The big questions include existence of extra dimension, the ultimate mechanism of electroweak symmetry breaking, the quest of large energy scale difference between the Planck scale and the electroweak scale.
Students will learn hadron collider physics, Monte Carlo simulation, statistical analysis and computing skills – C++ and Linux.
Requirements:
PHYS 226 or equivalent knowledge. C++/Linux skill is preferable.
Research Opportunity: Algebraic graph theory
Contact Name: Andrew Berget
Contact Email: aberget[at]uw.edu
Department: Mathematics
Description:
The student would learn the relevant background in algebra and graph theory, in particular the matrix-tree theorem and the fundamental theorem of finitely generated abelian groups. With this knowledge, we would embark on studying the critical group of a graph. This would involve extensive computer exploration of these groups using the computer algebra system Macaulay2.
Requirements:
4xx level abstract algebra or real analysis or combinatorics in the UW Department of Math, or equivalent coursework at another institution.
The student should supply the name of a mathematics professor who can recommend them.