Clustering Long Read Amplicon Sequencing Data
- Date: Oct, 2017 - Oct, 2018
- Advisor: Dr. Jeremy Wang
- We present a method to identify and partition clusters of unique amplicons from a complex population of full-length amplicon sequences.
- Paper "Resolution of Complex Amplicon Populations Using Long Read Sequencing" submitted to RECOMB 2019.
Kmer Based Phylogenetic Modeling
- January 2017 – October 2017
- Advisor: Dr. Corbin Jones, Dr. Jeremy Wang
- Build the accurate phylogenetic model from DNA sequencing data based on kmer without assembly and alignment
- Successfully generate phylogenetic tree from simulated reference primate and raw DNA sequencing data of Drosophila
- PhylgTree Github Page
MinHash on Mercator
- Date: Oct, 2018 - Nov, 2018
- Advisor: Dr. Jeremy Buhler
- Implementing a parallel algorithm to get minhash sketches with DNA sequence as input on Mercator, A framework to implement irregular streaming applications on NVIDIA GPUs
Online Resource Allocation Using Primal-dual Techniques
- Date: Nov, 2018 - Dec, 2018
- Advisor: Dr. Chien-Ju Ho
- Study online resource allocations problems, such as assigning tasks to workers who arrive online, assigning kidneys to patients, and assigning passengers to Uber drivers. The goal is to maximize the total system utility (e.g., social welfare) subject to various constraints (e.g., budget constraints, fairness constraints, or assignment constraints.)
- Date: Mar, 2018
- Submit(sbatch) Slurm cluster job inside python and avoid shell script for complicated pipeline jobs. For sbatch options, now only supports job name, memory size(in GBs), time limit(in days), dependency and ouput file. But you can use add_option parameter to add more.
- Pysbatch Github Page
pip install pysbatch to install
- or use
conda install -c luptior pysbatch to install
2D Graphics Canvas
- September 2017 – December 2017
- Language and Tools: C++, libpng, libsdl2
- Implements fundamentals of modern software 2D graphics: geometric primitives, scan conversion, clipping, transformations, compositing, texture sampling.
- Advanced functions include gradients, antialiasing, filtering, parametric curves, and geometric stroking.
Mail Client and Server
- January 2017 – April 2017
- Language: Python
- Constructed a mail client and server based on Simple Mail Transfer Protocol(SMTP)
- Used socket programming in building the communication link between client and server