As part of the ENCODE Data Coordination Center, this repository is where we maintain and update the ENCODEd database. As an associate data wrangler, I help to update/code review the schemas, tests, and front-end scripts.
You can find the repository on Github. Click here to be redirected. You can access the database here: ENCODE home page
Automated validation scripts to help validate Files and Experiment objects on the ENCODE data portal. I help to maintain and manage these scripts to stay up to date for the newest submissions.
You can find the repository on Github. Click here to be redirected.
Sudden cardiac death (SCD) is one of the major leading causes of deaths in the United States and is known to be caused by abnormalities of heart rhythm, or cardiac arrhythmias, such as ventricular fibrillation and tachycardia. Simulated a mathematical model of a rabbit ventricular myocyte and explored the effects of changes in ion channel conductances and investigated how these changes corresponded to the slope of a 0D simulation in relation to the phenomena of spiral wave break-up and reentry in 2D tissue. By studying the relationship between the two, we can theoretically predict how APD alternans appear, establish the severity of a cardiac arrhythmia without actual experimentation or patient contact, and decide where the best area to consider innovative treatments would be. 0D mathematical analysis and data visualization in Matlab. 2D tissue simulation in C/C++.
Investigating intracellular calcium dynamics by modeling the Calcium Induced Calcium Release (CICR) process within cardiac myocytes using the stochastic fire-diffuse-fire model of calcium release units (CRUs). Focused on describing the behaviors of calcium ions using random walks for a subcellular microdomain known as the dyad, as well as structural and spatial implications of RyR size heterogenity. Mathematical modeling and stochastic implementation in C/C++. Structured programming in C/C++ to simplify algorithm for readability and reuseability. Parallel programming in C/C++ to improve efficiency while dealing with large amounts of data points. Data Analysis and visualization in Matlab/GNU Octave to quanitfy results and make accurate comparisons to proven experiemental results. Bash scripts to run code on Lab computer cluster
Scripted in Python Group project where we created digital fireflies using the Raspberry Pi 3, LEDs, and photosensors. We had them synchronize their frequencies as would live fireflies in the wild in a phenomenon known as entrainment. Modeled with the Fitzhugh-Nagumo system and Hodgkin-Huxley model as nonlinear oscillators to control the period of flashing.
Utilized Scripts in Python & R Structure implies functionality. With emerging techniques such as chromatin conformation capture assays, we are able to make inferences regarding the structure of DNA. Further, the possibility of local knotting increases as a chain increases in length. By using the BFACF algorithm, we investigate how changes in different levels of confinement affect the transition probabilities of lower crossing topological knots through local reconnection moves. We investigate how changes in certain parameters affected inherent properties of self-avoiding polygons in 3D space. Use of Python for string processing and subsequent knot type identification. Use of R for statistical analysis and data management for visualizing transition probabilities within a Markov Chain
There is no available source code. However, here is a link to see my poster that was presented at a conference. Click here to be redirected.
Utilized integer linear programming (ILP) in DNA sequence analysis, in comparison to dynamic programming methods. Used longest common subsequence (LCS) as a criteria for similarity between 2 or more DNA sequences. ILP formulations generated using Python, solved using Gurobi Optimizer.
You can find my source code and results on Github. Click here to be redirected.
These scripts were all written as part of lab assignments in a computer science course. The course title was Data Abstraction and Structures - where we were tasked with implementing different containers/data structures, and specific algorithms using those them. Containers/structures include: doubly linked lists, stacks, queues, hash tables, binary trees, and graphs. Algorithms include searching, sorting, traversal, and Dijkstra's algorithm.
You can find my scripts on my Github. Click here to be redirected.
Binary Trees, Hash Tables, Linked Lists, Dictionaries in Python
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Utillized dynamic programming in Perl to answer the Longest Common Subsequence problem in DNA sequence analysis.
You can find my scripts on my Github. Click here to be redirected.
Utilized dynamic programming in Perl to recreate a small portion of a popular sequence alignment algorithm known as BLAST
You can find my scripts on my Github. Click here to be redirected.
Needleman-Wunsch Algorithm using dynamic programming in Perl in order to do DNA sequence analysis
You can find my scripts on my Github. Click here to be redirected. There are two versions- with Gaps, or no Gaps.
Runge Kutta Method to solve ODEs
You can find my source code on Github. Click here to be redirected.
Finite Elements Methods to solve PDEs
You can find my source code on Github. Click here to be redirected.
Scripted in C++ Final Project for Software Development and Object-Oriented Programming course, ECS 30 UC Davis. We were asked to implement a functioning program recreating the game, Tetris. Initializing a certain board size, we create tetrominos (https://en.wikipedia.org/wiki/Tetromino) as they are read. We have functions in order to add the tetromino, checks to see if it will fit on the board, and if it would overlap with any exisiting tetromino. That said, we also implemented rotate functions in order to rotate the tetrominos clockwise.
You can find my source code on Github. Click here to be redirected.
Scripted in Python. Final Project for Introduction to Programming, ECS 10 UC Davis. We were asked to implement a functioning program to recreate the game Hangman.
You can find my source code on Github. Click here to be redirected.
Scripted in C Final project for Programming and Problem solving course in collaboration with 3 other members, Winter 2015 UC Davis. We were asked to implement a functioning program to recreate the classic minesweeper game. Given a rectangular grid of tiles, we initialize and hide some mines under these tiles. The goal is to mark all the tiles containing mines and uncover all other tiles not containing any mines. Uncovering a tile containing a mine will cause you to lose the game. Uncovering a tile without a hidden mine, will tell you how many mines are hidden in its surrounding 8 tiles.
You can find my source code on Github.Clickhere to be redirected.
