Joshua Cook

Joshua Cook

Graduate Student

Harvard Medical School

Biography

Josh is a computational biologist pursuing his PhD. at Harvard Medical School. There, he is co-advised by Professor Kevin Haigis and Professor Peter Park as he studies cancer genetics and evolution. Specifically, he is working to understand the tissue-specific impacts of KRAS mutations on the behavior of cancers.

In his free time, Josh enjoys learning about programming and computer science - his current project is creating an iOS app in Swift. Off the computer, his hobbies include running and caring for his plants.

Interests

  • Cancer genetics and evolution
  • Swift and iOS development

Education

  • BS in Biochemistry and Molecular Biology, 2017

    University of California, Irvine

  • BS in Chemistry, 2017

    University of California, Irvine

Skills

R

Proficient

Python

Intermediate

Swift

Beginner

Linux

Sufficient

Statistics

Moderate

iOS

Beginner

Projects

.js-id-programming

mustashe

A simple system for saving and loading objects in R. Long running computations can be stashed after the first run and then reloaded the next time. Dependencies can be added to ensure that a computation is re-run if any of its dependencies or inputs have changed.

Frailea castanea from seed

My attempt at growing Frailea castanea from seed.

Germination Tracker iOS App

A simple app to help me record data on my seedlings.

Growing Lithops from seed

Documenting my journey from seed to Lithops.

ggasym (“gg-awesome”)

‘ggasym’ (pronounced “gg-awesome”) plots a symmetric matrix with three different fill aesthetics.

Plant Tracker iOS App

An app to help my mom keep track of and care for her plants.

Riddler: Can You Roll The Perfect Bowl?

I used simulation with to approximate the solution an older Riddler. I used an gradient descent-like method to gradually narrow in on a precise estimate.

Riddler: Can You Solve This Rather Pedestrian Puzzle?

I used graphs to solve this weeks Riddler to find the difference in shortest paths resulting from a change to the sidewalk layout of Riddler City.

Riddler: Can You Tell When The Snow Started?

This puzzle was to find the shortest paths of two indivduals sharing a sidewalk while obsering the COVID-19 6-foot social distancing guideline. I simulated the scenario in R and plotted the travels of the individuals using ‘gganimate’.

Riddler: Can You Flip Your Way To Freedom?

For this week’s Riddler, we were asked to solve the 3D structure given a series of cross-sections. I used R to reconstruct this structure and presented it as an interactive plot.

Riddler: Can You Solve The Chess Mystery?

This week’s Riddler involves finding the path used by the knight to kill the opposing queen in a game of chess. I show how I solved puzzle using two methods: a siumulation of the chessboard and by building a graph of the possible paths for the knight.

Accomplish­ments

mustashe

My R package, ‘mustashe’, has been accepted to CRAN. It is ‘A simple system for saving and loading objects in R. Long running computations can be stashed after the first run and then reloaded the next time. Dependencies can be added to ensure that a computation is re-run if any of its dependencies or inputs have changed.’

100 Days of Python

To become comfortable with Python, I completed an hour (usually more) of deliberate practice. I primarily followed data science-centered tutorials, namely Python for Data Analysis and Hands-On Machine Learning with Scikit-Learn, Keras, and TensorFlow. I also followed the tutorials for the common plotting libraries, Matplotlib, Seaborn, and Plotly. I recorded my progress at the linked GitHub repository. I did not finish the Hands on ML book in the 100 days, but I continued working through it afterwords.

Completed Hacktoberfest 2019

I opened four pull requests to open source projects to complete the Hacktoberfest challenge. I merged large features into my Germination and Plant Tracker apps (1, 2, 3). Also, I made a pull request to add documentation for a statsitcal test using by Hierarchical HotNet (Reyna, et al.. Bioinformatics. 2018) from the Raphael Lab at Princton University (4).

100 Days of Swift

I challenged myself to do at least an hour of Swift every day for 100 days. I recorded my progress at the linked GitHub repository. Towards the end of the challenge, I started developing two iOS apps, a Plant Tracker and a Germinaton Tracker.

Tissue-specific oncogenic activity of KRAS A146T

The Haigis Lab published on a biochemical, signaling, and computational description of the KRAS A146T allele.

Honorable Mention NSF GRFP

I have been awarded an Honorable Mention in the 2019 National Science Foundation (NSF) Graduate Research Fellowship Program competition

ggasym

My R package, ‘ggasym’, has been accepted to CRAN. It was further promoted by RStudio in their March edition of Top 40 New CRAN Packages and R Weekly (March 18, 2019).

Toxoplasma gondii disrupts β1 integrin signaling and focal adhesion formation during monocyte hypermotility

My undergraduate reseach in the Lodoen Lab at UC Irvine on the interactions between the single-celled parasite, T. gondii, and human monocytes was accepted by JBC.

Contact

  • Boston, MA 02215