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18s191

Course 18.S191 at MIT, fall 2020 - Introduction to computational thinking with Julia:

3d-eden-model

Codes for simulating the Eden model in 3D

3dtumorsimulator

simulated the spatiotemporal dynamics of a multicellular tumor using a three-dimensional (3D) agent-based model, in which the cells in the tumor are represented as interacting objects. In this model, the cells grow stochastically as a function of time and divide upon reaching a critical size. The cell-to-cell interaction is characterized by direct elastic and adhesive forces. We also consider cell-to-cell and cell-to-matrix damping as a way of accounting for the effects of friction experienced by a moving cell because of other cells and by the extracellular matrix (ECM) (or collagen matrix), respectively. Each cell is modeled as a deformable sphere with a time-dependent radius. Several physical properties, such as the radius, elastic modulus, membrane receptor and ligand concentration, and adhesive interaction, characterize each cell.

ads1-notebooks

Copies of notebooks used in the practical sessions for Algorithms for DNA Sequencing

agent-based-modeling

aws-machine-learning-university-accelerated-cv

aws-machine-learning-university-accelerated-tab

bad-data-guide

An exhaustive reference to problems seen in real-world data along with suggestions on how to resolve them.

bayesian-analysis-with-python

Bayesian Analysis with Python by Packt

breast-cancer-detection-using-deep-learning

Experiments to show the usage of deep learning to detect breast cancer from breast histopathology images

breast-cancer-scikitlearn

simple tutorial on Machine Learning with Scikitlearn

breast_cancer_classifier

Deep Neural Networks Improve Radiologists' Performance in Breast Cancer Screening

bumpy

Quick tutorial of scientific computing with Python using a real physics application.

cancer_modeling

Modeling signaling networks in cancer

cancerecologypaperscripts

jupyter python scripts for treatment options and success rates for cancer and rat eradication

cancertypeprediction

This is the repository for paper titled as "Convolutional neural network models for cancer type prediction based on gene expression".

clonal_evolution

code associated with thesis chapters for clonal evolution

colon_cancer_parameter_estimation_sensitivity_analysis

Codes for parameter estimation and sensitivity analysis of QSP models for colon cancer. This is a part of the National Cancer Institute funded project titled "Data-driven QSP software for personalized colon cancer treatment" Achyuth Manoj, Susanth Kakarla, Suvra Pal and Souvik Roy.

covid19-immune-model

QSP model of immune response to COVID19

covid19-qsp-model

Open Source QSP model describing SARS-CoV-2 virus and host cell life cycles, immune response and therapeutic treatments

cpt_qsptutorial

Supplementary material for CPT tutorial on logic modeling for quantitative systems pharmacology

cultural_evolution_abm_tutorial

This tutorial shows how to create very simple simulation or agent-based models of cultural evolution in R

data-visualization

R Markdown code for visualizing raw and summarized data + regression models

deep-learning

Repo for the Deep Learning Nanodegree Foundations program.

deep-learning-tutorial

dnds-clonesize

Snakemake pipeline to produce figures for "Measuring the distribution of fitness effects in somatic evolution by combining clonal dynamics with dN/dS ratios"

dynamicmodeling

These are MATLAB code I wrote while having Coursera Course Dynamic Modeling Methods for System Biology

evoldynamics1

A 4-compartment (which can be egeneralized to higher compartments) was studied to understand the phenotypic heterogeneity in modeling cancer evolution.

evolutionary-dynamics-to-treatment-of-mcrpc

evolutionary-triage-in-cancer

Evolutionary triage in Cancer: Drivers, Passengers, and “Never” Mutations