posts

Inference of Causality from Correlations

Posted on December 15, 2018

The source for this post is available here Intro & Motivation Yes, there is a mantra, that causality can not be inferred from correlation. No doubt if A correlates with B, it is generally impossible to say if A or B is the cause. Moreover there can be... [Read More]

An Overlooked Regression - Total Least Squares

Posted on December 12, 2018

The source for this post is available here Intro & Motivation When someone needs to perform a linear regression, the first thing that comes to mind is lm function from the the stats R package. However, this linear model relies on assumption that the... [Read More]

Analytical Solution of Linear ODE System with Complex Roots

minimal example from Edelstein-Keshet textbook page 140

Posted on January 14, 2017

The source for this post is available here Intro & Motivation Model Specification Numerical Solution Analytical Solution Comparing the results Solving it in Mathematica Intro & Motivation A typical way of handling ODEs... [Read More]

Non-Standard Evaluation in R

Posted on October 24, 2016

Non-standard evaluation (NSE) in R is a topic that unfairly not discussed as much as it should. At least understading NSE helps to better understand how R works. At this point this post is a stub with collection of links to the scarse decent resources on this topic. <a... [Read More]

Simulating Random Chemical Systems

random first order chemical reaction or linear dynamic systems

Posted on September 17, 2016

Intro Simple Case: X1 -> X2 -> X3 More Complicated Example Intro Linear dynamic systems can describe a number of phenomena... [Read More]

Chemical Bistability Switch

reproducing the minimal example of the bistability switch

Posted on July 19, 2016

Intro Bistability switch that is described here is a chemical reaction system that can jump from one steady state solution into another, drastically different, over a slight change of the input reactant concentration. Presumably a lot of signal transduction pathways downstream of the hormone receptor work as bistability... [Read More]

Checklist for Peer Review

items that I pay a particular attention to

Posted on June 3, 2016

Different peer reviewers pay attention to different thing in the manuscripts. Here is what I care about and pay a particular attention to. Is the ‘omics data uploaded into any of the public repositories (e.g. PRIDE)? Is the statistical analysis done correctly and the corresponding claims and conclusions of... [Read More]

Lotka-Volterra Model

forward and reverse ODE problem solving in R

Posted on December 1, 2015

Intro Lotka-Volterra is a small model that describes a number of biological processes. Perhaps the most know example is describing the populations of prey and predator specie. Although the model is (as low as 2 ODE) it possesses some interesting properties that makes it challending and interesting to... [Read More]

Testing R

How to make an R post with a graph

Posted on November 18, 2015

I am planning to post quite a few things on computation and R. This is a basic post that demonstrates the capability. the .Rmd file is created as usual. It should be in /blog/_R folder Run _knitposts.R from the main directory of the... [Read More]

T-test 101

What is t-test and why it works

Posted on November 18, 2015

The source code of this post is right here. T-test is one of the basic tests used in biology (and perhaps most others scientific disciplines). However, it is not always interpreted correctly. Hopefully, this small demo will help understanding what the t-test is and what question is answers. Let’s... [Read More]

Hello World

one day this gotta happen

Posted on November 18, 2015

It did really feel that I need a place on the web for self-expression. I think I can add some value with my posts of my biomedical research, R, computational biology and perhaps math in general. As an acknowledgement I’d like to point out a few folks & sites that... [Read More]