Recently I've been thinking about developing scientific web apps. I wanted to discuss my experiences with making web apps, and an overview of what I've made. A more technical/development discussion will follow in a subsequent post. I was introduced to R Shiny at a gerrymandering workshop a few years ago. Since then, I've created a… Continue reading Scientific web apps

## Collaborative Website: InitMathBio

Although most people can recognize the utility of collaborative workshops, and they are increasing in popularity, how to match possible collaborators together remains a problem. After all, hands-on experience is the best educator, particularly for skeptics of computational methods. A couple years ago I developed a research interest based matchmaking program and put it into… Continue reading Collaborative Website: InitMathBio

## Hardy-Weinberg population simulator

As a grad student, I was a TA for the introductory biology labs at LSU. The second semester lab had some modules on evolution, including a population simulator. This simulator was developed about 20 years ago, and was difficult to install, as well as having a layout that was unfamiliar to the students. When I… Continue reading Hardy-Weinberg population simulator

## Why we should stop publishing in open-access journals with article processing charges

Interesting argument that many researchers are essentially ‘forced’ to publish in non OA journals (so, at the very least not appropriate as a yardstick to gauge commitment to open science). In my field, I’m aware of Biomathematics as gold-standard OA (no APC and open access society journal), but haven’t heard of any others.

Reading time: 4 minutes

*Guest author: Francesco Chiodelli (University of Turin)*

In recent years, a new generation of academic journals has emerged and grown rapidly. It is a particular type of open-access journal with an article processing charge [hereafter: APC journal] . An APC journal is a scientific journal that requires authors to pay a fee to publish their article after it has been accepted. Such fees are usually quite high (ranging from around 1,000 Euros per article in most cases to over 3,000 Euros in some instances). The new generation of APC journals is not constituted by ‘traditional predatory journals’, that is to say a sort of fake-scientific-journals, characterized by false or misleading information, deviation from good editorial practices, and a lack of transparency and a serious peer-review process. This new generation consists of journals that appear to be more serious and on paper seem to respect…

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## Introduction to an Introduction to Approximate Bayesian Computation (ABC)

Last week I re-blogged a post introducing Approximate Bayesian Computation. I thought some of the content was a little foreign, so I wanted to give an intro to the intro. ABC core concept Say we have a process that is controlled by a parameter - say the slope in $latex y = m\cdot x+b$, or… Continue reading Introduction to an Introduction to Approximate Bayesian Computation (ABC)

## Introduction to Approximate Bayesian Computation (ABC)

Many of the posts in this blog have been concerned with using MCMC based methods for Bayesian inference. These methods are typically “exact” in the sense that they have the exact posterior distribution of interest as their target equilibrium distribution, but are obviously “approximate”, in that for any finite amount of computing time, we can only generate a finite sample of correlated realisations from a Markov chain that we hope is close to equilibrium.

Approximate Bayesian Computation (ABC) methods go a step further, and generate samples from a distribution which is not the true posterior distribution of interest, but a distribution which is hoped to be close to the real posterior distribution of interest. There are many variants on ABC, and I won’t get around to explaining all of them in this blog. The wikipedia page on ABC is a good starting point for further reading. In this post I’ll…

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## Why I got a statistics masters during my PhD

In this post I talk about my motivation to complete a degree in statistics during my PhD, and all the failures that went into that decision.

## Happy New Year!

I hope you had a nice end to 2020, however symbolic that may be. I love making new year's resolutions, although I am over-ambitious, as usual. (I'm still checking things off from 2018, and that's just because its the oldest list I have). 2020 wasn't incredibly productive, but I did accomplish a few things. I… Continue reading Happy New Year!

## Dr Ingo Dreyer: Lessons on Modeling Biological Systems

Dr Ingo Dreyer's talk to the modeling community and some takeaways on biological modeling and presenting modeling results.

## Modeling and Beyond: Meeting 10/2 and discussion with Dr Dreyer on membrane transport modeling

If you're a modeler, join us this Friday to talk about using physics-based models to discriminate different membrane transporter networks https://amoghpj.github.io/modeling-and-beyond/