moving the lamppost

random musings of a molecular biologist turned code jockey in the era of big data and open science.

Comparison of Aedes aegypti and Anopheles gambiae midgut gene expression post bloodmeal: an overview



The links on the discussion slides are now fixed!

Introduction to New Post Category: My Presentations

This is my first post in a new category of posts called “My Presentations” which shockingly will consist of as many of my talks that I am able to share online. It will most likely only contain talks that I write going forward since most of my other talks are not in ‘website’ form, and I do not have time to convert them.

However, I recently discovered an approach to writing presentations that is pretty similar to how I write this blog (in ReST or Markdown then conversion to HTML and JavaScript with a special tool: Tinkerer for this blog and mdpress for the presentations). Therefore the resulting presentations are webpages and easily shareable! Yay Open Science!

So far I REALLY like the presentations it produces, but it IS a little flashy, and I have found some differences in how it is displayed depending on the browser being used (so sorry if it sucks for you). The underlying technology behind the presentations is a combination of JavaScript and CSS3. Specifically, an engine written by Bartek Szopka (hereafter referred to as his GitHub/coder handle: bartaz) called impress.js. Here is his introduction to it, written in it.

However, beware! In its native form, you write your whole presentation in HTML and CSS. It is not for folks that are looking for a flashier version of powerpoint. That’s where mdpress comes in (THANK GOD). Aditya Bhargava wrote mdpress and it is awesome.

I write my presentation mostly in markdown (certain more complicated things require jumping into HTML and/or editing the CSS style-sheets), and mdpress reads my markdown file and writes the HTML code for me. Also, as you saw if you played with his introduction, which you should, you might easily get carried away and end up distracting your audience at best, or nauseating them if you are not careful.

With great power comes great responsibility

– Uncle Ben to Peter Parker (Spiderman)

Anyway, enough introduction.

Presentation Background

This is a talk I gave to my lab yesterday at our weekly lab meeting. It represents my effort to update the group on my projects and provides an opportunity for lab-mates to ask questions, give comments and advice, etc. This data is part of my dissertation project (which really should get its own full introduction post soon...). Here is a bit of context.

These are preliminary RNA-seq results from an effort I am undergoing to characterize the degree to which conservation of the regulation of bloodmeal triggered gene expression may be described across the ~150 million year divergence time between the last common ancestor of my subject species (Anopheles gambiae, Anopheles stephensi, Aedes aegypti, and Culex quinquefasciatus).


The talk also served as a way for me to introduce them to the analyses and plots generated by cummeRbund that I have integrated into my development version of Blacktie my automated Tophat/Cufflinks/cummeRbund RNA-seq analysis pipeline.