Scientific Illustrations Part I: Schematics and Cartoons

Scientific Illustrations Part I: Schematics and Cartoons

Biologists have a long tradition of drawing specimens as a form of data collection before the invention of the camera. The ability to present information in the form of illustrations is an important but often understated skill in a scientist’s toolkit. Scientific illustrations in publications run the gamut from schematics, 3D models, cartoons, and even…

Have a BLAST With Your Protein Sequences

Have a BLAST With Your Protein Sequences

When I was being trained in microbiology as an undergrad, one of the first skills I acquired was the ability to quickly compare and visualize amino acid sequences using BLAST and ClustalW. 15 years later, those two programs have done nothing but improve by expanding the data contained in these databases and simplifying the user…

How to Choose The Appropriate Genomic NGS Data Simulator

How to Choose The Appropriate Genomic NGS Data Simulator

Let’s say that you’ve just finished gathering your NGS reads and you’re going to simulate the introduction of random mutations at specific rates into the reads. Before you move on to the next step, you need to determine which NGS data simulator will get the job done. With the ever-increasing advancement of NGS in the…

A Simple Method for Measuring Intracellular Fluorescence

A Simple Method for Measuring Intracellular Fluorescence

Fortunately for microscopy users, measuring intracellular fluorescence has been made relatively simple through an ImageJ plugin called the Cell Magic Wand. For those of you unfamiliar with ImageJ, it’s a popular image processing program that runs on Mac, Windows, and Linux. How to use ImageJ for measuring intracellular fluorescence First of all, to begin measuring…

Top 5 Tricks for Using FlowJo

Top 5 Tricks for Using FlowJo

Are you planning to do cellular immunology research?  Then chances are you will be introduced to the flow cytometer –  “a modern immunologist’s best friend.” This modern magic box is a highly versatile machine packed with cutting-edge fluidics and photonics (lasers). Combined with the monoclonal antibodies conjugated to fluorochromes capable of emitting light signals from a…

Using a Genome Viewer to Scope your Sequencing Data

Using a Genome Viewer to Scope your Sequencing Data

Now you’ve got great sequencing results, thanks to Nick’s article on improving sequencing results. Now what? Well now you need some software (preferably free) to analyze your data. BioEdit is a good option. But what I have to offer today is a much lighter and equally handy tool. It’s called Artemis and was developed by…

Get Your Single Nucleotide Polymorphisms Straight From the Oven!

Get Your Single Nucleotide Polymorphisms Straight From the Oven!

While it is true that there are some useful websites like SNPedia, or NCBI that can help you find rs codes for genetic variants, sometimes you need that info coming straight from the oven – particularly when you want to look at atypic SNPs or substitutions that have not been validated. So, in this post I…

Publishing Online?  Consider a Graphical Abstract

Publishing Online? Consider a Graphical Abstract

There is a new way to present your paper, and some journals are even beginning to require it. Introducing… the Graphical Abstract. When submitting for online journals, not only do you have to write your normal abstract, you may also need to provide a graphical abstract. Various publishers, such as Elsevier, Springer, Taylor & Francis,…

How to Start Using Coding to Automate Image Analysis Part 1: The Simple Process

Pat yourself on the back, you saw a post with the word “coding” in the title and you didn’t freak out or glaze over. That’s the first step. Coding seems to have such a stigma attached to it; people tend to think that it’s incomprehensible nonsense that they could never learn, and that it has…

How to Start Using Coding to Automate Image Analysis Part 2: Batch Processing Multiple Images

How to Start Using Coding to Automate Image Analysis Part 2: Batch Processing Multiple Images

In Part 1 of this article, I introduced you to using code for basic image manipulation in ImageJ and working with the command recorder to expand your coding vocabulary. I covered how to make a simple macro, how to edit it and then save it to be run again another time. If you skipped the…

Being “Accuri-te” Through Cytometry: A Guide to Accuri C6 Software

Being “Accuri-te” Through Cytometry: A Guide to Accuri C6 Software

A new lab toy to make it big in the last 5–10 years is the Accuri C6 cytometer (now under the BD umbrella), a low-cost instrument in comparison to the big boys. Lightweight, with a small footprint and straightforward maintenance, it’s often the cytometer of choice. It may be suitable for those labs that require…

A Guide to Flow Cytometry Software: Becton Dickinson’s ‘Diva’

A Guide to Flow Cytometry Software: Becton Dickinson’s ‘Diva’

If you use a Becton Dickinson (BD) cytometer in your lab, the chances are you are acquiring your data using ‘Diva’ software. Diva software is used to acquire your cytometry data on LSRII, LSRFortessa, CantoII and Aria cell sorters. As well as acquiring your data using Diva software, you can also analyse your data after…