My Zotero bib has over 7000 entries. I can't submit that to a journal! They usually only want it when the paper has been accepted. Zotero should be able to do this for you with bbt, but it never seems to work. Simplest way I found: Download the bib file from overleaf. Look in the … Continue reading You’ve got a paper accepted and now you need a reasonable bib file →

Western Blot for Histone Proteins Protocol

Adapted from Abcam Histone Western Blot Protocol, Invitrogen NuPAGE Technical Guide and Dr Ben Cooper’s Western Blotting Protocol for HSP90 v5. Histone Extraction - using the Abcam Histone Extraction Kit Prepare reagents: 1x Pre-Lysis Buffer: dilute 1ml of 10x buffer with 9ml distilled water. Balance DTT Buffer: add 1μl of DTT solution to 500μl Balance … Continue reading Western Blot for Histone Proteins Protocol →

ALICE2 Basics

Here are a few tips for using the ALICE2 high performance computing cluster. This post is not designed to teach you how to use a command line interface, rather to just introduce you to the specifics of ALICE2. Logging in: ssh <username>@alice2.le.ac.uk, enter your password and text message verification code if off campusDo all of … Continue reading ALICE2 Basics →

Sanger Sequencing

Here is how we do Sanger sequencing in the lab for PCR products using https://www.sourcebioscience.com/. NOTE: we now have a lab account for Source Bioscience set up. You can also set up your own account as long as you use the lab purchase order number. Carry out your PCR reactionClean up using one of the … Continue reading Sanger Sequencing →

A labscrum refresh

The original labscrum document https://sel.home.blog/wp-content/uploads/2022/03/b4c3c-labscrumguide.pdf. Overall I think these meetings have worked better than expected due mainly to your engagement with them. Below is a refresh of what each meeting should be. Sprint planning (first Monday) Tell us your goals for this sprint. This is not a todo list. Rather it is the high level things … Continue reading A labscrum refresh →

How to read a scientific paper

Those were the days Recently, I've read alot around how to read a scientific paper. There seems to be three types of advice: The blindingly obvious ("an abstract is a summary of the paper")The too abstract to be useful ("you must become an active reader")Some version of a system I already use. So I'll just … Continue reading How to read a scientific paper →

Making a Conda environment on ALICE

Here are the instructions for making a Conda environment on ALICE. https://uniofleicester.sharepoint.com/sites/Research-Computing/SitePages/python.aspx Specifically, in your home (~) directory run: wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -P ~ bash Miniconda3-latest-Linux-x86_64.sh Then you can make your environments and install what you need as so: conda create -n ENVNAME python=3.8 conda activate ENVNAME conda install numpy Then to call an environment from … Continue reading Making a Conda environment on ALICE →

Ensuring correct coverage in MethylKit

Ben (previous postdoc in the lab) recently discovered that MethylKit automatically filters data based on coverage when the files are first read into R. We usually destrand our data (i.e. merge the reads from the positive and negative DNA strand to increase coverage at each CpG site) after we have read the data in and … Continue reading Ensuring correct coverage in MethylKit →

Converting markdown to rtf without files

I often would like to paste my markdown into an email and have it be rendered into something pretty. This is something airmail did automatically, but the Uni won't support that anymore. So what to do with Outlook? I could always convert to docx file using pandoc and then cut and paste the contents. Bit … Continue reading Converting markdown to rtf without files →