Using rclone, teams channels, and onedrive on deepthought
Recently, our HPC, deepthought has been running low on storage space. There are several options, but one that we are using is to combine deepthought, rclone,...
Recently, our HPC, deepthought has been running low on storage space. There are several options, but one that we are using is to combine deepthought, rclone,...
Heres a way to get some PDB files from Google cloud
How to search for all the WGS metagenomes in the cloud
Starting a Google VM Sometimes you might want to spin up a Google VM to use: WARNING: There maybe charges for starting a VM, running BigQuery searches, or ...
This is another in our series of posts on searching things in the SRA. As we noted previously, NCBI has moved most of the SRA into the clouds, which makes se...
how to update your repo to match code that was added upstream
a quick set of commands to clone a repository to update code
Instructions and guidelines for Flinders researchers
Congrats to FAME’s first honours student, Amber Skye on her graduation!
A wrap up of the FAME labs’ trip to the Australian Society for Microbiology conference in Sydney
Most of these instructions come from the official jupyter docs and you should use those as a guide
Congrats to FAMEous person - Laura Inglis on her recent achievements!
Elizabeth Dinsdale talks Shark Epidermis Microbiomes on American Society for Microbiology podcast.
Celebrating World Oceans Days with the Dinsdale Lab research group.
What should we worry about before we inject phage into people?
Congrats to FAMEous person - Susie Grigson on her recent achievements!
Southern eagle ray sampling with the Southern Shark Ecology Group (Huveneers lab).
Women’s History month commemorates women’s contribution to history, science, culture, and society.
On Feb 11th we acknowledge and celebrate the incredible women of STEM on Women in Science Day.
Krona plots are a fantastic way of representing heirarchial data such as taxonomic annotations. These plots are interactive, visually appealing, and best of...
DeepMind’s AlphaFold is winning at predicting tertiary structures from primary amino acid sequences. We thought it would be fun to investigate how it perfo...
Recently, NCBI released their new datasets API that might replace NCBI E-utils. At the moment, datasets is focused on genomes, genes, and viruses, but no dou...
We often want to calculate Pearson correlation between different datasets, for example, we have used it to identify the hosts of different phages. Often, we...
This post is one of a multipart series about analysing your metagenomics samples with Atavide. It is intended to be a quick and dirty look at the superfocus ...
A simple pipeline for complex annotations of metagenomes incorporating lots of tools
Why would I want to connect to the network. When you connect to the VPN it makes it seem like you are on the Flinders University Network even if you are at ...
Why would I want to do this? I am not really sure, but if you want to use Qiime2 you should install it on deepthought using conda. The sysadmins (may they ...
super-FOCUS Super-FOCUS is a tool to identify the functions that the sequences in your metagenome are doing. As a benefit, it also identifies the taxonomy a...
Kraken2 Kraken2 is a tool to identify the taxonomy of the things in your environmental sample. It does not identify what those things are doing, but what is...
This is an update from a previous post https://fame.flinders.edu.au/blog/2020/09/04/snakemakeprofile where Rob outlines a simple Snakemake profile for runnin...
Snakemake checkpoints are a little complex to get your head around, and so here are two examples that will hopefully clarify some use cases. Before we begin...
“Prophages, Phages, and Viruses Associated with Irritable Bowel Disease and Crohn’s Disease Notes”
It can be daunting when you’re just starting out using the Linux command line to access the University’s HPC resources.
I’m working on a pipeline that uses and generates tens of thousands of files, and there’s a good chance this could be expanded to produce hundreds of thousa...
PyCharm is a terrific Python IDE, and you should use it for code development
Most of these instructions come from the official jupyter docs and you should use those as a guide
We have a computational problem searching the Non-Redundant database, but we can solve that! If you use MMSeqs2 to search the NR database, it needs about 1....
Setting up a snakemake profile for deepthought will make your life much easier
snakemake is a pipelining tool that allows you to recreate reusable pipelines to analyse data
We are going to use conda to install and update software
Introduction To Using the Flinders HPC ‘DeepThought’ For Bioinformatics
Research Associate in the Edwards lab
PhD Student in the Edwards lab
Research Associate in the Edwards lab
PhD student in the Dinsdale lab
Rob is the Director of Bioinformatics and Human Microbiology for FAME.
PhD student in the Edwards lab
Research Associate in Microbiome Research in the Dinsdale lab
Research Fellow in Bioinformatics in the Edwards lab and FAME webmaster
FAME Liaison and Research Fellow in the Dinsdale lab
My research uses genomics to investigate the biodiversity and ecology of microbes and viruses on coral reefs, kelp forest and shark epidermis.
PhD student in the Edwards lab
Honours student in the Dinsdale lab
Research Associate in the Dinsdale lab
Research Associate in the Edwards lab
Honours student in the Dinsdale lab
Honours student in the Dinsdale lab
Honours student in the Edwards lab
PhD student in the Dinsdale lab
Research Associate in the Dinsdale lab
Honours student in the Dinsdale lab and FAME Webmaster
Phables is a tool developed to resolve bacteriophage genomes using phage bubbles in viral metagenomic data.
Hecatomb is a pipeline for accurately classifying viral sequences in metagenome samples.
SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data
PRINSEQ is used for easy and rapid quality control and data preprocessing of genomic and metagenomic datasets.
PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes.
PHANOTATE is a tool to annotate phage genomes.
FOCUS: An Alignment-Free Model To Identify Organisms In Metagenomes Using Non-Negative Least Squares Usage.
Past speakers at FAME events in 2021
Microbiomes of Chondrichthyes: Using basal vertebrates to investigate phylosymbiosis
Microbiome and metagenome monthly meetings (feat. talks + networking)
Fortnightly meeting at Flinders Uni to discuss bioinformatics-related problems/ideas
View all FAME posters and talks presented at ASM 2022!
View project summaries for the FAME seed projects for 2021
With the new release of Phispy2, we present a framework for prophage prediction software comparison
Understanding the role of Bacteriophages in IBD
Learn all about deduplicating highly heterozygous genome assemblies
Yet another Snakemake tutorial, part 2
Yet another Snakemake tutorial…