How to run a Jupyter notebook on a deepthought node
Most of these instructions come from the official jupyter docs and you should use those as a guide
Most of these instructions come from the official jupyter docs and you should use those as a guide
It can be daunting when you’re just starting out using the Linux command line to access the University’s HPC resources.
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
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
Research Associate 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
Research Associate in the Edwards lab
Research Associate in the Dinsdale lab
PhD Student in the Edwards lab
PhD student in the Dinsdale lab
PhD student in the Edwards lab
PhD student in the Edwards lab
Honours student in the Dinsdale lab
Honours student in the Dinsdale lab
PhD student in the Dinsdale lab
Most of these instructions come from the official jupyter docs and you should use those as a guide
Most of these instructions come from the official jupyter docs and you should use those as a guide
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
Phables is a tool developed to resolve bacteriophage genomes using phage bubbles in viral metagenomic data.
“Prophages, Phages, and Viruses Associated with Irritable Bowel Disease and Crohn’s Disease Notes”
PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes.
PHANOTATE is a tool to annotate phage genomes.
With the new release of Phispy2, we present a framework for prophage prediction software comparison
Understanding the role of Bacteriophages in IBD
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...
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...
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
Honours student in the Dinsdale lab
Research Associate in the Dinsdale lab
Honours student in the Edwards lab
Honours student in the Dinsdale lab and FAME Webmaster
Krona plots are a fantastic way of representing heirarchial data such as taxonomic annotations. These plots are interactive, visually appealing, and best of...
Hecatomb is a pipeline for accurately classifying viral sequences in metagenome samples.
SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data
FOCUS: An Alignment-Free Model To Identify Organisms In Metagenomes Using Non-Negative Least Squares Usage.
Most of these instructions come from the official jupyter docs and you should use those as a guide
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
A wrap up of the FAME labs’ trip to the Australian Society for Microbiology conference in Sydney
View all FAME posters and talks presented at ASM 2022!
“Prophages, Phages, and Viruses Associated with Irritable Bowel Disease and Crohn’s Disease Notes”
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,...
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...
It can be daunting when you’re just starting out using the Linux command line to access the University’s HPC resources.
We are going to use conda to install and update software
Microbiome and metagenome monthly meetings (feat. talks + networking)
Fortnightly meeting at Flinders Uni to discuss bioinformatics-related problems/ideas
Rob is the Director of Bioinformatics and Human Microbiology for FAME.
My research uses genomics to investigate the biodiversity and ecology of microbes and viruses on coral reefs, kelp forest and shark epidermis.
“Prophages, Phages, and Viruses Associated with Irritable Bowel Disease and Crohn’s Disease Notes”
Understanding the role of Bacteriophages in IBD
“Prophages, Phages, and Viruses Associated with Irritable Bowel Disease and Crohn’s Disease Notes”
With the new release of Phispy2, we present a framework for prophage prediction software comparison
“Prophages, Phages, and Viruses Associated with Irritable Bowel Disease and Crohn’s Disease Notes”
Hecatomb is a pipeline for accurately classifying viral sequences in metagenome samples.
How to search for all the WGS metagenomes in the cloud
A simple pipeline for complex annotations of metagenomes incorporating lots of tools
What should we worry about before we inject phage into people?
A simple pipeline for complex annotations of metagenomes incorporating lots of tools
Heres a way to get some PDB files from Google cloud
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...
What should we worry about before we inject phage into people?
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...
how to update your repo to match code that was added upstream
a quick set of commands to clone a repository to update code
Heres a way to get some PDB files from Google cloud
How to search for all the WGS metagenomes in the cloud
Heres a way to get some PDB files from Google cloud
How to search for all the WGS metagenomes in the cloud
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....
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....
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....
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....
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....
PRINSEQ is used for easy and rapid quality control and data preprocessing of genomic and metagenomic datasets.
PyCharm is a terrific Python IDE, and you should use it for code development
Microbiomes of Chondrichthyes: Using basal vertebrates to investigate phylosymbiosis
It can be daunting when you’re just starting out using the Linux command line to access the University’s HPC resources.
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...
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...
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...
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...
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...
View project summaries for the FAME seed projects for 2021
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 ...
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 ...
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 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 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 ...
A simple pipeline for complex annotations of metagenomes incorporating lots of tools
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 ...
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 ...
Past speakers at FAME events in 2021
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...
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...
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...
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...
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...
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...
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...
Krona plots are a fantastic way of representing heirarchial data such as taxonomic annotations. These plots are interactive, visually appealing, and best of...
Krona plots are a fantastic way of representing heirarchial data such as taxonomic annotations. These plots are interactive, visually appealing, and best of...
What should we worry about before we inject phage into people?
A wrap up of the FAME labs’ trip to the Australian Society for Microbiology conference in Sydney
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...
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 ...
How to search for all the WGS metagenomes in the cloud
Heres a way to get some PDB files from Google cloud
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,...
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,...