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
Archive
- Tutorial 8
- Researchers 7
- Students 7
- DeepThought 6
- Phage 6
- Snakemake 5
- Alumni 4
- Metagenome 4
- Jupyter 3
- Presentation 3
- deepthought 3
- Conda 2
- Regular meetings 2
- Group Leaders 2
- IBD 2
- Prophage 2
- Virus 2
- metagenome 2
- annotation 2
- alphafold 2
- phage 2
- git 2
- google 2
- cloud 2
- mmseqs 1
- mmseqs2 1
- non-redundant 1
- database 1
- search 1
- QC 1
- PyCharm 1
- Upcoming events 1
- Linux 1
- Checkpoints 1
- Deepthought 1
- Kraken2 1
- superfocus 1
- super-focus 1
- collaborate 1
- qiime2 1
- conda 1
- vpn 1
- remote 1
- ssh 1
- microbiome 1
- atavide 1
- R 1
- Past presentations 1
- turbocor 1
- pearson 1
- correlation 1
- statistics 1
- ncbi 1
- ncbi_dataset 1
- lambda 1
- Krona 1
- FOCUS 1
- genomics 1
- Conference 1
- SRA 1
- Google 1
- sra 1
- colabfold 1
- teams 1
- onedrive 1
- microsoft 1
- rclone 1
Tutorial
Getting started with linux
It can be daunting when you’re just starting out using the Linux command line to access the University’s HPC resources.
Using PyCharm and Jupyter Notebooks
PyCharm is a terrific Python IDE, and you should use it for code development
How to run a Jupyter notebook on deepthought
Most of these instructions come from the official jupyter docs and you should use those as a guide
Part 4: Snakemake profiles for DeepThought
Setting up a snakemake profile for deepthought will make your life much easier
Part 3: Using snakemake on deepthought
snakemake is a pipelining tool that allows you to recreate reusable pipelines to analyse data
Part 2: Using conda on deepthought
We are going to use conda to install and update software
Part 1: DeepThought General Overview
Introduction To Using the Flinders HPC ‘DeepThought’ For Bioinformatics
Researchers
Vijini Mallawaarachchi
Research Associate in the Edwards lab
Sarah Giles
Research Associate in the Edwards lab
Nick Falk
Research Associate in Microbiome Research in the Dinsdale lab
Michael Roach
Research Fellow in Bioinformatics in the Edwards lab and FAME webmaster
Michael Doane
FAME Liaison and Research Fellow in the Dinsdale lab
Jessica Carlson-Jones
Research Associate in the Edwards lab
Belinda Martin
Research Associate in the Dinsdale lab
Students
Susie Grigson
PhD Student in the Edwards lab
Ryan Hesse
PhD student in the Dinsdale lab
Bhavya Papudeshi
PhD student in the Edwards lab
Laura Inglis
PhD student in the Edwards lab
Haylee Smith
Honours student in the Dinsdale lab
Ewan Burns
Honours student in the Dinsdale lab
Emma Kerr
PhD student in the Dinsdale lab
DeepThought
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
How to run a Jupyter notebook on deepthought
Most of these instructions come from the official jupyter docs and you should use those as a guide
Part 4: Snakemake profiles for DeepThought
Setting up a snakemake profile for deepthought will make your life much easier
Part 3: Using snakemake on deepthought
snakemake is a pipelining tool that allows you to recreate reusable pipelines to analyse data
Part 2: Using conda on deepthought
We are going to use conda to install and update software
Part 1: DeepThought General Overview
Introduction To Using the Flinders HPC ‘DeepThought’ For Bioinformatics
Phage
Phables
Phables is a tool developed to resolve bacteriophage genomes using phage bubbles in viral metagenomic data.
Rob’s presentation at ASM 2021
“Prophages, Phages, and Viruses Associated with Irritable Bowel Disease and Crohn’s Disease Notes”
Phispy
PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes.
PHANOTATE
PHANOTATE is a tool to annotate phage genomes.
Prophage prediction software comparison
With the new release of Phispy2, we present a framework for prophage prediction software comparison
Phages and IBD
Understanding the role of Bacteriophages in IBD
Snakemake
Snakemake profiles updated
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...
How to use Snakemake Checkpoints
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...
Managing thousands of files in your Snakemake pipelines
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...
Part 4: Snakemake profiles for DeepThought
Setting up a snakemake profile for deepthought will make your life much easier
Part 3: Using snakemake on deepthought
snakemake is a pipelining tool that allows you to recreate reusable pipelines to analyse data
Alumni
Kale Christopher
Honours student in the Dinsdale lab
Jody McKerral
Research Associate in the Dinsdale lab
Evan Pargin
Honours student in the Edwards lab
Amber Skye
Honours student in the Dinsdale lab and FAME Webmaster
Metagenome
Krona plots are easy (metagenomics example)
Krona plots are a fantastic way of representing heirarchial data such as taxonomic annotations. These plots are interactive, visually appealing, and best of...
Hecatomb
Hecatomb is a pipeline for accurately classifying viral sequences in metagenome samples.
SUPER-FOCUS
SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data
FOCUS
FOCUS: An Alignment-Free Model To Identify Organisms In Metagenomes Using Non-Negative Least Squares Usage.
Jupyter
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
Using PyCharm and Jupyter Notebooks
PyCharm is a terrific Python IDE, and you should use it for code development
How to run a Jupyter notebook on deepthought
Most of these instructions come from the official jupyter docs and you should use those as a guide
Presentation
FAME's fabulous ASM tour
A wrap up of the FAME labs’ trip to the Australian Society for Microbiology conference in Sydney
Presentations and posters at ASM 2022
View all FAME posters and talks presented at ASM 2022!
Rob’s presentation at ASM 2021
“Prophages, Phages, and Viruses Associated with Irritable Bowel Disease and Crohn’s Disease Notes”
deepthought
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,...
How to install and use super-focus on deepthought
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...
How to install and use Kraken2 on deepthought
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...
Conda
Getting started with linux
It can be daunting when you’re just starting out using the Linux command line to access the University’s HPC resources.
Part 2: Using conda on deepthought
We are going to use conda to install and update software
Regular meetings
JAMS sponsored by FAME
Microbiome and metagenome monthly meetings (feat. talks + networking)
FAME Fortnightly Bioinf Meeting
Fortnightly meeting at Flinders Uni to discuss bioinformatics-related problems/ideas
Group Leaders
Rob Edwards
Rob is the Director of Bioinformatics and Human Microbiology for FAME.
Liz Dinsdale
My research uses genomics to investigate the biodiversity and ecology of microbes and viruses on coral reefs, kelp forest and shark epidermis.
IBD
Rob’s presentation at ASM 2021
“Prophages, Phages, and Viruses Associated with Irritable Bowel Disease and Crohn’s Disease Notes”
Phages and IBD
Understanding the role of Bacteriophages in IBD
Prophage
Rob’s presentation at ASM 2021
“Prophages, Phages, and Viruses Associated with Irritable Bowel Disease and Crohn’s Disease Notes”
Prophage prediction software comparison
With the new release of Phispy2, we present a framework for prophage prediction software comparison
Virus
Rob’s presentation at ASM 2021
“Prophages, Phages, and Viruses Associated with Irritable Bowel Disease and Crohn’s Disease Notes”
Hecatomb
Hecatomb is a pipeline for accurately classifying viral sequences in metagenome samples.
metagenome
Searching for metagenomes on the SRA in the cloud
How to search for all the WGS metagenomes in the cloud
Atavide: atavistic metagenome analysis with a vision
A simple pipeline for complex annotations of metagenomes incorporating lots of tools
annotation
Therapeutic Annotation of Phage Genomes
What should we worry about before we inject phage into people?
Atavide: atavistic metagenome analysis with a vision
A simple pipeline for complex annotations of metagenomes incorporating lots of tools
alphafold
Extracting some data from Google Cloud
Heres a way to get some PDB files from Google cloud
Running AlphaFold on phage lambda
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...
phage
Therapeutic Annotation of Phage Genomes
What should we worry about before we inject phage into people?
Running AlphaFold on phage lambda
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...
git
Forking a git repo and then updating the upstream changes
how to update your repo to match code that was added upstream
How to clone a git repository to develop code
a quick set of commands to clone a repository to update code
Extracting some data from Google Cloud
Heres a way to get some PDB files from Google cloud
Searching for metagenomes on the SRA in the cloud
How to search for all the WGS metagenomes in the cloud
cloud
Extracting some data from Google Cloud
Heres a way to get some PDB files from Google cloud
Searching for metagenomes on the SRA in the cloud
How to search for all the WGS metagenomes in the cloud
mmseqs
Searching the NR database with MMSeqs2
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....
mmseqs2
Searching the NR database with MMSeqs2
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....
non-redundant
Searching the NR database with MMSeqs2
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....
database
Searching the NR database with MMSeqs2
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....
search
Searching the NR database with MMSeqs2
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....
QC
Prinseq
PRINSEQ is used for easy and rapid quality control and data preprocessing of genomic and metagenomic datasets.
PyCharm
Using PyCharm and Jupyter Notebooks
PyCharm is a terrific Python IDE, and you should use it for code development
Upcoming events
Royal Society of South Australia lecture feat. Liz Dinsdale
Microbiomes of Chondrichthyes: Using basal vertebrates to investigate phylosymbiosis
Linux
Getting started with linux
It can be daunting when you’re just starting out using the Linux command line to access the University’s HPC resources.
Checkpoints
How to use Snakemake Checkpoints
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...
Deepthought
Snakemake profiles updated
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
How to install and use Kraken2 on deepthought
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...
superfocus
How to install and use super-focus on deepthought
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
How to install and use super-focus on deepthought
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...
collaborate
FAME seed projects for 2021
View project summaries for the FAME seed projects for 2021
qiime2
How to install qiime2 on deepthought
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 ...
conda
How to install qiime2 on deepthought
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 ...
vpn
How to use the VPN to connect to Flinders network
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 ...
remote
How to use the VPN to connect to Flinders network
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 ...
ssh
How to use the VPN to connect to Flinders network
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 ...
microbiome
Atavide: atavistic metagenome analysis with a vision
A simple pipeline for complex annotations of metagenomes incorporating lots of tools
atavide
Atavide: importing your data into R
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 ...
R
Atavide: importing your data into R
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 presentations
2021 Presentations
Past speakers at FAME events in 2021
turbocor
Fast correlations with turbocor
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...
pearson
Fast correlations with turbocor
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...
correlation
Fast correlations with turbocor
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...
statistics
Fast correlations with turbocor
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...
ncbi
NCBI datasets and genome assembly data
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...
ncbi_dataset
NCBI datasets and genome assembly data
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...
lambda
Running AlphaFold on phage lambda
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
Krona plots are easy (metagenomics example)
Krona plots are a fantastic way of representing heirarchial data such as taxonomic annotations. These plots are interactive, visually appealing, and best of...
FOCUS
Krona plots are easy (metagenomics example)
Krona plots are a fantastic way of representing heirarchial data such as taxonomic annotations. These plots are interactive, visually appealing, and best of...
genomics
Therapeutic Annotation of Phage Genomes
What should we worry about before we inject phage into people?
Conference
FAME's fabulous ASM tour
A wrap up of the FAME labs’ trip to the Australian Society for Microbiology conference in Sydney
SRA
Searching SRA Metadata in the Cloud
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 start a Google VM
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 ...
sra
Searching for metagenomes on the SRA in the cloud
How to search for all the WGS metagenomes in the cloud
colabfold
Extracting some data from Google Cloud
Heres a way to get some PDB files from Google cloud
teams
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,...
onedrive
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,...
microsoft
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,...
rclone
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,...