Available Apps¶

Blender¶

Blender is a free and open source 3D creation suite.

The Blender GUI can be accessed via the Open OnDemand Applications. This requires 3D acceleration for visualisation and rendering so needs to be run on a GPU partition.

ChimeraX¶

The ChimeraX GUI can be accessed via the Open OnDemand Applications. This requires 3D acceleration for visualisation so needs to be run on a GPU VirtualGL partition.

CLC genomics Workbench¶

QIAGEN CLC genomics Workbench is a user-friendly sequence analysis platform for genomics, epigenomics and metagenomics.

Warning

CLC Genomics Workbench is licensed software. The Research Cluster currently has a small number of floating licenses available for trial purposes, facilitated by Dr Sunali Mehta <mailto:sunali.mehta@otago.ac.nz>_, Pathology dept. Please ensure you are authorised to consume a license.

The CLC genomics Workbench GUI can be accessed via the Open OnDemand Applications.

Optionally tick the '3D hardware-accelerated rendering option and select a GPU partition if using the 3D viewers.

EcoAssist¶

The EcoAssist GUI can be accessed via the Open OnDemand Applications.

EPI2ME Desktop¶

Oxford Nanopore's EPI2ME Desktop is a data analysis platform providing a user-friendly graphical interface to running various bioinformatics pipelines.

Note

Apart from the list of ONT workflows prepopulated in the Available Workflows tab, EPI2ME Desktop allows for the importation of other generic Nextflow workflows, such as the 100+ curated pipelines of []nf-core](https://nf-co.re/pipelines).

Under Workflows, click Import workflow and copy-paste the workflow's git repository URL. (i.e. https://github.com/nf-core/<wf>)

The EPI2ME GUI can be accessed via the Open OnDemand Applications.

Individual pipeline tasks will be sent to the Slurm cluster scheduler and scheduled as separate jobs with their own allocated resources (as per the workflow defaults, or as specified in the Nextflow configuration tab).
For pipelines requiring GPU compute, there is no need to run the EPI2ME OOD app on a GPU partition -In fact, the OOD app form doesn't give you that option-; Individual tasks requiring GPUs will be automatically scheduled on GPU-capable cluster nodes.
In the EPI2ME Launch Wizard, there is also no need to change the Profile setting (in Nextflow configuration); This instance has been patched to default to the singularity profile (which uses apptainer).

To accomplish this, running the OnDemand app for the first time will automatically create the global nextflow config $HOME/.nextflow/config to support running the tasks via the cluster scheduler and make use of the GPU partition when appropriate. However if this file already exists, you may need to manually add this functionality:

Terminal

  process {
    executor = 'slurm'
    time = 6.h
    withLabel: 'gpu' {
      queue = 'aoraki_gpu'
    }
  }

Warning

EPI2ME Desktop isn't designed with HPC cluster use in mind. As such we have had to devise a number of workarounds to make this work and integrate with the cluster scheduler. While initial testing has been promising, the added complexity of running EPI2ME Desktop this way, as well as the application's general lack of (Nextflow) configurability may introduce hard-to-troubleshoot issues.

Consider running the workflows directly from the commandline using Nextflow instead.

Fiji¶

Fiji is an image processing package — a "batteries-included" distribution of ImageJ, bundling many plugins which facilitate scientific image analysis. .

The Fiji GUI is available as an Open OnDemand app.

FlexPDE¶

The FlexPDE GUI can be accessed via the Open OnDemand Applications.

The FlexPDE Lite (evaluation) configuration is free to use but wil be restricted in the number of simultaneous equations and mesh cells.

FlexPDE Professional can be Internet-activated with an appropriate serial number. Do note that the license activation is machine-based so will need to be deactivated and reactivated on subsequent runs unless the same node is selected.

GRASS GIS¶

The GRASS GUI can be accessed via the Open OnDemand Applications.

ilastik¶

ilastik is a user-friendly open-source tool for interactive image classification, segmentation and analysis leveraging machine learning algorithms.

via OnDemand¶

The ilastik GUI is available as an Open OnDemand app.

Jupyter Lab¶

Jupyter Lab can be accessed via the Open OnDemand applications.

This app features a number of domain-focused or application-specific variants. These containerised software stacks are immutable which promotes consistency and reproducibility.

The different environments are based on the Jupyter Docker Stacks images, maintained by the Jupyter team.

Contact us if you require a customised environment.

Kilosort4¶

Kilosort4 is a tool for clustering spikes from multi-channel electrophysiological recordings.

https://kilosort.readthedocs.io

via OnDemand¶

The Kilosort4 GUI is available as an Open OnDemand app.

MELTS¶

Legacy software for thermodynamic modeling of phase equilibria in magmatic systems experimental

🔗 https://melts.ofm-research.org

The MELTS GUI can be accessed via the Open OnDemand Applications.

The launcher allows for the selection of the different versions/models;

rhyolite-MELTS v. 1.0.2 (original version, with corrections) - old H2O model, no mixed fluids.
rhyolite-MELTS v, 1.1.0 (mixed fluid version that perserves the ternary minimum) - old H2O model.
rhyolite-MELTS v. 1.2.0 (mixed fluid version optimal for mafic and alkalic melts) - new H2O model.
pMELTS v. 5.6.1 (original version, with corrections) - - old H2O model, no mixed fluids.

NetLogo¶

The NetLogo GUI can be accessed via the Open OnDemand Applications.

QGIS¶

The QGIS GUI can be accessed via the Open OnDemand Applications.

RELION¶

The RELION GUI can be accessed via the Open OnDemand Applications.

RStudio Server¶

The RStudio Server web UI can be accessed via the Open OnDemand Applications.

SAGA GIS¶

The SAGA GUI can be accessed via the Open OnDemand Applications.

SaTScan¶

The SaTScan GUI can be accessed via the Open OnDemand Applications.

Specify¶

The Spcify 6 GUI can be accessed via the Open OnDemand Applications.

Stata¶

The Stata GUI can be accessed via the Open OnDemand Applications.

UGENE¶

https://ugene.net

UGENE is a GUI for DNA and protein sequence visualization, alignment, assembly and annotation. It integrates dozens of well-known biological tools, algorithms, and original tools in the context of genomics, evolutionary biology, virology, and other branches of life science.

GUI¶

The UGENE GUI can be accessed via the Open OnDemand Applications. https://ondemand.otago.ac.nz/pun/sys/dashboard/batch_connect/sys/ood_ugene_apptainer

hardware-accelerated 3D visualisation can be enabled to improve 3D visualisation (e.g. the 3D viewer)
OpenCL can be enabled to improve performance of a few select algorithms (Smith-Waterman, UGENE Genome Aligner)

VSCodium¶

VSCodium is a community-driven, freely-licensed distribution of Microsoft's editor VSCode.

The VSCodium GUI can be accessed via the Open OnDemand Applications.