diff --git a/_data/sidebars/main.yml b/_data/sidebars/main.yml index 354a004..c6280b7 100644 --- a/_data/sidebars/main.yml +++ b/_data/sidebars/main.yml @@ -6,8 +6,8 @@ subitems: url: /processes - title: Available resources url: /resources - - title: Existing projects - url: /projects + - title: ABLeS Participants + url: /participants - title: Shared software and reference data url: /if89 - title: Acknowledging ABLeS diff --git a/faq.md b/faq.md index f432be6..0e96b7f 100755 --- a/faq.md +++ b/faq.md @@ -29,19 +29,19 @@ toc: false
- The allocation of SUs is on a quarterly basis. At the beginning of each quarter, BioCommons will allocate 100 kSU of computational resources to each community. Additional resources will be allocated according to the quarterly plan proposed by the community, as well as the resources still available in that quarter. -
Communities should utilise the allocated SUs: + The allocation of SUs is on a quarterly basis. At the beginning of each quarter, BioCommons will allocate 100 kSU of computational resources to each participant. Additional resources will be allocated according to the quarterly plan proposed by the participant, as well as the resources still available in that quarter. +
Groups should utilise the allocated SUs:
  1. For projects approved by the steering committee.
    2. -
  2. Using the tools, methods and/or workflows that are suited to their community requirements.
    3. -
  3. While making sure to consider that the allocation is a shared resource for their community (if in doubt, consult with your community bioinformatics lead, or the BioCommons)
    4. +
  4. Using the tools, methods and/or workflows that are suited to their participant requirements.
    5. +
  5. While making sure to consider that the allocation is a shared resource for their participant (if in doubt, consult with your participant bioinformatics lead, or the BioCommons)
Note:
    -
  • Communities can request additional resources when needed through the GoogleForm, if the quarterly plan did not accurately predict resource requirements.
    • +
  • Groups can request additional resources when needed through the GoogleForm, if the quarterly plan did not accurately predict resource requirements.
  • Unused SUs **can NOT** be rolled-over to the next quarter.
    • -
  • As ABLeS is a shared resource covering many communities, it is expected that each community will adopt a best-effort approach to firstly estimate their computational requirement realistically and accurately, and also actively manage the allocations which are provided (i.e. don’t waste your allocation, as the resource is still finite).
    • +
  • As ABLeS is a shared resource covering many participants, it is expected that each participant will adopt a best-effort approach to firstly estimate their computational requirement realistically and accurately, and also actively manage the allocations which are provided (i.e. don’t waste your allocation, as the resource is still finite).
diff --git a/if89-technical.md b/if89-technical.md index 777ff8c..2b5fbf2 100755 --- a/if89-technical.md +++ b/if89-technical.md @@ -6,7 +6,7 @@ title: ABLeS - Application Installation Guidelines The following documentation describes the installation procedures for bioinformatics software at the National Computational Infrastructure (NCI project allocation if89) enabled by the Australian BioCommons and included in Tools and Workflows repository. -The maintenance process is purposely standardised using scripts to allow for sustainability. These scripts were developed to be similar to the NCI software management scripts to enable transferability. NCI staff, AusARG bioinformatics community, and bioinformatics/computational biology leads for the Australian BioCommons Leadership Share (ABLeS) program contributed to these scripts. +The maintenance process is purposely standardised using scripts to allow for sustainability. These scripts were developed to be similar to the NCI software management scripts to enable transferability. NCI staff, AusARG bioinformatics participant, and bioinformatics/computational biology leads for the Australian BioCommons Leadership Share (ABLeS) program contributed to these scripts. >* All software on if89 should be installed into `/g/data/if89/apps directory`. >* One directory for each software, then a subdirectory for each version of this software. @@ -22,7 +22,7 @@ This script should be added to the repository of all scripts and patches, which In order to contribute to `if89`, you need to satisfy the following conditions: 1. **Obtain access to the `if89` project**: Everyone can request access to `if89` if they have a user account on GADI. Simply, request to join at this [link](https://my.nci.org.au/mancini/project/if89). -2. **Request to join the writer group under `if89`**: request to join at this [link](https://my.nci.org.au/mancini/project/if89_w) +2. **Request to join the writer participant under `if89`**: request to join at this [link](https://my.nci.org.au/mancini/project/if89_w) 3. **Request access to `ables-software-installations` repository**: The repository link is [https://git.nci.org.au/dsr900/ables-software-installations](https://git.nci.org.au/dsr900/ables-software-installations). Access is managed through your Gadi username and password. If you do not have access, please contact one of the following repository maintainers and they will add you: diff --git a/if89.md b/if89.md index fa6181c..5c30b50 100755 --- a/if89.md +++ b/if89.md @@ -3,9 +3,9 @@ title: Shared repository of tools and software (`project if89` on NCI) toc: false --- -ABLeS communities have access to the Australian BioCommons Tools and Workflows project, in project allocation if89. This -is a repository of popular tools, containers and workflows that can be used by anyone in the NCI user community. Anyone -from an NCI community can contribute to if89 and add more tools that will be shared with others. +ABLeS participants have access to the Australian BioCommons Tools and Workflows project, in project allocation if89. This +is a repository of popular tools, containers and workflows that can be used by anyone in the NCI user participant. Anyone +from an NCI participant can contribute to if89 and add more tools that will be shared with others. # Software diff --git a/index.md b/index.md index 288e28e..0a53705 100644 --- a/index.md +++ b/index.md @@ -18,7 +18,7 @@ toc: false The ABLeS (Australian BioCommons Leadership Share) program was established in April 2021 to more readily support data-driven bioinformatics. This effort is supported by the [Australian BioCommons](https://www.biocommons.org.au/) in partnership with Bioplatforms Australia, the [National Computational Infrastructure (NCI, Canberra)](https://nci.org.au/), and the [Pawsey Supercomputing Research Centre (Pawsey, Perth)](https://pawsey.org.au/). -ABLeS targets established groups and communities that are focused on a common research theme, create reference data and/or software, and have the ability to plan and prioritise a computational research program. +ABLeS targets established participants and participants that are focused on a common research theme, create reference data and/or software, and have the ability to plan and prioritise a computational research program. ABLeS projects broadly align with the following three principles: @@ -28,7 +28,7 @@ ABLeS projects broadly align with the following three principles: 3. Resources are planned and approached with a level of care appropriate to their status as limited and consumable resources. -The support available includes access to computational and data infrastructure, specialist expertise, support to adopt best practices and share outputs effectively, and a community led and shared repository of bioinformatics software (i.e. tools and workflows). +The support available includes access to computational and data infrastructure, specialist expertise, support to adopt best practices and share outputs effectively, and a participant led and shared repository of bioinformatics software (i.e. tools and workflows). More details are available in the ABLeS publication: @@ -39,11 +39,11 @@ More details are available in the ABLeS publication: ### Creation of reference data assets -ABLeS reference data allocations support research groups and consortia within the life sciences to access the dedicated compute capacity required to efficiently construct reference data. +ABLeS reference data allocations support research participants and consortia within the life sciences to access the dedicated compute capacity required to efficiently construct reference data. ### Production bioinformatics -Institutes, consortia and core facilities are increasingly facing issues scaling their in-house compute and data infrastructure to the questions, sample sizes, and data set sizes they are addressing as part of their research programs. ABLeS production allocations support these groups to implement and run their computational workflow approaches for omics data analysis *at scale*. +Institutes, consortia and core facilities are increasingly facing issues scaling their in-house compute and data infrastructure to the questions, sample sizes, and data set sizes they are addressing as part of their research programs. ABLeS production allocations support these participants to implement and run their computational workflow approaches for omics data analysis *at scale*. ### Software accelerator diff --git a/projects.md b/participants.md similarity index 94% rename from projects.md rename to participants.md index dab6af3..628b66c 100755 --- a/projects.md +++ b/participants.md @@ -1,5 +1,5 @@ --- -title: ABLeS projects +title: ABLeS Participants toc: false --- @@ -27,5 +27,5 @@ toc: false ## ABLeS projects -{% include section-navigation-tiles.html type="projects" search=true col="4" %} +{% include section-navigation-tiles.html type="ABLeS Participant" search=true col="4" %} diff --git a/projects/ausARG.md b/participants/ausARG.md similarity index 50% rename from projects/ausARG.md rename to participants/ausARG.md index d1f124c..d45d275 100755 --- a/projects/ausARG.md +++ b/participants/ausARG.md @@ -1,17 +1,25 @@ --- -title: Australian Amphibian and Reptile Genomics (AusARG) +title: Workspace for the Australian Amphibian and Reptile Genomics (AusARG) description: Bioinformatics analyses for the Australian Amphibian and Reptile Genomics initiative. toc: false -type: projects +type: ABLeS Participant --- -## Bioinformatics leads + +## Project title + +Workspace for the Australian Amphibian and Reptile Genomics (AusARG) + +## Collaborators and funding + + +## Contact(s) - Hardip Patel - Terry Bertozzi -## Details +## Project description and aims The [Australian Amphibian and Reptile Genomics Initiative (AusARG)](https://ausargenomics.com/) is a national collaborative project that will facilitate research using genomics approaches towards a more thorough understanding of evolution and conservation of Australia’s unique native amphibians and reptiles that are now under threat, through climate, disease or habitat modification. @@ -21,4 +29,15 @@ AusARG's mission is to build genomic resources to understand and protect Austral + Phylogenomics + Conservation and Taxonomy genomics -### [GitHub link](https://github.com/AusARG) +[GitHub link](https://github.com/AusARG) + + +## How is ABLeS supporting this work? + +This work is supported through the reference data asset creation scheme provided by ABLeS. The support includes 135 TB long term storage, 1 TB temoprary storage on scratch and 100 KSUs per quarter. + +## Expected outputs enabled by participation in ABLeS + +
+ +> *These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.* diff --git a/projects/awri.md b/participants/awri.md similarity index 56% rename from projects/awri.md rename to participants/awri.md index 577a68b..5668057 100755 --- a/projects/awri.md +++ b/participants/awri.md @@ -1,17 +1,35 @@ --- -title: Australian Wine Research Institute +title: Workspace for Australian Wine Research Institute description: Genetic diversity of Australian wine grapevine germplasm. toc: false -type: projects +type: ABLeS Participant --- -## Bioinformatics leads +## Project title -Markus Herderich +Workspace for Australian Wine Research Institute +## Collaborators and funding -## Details + +## Contact(s) + +- Markus Herderich + +## Project description and aims Grapevine cultivars can be unequivocally typed by both physical differences (ampelography) and genetic tests. However, due to their very similar characteristics, the identification of clones within a cultivar relies on the accurate tracing of supply records to the point of origin. Such records are not always available or reliable, particularly for older accessions. Whole genome sequencing (WGS) provides the most highly detailed methodology for defining grapevine cultivars and more importantly, this can be extended to differentiating clones within those cultivars. The [AWRI](https://www.awri.com.au/) has developed a world-first clonal sequencing pipeline that has been successfully used to define grapevine clones as true-to-sequence. This information will underpin investments in replanting, facilitate vineyard recovery and improve income for Australian grape grower and wine producers. + + +## How is ABLeS supporting this work? + +This work is supported through the production bioinformatics scheme provided by ABLeS. The supports includes unlimited temporary storage on scratch, 1 TB permenant storage and 50 KSUs per quarter. + + +## Expected outputs enabled by participation in ABLeS + +
+ +> *These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.* diff --git a/projects/benchmarking.md b/participants/benchmarking.md similarity index 58% rename from projects/benchmarking.md rename to participants/benchmarking.md index 32c7acb..05c0634 100755 --- a/projects/benchmarking.md +++ b/participants/benchmarking.md @@ -2,15 +2,25 @@ title: Benchmarking life science software on national and institutional HPC platforms. description: A benchmarking project across multiple research organisations. toc: false -type: projects +type: ABLeS Participant --- -## Bioinformatics leads +## Project title -Johan Gustafsson , Ziad Al Bkhetan , Edward Yang , Julie Iskander +Benchmarking life science software on national and institutional HPC platforms. +## Collaborators and funding -## Details + +## Contact(s) + +- Johan Gustafsson +- Ziad Al Bkhetan +- Edward Yang +- Julie Iskander + + +## Project description and aims The goal of this project is to benchmark software that is commonly used throughout the life sciences on Australia’s national HPC facilities. The software benchmarked will span research areas such as bioinformatics and molecular dynamics, as well as general software that is commonly used such as [`NumPy`](https://bio.tools/numpy) and [`R`](https://bio.tools/r). The benchmarks also aim to test a variety of workloads, such as machine learning & artificial intelligence (ML/AI), traditional HPC (on a small to moderate scale), I/O dependent software (latency and bandwidth), and high throughput workloads. @@ -22,3 +32,18 @@ Life science researchers will benefit from this as it will: - Establish an easy-to-setup benchmarking pipeline – facilitated by [`Nextflow`](https://bio.tools/nextflow). All results and the pipeline will be made publicly available via GitHub. + + + +## How is ABLeS supporting this work? + +This work is supported through the production bioinformatics scheme provided by ABLeS. The supports includes 1 TB temprary storage, 1 TB long term storage and 10 KSUs per quarter. + +## Expected outputs enabled by participation in ABLeS + +Sharing benchmarking results with the broader bioinformatics comunity in Australia. + + +
+ +> *These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.* diff --git a/participants/csbn.md b/participants/csbn.md new file mode 100755 index 0000000..2abe914 --- /dev/null +++ b/participants/csbn.md @@ -0,0 +1,56 @@ +--- +title: Computational Structural Biology Node +description: explore software and hardware efficiencies in the current deep learning revolution in computational structural biology. +toc: false +type: ABLeS Participant +--- + +## Project title + +Computational Structural Biology Node + +## Collaborators and funding + + +- [Structural Biology Facility, The University of New South Wales](https://www.analytical.unsw.edu.au/facilities/sbf) + +- [The Australian BioCommons](https://www.biocommons.org.au/) + +- [Pawsey Supercomputing Centre](https://pawsey.org.au/) + +## Contact(s) + +- Keiran Rowell - Scientific Officer - UNSW, Structural Biology Facility - +- Kate Michie - Chief Scientist - UNSW, Structural Biology Facility - + +## Project description and aims + +Computational techniques applicable to all species, the focus is optimised and exploratory computation rather than investigation of any particular species. But we have local expertise in: + +- Fundamental evolutionary biology: archeal protein development and divergence into eukaryotes + +- Biomedical therapies in human genetic disorders: cardiomyopathy implicated protein mutations + + +The structural biology node will explore software and hardware efficiencies in the current deep learning revolution in computational structural biology. +These findings will be shared with local and national HPC facilities, the steering committee, and scientific advisory board in order to formulate best-practice in this new style of compute for biomolecules and drive widespread adoption by biochemical/medical researchers in Australia. + + +Aims: +- Benchmarking AlphaFold variants (e.g. OpenFold, FastFold) and optimising their use on HPC facilities +- Apply protein generative AI (e.g. RFDiffusion, EvoDiff, ProteinMPNN) for generation of novel protein designs in fundamental biology (molecular motors) and antibodies therapeutics +- Validating compilation of CUDA code of the above software onto AMD GPUs. + +## How is ABLeS supporting this work? + +This work is supported through the production bioinformatics scheme provided by ABLeS. The supports includes unlimited temporary storage on scratch, 5 TB permenant storage and 150 KSUs per quarter. + + +## Expected outputs enabled by participation in ABLeS + +This project is to support the Structural Biology Node being responsive to the deep learning developments in structural biology compute, which is producing pre-print code at a rapid which, many of which find eventual publication in top-rank journals. This is the beginning of software explosion in this ecosystem, and so we will be continually validating new code as the leading-edge validators for wide use by the biological research participant. + + +
+ +> *These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.* diff --git a/projects/diann.md b/participants/diann.md similarity index 59% rename from projects/diann.md rename to participants/diann.md index 0cedac5..8b1a2fe 100755 --- a/projects/diann.md +++ b/participants/diann.md @@ -2,26 +2,44 @@ title: Development and optimisation of a DIA-NN workflow description: Development of a scalable DIA-NN workflow for the processing of scanning SWATH mass spectra. toc: false -type: projects +type: ABLeS Participant --- -## Bioinformatics leads +## Project title + +Development and optimisation of a DIA-NN workflow + +## Collaborators and funding + +This is a new collaboration at the University of Sydney between the Precision Nutrition research participant, School of Life and Environmental Sciences (CSP) and the Bioinformatics Group, Sydney Informatics Hub. + +## Contact(s) - Cali Willet - Carsten Schmitz-Peiffer - Nathaniel Butterworth -## Details +## Project description and aims Scanning SWATH is a novel method that now enables rapid mass spectrometry of hundreds of peptide samples, but the ability to process the resulting spectra using DIA-NN software is much more demanding and extends beyond the capability of most mass spectrometry facilities. This workflow will be available to all future users. The workflow will enable rapid generation of unbiased quantitative data concerning the proteins present in high numbers of complex tissue samples, obtained for example under different dietary or genetic conditions. This will enable further mechanistic investigation of the phenotypes observed. -We aspire to publish our studies in journals such as Cell Metabolism or Nature Communications. Data will be made freely available in a public database such as the ProteomeXchange Consortium. Mouse species will be investigated during this project. -This is a new collaboration at the University of Sydney between the Precision Nutrition research group, School of Life and Environmental Sciences (CSP) and the Bioinformatics Group, Sydney Informatics Hub. -## [GitHub](https://github.com/Sydney-Informatics-Hub/Scalable-DIA-NN) +[GitHub account](https://github.com/Sydney-Informatics-Hub/Scalable-DIA-NN). + +## How is ABLeS supporting this work? + +This work is supported through the software accelerator scheme provided by ABLeS. The supports includes 44 TB temporary storage and 10 KSUs per quarter. + +## Expected outputs enabled by participation in ABLeS + +We aspire to publish our studies in journals such as Cell Metabolism or Nature Communications. Data will be made freely available in a public database such as the ProteomeXchange Consortium. + +
+ +> *These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.* diff --git a/projects/gap.md b/participants/gap.md similarity index 60% rename from projects/gap.md rename to participants/gap.md index 0334401..b1813d3 100755 --- a/projects/gap.md +++ b/participants/gap.md @@ -1,16 +1,25 @@ --- -title: Genomics of Australian Plants (GAP) +title: Workspace for Genomics of Australian Plants (GAP) description: Development of genomics resources to enhance our understanding of the evolution and conservation of the unique Australian flora. toc: false -type: projects +type: ABLeS Participant --- -## Bioinformatics leads +## Project title + +Workspace for Genomics of Australian Plants (GAP) + + +## Collaborators and funding + + +## Contact(s) - Theodore Allnutt -## Details +## Project description and aims + [Genomics for Australian Plants](https://www.genomicsforaustralianplants.com/) was initiated by Bioplatforms in partnership with researchers from the Australian State and National Herbaria and Botanic Gardens. @@ -21,3 +30,14 @@ Broadly, the key aims of the Initiative are: + Build genomic capacity across Australian Botanic Gardens and Herbaria to create networks collaborating in the collection, management, dissemination and application of genomic data for Australian plants; + Provide tools to enable genomic data to be used to identify and classify biodiversity at a range of scales and to use these tools to inform conservation management and enable better decision making. + + +## How is ABLeS supporting this work? + +This work is supported through the reference data asset creation scheme provided by ABLeS. The support includes 33 TB long term storage, 1 TB temoprary storage on scratch and 100 KSUs per quarter. + +## Expected outputs enabled by participation in ABLeS + +
+ +> *These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.* diff --git a/participants/gap2.md b/participants/gap2.md new file mode 100755 index 0000000..373aa16 --- /dev/null +++ b/participants/gap2.md @@ -0,0 +1,31 @@ +--- +title: Genome Assembly for Genomics of Australian Plants (GAP) +description: Genome Assembly and base calling for genomes genreated by GAP. +toc: false +type: ABLeS Participant +--- + +## Project title + +Genome Assembly for Genomics of Australian Plants (GAP) + +## Collaborators and funding + + +## Contact(s) + +- Theodore Allnutt + + +## Project description and aims + + +## How is ABLeS supporting this work? + +This work is supported through the reference data asset creation scheme provided by ABLeS. The support includes 20 TB long term storage, 10 TB temoprary storage on scratch and 100 KSUs per quarter. + +## Expected outputs enabled by participation in ABLeS + +
+ +> *These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.* diff --git a/participants/if89.md b/participants/if89.md new file mode 100755 index 0000000..a7ee460 --- /dev/null +++ b/participants/if89.md @@ -0,0 +1,43 @@ +--- +title: The Australian BioCommons tools and workflows repository +description: A shared repository for bioinformatics tools, workflows, databases, and containers. +toc: false +type: ABLeS Participant +--- + +## Project title + +The Australian BioCommons tools and workflows repository + + +## Collaborators and funding + +[The Australian BioCommons](https://www.biocommons.org.au/) + +[National Computational Infrastructure](https://nci.org.au/) + + + +## Contact(s) + +- Ziad Al-Bkhetan +- Johan Gustafsson + + +## Project description and aims + +ABLeS participants and NCI users have access to the Australian BioCommons Tools and Workflows project, in project allocation `if89`. This is a repository of popular tools, containers and workflows that can be used by anyone in the NCI user participant. Anyone from an NCI participant can contribute to if89 and add more tools that will be shared with others. + + +## How is ABLeS supporting this work? + +This work is supported through the software accelerator scheme provided by ABLeS. The supports includes 10 TB long term storage. + +## Expected outputs enabled by participation in ABLeS + +A shared repository for popular bioinformatics tools, workflows, databases, and containers that can be usilised directly by all NCI users including ABLeS participants. This will avoid effort replication to deploy all these resources by the individual users. + + +
+ +> *These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.* diff --git a/participants/janis.md b/participants/janis.md new file mode 100755 index 0000000..bffd35c --- /dev/null +++ b/participants/janis.md @@ -0,0 +1,34 @@ +--- +title: Janis +description: Janis is a framework creating specialised, simple workflow definitions that are then transpiled to Common Workflow Language (CWL) or Workflow Definition Language (WDL). +toc: false +type: ABLeS Participant +--- + +## Project title + +Janis development + +## Collaborators and funding + + +## Contact(s) + +- Richard Lupat + +## Project description and aims + +[Website](https://janis.readthedocs.io/en/latest/about.html) + +[GitHub](https://github.com/PMCC-BioinformaticsCore/janis) + + + +## How is ABLeS supporting this work? +This work is supported through the software accelerator scheme provided by ABLeS. The support includes 5 TB long term storage, 1 TB temoprary storage on scratch and 10 KSUs per quarter. + +## Expected outputs enabled by participation in ABLeS + +
+ +> *These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.* diff --git a/participants/neuropathies.md b/participants/neuropathies.md new file mode 100755 index 0000000..23ceff0 --- /dev/null +++ b/participants/neuropathies.md @@ -0,0 +1,34 @@ +--- +title: Whole-genome structural variant profiling in heritable neuropathies. +description: +toc: false +type: ABLeS Participant +--- + +## Project title + +Whole-genome structural variant profiling in heritable neuropathies. + +## Collaborators and funding + + + +## Contact(s) + +- Georgina Samaha + + +## Project description and aims + +This project is a use case for the Australian BioCommons Nextflow Tower service. For this use case we will be processing 100 human genomes to identify, annotate and prioritise structural variations in the genome potentially associated with heritable motor neuropathies. + + +## How is ABLeS supporting this work? + +This work is supported through the production bioinformatics scheme provided by ABLeS. The support includes 2 TB long term storage, 11 TB temoprary storage on scratch and 50 KSUs per quarter. + +## Expected outputs enabled by participation in ABLeS + +
+ +> *These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.* diff --git a/projects/nf-ont-visc.md b/participants/nf-ont-visc.md similarity index 57% rename from projects/nf-ont-visc.md rename to participants/nf-ont-visc.md index 42d5d63..a6d5520 100755 --- a/projects/nf-ont-visc.md +++ b/participants/nf-ont-visc.md @@ -2,15 +2,21 @@ title: Development of an end-to-end nextflow ONT-based viral screening for plants. description: toc: false -type: projects +type: ABLeS Participant --- -## Bioinformatics leads +## Project title + +Development of an end-to-end nextflow ONT-based viral screening for plants. + +## Collaborators and funding -- Magdalena Antczak +## Contact(s) + +- Magdalena Antczak -## Details +## Project description and aims This project is funded by Queensland University of Technology (QUT) and the Australian BioCommons. @@ -22,3 +28,13 @@ Objectives: - Prepare a hands-on training user guide for the upskilling of end users and make the resource available through appropriate platforms. + +## How is ABLeS supporting this work? + +This work is supported through the software accelerator scheme provided by ABLeS. The support includes 0.5 TB long term storage, 1 TB temoprary storage on scratch and 10 KSUs per quarter. + +## Expected outputs enabled by participation in ABLeS + +
+ +> *These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.* diff --git a/projects/parabricks.md b/participants/parabricks.md similarity index 58% rename from projects/parabricks.md rename to participants/parabricks.md index cf5ae73..6d818b9 100755 --- a/projects/parabricks.md +++ b/participants/parabricks.md @@ -2,15 +2,21 @@ title: Parabricks and GATK benchmarking description: Benchmarking for NVIDIA Parabricks and GATK RNA-Seq variant calling workflows. toc: false -type: projects +type: ABLeS Participant --- -## Bioinformatics leads +## Project title -- Locedie Mansueto +Parabricks and GATK benchmarking +## Collaborators and funding -## Details + +## Contact(s) + +- Locedie Mansueto + +## Project description and aims This project is for an updated analysis for NVIDIA Parabricks and GATK benchmarking for RNA-Seq, based on NVIDIA recommendations. @@ -23,3 +29,14 @@ The number of discovered variants, service unit (SU) usage and runtime will be c This is a follow-up run based on the recommendation from NVIDIA to use specific versions (`Parabricks 3.8`, `GATK v4.2.0.0`, `STAR v2.7.2`) for compatibility. The test data are from 21 RNA-Seq Cannabis samples and cs10 genome assembly. + + +## How is ABLeS supporting this work? + +This work is supported through Software accelerator scheme provided by ABLeS. The support includes 2 TB long term storage, 5 TB temoprary storage on scratch and 20 KSUs per quarter. + +## Expected outputs enabled by participation in ABLeS + +
+ +> *These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.* diff --git a/projects/perkins.md b/participants/perkins.md similarity index 79% rename from projects/perkins.md rename to participants/perkins.md index 553782d..858b848 100755 --- a/projects/perkins.md +++ b/participants/perkins.md @@ -2,16 +2,24 @@ title: Rare Disease Genetics and Functional Genomics description: Workflow consolidation, testing and implementation for Rare Disease Genetics and Functional Genomics managed by the Harry Perkins Institute of Medical Research. toc: false -type: projects +type: ABLeS Participant --- -## Bioinformatics leads +## Project title + +Rare Disease Genetics and Functional Genomics + +## Collaborators and funding + + +## Contact(s) - Gina Ravenscroft - Mridul Johari -## Details + +## Project description and aims We are analysing DNA and RNA sequencing data from rare disease patients to identify genomic variants that may be contributing to disease. This first requires the processing of the raw sequencing read (FASTQ) files to file formats that are compatibile with variant calling (BAM and VCF). @@ -42,3 +50,15 @@ The general workflows/analyses for this project are as follows: 4. RNA-seq data processing using [nfcore/rnaseq](https://github.com/nf-core/rnaseq) 5. Detecting aberrant splicing and expression outliers in RNAseq data using the [Detection of RNA Outliers Pipeline (DROP)](https://gagneurlab-drop.readthedocs.io/en/latest/) 6. Model protein structures using [AlphaFold](https://bio.tools/alphafold_2) + + +## How is ABLeS supporting this work? + +This work is supported through Production bioinformatics scheme provided by ABLeS. The supports includes unlimited temporary storage on scratch, 1 TB permenant storage and 50 KSUs per quarter. + + +## Expected outputs enabled by participation in ABLeS + +
+ +> *These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.* diff --git a/participants/plant-pathogens.md b/participants/plant-pathogens.md new file mode 100755 index 0000000..44f0294 --- /dev/null +++ b/participants/plant-pathogens.md @@ -0,0 +1,49 @@ +--- +title: Workspace for Plant Pathogen Initiative +description: +toc: false +type: ABLeS Participant +--- + +## Project title + +Workspace for Plant Pathogen Initiative + +## Collaborators and funding + + +## Contact(s) + +- Benjamin Schwessinger + + + +## Project description and aims + +This project aims to investigate plant pathogen genomics, population genetics, virulence evolution, fungicide resistance evolution, and diagnostics. + +Methods: + +- Genome assembly, +- Annotation, +- Population genetics, and +- Variation analysis + + +## How is ABLeS supporting this work? + +This work is supported through the reference data asset creation scheme provided by ABLeS. The support includes 5 TB long term storage, 2 TB temoprary storage on scratch and 100 KSUs per quarter. + +## Expected outputs enabled by participation in ABLeS + ++ Genome resources for Australian biosecurity, ++ New workflows, ++ Publications, and ++ Policy documents. + +Raw data and genomes under embargo will be stored on the Bioplatforms Australia data portal. At the time of publication, data will be at NCBI / SRA for long term storage. + + +
+ +> *These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.* diff --git a/projects/platypusbio.md b/participants/platypusbio.md similarity index 100% rename from projects/platypusbio.md rename to participants/platypusbio.md diff --git a/participants/svi.md b/participants/svi.md new file mode 100755 index 0000000..1d3501a --- /dev/null +++ b/participants/svi.md @@ -0,0 +1,36 @@ +--- +title: Crismani Bioinformatics at St. Vincent’s Institute of Medical Research +description: Bioinformatics analyses by Crismani Bioinformatics. +toc: false +type: ABLeS Participant +--- + + +## Project title + +Crismani Bioinformatics at St. Vincent’s Institute of Medical Research + +## Collaborators and funding + + +## Contact(s) + +- Caitlin Harris + + +## Project description and aims + +This project aims to utilise bioinformatic tools and techniques to investigate the effects of mutations in the Fanconi Anaemia DNA-repair pathway. + +Genomic research will be conducted in this project using high throughput sequencing methods, including whole genome sequencing as well as additional methods where appropriate. + + +## How is ABLeS supporting this work? + +This work is supported through the production bioinformatics scheme provided by ABLeS. The supports includes unlimited temporary storage on scratch, 1 TB permenant storage and 50 KSUs per quarter. + +## Expected outputs enabled by participation in ABLeS + +
+ +> *These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.* diff --git a/projects/tasmanian-devil.md b/participants/tasmanian-devil.md similarity index 84% rename from projects/tasmanian-devil.md rename to participants/tasmanian-devil.md index 6227e16..b1f7eb4 100755 --- a/projects/tasmanian-devil.md +++ b/participants/tasmanian-devil.md @@ -2,17 +2,22 @@ title: Genomic analysis of Tasmanian Devil description: The project will analyse Tasmanian Devil genome to shed light on causes of Tasmanian Devil facial tumour disease (DFTD) disease. toc: false -type: projects +type: ABLeS Participant --- -## Bioinformatics leads +## Project title + +Genomic analysis of Tasmanian Devil + +## Collaborators and funding -- Ambikesh Jayal +## Contact(s) + +- Ambikesh Jayal -## Details -### Background and Aims +## Project description and aims The project deals with the characterisation of the subtelomeres in the Tasmanian devil (TD) which is the largest carnivore marsupial in the Australian Dasyuridae family. TD is listed as a threatened species due to two facial tumours (devil facial tumour 1 (DFT1) and devil facial tumour 2 (DFT2)). These tumours have resulted in about 90% reduction in the TD population. The exact cause of these facial tumours is yet unknown (McCallum et al., 2007); however, the DFT1 is believed to have originated from telomeres (the end cap of linear chromosomes that protects it from degradation and end-to-end fusion) on one homologue of chromosomes 1 and X (Taylor et al., 2017). @@ -30,4 +35,14 @@ The subtelomeres of only a few species have been characterised so far; this incl 3. Explore the subtelomere's role in regulating the Tasmanian devil's unique telomere and its facial tumours. - \ No newline at end of file + + +## How is ABLeS supporting this work? + +This work is supported through the production bioinformatics scheme provided by ABLeS. The supports includes 1 TB temporary storage on scratch, 0.5 TB permenant storage and 50 KSUs per quarter. + +## Expected outputs enabled by participation in ABLeS + +
+ +> *These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.* diff --git a/projects/telethon-kids.md b/participants/telethon-kids.md similarity index 64% rename from projects/telethon-kids.md rename to participants/telethon-kids.md index ca5ffb3..b75faa1 100755 --- a/projects/telethon-kids.md +++ b/participants/telethon-kids.md @@ -1,16 +1,23 @@ --- -title: Telethon Kids Institute +title: Prenatal programming of respiratory epithelial progenitors and early postnatal respiratory disease. description: Prenatal programming of respiratory epithelial progenitors and early postnatal respiratory disease. toc: false -type: projects +type: ABLeS Participant --- -## Bioinformatics leads +## Project title + +## Collaborators and funding + +Telethon Kids Institute + + +## Contact(s) - Patricia Agudelo-romero -## Details +## Project description and aims Viral-induced wheezing and asthma in children have a significant burden in families and healthcare, with around 20% of all children developing recurrent respiratory disorders during childhood. @@ -18,3 +25,11 @@ Our team have identified a vulnerable epithelial signature in young children sus Poorly controlled maternal asthma and prenatal exposures to smoke and viral infections in pregnancy have been identified as risk factors to the development of respiratory disorders. We propose that wheezing in early life is related to an in utero epigenetic reprogramming that can be identified in the amnion, providing new opportunities for early disease prevention. One of our objectives is to determine whether maternal epigenetic imprinting due to smoke exposure is a risk factor for increasing the development of early-life respiratory diseases. +## How is ABLeS supporting this work? +This work is supported through the production bioinformatics scheme provided by ABLeS. The supports includes unlimited temporary storage on scratch, 50 TB permenant storage and 50 KSUs per quarter. + +## Expected outputs enabled by participation in ABLeS + +
+ +> *These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.* diff --git a/participants/tsi.md b/participants/tsi.md new file mode 100755 index 0000000..cf55759 --- /dev/null +++ b/participants/tsi.md @@ -0,0 +1,31 @@ +--- +title: Workspace for Threatened Species Initiative +description: Bioinformatics analyses for the Threatened Species Initiative. +toc: false +type: ABLeS Participant +--- + +## Project title + +Workspace for Threatened Species Initiative + +## Collaborators and funding + + +## Contact(s) + +- Kate Farquharson + +## Project description and aims + +The [Threatened Species Initiative (TSI)](https://threatenedspeciesinitiative.com/) aims to improve conservation practices through the use of cutting-edge genomics technology and advanced computational biology to transform the way the conservation industry manages wildlife recovery programs. + +## How is ABLeS supporting this work? + +This work is supported through the reference data asset creation scheme provided by ABLeS. The support includes 5 TB long term storage, 1 TB temoprary storage on scratch and 100 KSUs per quarter. + +## Expected outputs enabled by participation in ABLeS + +
+ +> *These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.* diff --git a/participants/zero.md b/participants/zero.md new file mode 100755 index 0000000..2d8e1b4 --- /dev/null +++ b/participants/zero.md @@ -0,0 +1,33 @@ +--- +title: Workspace for ZERO Childhood Cancer +description: Analysis of a large number of healthy and tumour samples by the Zero Childhood Cancer initiative. +toc: false +type: ABLeS Participant +--- + +## Project title + +Workspace for ZERO Childhood Cancer + +## Collaborators and funding + + +## Contact(s) + +- Marie Wong-Erasmus + + +## Project description and aims + + +This project will develop, test and run tools and pipelines from the [Zero Childhood Cancer initiative](https://www.zerochildhoodcancer.org.au/) on the National Computational Infrastructure (NCI) and Pawsey Supercomputing Centre. + +## How is ABLeS supporting this work? + +This work is supported through the production bioinformatics scheme provided by ABLeS. The supports includes 800 TB temprary storage, 5 TB long term storage and 100 KSUs per quarter. + +## Expected outputs enabled by participation in ABLeS + +
+ +> *These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.* diff --git a/projects/zero2.md b/participants/zero2.md similarity index 58% rename from projects/zero2.md rename to participants/zero2.md index 422e034..f5b51b6 100755 --- a/projects/zero2.md +++ b/participants/zero2.md @@ -1,17 +1,35 @@ --- -title: ZERO Childhood Cancer - transcriptomics +title: Transcriptomics analysis for ZERO Childhood Cancer description: Analysis of high-risk paediatric children enrolled in the Zero Childhood Cancer initiative. toc: false -type: projects +type: ABLeS Participant --- -## Bioinformatics leads +## Project title + +Transcriptomics analysis for ZERO Childhood Cancer + +## Collaborators and funding + + +## Contact(s) - Chelsea Mayoh -## Details +## Project description and aims The aim of the project is to develop and analyse the splicing profiles and structural rearrangement events within the RNA samples that cannot be identified through fusion detection algorithms. This project will develop the pipeline and then analyse all 700+ patients to identify novel structural rearrangement events occurring in the RNA and unique splicing profiles that are specific to high-risk paediatric cancers. The development of this pipeline and analysis will then be integrated into the current RNA pipeline that will be ran prospectively on all new patients enrolled on ZERO. The analysis will be carried out using [MINTIE](https://github.com/Oshlack/MINTIE) and rMATS. Both methodologies will be tested and compared to determine which algorithm to continue using, or if both are required. + + +## How is ABLeS supporting this work? + +This work is supported through the production bioinformatics scheme provided by ABLeS. The supports includes 1 TB temprary storage, 5 TB long term storage and 100 KSUs per quarter. + +## Expected outputs enabled by participation in ABLeS + +
+ +> *These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.* diff --git a/processes.md b/processes.md index 159e44c..cc2645b 100755 --- a/processes.md +++ b/processes.md @@ -37,7 +37,7 @@ If you are new to the ABLeS program, please read the processes below to get star Data centric outcomes - Production of reference and derived data assets that will be published to enable use / reuse by others outside the community. + Production of reference and derived data assets that will be published to enable use / reuse by others outside the participant. Yes Yes @@ -51,19 +51,19 @@ If you are new to the ABLeS program, please read the processes below to get star Software centric outcomes - Creation, development, installation, testing and/or optimisation of software that will be made available for use / reuse by others in the life sciences community. + Creation, development, installation, testing and/or optimisation of software that will be made available for use / reuse by others in the life sciences participant. Yes Common research theme - A defined cross-institutional collaboration, project, community, consortium, or some other collaborative construct, that is focused on a common research theme. + A defined cross-institutional collaboration, project, participant, consortium, or some other collaborative construct, that is focused on a common research theme. Yes Development & optimisation - Communities work to understand their software, methods and the optimal approaches to solving the bioinformatics problems at hand. ABLeS will facilitate both the experimental / testing and production phases of computational analyses. + Groups work to understand their software, methods and the optimal approaches to solving the bioinformatics problems at hand. ABLeS will facilitate both the experimental / testing and production phases of computational analyses. Yes @@ -73,7 +73,7 @@ If you are new to the ABLeS program, please read the processes below to get star Sharing - Appropriate mechanisms are used to share outputs that support and assist other communities, with examples provided in the ABLeS publication. Outputs include software, methods, training, resource usage and quality assessments for derived reference data sets, submissions to data international repositories and research publications. + Appropriate mechanisms are used to share outputs that support and assist other participants, with examples provided in the ABLeS publication. Outputs include software, methods, training, resource usage and quality assessments for derived reference data sets, submissions to data international repositories and research publications. Yes @@ -91,7 +91,7 @@ ABLeS users will follow one of the paths illustrated below as per the three sche ## ABLeS process for different stages of a project's lifetime -The Australian BioCommons and the bioinformatics leads for each group have different roles during ABLeS project initiation, operation and close. +The Australian BioCommons and the bioinformatics leads for each participant have different roles during ABLeS project initiation, operation and close. ABLeS projects are led and maintained by their users with the support of the ABLeS team to facilitate access to ABLeS resources. @@ -107,13 +107,13 @@ ABLeS projects are led and maintained by their users with the support of the ABL Project bioinformatics lead's role:
  1. Familarise themselves with ABLeS schemes, expectations, and responsibilities.
    2. -
  2. Submit a project plan that contains the details of the project (link). The community’s steering committee (or bioinformatics leads) should approve the plan.
    3. +
  3. Submit a project plan that contains the details of the project (link). The participant’s steering committee (or bioinformatics leads) should approve the plan.
  4. Identify known challenges that BioCommons, NCI, or Pawsey may be able to address and / or support as part of ABLeS. You can use the GoogleForm to let us know about these challenges.
Australian BioCommons' role:
    -
  1. Create of a project allocation (at NCI or Pawsey) for a community
    2. -
  2. Invite community bioinformatics leads to a project allocation as Chief Investigators
    3. +
  3. Create of a project allocation (at NCI or Pawsey) for a participant
    4. +
  4. Invite participant bioinformatics leads to a project allocation as Chief Investigators
  5. Provide information on how to utilise ABLeS resources and contribute to the shared tool and software repository.
  6. Manage the resources available to the ABLeS programme across all active projects.
@@ -131,12 +131,12 @@ ABLeS projects are led and maintained by their users with the support of the ABL Project bioinformatics lead's role:
  1. Request additional resources when the project needs more resources than are available. Each project gets default resources automatically at the beginning of each quarter without the need to request them.
    2. -
  2. Attend a quarterly meeting with BioCommons to discuss and report the outcomes of the community work (data, methods, publications etc.) in the previous quarter.
    3. +
  3. Attend a quarterly meeting with BioCommons to discuss and report the outcomes of the participant work (data, methods, publications etc.) in the previous quarter.
  4. Manage the resources provided by ABLeS including:
    • Adding members to the project(s).
    • Educating / onboarding new project members.
      • -
    • Contributing and / or coordinating contributions to the shared tool and software repository (if89), as well as encouraging community contribution.
      • +
    • Contributing and / or coordinating contributions to the shared tool and software repository (if89), as well as encouraging participant contribution.
@@ -188,9 +188,9 @@ ABLeS projects are led and maintained by their users with the support of the ABL |Principle| Description| |-------------|------------------------------------------------------------------| |**Project leadership**| A project lead is responsible for all use of resources provided, which will need to adhere to relevant facility processes and policies. The lead will also monitor and manage reasonable usage of their project computational infrastructure allocations.| -|**Community-level decision making**| A collaborative decision making mechanism to prioritise the bioinformatics work using relevant computational resources must exist. This can be a formalised steering committee, a working group, or some other forum which is representative of the collaboration. Resources used must be agreed upon / in line with the community’s decision making mechanism and align with community priorities.| -|**Community-level expertise**|The community has expertise which will drive and execute its bioinformatics agenda. This expertise offers a strong collaboration link with the expertise and support available through ABLeS, NCI and Pawsey.| -|**Collaboration & consultation**|ABLeS is collaborative and involves BioCommons, the research community, and the computational facilities. It is also a standing item for discussion and forums play a strong role in managing the use of ABLeS: communities will thus engage with BioCommons in an open and collaborative manner, with regular meetups.| +|**Group-level decision making**| A collaborative decision making mechanism to prioritise the bioinformatics work using relevant computational resources must exist. This can be a formalised steering committee, a working participant, or some other forum which is representative of the collaboration. Resources used must be agreed upon / in line with the participant’s decision making mechanism and align with participant priorities.| +|**Group-level expertise**|The participant has expertise which will drive and execute its bioinformatics agenda. This expertise offers a strong collaboration link with the expertise and support available through ABLeS, NCI and Pawsey.| +|**Collaboration & consultation**|ABLeS is collaborative and involves BioCommons, the research participant, and the computational facilities. It is also a standing item for discussion and forums play a strong role in managing the use of ABLeS: participants will thus engage with BioCommons in an open and collaborative manner, with regular meetups.| |**Follow compute facility access policies**|All users must abide by the relevant access policies of Pawsey and NCI. [NCI Terms and Conditions of Access](https://nci.org.au/users/nci-terms-and-conditions-access); [NCI Data Collections Management](https://opus.nci.org.au/display/NDP/NCI+Data+Collections+and+Publishing); and [Pawsey Conditions of Access](https://support.pawsey.org.au/documentation/display/US/Conditions+of+Use).| |**Time frame / duration of allocations**|Each project is reviewed at the 6 month mark, to ensure resources are being used as efficiently as practical and so challenges can be identified / addressed by the ABLeS team. Reference data and production projects are ongoing by definition, while software accelerator projects need to be renewed at 6 months if the work originally described for the project has not been completed.| diff --git a/projects/janis.md b/projects/janis.md deleted file mode 100755 index 2bf6d40..0000000 --- a/projects/janis.md +++ /dev/null @@ -1,17 +0,0 @@ ---- -title: Janis -description: Janis is a framework creating specialised, simple workflow definitions that are then transpiled to Common Workflow Language (CWL) or Workflow Definition Language (WDL). -toc: false -type: projects ---- - -## Bioinformatics leads - -- Richard Lupat - -## Details - - -## [Website](https://janis.readthedocs.io/en/latest/about.html) - -## [GitHub](https://github.com/PMCC-BioinformaticsCore/janis) diff --git a/projects/neuropathies.md b/projects/neuropathies.md deleted file mode 100755 index 7ba0fef..0000000 --- a/projects/neuropathies.md +++ /dev/null @@ -1,15 +0,0 @@ ---- -title: Whole-genome structural variant profiling in heritable neuropathies. -description: -toc: false -type: projects ---- - -## Bioinformatics leads - -- Georgina Samaha - - -## Details - -This project is a use case for the Australian BioCommons Nextflow Tower service. For this use case we will be processing 100 human genomes to identify, annotate and prioritise structural variations in the genome potentially associated with heritable motor neuropathies. diff --git a/projects/plant-pathogens.md b/projects/plant-pathogens.md deleted file mode 100755 index 1cda5bb..0000000 --- a/projects/plant-pathogens.md +++ /dev/null @@ -1,31 +0,0 @@ ---- -title: Plant Pathogen Initiative -description: -toc: false -type: projects ---- - -## Bioinformatics leads - -- Benjamin Schwessinger - - -## Details - -This project aims to investigate plant pathogen genomics, population genetics, virulence evolution, fungicide resistance evolution, and diagnostics. - -## Methods - -- Genome assembly, -- Annotation, -- Population genetics, and -- Variation analysis - -## Expected outcomes of the project - -+ Genome resources for Australian biosecurity, -+ New workflows, -+ Publications, and -+ Policy documents. - -Raw data and genomes under embargo will be stored on the Bioplatforms Australia data portal. At the time of publication, data will be at NCBI / SRA for long term storage. diff --git a/projects/svi.md b/projects/svi.md deleted file mode 100755 index 3bc55ae..0000000 --- a/projects/svi.md +++ /dev/null @@ -1,17 +0,0 @@ ---- -title: St. Vincent’s Institute of Medical Research - Crismani Bioinformatics -description: Bioinformatics analyses by Crismani Bioinformatics. -toc: false -type: projects ---- - -## Bioinformatics leads - -- Caitlin Harris - - -## Details - -This project aims to utilise bioinformatic tools and techniques to investigate the effects of mutations in the Fanconi Anaemia DNA-repair pathway. - -Genomic research will be conducted in this project using high throughput sequencing methods, including whole genome sequencing as well as additional methods where appropriate. diff --git a/projects/tsi.md b/projects/tsi.md deleted file mode 100755 index c8b1524..0000000 --- a/projects/tsi.md +++ /dev/null @@ -1,15 +0,0 @@ ---- -title: Threatened Species Initiative -description: Bioinformatics analyses for the Threatened Species Initiative. -toc: false -type: projects ---- - -## Bioinformatics leads - -- Kate Farquharson - - -## Details - -The [Threatened Species Initiative (TSI)](https://threatenedspeciesinitiative.com/) aims to improve conservation practices through the use of cutting-edge genomics technology and advanced computational biology to transform the way the conservation industry manages wildlife recovery programs. diff --git a/projects/zero.md b/projects/zero.md deleted file mode 100755 index 8e2db1c..0000000 --- a/projects/zero.md +++ /dev/null @@ -1,16 +0,0 @@ ---- -title: ZERO Childhood Cancer -description: Analysis of a large number of healthy and tumour samples by the Zero Childhood Cancer initiative. -toc: false -type: projects ---- - -## Bioinformatics leads - -- Mark Cowley -- Marie Wong-Erasmus - - -## Details - -This project will develop, test and run tools and pipelines from the [Zero Childhood Cancer initiative](https://www.zerochildhoodcancer.org.au/) on the National Computational Infrastructure (NCI) and Pawsey Supercomputing Centre. diff --git a/resources.md b/resources.md index 4977c99..2da77b8 100755 --- a/resources.md +++ b/resources.md @@ -1,5 +1,5 @@ --- -title: Resources available for ABLeS communities +title: Resources available for ABLeS participants ---