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finor update
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ziadbkh committed Jan 18, 2024
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8 changes: 4 additions & 4 deletions faq.md
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</h2>
<div id="collapse-faq-2" class="accordion-collapse collapse" aria-labelledby="heading-faq-2" data-bs-parent="#accordion-faq">
<div class="accordion-body">
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.
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 group. Additional resources will be allocated according to the quarterly plan proposed by the group, as well as the resources still available in that quarter.
<br/>Groups should utilise the allocated SUs:
<ol>
<li>For projects approved by the steering committee.</li>
<li>Using the tools, methods and/or workflows that are suited to their participant requirements.</li>
<li>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)</li>
<li>Using the tools, methods and/or workflows that are suited to their group requirements.</li>
<li>While making sure to consider that the allocation is a shared resource for their group (if in doubt, consult with your group bioinformatics lead, or the BioCommons)</li>
</ol>
<blockquote>
<strong>Note:</strong>
<ul>
<li>Groups can request additional resources when needed through the <a href="https://docs.google.com/forms/d/e/1FAIpQLSfzHJajEKTnGuYWb1gLRR2nlUExLIRM7qSGy_hhbiCKB3KX2Q/viewform?usp=sf_link"><strong>GoogleForm</strong></a>, if the quarterly plan did not accurately predict resource requirements.</li>
<li>Unused SUs **can NOT** be rolled-over to the next quarter. </li>
<li>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). </li>
<li>As ABLeS is a shared resource covering many groups, it is expected that each group 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). </li>
</ul>
</blockquote>
</div>
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4 changes: 2 additions & 2 deletions if89-technical.md
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Expand Up @@ -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 participant, 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 community, 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.
Expand All @@ -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 participant under `if89`**: request to join at this [link](https://my.nci.org.au/mancini/project/if89_w)
2. **Request to join the writer group 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:
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4 changes: 2 additions & 2 deletions if89.md
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---

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.
is a repository of popular tools, containers and workflows that can be used by anyone in the NCI user group. Anyone
from an NCI users can contribute to if89 and add more tools that will be shared with others.

# Software

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8 changes: 4 additions & 4 deletions index.md
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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 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 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 projects broadly align with the following three principles:

Expand All @@ -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 participant 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 community led and shared repository of bioinformatics software (i.e. tools and workflows).

More details are available in the ABLeS publication:

Expand All @@ -39,11 +39,11 @@ More details are available in the ABLeS publication:

### Creation of reference data assets

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.
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.

### 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 participants 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 groups to implement and run their computational workflow approaches for omics data analysis *at scale*.

### Software accelerator

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26 changes: 13 additions & 13 deletions processes.md
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Expand Up @@ -37,7 +37,7 @@ If you are new to the ABLeS program, please read the processes below to get star
<tbody>
<tr>
<td class="tg-baqh">Data centric outcomes</td>
<td class="tg-0lax">Production of reference and derived data assets that will be published to enable use / reuse by others outside the participant.</td>
<td class="tg-0lax">Production of reference and derived data assets that will be published to enable use / reuse by others outside the group.</td>
<td class="tg-ibb5">Yes</td>
<td class="tg-ibb5">Yes</td>
<td class="tg-baqh"></td>
Expand All @@ -51,14 +51,14 @@ If you are new to the ABLeS program, please read the processes below to get star
</tr>
<tr>
<td class="tg-baqh">Software centric outcomes</td>
<td class="tg-0lax">Creation, development, installation, testing and/or optimisation of software that will be made available for use / reuse by others in the life sciences participant.</td>
<td class="tg-0lax">Creation, development, installation, testing and/or optimisation of software that will be made available for use / reuse by others in the life sciences community.</td>
<td class="tg-baqh"></td>
<td class="tg-baqh"></td>
<td class="tg-ibb5">Yes</td>
</tr>
<tr>
<td class="tg-baqh">Common research theme</td>
<td class="tg-0lax">A defined cross-institutional collaboration, project, participant, consortium, or some other collaborative construct, that is focused on a common research theme.</td>
<td class="tg-0lax">A defined cross-institutional collaboration, project, community, consortium, or some other collaborative construct, that is focused on a common research theme.</td>
<td class="tg-ibb5" colspan="3">Yes</td>
</tr>
<tr>
Expand All @@ -73,7 +73,7 @@ If you are new to the ABLeS program, please read the processes below to get star
</tr>
<tr>
<td class="tg-baqh">Sharing</td>
<td class="tg-0lax">Appropriate mechanisms are used to share outputs that support and assist other participants, with examples provided <a href="https://doi.org/10.5281/zenodo.10139651">in the ABLeS publication</a>. Outputs include software, methods, training, resource usage and quality assessments for derived reference data sets, submissions to data international repositories and research publications.</td>
<td class="tg-0lax">Appropriate mechanisms are used to share outputs that support and assist other groups, with examples provided <a href="https://doi.org/10.5281/zenodo.10139651">in the ABLeS publication</a>. Outputs include software, methods, training, resource usage and quality assessments for derived reference data sets, submissions to data international repositories and research publications.</td>
<td class="tg-ibb5" colspan="3">Yes</td>
</tr>
</tbody>
Expand All @@ -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 participant have different roles during ABLeS project initiation, operation and close.
The Australian BioCommons and the bioinformatics leads for each group 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.

Expand All @@ -107,13 +107,13 @@ ABLeS projects are led and maintained by their users with the support of the ABL
<b>Project bioinformatics lead's role:</b>
<ol>
<li>Familarise themselves with ABLeS schemes, expectations, and responsibilities.</li>
<li>Submit a project plan that contains the details of the project (<a href="https://docs.google.com/forms/d/e/1FAIpQLSf9UVEuhbAsbvVzTEvvE9mLoietryb7e3sDmv74Xhl-1YWj2Q/viewform?usp=sf_link">link</a>). The participant’s steering committee (or bioinformatics leads) should approve the plan.</li>
<li>Submit a project plan that contains the details of the project (<a href="https://docs.google.com/forms/d/e/1FAIpQLSf9UVEuhbAsbvVzTEvvE9mLoietryb7e3sDmv74Xhl-1YWj2Q/viewform?usp=sf_link">link</a>). The community’s steering committee (or bioinformatics leads) should approve the plan.</li>
<li>Identify known challenges that BioCommons, NCI, or Pawsey may be able to address and / or support as part of ABLeS. You can use the <a href="https://docs.google.com/forms/d/e/1FAIpQLSere1PvgPEuJkpvQUk1-11C88IAeQNQKEUFc-Qgbn5GgKK2jw/viewform?usp=sf_link">GoogleForm</a> to let us know about these challenges.</li>
</ol>
<b>Australian BioCommons' role:</b>
<ol>
<li>Create of a project allocation (at NCI or Pawsey) for a participant</li>
<li>Invite participant bioinformatics leads to a project allocation as Chief Investigators</li>
<li>Create of a project allocation (at NCI or Pawsey) for a group</li>
<li>Invite the group bioinformatics leads to a project allocation as Chief Investigators</li>
<li>Provide information on how to utilise ABLeS resources and contribute to the shared tool and software repository.</li>
<li>Manage the resources available to the ABLeS programme across all active projects.</li>
</ol>
Expand All @@ -131,12 +131,12 @@ ABLeS projects are led and maintained by their users with the support of the ABL
<b>Project bioinformatics lead's role:</b>
<ol>
<li><a href="https://docs.google.com/forms/d/e/1FAIpQLSfzHJajEKTnGuYWb1gLRR2nlUExLIRM7qSGy_hhbiCKB3KX2Q/viewform?usp=sf_link">Request additional resources</a> when the project needs more resources than are available. Each project gets <a href="ables/resources">default resources</a> automatically at the beginning of each quarter without the need to request them.</li>
<li>Attend a quarterly meeting with BioCommons to discuss and report the outcomes of the participant work (data, methods, publications etc.) in the previous quarter.</li>
<li>Attend a quarterly meeting with BioCommons to discuss and report the outcomes of the project (data, methods, publications etc.) in the previous quarter.</li>
<li>Manage the resources provided by ABLeS including:
<ul>
<li>Adding members to the project(s).</li>
<li>Educating / onboarding new project members.</li>
<li>Contributing and / or coordinating contributions to the shared tool and software repository (if89), as well as encouraging participant contribution.</li>
<li>Contributing and / or coordinating contributions to the shared tool and software repository (if89), as well as encouraging community contribution.</li>
</ul>
</li>
</ol>
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|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.|
|**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.|
|**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 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.|
|**Group-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: groups 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.|

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