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Expand Up @@ -3,14 +3,97 @@ title: ABLeS processes
toc: false
---

If you are new to the ABLeS program, please read the processes below in order to start using ABLeS resources or **[contact us](contact-us.md)** for more information and assistance.

## ABLeS process for different stages of a project's lifetime
## Characteristics of the different ABLeS project types

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<table class="tg">
<thead>
<tr>
<th class="tg-kcp5" rowspan="2">Principle</th>
<th class="tg-kcp5" rowspan="2">Characteristics of an ABLeS project</th>
<th class="tg-kcp5" colspan="3">Project Type</th>
</tr>
<tr>
<th class="tg-7o2y">Reference Data</th>
<th class="tg-7o2y">Production bioinformatics</th>
<th class="tg-7o2y">Software Accelerator</th>
</tr>
</thead>
<tbody>
<tr>
<td class="tg-baqh">Data centric outcomes</td>
<td class="tg-0lax">It is producing reference and derived data assets that will be published to enable use / reuse by others outside the community.</td>
<td class="tg-ibb5">Yes</td>
<td class="tg-ibb5">Yes</td>
<td class="tg-baqh"></td>
</tr>
<tr>
<td class="tg-baqh">Research centric outcomes</td>
<td class="tg-0lax">It is producing data assets and outputs that are critical to research projects and consortia making use of best practice production level bioinformatics approaches.</td>
<td class="tg-baqh"></td>
<td class="tg-ibb5">Yes</td>
<td class="tg-baqh"></td>
</tr>
<tr>
<td class="tg-baqh">Software centric outcomes</td>
<td class="tg-0lax">It is creating, developing, installing, testing and/or optimising software that will be made available for use / reuse by others in the life science 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">It is 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>
<td class="tg-baqh">Development & optimisation</td>
<td class="tg-0lax">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.</td>
<td class="tg-ibb5" colspan="3">Yes</td>
</tr>
<tr>
<td class="tg-baqh">Planned usage of ABLeS resources</td>
<td class="tg-0lax">The use of ABLeS resources is planned and approached with a level of care appropriate to their status as limited and consumable resources.</td>
<td class="tg-ibb5" colspan="3">Yes</td>
</tr>
<tr>
<td class="tg-baqh">Sharing</td>
<td class="tg-0lax">Appropriate mechanisms are used to share outputs that support and assist other communities, with examples provided in Table 3. 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>
</table>

The Australian BioCommons and the bioinformatics leads for each group have different roles in initiation, onboarding and reporting for ABLeS.

ABLeS projects are led and maintained by their users with the support of the ABLeS team to facilitate access to ABLeS resources.
## Which ABLeS project matches your work?

If you are new to the ABLeS program, please read the processes below in order to start using ABLeS resources or **[contact us](contact-us.md)** for more information and assistance.
Considering the three schemes supported by ABLeS (`Creation of reference data assets`, `Production analysis`, and `Software accelerator`), ABLeS users will follow one of the paths demonstrated below.

<br/>

![ABLeS pathways](images/ABLeS.png){: height="85%" width="80%" style="display: block; margin-left: auto; margin-right: auto;"}


## ABLeS process for different stages of a project's lifetime

The Australian BioCommons and the bioinformatics leads for each group have different roles in 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.

<div class="accordion" id="accordion-processes">
<div class="accordion-item">
Expand All @@ -24,12 +107,12 @@ If you are new to the ABLeS program, please read the processes below in order to
<b>Project bioinformatics lead 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 community’s steering committee should approve the plan.</li>
<li>Identify known existing 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.</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 existing challenges that the 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>The Australian BioCommons role:</b>
<ol>
<li>Creation of a project allocation at the NCI for a community</li>
<li>Creation of a project allocation (at NCI / Pawsey) for a community</li>
<li>Inviting community bioinformatics leads to a project allocation as Chief Investigators</li>
<li>Providing information on how to utilise ABLeS resources and contribute to the shared tool and software repository.</li>
<li>BioCommons manage the resources available to the ABLeS programme across all active projects.</li>
Expand All @@ -47,8 +130,8 @@ If you are new to the ABLeS program, please read the processes below in order to
<div class="accordion-body">
<b>Project bioinformatics lead role:</b>
<ol>
<li>Request additional resources (<a href="https://docs.google.com/forms/d/e/1FAIpQLSfzHJajEKTnGuYWb1gLRR2nlUExLIRM7qSGy_hhbiCKB3KX2Q/viewform?usp=sf_link">link</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 community work (data, methods, publications..) in the previous quarter.</li>
<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 community work (data, methods, publications etc.) in the previous quarter.</li>
<li>Project bioinformatics leads manage the resources provided by ABLeS including:
<ul>
<li>Adding members to the projects.</li>
Expand All @@ -59,17 +142,17 @@ If you are new to the ABLeS program, please read the processes below in order to
</ol>
<b>Project members role:</b>
<ol>
<li>Try their best to utilise ABLeS resources efficiently and use the resource for the project purposes</li>
<li>Try their best to utilise ABLeS resources efficiently and use the resource for the project purposes.</li>
<li>Help to deploy and install software, tools and workflows to the shared repository (this activity may be coordinated by the project bioinformatics leads, as needed)</li>
</ol>
<b>The Australian BioCommons role:</b><br/>Biocommons helps communities to overcome different challenges that may appear:
<b>The Australian BioCommons helps ABLeS projects to overcome different challenges that may appear:</b>
<ol>
<li>Installing tools, software, pipelines when a special support is needed. </li>
<li>Installing tools, software, pipelines when special support is needed. </li>
<li>Optimising workflows and software to be used by all projects.</li>
<li>Developing and improving cross-cutting tools and workflows.</li>
<li>Managing the allocation of resources for projects and add default resources at the begining of each quarter.</li>
<li>Managing the allocation of resources for projects and adding default resources at the beginning of each quarter.</li>
</ol>
We realise that communities will have different capabilities and different needs. Therefore, ABLeS support will adapt to suit these aspects and aim to provide the best possible support to the communities in order to do their work efficiently.
We realise that project members will have different capabilities and different needs. Therefore, ABLeS support will adapt to suit these aspects and aims to provide the best possible support to users in order to do their work efficiently.
</div>
</div>
</div>
Expand All @@ -83,10 +166,10 @@ If you are new to the ABLeS program, please read the processes below in order to
<div class="accordion-body">
<b>Project bioinformatics lead role:</b>
<ol>
<li>Notify the AUstralian BioCommons when you are ready to close your project.</li>
<li>Notify the Australian BioCommons when you are ready to close your project.</li>
<li>Make sure all project data is archived as the project storage will be released.</li>
<li>Make sure all workflows are registered at <a>workflowhub</a> and well documented so they are findable.</li>
<li>Report the project outcomes to the Australian BioCommons.</li>
<li>Make sure all workflows are registered with <a href="https://workflowhub.eu/">WorkflowHub</a> and well documented so they are findable.</li>
<li><a href="https://docs.google.com/forms/d/e/1FAIpQLSdO1w-RY8OexUBwJx8BHNMwSRNPA3_-5r6pefdQW8ancbKZqw/viewform?usp=sf_link">Report the project outcomes</a> to the Australian BioCommons.</li>
</ol>
<b>The Australian BioCommons role:</b>
<ol>
Expand All @@ -97,85 +180,8 @@ If you are new to the ABLeS program, please read the processes below in order to
</div>
</div>


## Pathways within the Australian BioCommons Leadership Share (ABLeS)

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<thead>
<tr>
<th class="tg-kcp5" rowspan="2">Principle</th>
<th class="tg-kcp5" rowspan="2">Characteristics of an ABLeS project</th>
<th class="tg-kcp5" colspan="3">Project Type</th>
</tr>
<tr>
<th class="tg-7o2y">Reference Data</th>
<th class="tg-7o2y">Production bioinformatics</th>
<th class="tg-7o2y">Software Accelerator</th>
</tr>
</thead>
<tbody>
<tr>
<td class="tg-baqh">Data centric outcomes</td>
<td class="tg-0lax">It is producing reference and derived data assets that will be published to enable use / reuse by others outside the community.</td>
<td class="tg-ibb5">Yes</td>
<td class="tg-ibb5">Yes</td>
<td class="tg-baqh"></td>
</tr>
<tr>
<td class="tg-baqh">Research centric outcomes</td>
<td class="tg-0lax">It is producing data assets and outputs that are critical to research projects and consortia making use of best practice production level bioinformatics approaches.</td>
<td class="tg-baqh"></td>
<td class="tg-ibb5">Yes</td>
<td class="tg-baqh"></td>
</tr>
<tr>
<td class="tg-baqh">Software centric outcomes</td>
<td class="tg-0lax">It is creating, developing, installing, testing and/or optimising software that will be made available for use / reuse by others in the life science 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">It is 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>
<td class="tg-baqh">Development & optimisation</td>
<td class="tg-0lax">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.</td>
<td class="tg-ibb5" colspan="3">Yes</td>
</tr>
<tr>
<td class="tg-baqh">Planned usage of ABLeS resources</td>
<td class="tg-0lax">The use of ABLeS resources is planned and approached with a level of care appropriate to their status as limited and consumable resources.</td>
<td class="tg-ibb5" colspan="3">Yes</td>
</tr>
<tr>
<td class="tg-baqh">Sharing</td>
<td class="tg-0lax">Appropriate mechanisms are used to share outputs that support and assist other communities, with examples provided in Table 3. 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>
</table>

<br/>
Considering the three schemes supported by ABLeS (Creation of reference data assets, Production analysis, and Bioinformatics software accelerator), ABLeS users will follow one of the paths demonstrated below.<br/>

![ABLeS pathways](images/ABLeS.png){: height="85%" width="80%" style="display: block; margin-left: auto; margin-right: auto;"}

## ABLeS Expectations

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