BioCompute Spring Workshop 2024: Difference between revisions
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{{DISPLAYTITLE:BioCompute Spring Workshop Summer 2023}} | {{DISPLAYTITLE:BioCompute Spring Workshop Summer 2023}} | ||
'' | ''<big>This hybrid workshop provides an opportunity to learn about BioCompute Objects and interoperability between 3 platforms that host BioCompute Objects. It will also cover BCODB and Portal at the FDA, real-world applications, and potential AL/ML-related BCO implementations. We encourage everyone to attend in person for hands-on experience.</big>'' | ||
'''Date & Time:''' May 10th, 2024, 8 AM - 5 PM | <big>'''Date & Time:''' May 10th, 2024, 8 AM - 5 PM</big> | ||
'''Location:''' Great Room, White Oak Campus, FDA center | <big>'''Location:''' Great Room, White Oak Campus, FDA center</big> | ||
'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite] | <big>'''Event Registration:''' [https://www.eventbrite.com/e/biocompute-objects-workshop-2024-tickets-700473915337?aff=oddtdtcreator Eventbrite]</big> | ||
== Abstract == | == <big>Abstract</big> == | ||
Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for describing workflows in a precise yet adaptable manner. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility. | <big>Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for describing workflows in a precise yet adaptable manner. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.</big> | ||
As the field continues to evolve, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes. | <big>As the field continues to evolve, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.</big> | ||
The [https://www.biocomputeobject.org/ BioCompute Portal], serving as the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. Overall, this project strives to streamline and secure the submission process. The FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly. | <big>The [https://www.biocomputeobject.org/ BioCompute Portal], serving as the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. Overall, this project strives to streamline and secure the submission process. The FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly.</big> | ||
== Workshop Topics == | == <big>Workshop Topics</big> == | ||
* Updates on BioComput | * <big>Updates on BioComput</big> | ||
* BCO Portal at the FDA | * <big>BCO Portal at the FDA</big> | ||
* Platform interoperability, | * <big>Platform interoperability,</big> | ||
* Exemplar workflows and real-world applications | * <big>Exemplar workflows and real-world applications</big> | ||
* BCO-Nextflow | * <big>BCO-Nextflow</big> | ||
* AI/ML-related implementations | * <big>AI/ML-related implementations</big> | ||
== Schedule == | == <big>Schedule</big> == | ||
TBD | <big>TBD</big> | ||
== Organization Committee == | == <big>Organization Committee</big> == | ||
Mark Walderhaug - U.S Food & Drug (FDA) | <big>Mark Walderhaug - U.S Food & Drug (FDA)</big> | ||
Luis Santana-Quintero - U.S Food & Drug (FDA) | <big>Luis Santana-Quintero - U.S Food & Drug (FDA)</big> | ||
Raja Mazumder - The George Washington University (GWU) | <big>Raja Mazumder - The George Washington University (GWU)</big> | ||
Jonathon Keeney - The George Washington University (GWU) | <big>Jonathon Keeney - The George Washington University (GWU)</big> | ||
Charles Hadley King - The George Washington University (GWU) | <big>Charles Hadley King - The George Washington University (GWU)</big> | ||
Tianyi Wang - The George Washington University (GWU) | <big>Tianyi Wang - The George Washington University (GWU)</big> | ||
Chinweoke Okonkwo - The George Washington University (GWU) | <big>Chinweoke Okonkwo - The George Washington University (GWU)</big> | ||
Omar Serang - DNAnexus | <big>Omar Serang - DNAnexus</big> | ||
Sam Westreich - DNAnexus | <big>Sam Westreich - DNAnexus</big> | ||
Dennis A. Dean, II - Velsera | <big>Dennis A. Dean, II - Velsera</big> | ||
Phil Webster- Velsera | <big>Phil Webster- Velsera</big> | ||
Revision as of 19:16, 11 October 2023
This hybrid workshop provides an opportunity to learn about BioCompute Objects and interoperability between 3 platforms that host BioCompute Objects. It will also cover BCODB and Portal at the FDA, real-world applications, and potential AL/ML-related BCO implementations. We encourage everyone to attend in person for hands-on experience.
Date & Time: May 10th, 2024, 8 AM - 5 PM
Location: Great Room, White Oak Campus, FDA center
Event Registration: Eventbrite
Abstract
Documenting computational workflows has historically been a challenge for researchers and reviewers. Often, there are no clear guidelines for describing these workflows, leading to ad hoc definitions and descriptions that are insufficient for comprehension and reproducibility. BioCompute, an abbreviation for the IEEE standard 2791-2020, offers a structured framework for describing workflows in a precise yet adaptable manner. A BioCompute Object (BCO) represents a workflow that adheres to this standard. This standard breaks down a workflow into its core components, aligning them with established data standards and ontologies. BioCompute significantly aids in streamlining workflow data, managing complexity across multiple versions, and enhancing reproducibility.
As the field continues to evolve, addressing regulatory concerns becomes paramount, necessitating a common language for all stakeholders. The BioCompute community, comprised of over 400 individuals, has crafted a framework that offers guidance without imposing undue burdens on sponsors or reviewers. To date, BCO has been embraced by three FDA centers, effectively reducing delays in regulatory submissions. An ongoing pilot project involving the BioCompute team, FDA, and industry sponsors aims to improve communication efficiency and fluidity during submission and review processes.
The BioCompute Portal, serving as the central platform for creating and submitting BCOs, has seen significant improvements in the past year, including Google and ORCID integration and an enhanced user interface. Furthermore, a new Portal instance at the FDA, along with four tools for authoring BCOs directly from various platforms (BCOnexus, Seven Bridges APP, the HIVE, and Galaxy platforms), and expanded documentation, make it easier to create, share, edit, and publish BCOs online. Overall, this project strives to streamline and secure the submission process. The FDA can retrieve BCOs from the public BCODB upon request, and with APIs and authentication tokens, users can directly submit to FDA portal API endpoints and interact with BCOs and their implementations seamlessly.
Workshop Topics
- Updates on BioComput
- BCO Portal at the FDA
- Platform interoperability,
- Exemplar workflows and real-world applications
- BCO-Nextflow
- AI/ML-related implementations
Schedule
TBD
Organization Committee
Mark Walderhaug - U.S Food & Drug (FDA)
Luis Santana-Quintero - U.S Food & Drug (FDA)
Raja Mazumder - The George Washington University (GWU)
Jonathon Keeney - The George Washington University (GWU)
Charles Hadley King - The George Washington University (GWU)
Tianyi Wang - The George Washington University (GWU)
Chinweoke Okonkwo - The George Washington University (GWU)
Omar Serang - DNAnexus
Sam Westreich - DNAnexus
Dennis A. Dean, II - Velsera
Phil Webster- Velsera