PSB Workshops
Pacific Symposium on Biocomputing
Big Island of Hawaii - January 4-8, 2025
PSB is offering four workshops during the meeting. These workshops were created to provide an opportunity for a gathering that will not be based on peer-reviewed papers included in the proceedings book. The workshops will consist of presentations by invited speakers. Abstract submissions for the workshops will be evaluated by the workshop co-chairs.
Each workshop has a chair who is responsible for organizing submissions. Please contact the specific workshop chair relevant to your interests for further information. Links on each of the titles below lead to more detailed calls for participation.
- All Together Now: Data Work to Advance Privacy, Science, and Health in the Age of Synthetic Data
- Command Line to PipeLine: Cross-Biobank Analyses with Nextflow
- Leveraging Foundational Models in Computational Biology: Validation, Understanding, and Innovation
- Opportunities and Pitfalls with Large Language Models for Biomedical Annotation
All Together Now: Data Work to Advance Privacy, Science, and Health in the Age of Synthetic Data
Organizers: Lindsay Fernandez-Rhodes, Jennifer K. Wagner
Description: Transparency alone is insufficient to bridge the gap between data practices and public understanding in an era of synthetic data and artificial intelligence. “Data work” is needed to have scientific data be deemed trustworthy, meaningful and actionable–not only for scientists but also for the individuals from whom those data were derived or to whom those data relate. This workshop is intended to nurture a discussion of these issues and describe the interdisciplinary competencies necessary to become equipped to embed ethical, legal and social considerations into their research.
Contact: Lindsay Fernandez-Rhodes
Email: Fernandez-rhodes at psu dot edu
Command Line to PipeLine: Cross-Biobank Analyses with Nextflow
Organizers: Anurag Verma, Lindsay Guare, Katie Cardone, Christopher Carson, Zachary Rodriguez
Biobanks hold immense potential for genomic research, but fragmented data and incompatible tools slow progress. This workshop equips you with Nextflow, a powerful workflow language to streamline bioinformatic analyses across biobanks. Write code in your preferred language and Nextflow handles the complexities, ensuring consistent, reproducible results across different platforms. This interactive session is ideal for beginner-to-intermediate researchers who want to (1) Leverage biobank data for genomic discoveries, (2) Build portable and scalable analysis pipelines, (3) Ensure reproducibility in their findings, (4) Gain hands-on experience through presentations, demonstrations, tutorials, and discussions with bioinformatics experts.
Contact: Anurag Verma
Email: anurag.verma at pennmedicine dot upenn dot edu
Leveraging Foundational Models in Computational Biology: Validation, Understanding, and Innovation
Organizers: Steven Brenner, Brett Beaulieu-Jones
Large Language Models (LLMs) have demonstrated immense potential within and outside of the biomedical domain but currently have substantial limitations when applied to biomedical research. These models promise a new paradigm for data analysis, interpretation and hypothesis generation, but it is not clear how fully this promise will be fulfilled. LLMs are just one class of foundational models, and while they have already made a significant impact to computational biology, it is unlikely that a singular architecture geared at processing natural language will be the ideal framework for general learning in computational biology. This workshop aims to provide an understanding of the state of the art today, current challenges in the application or development of models tailored to computational biology, as well as to start a discussion of what the future holds for our community.
Contact: Brett Beaulieu-Jones
Email: beaulieujones at uchicago dot edu
Opportunities and Pitfalls with Large Language Models for Biomedical Annotation
Organizers: Fabio Rinaldi, Jin-Dong Kim, Zhiyong Lu, Cecilia Arighi
Coming soon.
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