PSB Workshops

Pacific Symposium on Biocomputing

Big Island of Hawaii -- January 3-7, 2020

PSB is offering four workshops during the meeting (exact dates to be determined). 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 session chair relevant to your interests for further information. Links on each of the session titles below lead to more detailed calls for participation.

AI Ethics and Values in Biomedicine – Technical Challenges and Solutions

Organizers: D. Petkovic, L. Kobzik, R. Ghanadan

There is increasing recognition of the need to ensure better consideration of ethics and values in artificial intelligence (AI) applications for biomedicine. This 3-hour workshop will provide an overview and discussion on the technical challenges and potential solutions that can enable ethical and value-based AI algorithms and tools in biomedicine. Five expert speakers will present their work and engage the audience in discussion with the aim of defining the best ways to move forward.

Contact: D. Petkovic
Email: Petkovic at sfsu dot edu


Can the circle be squared? Navigating ethical quandaries with the privacy dilemma of biomedical datasets

Organizers: Gamze Gursoy, Megan Doerr, Steven E. Brenner, Haixu Tang

With decreasing cost of biomedical technologies, the amount and the size of the available genetic and healthcare data have exponentially increased and become available to wider audiences. Hence, privacy of patients and study participants has recently emerged as one of the major foci of studies. Availability of genetic and health care information gives rise to privacy concerns such that people suffer dignitary harm when their data is used in ways they did not desire or intend, even if no concrete economic damage results. In this workshop, we propose a practical and interactive exploration of the regulatory and ethical frames that govern data use to advance human health from a privacy perspective. We will have two sections: (1) Ethics of privacy, which we will discuss the ethical and moral frames through which we can consider privacy, the existing regulations regarding privacy and what is on the horizon, and implementation of such ethical considerations for data with the new Common Rule. (2) Approaches to ensuring privacy using technology, in which we will discuss the technologies that allow responsible use and sharing of data such as encryption and the quantification of privacy leakages in publicly available data through privacy attacks for better risk-assessment tools. We will end the workshop with a panel discussion. The mission is to bring together computational biologists, experimental biologists, computer scientists, ethicists, and policy and lawmakers to share ideas, discuss the challenges related to biological data and privacy and hopefully create collaborations.

Contact: Gamze Gursoy and Megan Doerr
Email: gamze.gursoy at yale.edu and megan.doerr at sagebionetworks.org


Packaging Biocomputing Software to Maximize Distribution and Reuse

Organizers: William S. Bush, Nicholas Wheeler, Brett Beaulieu-Jones, Christian Darabos

In this tutorial, we will guide PSB attendees through the process of creating containerized and distributable collections of software and source code. Our session co-chairs will provide hands-on experience creating the simple Docker containers that encapsulate code along with the libraries and software environments necessary to support them; R and python packages that contain validated source code and are distributed through widely available package repositories; and Jupyter/Colab notebooks which meld analysis workflows with data visualization.

Contact: William S. Bush
Email: wsb36 at case.edu


Translational Bioinformatics Workshop: Biobanks in the Precision Medicine Era

Organizers: Jason Moore, Ju Han Kim, Marylyn Ritchie

Translational bioinformatics (TBI) is a multi-disciplinary and rapidly emerging field of biomedical data sciences and informatics that includes the development of technologies that efficiently translate basic molecular, genetic, cellular, and clinical data into clinical products or health implications. We are hosting a TBI workshop at PSB 2020, which is co-sponsored by the Asia-Pacific Translational Bioinformatics Conference (TBC). The theme is "Biobanks in the Precision Medicine Era." Due to the increasing number of growing biobanks, and the opportunities for bioinformatics to drive discovery and implementation science, this topic is ripe for discussion at PSB 2020. We will have speakers from academia and industry discuss the strengths, challenges, and opportunities for using biobanks in precision medicine.

Contact: Marylyn Ritchie
Email: marylyn at upenn.edu