PSB Workshops

Pacific Symposium on Biocomputing

Big Island of Hawaii - January 3-7, 2022

PSB is offering five 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.

Emerging Topics in Cancer Evolution

Organizers: Mohammed El-Kebir, Quaid Morris, Layla Oesper, Cenk Sahinalp

Cancer results from an evolutionary process that yields a heterogeneous tumor with distinct subpopulations and varying sets of somatic mutations. Viewing cancer through the lens of evolution is critical to improve our understanding of tumorigenesis and ultimately treatment of cancer. The workshop will focus on algorithms and models of evolutionary processes in cancer. Specifically, we aim to bring together the algorithmically-focused side of the cancer evolution community with the biologically-focused side.

Contact: Mohammed El-Kebir
Email: melkebir at illinois dot edu

Genomic and Synthetic Biology Digital Biosecurity

Organizers: Ravishankar K. Iyer, Zbigniew T. Kalbarczyk, Nina Alli, Corey M. Hudson, Nicholas D. Pattengale

Trends toward automation and individualization in biology and medicine raise varied and critical security issues. We solicit talks addressing genomic resilience spanning semantic data protection and secure data sharing, security in synthetic biology automation (secure and reliable), application of ML-based models in prediction and decision making (e.g., an early detection of data tampering), and other related topics, for this workshop geared toward getting ahead of security issues related to the growing automated bioeconomy.

Contact: Corey M. Hudson
Email: cmhudso at sandia dot gov

Image-based profiling: a powerful and challenging new data type

Organizers: Gregory P. Way, Hannah Spitzer, Philip Burnham, Arjun Raj, Fabian Theis, Shantanu Singh, Anne E. Carpenter

In image-based profiling, scientists extract high-dimensional representations from biological images. These representations provide a unique perspective into the underpinnings of biological systems, but there also unique challenges. In this workshop, we will introduce image-based profiling as a concept, and discuss several exciting new application areas in industry and academia.

Contact: Gregory Way
Email: gregory.way at gmail dot com

Packaging Biocomputing Software to Maximize Distribution and Reuse

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

The majority of accepted papers in biocomputing describe new computational approaches to relevant biological problems, and while journals and conferences often require the availability of software and source code, there are limited resources available for trainees to maximize the distribution and use of their software within the scientific community. While the accepted standard is to make source code available for new approaches published work, the growing problem of system configuration issues, language and library version conflicts, and other implementation issues often impede the broad distribution and availability of software tools. There are a variety of solutions to these implementation issues, but the learning curve for applying these solutions is steep. In this tutorial workshop for the Pacific Symposium of Biocomputing, we will demonstrate tools and approaches for packaging and distribution of published code.

Contact: William Bush
Email: wsb36[at]

Social, Technical, and Ethical Challenges in Biomedical Data Privacy

Organizers: Gamze Gursoy, Steven Brenner, Bradley Malin, Barbara Koenig

With decreasing cost of biotechnology, the amount and the size of the available biomedical 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 technical and ethical frames that govern data sharing and use to advance human health from a privacy perspective. 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. We will also discuss the 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
Email: gamze.gursoy at yale dot edu