PSB 2013

PSB Workshops

Pacific Symposium on Biocomputing

Big Island of Hawaii -- January 3-7, 2013

PSB is offering three three-hour 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.

PSB 2013 Workshops:

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.

Modeling cell heterogeneity: from single-cell variations to mixed cells populations

Co-chairs: Eric Batchelor, Maricel G. Kann, Teresa M. Przytycka, Ben Raphael, and Damian Wojtowicz

Emerging technologies such as single cell gene expression analysis and single cell genome sequencing provide an unprecedented opportunity to quantitatively probe biological interactions at the single cell level. This new level of insight has begun to reveal a more accurate picture of cellular behavior, and to highlight the importance of understanding cellular variation in a wide range of biological contexts. The aim of this workshop is to bring together researchers working on identifying and modeling cell heterogeneity that arises by a variety of mechanisms, including but not limited to cell-to-cell noise, cell-state switches and cell differentiation, heterogeneity in immune responses, cancer evolution, and heterogeneity in disease progression. We will welcome algorithms to process single-cell experimental data and to provide a system-level view of the interplay of diverse, fluctuating biological components.

Workshop Schedule

Important Dates
Workshop Abstract Deadline: September 7, 2012 (extended deadline); submit online at
Notification: September 22, 2012
Workshop Date: January 3, 2013 1-4pm in Salon 2 & 3

Contact: Maricel Kann
Email: mkann at umbc dot edu

Computational biology in the cloud: methods and new insights from computing at scale

Co-chairs: Peter Kasson and David Konerding

The past few years have seen both explosions in the size of biological data sets and the proliferation of new, highly flexible on-demand computing capabilities. The sheer amount of information available from genomic and metagenomic sequencing, high-throughput proteomics, experimental and simulation datasets on molecular structure and dynamics affords an opportunity for greatly expanded insight, but it creates new challenges of scale for computation, storage, and interpretation of petascale data. Cloud computing resources have the potential to help solve these problems by offering a utility model of computing and storage: near-unlimited capacity, the ability to burst usage, and cheap and flexible payment models. Effective use of cloud computing on large biological datasets requires dealing with non-trivial problems of scale and robustness, since performance-limiting factors can change substantially when a dataset grows by a factor of 10,000 or more. New computing paradigms are thus often needed. The use of cloud platforms also creates new opportunities to share data, reduce duplication, and to provide easy reproducibility by making the datasets and computational methods easily available.

This workshop aims to bring together producers and consumers of large biological datasets with those working on cloud computing and "big data" methods. Presentations describing novel scientific results from the use of cloud computing are welcomed, as well as new platforms for collaboration and data sharing as well as new tools and methods to deal effectively with big data and cloud resources.

Workshop Abstract Deadline: September 7, 2012 (extended deadline)
Notification: September 15, 2012

Workshop Date: January 3, 2013 9am-noon in Salon 2 & 3

Peter Kasson
Email: kasson at virginia dot edu

Computational Challenges of Mass Phenotyping

Chair: Larry Hunter

One of the primary challenges in making sense the dramatic increase in human genotype data is finding suitable phenotype information for correlational analyses. Until recently, such phenotype data was primarily derived from assays or measurements made in clinical or research laboratories. However, laboratory phenotyping is expensive and low-throughput, and a variety of promising alternatives have arisen, including: mining electronic medical records, analyzing data from social networks of patients, and the advent and increasing general adoption of inexpensive wearable sensors. However, the extent and complexity of the data produced involve significant new computational challenges.

Issues to be addressed at the workshop include: Description of the many new modalities, granularities and frequencies of phenotypic data collection; integration across modalities and with other (e.g. epidemiological) data types; analytical approaches; transformation of data to be effective for research use; sharing, openness, consent and other legal/ethical issues; and applications to individual and public health.

Workshop Date: January 3, 2013 7:30-10:30pm in Salon 2 & 3

Larry Hunter
Email: Larry dot Hunter at ucdenver dot edu

The future of genome-based medicine

Chairs: Oliver Stegle, Jennifer Listgarten, Steven Brenner, and Quaid Morris

There has been unprecedented public investment in sequencing human and cancer genomes in the hopes of understanding disease. At the same time, large genome-wide association studies have helped elucidating the genetic underpinning of common diseases, identifying thousands of putative disease relevant loci. Complementary molecular profiling studies have revealed that several of these loci are co-associated with individual mRNA levels, suggesting candidate pathways that are putative mediators of genetic signals.

In this workshop, we hope to address questions about how much genome sequencing has helped our understanding of the causal factors in disease and how much will these data change the way we treat disease in the clinic. Are genome clinics even realistic? If not, what other data will we need on individual patients before genome-based personalized medicine is possible?

Workshop Abstract Deadline: September 1, 2012
Submission Webpage:
Author Notification: September 15, 2012

Workshop Date: January 5, 2013 2:30-5:30pm in Salon 2 & 3

Workshop Schedule

Contact: Oliver Stegle
Email: oliver dot stegle at

Back to the main PSB page