• Scott Cain, Adaptive Oncology, Ontario Institute for Cancer Research, United States
• Robert Buels, Dept of Bioengineering, University of California, Berkeley, United States
• Colin Diesh, Dept of Bioengineering, University of California, Berkeley, United States
• Garrett Stevens, Dept of Bioengineering, University of California, Berkeley, United States
• Peter Xie, Dept of Bioengineering, University of California, Berkeley, United States
• Teresa De Jesus Martinez, Dept of Bioengineering, University of California, Berkeley, United States
• Elliot Hershberg, Dept of Bioengineering, University of California, Berkeley, United States
• Angel Leung, Dept of Bioengineering, University of California, Berkeley, United States
• Junjun Zhang, Adaptive Oncology, Ontario Institute for Cancer Research, Canada
• Caroline Bridge, Adaptive Oncology, Ontario Institute for Cancer Research, Canada
• Gregory Hogue, Adaptive Oncology, Ontario Institute for Cancer Research, Canada
• Andrew Duncan, Adaptive Oncology, Ontario Institute for Cancer Research, Canada
• Robin Haw, Adaptive Oncology, Ontario Institute for Cancer Research, Canada
• Lincoln Stein, Adaptive Oncology, Ontario Institute for Cancer Research, Canada
• Ian Holmes, Dept of Bioengineering, University of California, Berkeley, United States

We present JBrowse 2, a new genome browser with special features for structural variant and comparative genomics. JBrowse 2 is capable of multi-model genome visualization with circular, dotplot, synteny, and linear view types. JBrowse 2 is available as a web based application that anyone can set up on their websites and is well suited for customers of bioinformatics core facilities. It has a graphical configuration editor that can make changes both on the user level and at an administrative level. In addition to a variety of built in view modes, JBrowse 2 has an extensive plugin architecture that can be used to extend views and create new ones. Examples of plug-ins include whole genome views and data adapters that connect JBrowse 2 to Reactome and International Cancer Genome Consortium. It can also be used as a desktop application that individuals can install on Windows, Mac, or Linux machines easily without any complicated setup or update processes.

• Patricia Carvajal-López, EMBL-EBI, United Kingdom
• Ezgi Karaca, Izmir Biomedicine and Genome Center, Dokuz Eylul University, Turkey
• Cath Brooksbank, EMBL-EBI, United Kingdom
• Salvador Capella-Gutierrez, Barcelona Supercomputing Center (BSC), Spanish National Bioinformatics Institute (INB/ELIXR-ES), Spain
• Eva Alloza, Barcelona Supercomputing Center (BSC), Spanish National Bioinformatics Institute (INB/ELIXR-ES), Spain

Bioinformatics core facilities (BCF) play an essential role in enabling research in life sciences. As deep learning and high-throughput sequencing methodologies are increasingly applied to analyse molecular data, there is a growing need for highly specialised services from BCFs and their supporting teams.

BCF scientists face many career progression challenges, often hampered by the lack of formal education as they transition from a research focus to a service focus and management role

Several efforts have emerged to strengthen management-related competencies for BCFs. Since 2017 EMBL-EBI runs a yearly BCF management course, and biannually since 2019, an EMBO Research to Service practical course takes place. These events have reached over 100 participants delving into topics such as BCF strengths and limitations, financial sustainability, project management, estimation of human/computing resources, communication, and networking within BCFs and their associates/users, and the courses keep evolving according to emerging needs. The participants enthusiastically apply the gained knowledge with their teams and beyond, becoming BCF management trainers themselves and taking these courses to other regions.

Diverse efforts are needed to support the BCF community of practice. The training targeted toward this community is essential to continue enabling research and development within the life sciences.

• Nikhil Kumar, Memorial Sloan Kettering Cancer Center, United States
• Christopher Bolipata, Memorial Sloan Kettering Cancer Center, United States
• Sinisa Ivkovic, Memorial Sloan Kettering Cancer Center, United States
• Timothy Song, Memorial Sloan Kettering Cancer Center, United States
• Stephen Kelly, Memorial Sloan Kettering Cancer Center, United States
• Suleyman Vural, Memorial Sloan Kettering Cancer Center, United States
• Amy Webber, Memorial Sloan Kettering Cancer Center, United States
• Nicholas Socci, Memorial Sloan Kettering Cancer Center, United States
• David Solit, Memorial Sloan Kettering Cancer Center, United States

The lack of reproducibility or portability are common problems for bioinformatic pipelines. In addition, complicated workflows can be difficult to run in production environments due to external factors such as non-deterministic errors in the server or filesystem. The Center for Molecular Oncology (CMO) at MSKCC has created a centralized bioinformatic service for labs to perform analysis on targeted cancer gene panels (MSK-IMPACT) and whole exome sequencing data. These pipelines need to be reproducible and portable so any lab can replicate the analysis, but at the same time, the pipelines need to be robust and easily debuggable for operations to run smoothly. To this end, the CMO has assembled, worked with, and developed a suite of open tools to be used in all phases of genomic analysis from pipeline development using Common Workflow Language, execution with TOIL an open-source pipeline management system, debugging with Elastic, Logstash, and Kibana, and testing with Jenkins. This presentation will highlight and discuss the open tech stack that is used at the CMO which can be used as a framework for other teams and organizations to develop and operate their own pipelines.

• Jie Liu, University of Michigan, United States
• Fan Feng, University of Michigan, United States
• Yuan Yao, University of Michigan, United States
• Xue Qing David Wang, University of Southern California, United States
• Xiaotian Zhang, University of Michigan, United States

The resolution of chromatin conformation capture technologies keeps increasing, and the recent nucleosome resolution chromatin contact maps allow us to explore how fine-scale 3D chromatin organization is related to epigenomic states in human cells. Using publicly available Micro-C datasets, we develop a deep learning model, CAESAR, to learn a mapping function from epigenomic features to 3D chromatin organization. The model accurately predicts fine-scale structures, such as short-range chromatin loops and stripes, that Hi-C fails to detect. With existing epigenomic datasets from ENCODE and Roadmap Epigenomics Project, we successfully impute high-resolution 3D chromatin contact maps for 91 human tissues and cell lines. In the imputed high-resolution contact maps, we identify the spatial interactions between genes and their experimentally validated regulatory elements, demonstrating CAESAR's potential in coupling transcriptional regulation with 3D chromatin organization at high resolution.

• Jonathan Dursi, Research Computing Teams, Canada

Leaders of supporting research with technology face common challenges: hiring and retention, keeping up to date, and balancing the countless possibilities of research against what's feasible with a small, under-resourced team. Like elsewhere in academia, we often work with team members who are trainees, not employees; like nonprofits we are called on to enact real changes with ongoing programmes or products while funded only by budgets dependent on multiple short-term grants. Like consultants, we can influence but not set directions of projects and efforts; like technology companies we try to stay on the cutting edge while maintaining legacy tools.

We can learn much from those groups, and each other, about what works and what doesn't in managing such complex teams. In this discussion, we cover some successful patterns seen in other research supporting teams.

• Shannan Ho Sui, Harvard T.H. Chan School of Public Health, USA
• George Bell
• Patricia Carvajal
• Ryan Dale, National Institute of Child Health and Human Development, National Institutes of Health, USA
• Jonathan Dursi, Research Computing Teams, Canada

Managers of Bioinformatics Cores take questions about core management.

• Small discussions

Attendees will break into small groups to discuss a variety of topics of interest to members of bioi...