Birds of a Feather (BoF) - ISMB/ECCB 2021
- Interpretability of Machine Learning Algorithms
- Bioinformatics Advances: Meet the Editors
- JBrowse
- Jalview and Friends
- Next steps for computational reproducibility toward fully executable papers
- Interoperability Challenges for Sensitive Biomedical Data
- New Methods of Programmatic, Web and Cloud Data Access from NCBI
Location: CafeConnect Round Table Group Sunday, July 25, 15:20 - 16:20 UTC
Organizer(s):
Thomas Y. Chen, U.S. Technology Policy Committee
Overview
In machine learning-based computational biology models, one of the many questions that is raised is whether or not the algorithm is interpretable/explainable. In other words, does the end user understand the inner decision making processes of the model? Some approaches are notorious as “black boxes” like CNNs and random forests.
Location: Research Exchange ForumWednesday, July 28, 15:20 - 16:20 UTC
Organizer(s):
Thomas Lengauer, Editor-in-Chief; Max Planck Institute for Informatics; University of Cologne
Overview
The editors-in-chief of the newly launched Bioinformatics Advances (https://academic.oup.com/bioinformaticsadvances) will give a brief overview of the journal, the Associate Editor team, and how the journal will serve the computational biology community with the ISCB at the core of its mission. Please join to hear more about the journal and ask the editors any questions you may have.
Location: Research Exchange Fortum Wednesday, July 28, 15:20 - 16:20 UTC
Organizer(s):
Scott Cain, Ontario Institute for Cancer Research
Overview
Devs, admins and users of JBrowse (1 and 2) gather to discuss new and established JBrowse and GMOD tools.
Location: Research Exchange Forum Wednesday, July 28, 15:20 - 16:20 UTC
Organizer(s):
Jim Procter, University of Dundee
Overview
Catch up with the latest news from the Jalview Team, and meet others using Jalview for teaching, research, and outreach.
Location: CafeConnect Round Table Group Thursday, July 29, 15:20 - 16:20 UTC
Organizer(s):
Geraldine Van der Auwera, Broad Institute
Overview
Think about the last time you wanted to reuse or adapt an analysis method that you read about in a published paper. How did it go? What were the biggest hurdles you ran into? What solutions are you aware of that you think everyone should know about, and what do you wish was available? Let's talk about problems and solutions, and how we might make progress toward fully executable papers.
Location: Research Exchange Forum Thursday, July 29, 15:20 - 16:20 UTC
Organizer(s):
Caitlin McHugh, Alzheimer's Disease Data Initiative (ADDI)
Overview
Advances in biomedical research and the advent of big data have opened doors to tremendous amounts of data. Often, data is siloed across technology platforms or is not easily sharable because of restrictive data governance policies. This underscores the need to create a platform that fosters data democratization, enables disparate data analysis, and serves all skill levels—from clinicians to data scientists. Let's discuss gaps and challenges to achieving data interoperability across datasets.
Location: Research Exchange Forum Thursday, July 29, 15:20 - 16:20 UTC
Organizer(s):
Nuala O'Leary, NCBI/NLM/NIH
Overview
National Center for Biotechnology Information (NCBI) at NIH has improved access to sequence and metadata by reimagining programmatic and web interfaces, data formats and cloud-based tools (e.g. ElasticBLAST). NCBI wants to update users on two new initiatives: 1) moving the complete Sequence Read Archive (>14 PB ) to AWS ODP and 2) improving access to GenBank data through NCBI Datasets. We welcome a discussion of use cases for working with the new data access options!