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Birds of a Feather (BoF) - ISMB/ECCB 2021

Interpretability of Machine Learning Algorithms

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.

Bioinformatics Advances: Meet the Editors

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.

JBrowse

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.

Jalview and Friends

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.

Next steps for computational reproducibility toward fully executable papers

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. 

Interoperability Challenges for Sensitive Biomedical Data

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.

New Methods of Programmatic, Web and Cloud Data Access from NCBI

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!