Please use the links below to view previous webinars:
- January 14, 2021 - Approaching Indigenous communities on theior own terms in microbiome research by Matthew Anderson, Ohio State University. Hosted by ISCB.
- January 26, 2021 - The ISCB Competency Framework: what is it and how does it support bioinformatics education and training? by Cath Brooksbank, EMBL-European Bioinformatics Institute. Hosted by ISCB
- January 28, 2021 - SaGePhy: A phylogenetic simulation framework for gene and subgene evolution by Soumya Kundu, University of Connecticut. Hosted by EvolCompGen COSI and SMBE
- February 18, 2021 - Responsibilities for the Stewardship of Indigenous Data in Open Science by Stephanie Russo Carroll, University of Arizona. Hosted by ISCB
- March 17, 2021 - Recognising Indigenous Rights in Digital Sequence Information by Maui Hudson, University of Waikato. Hosted by ISCB
- May 25, 2021 - The Evolution of the Data Sharing Culture in Structural Biology by Helen Berman, Rutgers University. Hosted by ISCB
- June 10, 2021 - How did they get there? Genetic History of Native Americans in the Central Andes by Victor Borda, University of Maryland. Hosted by ISCB
- June 28, 2021 - Early publication access and EMBL-EBI bio-molecular data tackle COVID-19 by Matt Pearce, EBI, and Michael Parkin, EBI. Hosted by ISCB
January 14, 2021
Principles of individual consent and sample deidentification stand as pillars of modern biomedical research but are flawed with respect to certain populations. Indigenous peoples have historically been targeted by unethical practices that continue into the present even when following best practices for conducting research with human subjects. This has led some studies in American Indian/Alaskan Native (AI/AN) populations to included additional safeguards that are reinforced through these communities’ unique legal status as domestic dependent nations. Yet, use of microbiome datasets generally lacks restriction on data sharing and other protections because of their perceived inability to significantly impact public health or individual welfare despite over a decade of work demonstrating the importance of microbial population in human development, metabolism, and immunopathologies. Additionally, raw datasets can contain large proportions of human-derived reads that include information on the host and not just microbes. Current projects in partnerships with the Cheyenne River Sioux Tribe serve as new models of community partnerships to address issues of sovereignty in human and non-human datasets.
The ISCB Competency Framework: what is it and how does it support bioinformatics education and training?
By Cath Brooksbank
January 26, 2021
Demand for the application of data science techniques to life science research is accompanied by an increased need for bioinformatics expertise across a broad range of professionals – from lab-based molecular life-scientists through computer scientists to software engineers; furthermore, the applications of data-driven biology are just as varied, encompassing fundamental life-science, medicine, agriculture and environmental science. Educating and training the individuals who choose career paths in this varied and fast-moving field is therefore challenging, and educators can struggle to keep up with the needs of employers.
The ISCB competency framework was developed by the ISCB Education Committee in consultation with a global community of bioinformatics professionals to bridge this gap. It provides a minimum information standard defining the competencies required, and the levels they’re required at, for a range of roles that require bioinformatics expertise, and it provides a tool to support bioinformatics educators to develop courses and curricula that meet the needs of employers.
In this webinar I will explain why the ISCB adopted a competency-based approach, describe the newly released version 3 of the framework, summarise how educators and trainers can use the framework to develop new learning interventions or update pre-existing ones, and outline how the ISCB is planning to support a competency-based approach to bioinformatics education and training in the future, both through continuing improvement of the framework and through initiatives to encourage the recognition of courses and curricula that make use of it.
January 28, 2021
SaGePhy (pronounced sage-phy) is a software package for improved phylogenetic simulation of gene and subgene evolution. SaGePhy can be used to generate species trees, gene trees, and subgene or (protein) domain trees using a probabilistic birth–death process that allows for gene and subgene duplication, horizontal gene and subgene transfer, and gene and subgene loss. SaGePhy implements a range of important features not generally found in other phylogenetic simulation frameworks; these include the ability to simulate (i) subgene or domain level events inside one or more gene families, (ii) both additive and replacing horizontal gene and subgene/domain transfers, (iii) distance-biased horizontal transfers, and (iv) probabilistic sampling of species tree and gene tree nodes, respectively, for gene- and domain-family birth. SaGePhy therefore makes it possible to perform more realistic simulation of gene and subgene/domain evolution.
February 18, 2021
As big data, open data, and open science advance to increase access to complex and large datasets for innovation, discovery, and decision-making, Indigenous Peoples’ rights to control and access their data within these data environments remain limited. Indigenous Data Sovereignty focuses on the protection of Indigenous rights and interests in the control and governance of Indigenous data. Indigenous data interests stretch across diverse disciplinary fields connecting community data governance ambitions with institutional and individual responsibilities in practice. Given this reach, a range of initiatives have been developed to strategically build new capabilities for strengthening control and governance of Indigenous data. These initiatives draw on a variety of methods and tactics across law, policy, ethics, and infrastructure. Applying these new tools and mechanisms in open science shifts Indigenous Peoples from invisibility within data ecosystems to vibrant contributors to open science.
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March 17, 2021
Indigenous concerns about genomic research have been strongly articulated over the past few years with accompanying suggestions about how to improve relationships with indigenous communities and the practice of research. Discussions are now moving towards how Indigenous rights can be recognised in the context of Digital Sequence Information including the recognition of provenance and sharing of protocols and permissions through labelling systems like Local Contexts.
May 25, 2021
The Protein Data Bank was established 50 years ago in 1971. In this Webinar I will describe its evolution from a small repository to a large international data resource. The roles that the many stakeholders played in creating a data sharing culture and how science has benefited from that culture will be discussed.
June 10, 2021
Central Andes, which extends from Southern Ecuador to Southern Peru, was the homeland of civilizations that reached the state-level society in pre-Columbian times. The term “Central Andes” do not include solely the highland mountains but also the regions affected by both slopes to the east (Amazon) and west (Pacific Coast). Cultural interaction involving these regions were described for the last 5000 years. Here we describe genetic evidence that these cultural connections were accompanied by gene flow across the Andes and Northern Peru was one of the main scenarios for these movements.
Early publication access and EMBL-EBI bio-molecular data tackle COVID-19
By Matt Pearce and Michael Parkin
June 28, 2021
The COVID-19 Data Portal (CDP) and Europe PMC’s full-text collection of COVID-19 preprints represent two efforts by EMBL-EBI to make data available to promote coronavirus research.
The COVID-19 Data Portal (CDP) was launched in April 2020 to provide access to SARS-CoV-2 and COVID-19 biomolecular data in an accessible manner. The data portal is part of the European COVID-19 Data Platform, which is provided by EMBL's European Bioinformatics Institute (EMBL-EBI), ELIXIR, partners from the ReCoDID and VEO projects and the European Open Science Cloud. There are national portals that complement the covid19dataportal.org and represent a broad international collaboration.
In recognition of many researchers publishing their COVID-19 results rapidly via preprints during the pandemic, Europe PMC (https://europepmc.org/), an EMBL-EBI database for life science literature, launched a project in July 2020 to make the full text of COVID-19 preprints available for reading and reuse via a standard XML format. Preprints are linked to journal-published articles, open peer review materials, as well as underlying data in community databases, including PDBe, ENA, and many more. The full text corpus of COVID-19 preprints with an open access license or similar is made available for download via a public API and FTP site, enabling deeper analysis.