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Neuroinformatics Assembly 2022

Program

17:00-18:30 CET INCF & the FAIR roadmap
icon keynoteChair: Maryann Martone, University of California, San Diego

Since the introduction in 2016, the FAIR data principles have gained increasing recognition and adoption in global neuroscience. FAIR defines a set of high level principles and practices for making digital objects, including data, software and workflows, Findable, Accessible, Interoperable and Reusable. But FAIR is not a specification; it leaves many of the specifics up to individual scientific disciplines to define. INCF has been leading the way in promoting, defining and implementing FAIR data practices for neuroscience. We have been bringing together researchers, infrastructure providers, industry and publishers through our programs and networks.

  • Welcome and introductions to INCF
  • FAIR Roadmap
  • Discussion
18:30-19:00 CET BREAK
19:00-20:30 CET
Parallel Session 1:FAIR Workflows for neuroscience research
icon keynoteCo-Chairs: Helena Cousijn, PhD (DataCite) and Prof. Lucia Melloni (MPIEA)

An exciting development we are witnessing in neuroscience research is the increase in large-scale collaboration. But on the other hand, the field faces significant reproducibility problems which introduces great uncertainty in the interpretation of study results. More specifically, consciousness research inherits this same challenge, while also facing further limitations of the contrastive method put forward almost a decade ago. Such complications have impeded the search for the neural correlate of consciousness, and thereby put to question the validity of the theories of consciousness that were built on those findings. To address the question of what anatomical structures and physiological processes in the human brain give rise to consciousness, would require countless studies, and critically, the aggregation of data across them. Yet, the lack of infrastructure to aggregate results in a consequential way, poses great challenges for researchers to fully understand the extent of a research study - including the experimental context, the methodology, analysis, stability of the results and data. Development of FAIR workflows will address that need, unleashing the possibility to better understand the ‘hard problem’ of consciousness.

  • Collaborative neuroscience research
  • FAIR principles / PID infrastructure
  • Metadata standards and templates for data and project
  • Implementing FAIR Workflows project
Parallel Session 2: Fully transparent ERP & MRI study methodology descriptions with ARTEM-IS and eCOBIDAS
icon keynoteAngela Šoškić, Suzy Styles and Remi Gau

Accurate reporting is critical for transparent, reproducible, replicable, FAIR-compliant research in the scientific record, and allows advanced forms of meta-science to be conducted. Two recent initiatives that address this challenge are ARTEM-IS and eCOBIDAS. Both are community collaborations that aim to design tools that facilitate detailed methodology documentation in neuroscience. These projects engage in broad consultation to maximise ease of use, clarity and specificity in the tools.

  • Walk users through the ARTEM-IS template for documenting an ERP study, and eCOBIDAS web-app for documenting an MRI study, in two parallel sessions.
20:30-20:45 CET BREAK
20:45-21:15 CET F1000 - Sharing and publishing your data
icon keynoteChair: James Barker, Publishing Executive, F1000 Research Ltd.

F1000 has upheld an Open Data policy on F1000Research and our Partner Platforms since 2014. Over this time, we have gained extensive experience in aiding authors in presenting and publishing the data support their publications. Through the workshop we will present how we go about supporting our authors in sharing their data through traditional and non-traditional article types, and how these practices can support discoverability and reuse of this data.

  • Data availability statements 
  • Preparing data to be shared  
  • Data publications – Data Notes
  • The INCF Community Gateway on F1000Research
21:15-22:15 CET Poster Session 1
02:00-03:00 CET Poster Session 2
09:00-10:00 CET Poster Session 3
16:30-17:00 CET Lightning talks 1
17:00-18:30 CET Diversity and inclusion in Neuroinformatics
icon keynoteTBD

The lack of diversity and inclusion continues to remain an issue in STEM. Even though it is well acknowledged, and there are initiatives that promote diversity and inclusion, progress is slow. The INCF, as an umbrella organization in Neuroscience, is incredibly well placed to help accelerate our progress by bringing its members (both institutional and individual) together to discuss what concrete steps we, as a community, can take.

  • Metrics from organisations/labs/conferences where available
  • Discuss the possibility of the INCF also acting as an umbrella organisation for Outreachy, in a way similar to how we conduct GSoC
  • Formation of a new working group explicitly to work on diversity, inclusion, and outreach
18:30-19:00 CET BREAK
19:00-20:30 CET
Parallel Session 1: Tools and formats for large scale network modelling
icon keynoteChair: Padraig Gleeson

A number of groups around the world are developing complex, experimentally constrained network models of neuronal function. Creating the software infrastructure to develop, simulate and share these types of models takes a significant amount of time for any of the groups involved and there can be a lot of overlap, duplication in work and repeated effort.

The purpose of this workshop is to highlight some of the initiatives currently underway to build biologically detailed neuronal network models as well as those projects building the infrastructure to make it easier to develop, disseminate and compare the models. This workshop is an activity of the INCF Working Group on Standardized Representations of Network Structures. .

  • Highlight some of the initiatives currently underway to build biologically detailed neuronal network models and projects
Parallel Session 2: Global brain consortium’s EEG normative initiative for creating standards for MEEG analysis
icon keynoteCo-Chairs: Pedro Valdes-Sosa and Jorge Bosch-Bayard

With the increase of large collaboration and data sharing, EEG data faces the critical barrier of replicability and data pooling problems. Especially for quantitative EEG (qEEG) analysis, the characterized age-frequency distribution of log-spectrum may lose reliability for clinical diagnosis when people gather datasets from different sites recorded at a different time with varying data acquisition protocols because of batch effects.This workshop will present the Global Brain Consortium’s multi-national EEG normative initiative for creating international standards for MEEG analysis.

  • Introduction to the GBC EEG norms initiative. Covers the rationale, partners, aims, and scope
  • Harmonized norms
  • EEGNet platform for annotating EEG data
  • EBRAINS intracranial EEG recordings
  • Discussion: Challenges, gaps, and opportunities
Parallel Session 3: Neuroimaging Quality control - focus on informatics aspects of the niQC methods, tools, and standards
icon keynoteCo-Chairs: Pradeep Reddy Raamana and Yaroslav Halchenko

The Neuroimaging Quality Control (niQC) working group (WG) proposes a symposium focused on the informatics aspects of the niQC methods, tools, and standards. Informatics has been and remains a crucial part of assisting the neuroscience community to improve the quality of their data. Virtually all stages of the data acquisition and processing in neuroimaging involve some sort of quality assurance (QA) and quality control (QC), that needs an informatics solution to deal with the complexity, heterogeneity, and scale of the neuroimaging datasets. While the community has already developed a number of tools, which are listed and categorized on the WG website (https://incf.github.io/niQC/tools), there are many unaddressed gaps in terms of interoperability and harmonization of the results across QA and processing ecosystems, where a number of decisions to be made based on the quality of the data at different stages of processing. Lack of standardization and cross-pollination of QA/QC “know-how” between ecosystems can lead to reduced reproducibility. We plan to invite various tool developers and methods researchers to discuss these gaps, and try to achieve or improve interoperability among different processing ecosystems. The focus would initially be on the anatomical (T1w) and functional MRI (EPI) data, at the stages of initial QA and QC on raw-data as well as QC on the derived measures.

  • Overview / tutorial talks from the relevant ecosystems and tools with a clear template
  • Open panel discussion ies
20:30-20:45 CET BREAK
20:45-21:15 CET EEG: the interface between neuroinformatics and clinical/basic science research
icon keynoteINCF Secretariat

This discussion panel will cover the challenges the EEG and neuroimaging community face as an interface between neuroinformatics and clinical/basic science research. Panelist to include: i. service providers: EEGLab, MNE, and FieldTrip and ii. data providers: Pakistan, Healthy Brain Network (Mike M.), Arnaud Willringer, Temple University, EEGManyLabs.

  • Data sharing
  • Interoperability
  • Harmonization
  • Data protection
  • Levels of evidence
16:30-17:00 CET Lightning talks 2
17:00-18:30 CET GA4BH
icon keynoteTBD

TBD

  • TBD
18:30-19:00 CET BREAK
19:00-20:30 CET
Parallel Session 1: Software arena (tool developers BoF)
icon keynoteCo-Chairs: Shailesh Appukuttan and Ankur Sinha

Contemporary neuroscience is heavily reliant on computing. From computational modelling to the analysis of data gathered from experiments, all tasks in the neuroscience research pipeline require a basic knowledge of common computing tools. Yet, the multi-disciplinary nature of neuroscience research implies that many of us do not hail from computing disciplines, and therefore have not received formal training in this area. Keeping in line with its goal of improving technical software/computing knowledge in the research community, the INCF/OCNS Software working group (WG) will conducting this session

  • Provide more visibility to all the software that is out there for Neuroinformatics/neuroscience research
  • Best practices that help in development and long term maintenance of software tools 
  • Potential pitfalls that tool developers are likely to encounter  
  • How testing should not be a post facto activity, but rather go hand-in-hand with software development  
  • Importance of software documentation and effective ways of handling it  
Parallel Session 2: Automatic spatial quantification of brain data from small animal models
icon keynoteCo-Chairs: Maja Puchades and Jan G. Bjaalie

This workshop will present and compare a series of neuroinformatics tools for performing feature extraction and advanced brain-wide distribution analysis in an atlas context. The speakers will be recruited from different projects and institutions developing complementary tools and services for brain-wide analysis of data originating from small animal experimental neuroscience. They will discuss alternative approaches for registration of images, segmentation, analyses, reuse of data, and smart combinations of new neuroinformatics tools originating from different laboratories and projects.

Attendees will be guided through use cases demonstrating how the tools can be used in different context and for different purposes.

  • Neuroinformatics tools for performing feature extraction and advanced brain-wide distribution analysis in an atlas contex
20:30-20:45 CET BREAK
20:45-21:15 CET How do I rigorously express where my manipulation occurred in the brain or nervous system?
icon keynoteChair: Stephen Van Hooser, Brandeis University
Presenters: UBERON team, Josh Siegel, Allen Institute, Yongsoo Kim, Penn State University

This workshop focuses on the problem of unambiguously and rigorously declaring where a probe or other manipulator is placed in the brain, so that it can be understood by humans or machines. We will hear about solutions that have been developed in highly used model organisms like the mouse, and hear about cross-species ontologies that have been developed. The goal of the workshop is to spread best practices and to identify needed digital infrastructure so that it may be developed.

  • "Where was I? The problem of rigorously identifying placement of electrodes or other probes in the brain, for many species"
  • UBERON, a comparative anatomy ontology
  • How does AI accurately trace the probes in ex vivo volumes?
  • How does AI align anatomical and physiological landmarks?
  • How does AI validate that our registration is accurate?
  • How are locations in the mouse brain developmental ontology being determined and specified?
  • How can the developmental CCF be used to rigorously specify locations in the mouse brain?
09:00 - 13:00 CET Enabling multi-scale data integration: Turning data to knowledge
icon keynoteChair: Hosted by NFDI-Neuro (Responsible Spokesperson Petra Ritter)
Contributors: Co-spokespersons of NFDI-Neuro

The workshop is organized by the German National Research Data Infrastructure Initiative Neuroscience (NFDI-Neuro). The initiative is community driven and comprises ca. 50 contributing national partners and collaborates. NFDI-Neuro partners with EBRAINS AISB, the coordinating entity of the EU Human Brain Project and the EBRAINS infrastructure. We will introduce common methods that enable digital reproducible Neuroscience. Each class of research data management method is first introduced conceptually - followed by a practical hands-on session. For hands-on sessions we will use the Collaboratory by EBRAINS as a joint digital workspace providing a range of functionalities including compute and storage resources.

  • Why is multilevel data integration important?
  • Introduction to data structure standards
  • Introduction to metadata schemas
  • Introduction to EBRAINS Knowledge Graph for data discovery
  • Introduction to reproducible digital workflows
  • Introduction to provenance tracking
13:00 - 13:30 CET BREAK
13:20 - 17:30 CET Continuation - Enabling multi-scale data integration: Turning data to knowledge
17:30 - 17:45 CET BREAK
17:45 - 18:00 CET INCF tools & training (pre-recorded)
17:45 - 18:00 CET Event and condition annotation of BIDS data using HED – from start to finish
icon keynoteCo-chairs: Scott Makeig and Kay Robbins

Hierarchical Event Descriptors (HED) fill a major gap in the neuroinformatics standards toolkit, namely the specification of the nature(s) of events and time-limited conditions recorded as having occurred during time series recordings (EEG, MEG, iEEG, fMRI, etc.). We, the HED Working Group, propose a half-day online INCF workshop on the need for, structure of, tools for, and use of HED annotation to prepare neuroimaging time series data for storing, sharing, and advanced analysis.

  • Documenting temporal structure in time series data (evolving concepts, history, needs and benefits)
  • Annotating a BIDS dataset from start to finish
  • Adding annotations to EEG data using the HED tools ecosystem
  • Using the SCORE HED library schema for clinical EEG data annotation
  • Applying HED annotation to fMRI datasets
17:45 - 18:00 CET BIDS Annotations, NIDM, and Query Across Datasets
icon keynoteChair: David Keator, Co-Chairs: Camille Maumet, JB Poline

This workshop will focus on teaching researchers how to annotate BIDS datasets to make them more findable and reusable. We will identify some sample BIDS datasets and attendees will learn how to create un-ambiguous data dictionaries (JSON sidecar files) for BIDS formatted datasets using the latest tools from the NIDM and ReproNim efforts. Attendees will then learn how to query across the sample BIDS datasets using concept annotations created during the annotation portion of the training. Attendees will be taught how to use the query tools developed for NIDM by ReproNim while also being taught the core NIDM model and how to write their own queries. Attendees will then be introduced to NIDM tools allowing them to learn relationships between variables contained within the sample BIDS datasets using simple linear regression and how these derived data can be described using the BIDS-Prov extension. At the completion of this workshop attendees should be able to create their own BIDS annotation files using multiple tools, query within their BIDS dataset or across multiple BIDS datasets, and understand the current state of derived data provenance in BIDS and NIDM.

17:45 - 18:00 CET NWB User Training Tutorial icon keynoteChair: Ben Dichter

This training will cover the basics of Neurodata Without Borders (NWB), a data standard for neurophysiology data designed to maximize reusability of the data. We will demonstrate converting experiment data to NWB in Python and publishing on the DANDI Archive. Then we will give a tour of the available training resources for automated conversion from proprietary formats, and for building and publishing extensions. We will conclude with a Q+A section to help users with specific conversion questions.

13:00 - 13:15 CET INCF tools & training (pre-recorded)
16:45 - 17:00 CET INCF tools & training (pre-recorded)
17:00 - 18:30 CET Neuroinformatics Reproducibility for Everyone icon keynoteChair: Dr. Alberto Antonietti

This workshop will introduce reproducible workflows and a range of tools along the themes of organisation, documentation, analysis, and dissemination. After a brief introduction to the topic of reproducibility, the workshop will provide specific tips and tools useful in improving daily research workflows. The content will include modules such as data management, electronic lab notebooks, reproducible bioinformatics tools and methods, protocol and reagent sharing, data visualisation, and version control. All modules include interactive learning, real-time participation, and active knowledge sharing. The methods and tools introduced help researchers share work with their future self, their immediate colleagues, and the wider scientific community.

Topics:
  • Apply a conceptual framework for reproducibility, replicability, and robustness of research.
  • Explore practical, accessible tools and methods for advancing the reproducibility of research.
  • Reuse and adapt the Reproducibility for Everyone modular curriculum to their own training and research needs.
  • Evaluate their reproducibility barriers and solutions through interactive knowledge sharing.
Target Audience: :

Every R4E workshop is customised for the audience. This workshop is for neuroinformatics students, postdoctoral scholars, and any active researchers. It is designed for participants without any prior knowledge of either the concepts or methods of reproducibility. This workshop introduces this curriculum to attendees, initiating them into the landscape of research data management, open research, and reproducible methods.