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Neuroinformatics Assembly 2023 - Program

14:00-14:20 CEST
Welcome!
icon keynoteChair: Maryann Martone

Location: Presentation Room 1

  • Welcome and introductions to INCF
14:30-16:00 CEST
Session 1: A FAIR roadmap for knowledge graphs and ontologies
icon keynoteChair: JB Poline

Speakers: Sourabh Prakash, Jeff Grethe, Fahim Imam, & John Senanu

Location: Presentation Room 1

This talk is an investigator session and will comprise of three talks, with questions moderated by chair Jean-Baptiste Poline, McGill University:
- Sourabh Prakash & Jeff Grethe, UC San Diego: Frictionless data infrastructure for ODC-SCI
- Fahim Imam, FAIR Data Informatics Lab, UC San Diego: The SPARC experience
- John Senanu, University of Ghana: Relationship between sensory sensitivity and cognitive ability in psychopathy

16:30-17:30 CEST
Session 2: FAIR sharing, integration, & analysis of neuroscience data
icon keynoteChairs: Trygve Brauns Leergaard

Location: Presentation Room 1

Speakers: Oliver Schmid, EBRAINS AISBL: The EBRAINS Knowledge Graph
Timo Dickscheid, Research Center Jülich: Brain atlases as tools for data integration
Sharon Yates, University of Oslo: Brain atlas-based analysis of disease models
Andrew Davison, CNRS: Live papers

This session will demonstrate opportunities for sharing, finding and using neuroscience data via the EBRAINS research infrastructure. The session will consist of four brief presentations, each highlighting distinct aspects of EBRAINS.
- The Knowledge Graph - a fundamental tool for organizing and accessing neuroscience data.
- Brain Atlases and tools - common anatomical frameworks, providing a context within which diverse neuroscience data can be explored, visualized, and analyzed using various tools and workflows.
- New and dynamic ways of working with data and models, particularly through live papers.

17:30-18:00 CEST
BREAK
Parallel sessions
18:00-21:00 CEST

18:00-21:00 CEST

Session 3: Streamlining Cross-Platform Data Integration: Processes and Solutions for Rapidly Developing an Integrated Workflow Across Independent Systems for the US BRAIN Initiative Cell Census

Speakers: Maryann Martone, Mike Hawrylycz, Anita Bandrowski, Owen White, GQ Zhang, Joost Wagenaar, Alex Ropelewski, Lydia Ng, Hanchuan Peng, Jesse Gillis, Carol Thompson, Yaroslav (Yarik) Halchenko

icon keynoteChairs: Bing-Xing Huo, Patrick Ray

Location: Zoom session

The workshop will cover topics at ecosystem level such as standardization, governance, and success metrics drawing from experiences in the US BRAIN Initiative Cell Census Network (BICCN) and its next phase, the BRAIN Initiative Cell Atlas Network (BICAN), with a focus on streamlining integrated workflows across independent systems. The challenge in both these projects was to quickly develop an end-to-end system to support the specific requirements of these consortia from systems that were developed independently. Projects like these present the ultimate use cases for FAIR, as FAIR practices should greatly reduce the barrier to integration and increase the usability of the data.

19:00-20:30 CEST

Session 4: “Is this FAIR?”: Transparency in EDI & career development & management
icon keynoteChair: Tanya Brown, TVB

Speakers: Tanya Brown, Karin Grasenick, Hannah Bayer, Zefan Zheng

Location: Presentation Room 2

There is a growing recognition and adoption of open and FAIR science practices in neuroscience research. This is predominately regarded as scientific progress and has enabled significant opportunities for large, collaborative, team science. The efforts and practical work that go into creating an open and FAIR landscape extend far beyond just the science. There is an exceptional amount of 'behind the scenes' processes, policies, and people that are necessary to ensure open and FAIR science prevails. This session aims to explore the implications, challenges, and solutions involved in making open and FAIR science effective at various levels of scientific organization. Karin Grasernick from the Human Brain Project and Convelop will explore the macro/system level, emphasizing equity, diversity, and inclusion within the scientific community. Hannah Bayer of the International Brain Lab will focus on the meso-scale, sharing essential principles for effectively leading and governing a large, diverse research lab committed to openness. Zefan Zheng, a PhD candidate at the Max Planck Institute, will provide insights into the micro-level experience, addressing the question of what it takes to be an open researcher and whether it's worth the effort. Finally, Tanya Brown from ARC-Cogitate Consortium at the Max Planck Institute will bridge the gap between these levels by examining the concepts of credit and contribution in open research. She will elucidate how change at each level is necessary to provide effective support and incentives for open and FAIR researchers to thrive.

21:00-21:30 CEST
BREAK
21:30-22:00 CEST
Lightning talks 1

Location: Presentation Room 2

21:30 CEST Alden Connor, The Alan Turing Institute - Bridging into AI: open source tools for computer vision
21:35 CEST Harsh Sinha, University of Pittsburgh - Building bridges in MR research: unified interface to different MRI dataset formats with MRdataset
21:40 CEST Kimberly Ray, UT Austin - Developing an International Data Governance Framework for Brain Data

22:00-23:00 CEST
Poster Session 1

Location: Poster Hall

02:00-03:00 CEST
Poster Session 2

Location: Poster Hall

Parallel sessions
13:00-14:00 CEST

13:00-14:00 CEST

Poster Session 3

Location: Poster Hall

13:00-14:00 CEST

Lightning talks 2

Location: Presentation ROOM 2

13:00 CEST Martijn de Neeling, state of brain-computer interface standards
13:15 CEST Aref Kalantari Sarcheshmeh, University Hostpital Cologne - How to establish and maintain a multimodal animal MRI dataset using DataLad
13:20 CEST Michał Szczepanik, Research Center Jülich - Distributed data management for large collaborative projects: DataLad ecosystem in Collaborative Research Center 1451
13:25 CEST Yoshimasa Tawatsuji, The University of Tokyo - BRAES: Developing Brain Reference Architecture Editorial System for Accumulating Hypotheses on Neural Functionality
13:30 CEST Joseph Ziminski, Sainsbury Wellcome Centre - Automated tools for (systems) neuroscience project standardisation, organisation and discovery
13:35 CEST David Abbott, TBA - Robust individual analysis of multi-band multi-echo functional MRI
13:40 CEST - Alessandro Felder, University College London - BrainGlobe: tools for neuroanatomy - improving the experience for both users and contributors
13:45 CEST - Sarah Faber, Simon Fraser University - What do network models of naturalistic data tell us? Lessons from music listening
13:50 CEST - Soodeh Moallemian - PET Pro: An Automated pipeline to estimate the image-derived input function for UCB-H PET

14:00-14:30 CEST
BREAK
14:30-18:30 CEST
Session 5.1: Infrastructure for Sensitive Data
icon keynoteChair: Petra Ritter

Speakers: Petra Ritter & Michael Schirner

Location: Presentation Room 1

Presentation of the new EBRAINS privacy-compliant and scalable services for brain research to store, share and analyze complex multi-modal FAIR sensitive neuroscience data originating from human subjects: Health Data Cloud (HDC). The workshop provides participants both lecture and hands-on training session.

18:30-19:00 CEST
BREAK
Parallel sessions
19:00-22:00 CEST

19:00-22:00 CEST

Session 5.2: Continuation: Hands on session for Infrastructure for Sensitive Data
icon keynoteChair: Petra Ritter

Speakers: Patrik Bey & Marc Sacks

Location: Presentation Room 1

Presentation of the new EBRAINS privacy-compliant and scalable services for brain research to store, share and analyze complex multi-modal FAIR sensitive neuroscience data originating from human subjects: Health Data Cloud (HDC). The workshop provides participants both lecture and hands-on training session.

19:00-22:00 CEST

Session 6: Research workflows for collaborative neuroscience
icon keynoteCo-Chairs: Dimitri Yatsenko (DataJoint), David Feng (Allen Institute), Erik C. Johnson (JHU APL)

Speakers: Kabilar Gunalan (DataJoint), Milagros Marin-Alejo (DataJoint), Frank Zappulla (Code Ocean), and Daniel Xenes (JHU/APL)

Location: Presentation Room 2

To tackle the challenging questions of the brain, scientists are turning to innovative strategies to automate and organize their research. Automated research workflows integrate computing infrastructure, automation, instrument integration, advanced data operations, and machine learning to enable researchers to process vast amounts of data and analyze complex patterns. This enhances the speed, accuracy, and reliability of collaborative research activities and enables scientists to generate new insights and knowledge that were previously unattainable.

The implementation of automated research workflows is not just about technical solutions but also about creating novel team structures that foster collaboration and innovation. With these tools, researchers can work more efficiently, share knowledge more easily, and focus on the intellectual challenges of their research. In this workshop, three teams will present approaches to workflow management, team organizations, software tools, and online platforms and resources for organizing studies. The presentation will comprise short lectures followed by hands-on tutorials.

The target audience are students, postdocs, and investigators in data-intensive neuroscience research.

Parallel sessions
11:30-15:30 CEST

11:30-15:30 CEST

Session 7: Practical guide to overcome the reproducibility crisis in small animal neuroimaging: workflows, tools, and repositories
icon keynoteChairs: Markus Aswendt, Joanes Grandjean

Location: Presentation Room 1

The workshop will include interactive seminars given by selected experts in the field covering all aspects of (FAIR) small animal MRI data acquisition, analysis, and sharing. The seminars will be followed by hands-on training where participants will perform use case scenarios using software established by the organizers. This will include an introduction to the basics of using command line interfaces, Python installation, working with Docker/Singularity containers, Datalad/Git, and BIDS.

14:00-15:30 CEST

Session 9: FAIR data: The role of journals
icon keynoteChair: Jan Bjaalie

Speakers: Jean-Baptiste Poline, McGill University
Franco Pistilli, The University of Texas at Austin
Petra Ritter, Charité University Hospital Berlin
Trygve B. Leergaard, University of Oslo
Iain Hrynaszkiewicz, Open Research Solutions, PLOS
Jan Bjaalie, University of Oslo and EBRAINS AISBL

Location: Presentation Room 2

Most neuroscience journals request authors to make their data publicly available in appropriate repositories. The requirements and policies put forward by journals vary, and the services provided for different types of data also differ considerably across repositories. Researchers trying to navigate to a suitable repository are challenged with several questions and a need to compromise parameters such as storage space available, time and efforts needed for data sharing, data governance considerations et cetera, all influencing the extent of FAIRness their data may achieve. Many journals provide data repository guidance, but with many options and priorities available, data tend to be dispersed across many repositories. In this session we discuss how journal policies and recommendations contribute to open and FAIR neuroscience and influence the findability and interoperability of public data.

  • How journal policies and recommendations contribute to open and FAIR neuroscience
  • Data governance challenges in global science collaborations
  • Sharing of human brain data in the European Union
  • Balancing open data sharing and data protection in scientific research
  • Relations between data repositories and journals
  • Data repositories recommended by journals
  • General vs domain specific data repositories
  • Journal article formats
15:30-16:00 CEST
MathWorks sponsored demo

Location: Presentation Room 1

16:00-19:00 CEST

16:00-19:00 CEST

Session 10: Event annotation in neuroimaging using HED: from experiment to analysis
icon keynoteChair: Scott Makeig

Speakers: Scott Makeig, Dung Truong, Dora Hermes, & Monique Denissen

Location: Presentation Room 1

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.

Scott Makeig, Institute for Neural Computation, University of California San Diego
“Documenting temporal structure in time series data (evolving concepts, history, needs and benefits)”
(45 mins + 10 minutes discussion)

Dung Truong, University of California San Diego
“Adding annotations to neuroimaging data: the path from experiment to analysis: tools and pipelines”
(50 mins + 10 min discussion)

Dora Hermes, Tal Pal Attia], Mayo Clinic, Rochester MN
“Using the SCORE HED library schema for clinical EEG data annotation.”
(30 mins + 10 min discussion)

Monique Denissen, University of Salzburg, Austria
“Applying HED annotation to fMRI datasets: strategies and pitfalls.”
(30 mins + 10 min discussion)

Panel discussion / Q&A (15 min)

09:00-12:00 CEST
Satellite Session 1.1: Neuroscience data integration through use of digital brain atlases

CREDIT COURSE - Level: PhD, Credits: 2 ECTS

icon keynoteTrygve Brauns Leergaard, Ingvild Elise Bjerke - University of Oslo

Location: Zoom

Speakers: Trygve Leergaard, Ingvild Bjerke, Jan G. Bjaalie, Nicola Palomero-Gallagher

The course will be arranged as a digital Satellite event to the 2023 INCF Neuroinformatics assembly. This two-day course will provide a hands-on introduction to three-dimensional reference atlases for the human, rat and mouse brain, and demonstrate how such atlases can be utilized to integrate and analyze heterogeneous neuroscience data. Students will gain updated knowledge about current approaches to assigning anatomical location to experimental data from the brain, and acquire basic skills in associated analytic tools.

Schedule
09:00-09:15 INTRODUCTION (Trygve Leergaard, Ingvild Bjerke)
09:15-10:00 SESSION 1: Concepts for sharing and integration of neuroscience research data (Jan Bjaalie)
10:00-10:15 SHORT BREAK
10:15-12:00 SESSION 2: Navigating the human brain (Nicola Palomero-Gallagher)

12:00-13:00 CEST
BREAK
13:00-16:00 CEST
Satellite Session 1.2: Neuroscience data integration through use of digital brain atlases

CREDIT COURSE - Level: PhD, Credits: 2 ECTS

icon keynoteTrygve Brauns Leergaard, Ingvild Elise Bjerke - University of Oslo

Location: Zoom/p>

Speakers: Menno Witter, Timo Dickscheid

Schedule
13:00-14.30 SESSION 3: Navigating the rodent brain (Menno Witter)
14:30-14:45 SHORT BREAK
14:45-15:55 SESSION 4: Introduction to EBRAINS digital brain atlas resources (Timo Dickscheid)
15:55-16:00 CLOSURE DAY 1

09:00-12:00 CEST
Satellite Session 1.3: Neuroscience data integration through use of digital brain atlases

CREDIT COURSE - Level: PhD, Credits: 2 ECTS

icon keynoteTrygve Brauns Leergaard, Ingvild Elise Bjerke - University of Oslo

Speakers: Ingvild Bjerke, Maja Puchades, Harry Carey

The course will be arranged as a digital Satellite event to the 2023 INCF Neuroinformatics assembly. This two-day course will provide a hands-on introduction to three-dimensional reference atlases for the human, rat and mouse brain, and demonstrate how such atlases can be utilized to integrate and analyze heterogeneous neuroscience data. Students will gain updated knowledge about current approaches to assigning anatomical location to experimental data from the brain, and acquire basic skills in associated analytic tools.

Schedule
09:00-10:00 SESSION 5: Sharing and assigning location parameters to murine data (Ingvild Bjerke, Maja Puchades)
09:45-10:00 SHORT BREAK
10:00-11:00 SESSION 5, continued
10:15-10:30 SHORT BREAK
10:30-11:30 SESSION 7: Advanced and automated image registration (Harry Carey, Maja Puchades)
11:30-12:00 SESSION 8: Quantification of experimental murine image data

12:00-13:00 CEST
BREAK
13:00-16:00 CEST
Satellite Session 1.4: Neuroscience data integration through use of digital brain atlases

CREDIT COURSE - Level: PhD, Credits: 2 ECTS

icon keynoteTrygve Brauns Leergaard, Ingvild Elise Bjerke - University of Oslo

Location: Zoom/p>

Speakers: Ingvild Bjerke, Jan G. Bjaalie, Maja Puchades, Trygve Leergaard, Sharon Yates

Schedule
13:00-13:45 SESSION 8: Continued (Sharon Yates)
13:45 - 14:00 SHORT BREAK
14:00-15:00 Session 9: Quantify and Visualize data points in 3D (Sharon Yates / Ingvild Bjerke)
15:00-15:15 SHORT BREAK
15:15-15:45 SESSION 10: Visions of data integration in the future (Jan Bjaalie)
15:45-16:00 CLOSURE DAY 2: Evaluation and preparation for exam task (Trygve Leergaard)