Neuroinformatics Assembly 2023 - Program
14:00-14:20 CEST | Welcome!![]() Location: Presentation Room 1
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14:30-16:00 CEST |
Session 1: A FAIR roadmap for knowledge graphs and ontologies![]() 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: |
16:30-17:30 CEST |
Session 2: FAIR sharing, integration, & analysis of neuroscience data![]() Location: Presentation Room 1 Speakers: Oliver Schmid, EBRAINS AISBL: The EBRAINS Knowledge Graph
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. |
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 CensusSpeakers: 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 ![]() 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![]() 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 1Location: Presentation Room 2
21:30 CEST Alden Connor, The Alan Turing Institute - Bridging into AI: open source tools for computer vision |
22:00-23:00 CEST | Poster Session 1Location: Poster Hall |
02:00-03:00 CEST | Poster Session 2Location: Poster Hall |
Parallel sessions 13:00-14:00 CEST |
13:00-14:00 CEST Poster Session 3Location: Poster Hall 13:00-14:00 CEST Lightning talks 2Location: Presentation ROOM 2
13:00 CEST Martijn de Neeling, state of brain-computer interface standards |
14:00-14:30 CEST | BREAK |
14:30-18:30 CEST |
Session 5.1: Infrastructure for Sensitive Data![]() 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![]() 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![]() 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![]() 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![]() Speakers: Jean-Baptiste Poline, McGill University 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.
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15:30-16:00 CEST | MathWorks sponsored demoLocation: 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![]() 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 Dung Truong, University of California San Diego Dora Hermes, Tal Pal Attia], Mayo Clinic, Rochester MN Monique Denissen, University of Salzburg, Austria Panel discussion / Q&A (15 min) |
09:00-12:00 CEST | Satellite Session 1.1: Neuroscience data integration through use of digital brain atlasesCREDIT COURSE - Level: PhD, Credits: 2 ECTS ![]() 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 |
12:00-13:00 CEST | BREAK |
13:00-16:00 CEST | Satellite Session 1.2: Neuroscience data integration through use of digital brain atlasesCREDIT COURSE - Level: PhD, Credits: 2 ECTS ![]() Location: Zoom/p> Speakers: Menno Witter, Timo Dickscheid
Schedule |
09:00-12:00 CEST | Satellite Session 1.3: Neuroscience data integration through use of digital brain atlasesCREDIT COURSE - Level: PhD, Credits: 2 ECTS ![]() 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 |
12:00-13:00 CEST | BREAK |
13:00-16:00 CEST | Satellite Session 1.4: Neuroscience data integration through use of digital brain atlasesCREDIT COURSE - Level: PhD, Credits: 2 ECTS ![]() Location: Zoom/p> Speakers: Ingvild Bjerke, Jan G. Bjaalie, Maja Puchades, Trygve Leergaard, Sharon Yates
Schedule |