Meeting Notes

• Date: 2026-03-17
• Time: 09:00AM (PT)
• Location: Teams Meeting

Agenda

Discussion on how to organize and focus future analysis:

Led by @Sarruedi and @lrudelt Some material for the meeting is available here

Meeting Recording

Meeting Notes

Organizing Future Analysis and Documentation: Lucas Rudelt, Jerome, and Sarah Ruediger Lee led a comprehensive discussion on structuring the group's analysis efforts, focusing on the use of visual maps and spreadsheets to document progress, assign tasks, and facilitate onboarding, with input from Alexander Maier, ali, Farzaneh Najafi, and others.

Analysis Map and Spreadsheet Proposal: Lucas Rudelt presented two main tools for organizing analysis: a visual map to display dependencies and progress, and a spreadsheet to track contributors, resources, and task details. The visual map would allow for easy identification of work packages and their relationships, while the spreadsheet would provide a more detailed, accessible record of ongoing work.

Feedback on Tools and Onboarding: Jerome and Sarah Ruediger Lee emphasized the value of the visual map for onboarding new members and providing a clear overview, while the spreadsheet was seen as essential for tracking specific contributions and code links. The group agreed that both tools are complementary and should be used together.

Editing and Coordination Responsibilities: The group discussed whether editing rights for the map and spreadsheet should be open to all or managed by designated individuals or teams. Lucas Rudelt suggested starting with open editing and adjusting based on engagement, while Jerome highlighted the importance of tools being useful and accessible to everyone.

Standardization of Documentation: Lucas Rudelt proposed establishing standards for analysis documentation, including the use of iPython notebooks for code sharing, analysis summaries outlining methods and results, and clear links to resources. The aim is to ensure consistency and traceability across all contributions.

Next Steps for Implementation: The group agreed to trial the proposed tools, with Lucas Rudelt making the visual map editable for everyone and creating a discussion thread for feedback. The spreadsheet and map will be linked and refined based on user experience, with the possibility of assigning editing responsibilities in the future.

Communication Platforms and Notification Challenges: Ali, Farzaneh Najafi, Sarah Ruediger Lee, and others discussed difficulties with current communication platforms (GitHub forums, Slack, Teams), focusing on notification issues, accessibility, and the need for improved visibility and feedback on analysis contributions.

Notification and Visibility Issues: Ali and Farzaneh Najafi raised concerns about missed notifications and limited visibility on GitHub forums, noting that unless users are specifically mentioned or subscribed, important analysis updates can be overlooked. Sarah Ruediger Lee and others echoed these challenges, emphasizing the need for a more reliable system to ensure all contributors are informed.

Platform Comparisons and Preferences: The group compared various platforms, including GitHub, Slack, Teams, and email. While Slack was favored by some for its centralized notifications, concerns were raised about access limitations and message retention. Teams was described by Hannah as the primary tool at the Allen Institute, with GitHub used for code and documentation. Email was considered less suitable due to its closed nature.

Suggestions for Improved Organization: Participants suggested creating dedicated threads or channels for specific analysis topics, using color coding and categories to organize discussions, and consolidating links to resources in a central, easily accessible location. The importance of adapting tools based on group engagement and feedback was highlighted by Ivana Bussi.

Decision to Continue with GitHub and Refine Structure: After weighing the pros and cons, the group decided to continue using GitHub forums for now, with plans to improve organization through dedicated threads, better use of categories and labels, and enhanced notification management. The goal is to maintain an open, accessible record of contributions while addressing current shortcomings.

Defining Work Packages and Data Release Paper Requirements: Lucas Rudelt, Jerome, Sarah Ruediger Lee, Farzaneh Najafi, and Alexander Maier discussed the structure and content of work packages for analysis, focusing on the requirements for an upcoming data release paper and the organization of tasks across different data modalities.

Essential Analyses for Data Release: The group identified key analyses required for the data release paper, including quality control, identification of responsive units, receptive field and visual tuning analysis, and basic demonstrations of data utility. The aim is to provide a well-documented, accessible dataset without preempting downstream research.

Work Package Organization by Modality: There was an in-depth discussion on whether to organize work packages and data release papers by individual data modalities (e.g., SLAP 2, electrophysiology, imaging) or to combine them. The consensus leaned toward creating one main paper with modality-specific sections, supported by separate spreadsheets and visual maps for each modality.

Assignment and Tracking of Tasks: The group agreed to use the visual map and spreadsheet to assign tasks, track progress, and allow contributors to indicate their involvement in specific analysis blocks. Color coding and deactivation of irrelevant boxes were suggested to clarify current priorities.

Next Steps and Timeline: Action items include preparing updated analysis plan figures for each modality, creating a central page for the data paper, and collecting feedback via a questionnaire on the minimum requirements for the data release paper. The goal is to have these materials ready for discussion at the next meeting.

Data Packaging and Accessibility Updates: Jerome provided an update on recent progress in data packaging, announcing that 25 SLAP 2 sessions have been reorganized and will soon be made available on Code Ocean, with similar efforts underway for other modalities.

SLAP 2 Data Packaging Progress: Jerome reported that 25 SLAP 2 sessions, covering 12 mice, have been reorganized and are scheduled for upload to Code Ocean in the coming weeks. This work is part of a broader effort to ensure all raw data is accessible to the group.

Plans for Other Modalities: Similar data packaging and upload processes are planned for the remaining data modalities, with the intention of providing direct access to raw data and later packaging in NWB format.