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Working Group outcomes

INCF Working Groups are composed of members working on short-term funded projects that aim to achieve a concrete deliverable. See below the outcomes of the working groups over the years.

Year Outcomes Working group
2023
  • Interactive web-based dashboard for Pydra workers
  • Pydra integration with PSI/J for submission and tracking of jobs
  • Bokeh implementation in Pydra dashboard
  • Examples and tutorials for users
Adding new workers and resource management to new dataflow engine written in Python: Pydra
2023
  • Making browsing experience less confusing by modifying chapter links and profile tags based on a selected ‘pathway’, rather than displaying all tags associated with a chapter.
  • Adding a feature to provide descriptions for each pathway which will improve user experience allowing meaningful use of books by all profile types.
  • Implementing the solutions proposed in this application and integrating them into The Turing Way via the open source framework.
Technical Improvements to enhance the usability of The Turing Way chapters by different user groups
2023

Comprehensive dashboard to measure and display INCF impact on global neuroscience and informatics community

Impact visualization portal for global neuroinformatics community
2023
  • Development of optimization functions for automatic parameter-space searching when modelling simulation
  • Algorithm development for more efficient tuning of model parameters
Generalize parameter optimization routines for the Human NeoCortical Neurosolver
2023
  • Develop code to convert publicly available neuroscience datasets to NWB format
  • Add structured metadata and annotation to datasets
  • Make converted datasets available to NWB Explorer on the Open Source Brain repository
Conversion of public neurophysiology datasets to Neurodata Without Borders (NWB) format
2023

Development and build of Sci-commons, a portal for users to anonymously review, comment on, and rate submitted article

A social web tool to facilitate rating and commenting on research reports
2023
  • Develop embedding capability for Jupyter notebooks, Observable HQ notebooks, and Google Colab notebooks on AnalySim site.
  • Interactive panel or interface that displays a dataset’s different types of features, including minimum, mean, number of non-zero, and the number of invalid values.
  • Ability for users to add publications related to the datasets in a project.
Implementing CSV data browser and querying component
2023
  • Remove bootstrap from the application and substitute the design with pure SCSS. 
  • Finish implementing the CSS global variables and add component wise CSS variables to improve the reusability of code in the application.
  • Add CSV viewing functionality on the datasets of AnalySim to view, filter, and browse through the columns of the file. 
  • Create a feature on the Jupyter notebooks to make the Notebooks downloadable.
  • Improve the Registration page, Explore section page, and My Dashboard page design.
  • Make the design of the application consistent throughout the application to create a great user experience.
Improving graphical interface and user experience on AnalySim
2023
  • Open-source project scenario simulation
  • Factor identification in successful or failing projects for informed decision making and strategy development
Exploring open-source sustainability via agent-based modelling
2023
  • Development of new IO routines for HNN-core objects
  • Maintenance of backwards compatibility with HNN-GUI
  • Implement hdf5 format for modular data storage
Develop IO routines for HNN-core outputs
2023
  • Improve existing LORIS Codebase and API features
  • Write test cases for code changes
  • Develop additional features based on need
  • Documentation for the new changes
Improving LORIS data platform
2023
  • Development of application suite which integrates hardware devices, deep learning-based infant eye trackers, and visual stimuli analysis
  • Development of GUI for easy user experience
Efficient app-based measurement of visual functions in infants and young children
2023
  • Enhanced SciBERT’s text-to-semantic meaning capture by fine tuning on data corpus and providing alternative and appropriate optimization approaches (e.g., contrastive learning, learning to rank diversely, lambda rank).
  • Improved SciBERT’s automatic reviewer assignment
Improving automatic reviewer assignment using large language models for NBDT journal
2023
  • Methods for optimization implementation in NumPy and Jax
  • Plotting functions for HOIs
  • HOI o-info integration with Frites Python package
Optimization of the computations of HOIs and integration in the Frites Python package
2023
  • Implementation of an interface between HippoUnit and Neuroptimus to enable the optimization of a broader range of neuronal behaviors, extend the current supported tests to include all HippoUnit tests.
  • Integrate the HippoUnit with the Neuroptimus’s GUI so that users can run optimizations directly from the interface.
  • Integration of HippoUnit's useful outputs and plots with Neuroptimus for visualization and analysis purposes.
Integration of automated model testing and parameter fitting tools for neuroscience applications
2023
  • Implementation of an interface between HippoUnit and Neuroptimus to enable the optimization of a broader range of neuronal behaviors, extend the current supported tests to include all HippoUnit tests.
  • Integrate the HippoUnit with the Neuroptimus’s GUI so that users can run optimizations directly from the interface.
  • Integration of HippoUnit's useful outputs and plots with Neuroptimus for visualization and analysis purposes.
D-GNNs: developing DevoGraph for computational developmental biology
2023
  • Utilization of the Optuna HPO toolkit to build model of auditory cortex (A1), with particular emphasis on schizophrenia-specific activity patterns
  • Quantification and simulation of connectivity and CB1/GABA receptors in A1
  • High-fidelity reconstruction of ASSR phenomenon in A1 model
Replicating Auditory Steady-State Response (ASSR) in an auditory cortex model
2023
  • Demo Jupyter notebook that runs the widget along with a set of classes that handle the features and tunable parameters
  • Integration of widget with Xcircuit extension
  • Unit test cases for the newly written code and readable documents of the entire project
A structural connectivity widget for The Virtual Brain
2023
  • Incorporate segmented raw microscopy data into DevoGraph pipeline
  • Refactoring of CNN models for understanding biological training datasets
  • Tighter integration of DevoGraph as a network structure
D-GNNs: developing DevoGraph for computational developmental biology (OpenWorm Foundation)
2023
  • ABM simulation using NETLOGO and GAMA platform
  • Development of AR/VR application, compatible with devices such as Meta Quest and Web XR
Virtual reality for distributed research
2023 INCF Working Group on Standardized Representations of Network Structures
2023
  • Google Doc per sub-group conveying recommendations to MathWorks Neuroscience team of 2+ priority existing MATLAB community toolbox projects, plus important new MATLAB community toolbox project opportunities, if any
  • Google Doc conveying recommendations to MathWorks product teams of 2+ priority enhancements or issue fixes for the MATLAB and Simulink product families
  • Written recommendations of 1+ key project improvements for 2+ identified priority MATLAB community toolbox projects 
INCF Working Group on Cellular Neuroscience with MATLAB
2023
  • Creation of common SQLite database 
  • ASP/IJ GUI integration
Image feature and classification database
2023
  • Zenodo API integration with TVB
  • Automatic downloading and unzipping of TVB data
Integrate Zenodo API with The Virtual Brain
2023
  • Fully functional extension that can be installed and used with VS code
  • Documentation on extension installation and use
Code editor support for Brian model equations
2022 INCF Working Group on Reproducibility and Best Practices in Human Brain Imaging
2022

An app facilitating completion of the template using an onscreen interface

INCF Working Group on ARTEM-IS
2022 INCF Working Group on NIDM (NeuroImaging Data Model)
2022 INCF Working Group on Neuroimaging Quality Control
2021

 

INCF Working Group on Electrophysiology Stimulation Ontology
2021

Brainconnects 2021

INCF Working Group on Neuroinformatics for Aging
2021 INCF Working Group on Reproducibility and Best Practices in Human Brain Imaging
2020

“Neuroimaging and Informatics for Successful Aging” Research Topic in Frontiers

INCF Working Group on Neuroinformatics for Aging
2020 INCF Working Group on Standardized Representations of Network Structures
2020 INCF Working Group on Neuroinformatics for cell types
2019

Brainconnects 2019

INCF Working Group on Neuroinformatics for Aging
2019 INCF Working Group on NIDM (NeuroImaging Data Model)
2019 INCF Working Group on Neuroimaging Quality Control
2018 INCF Working Group on NIDM (NeuroImaging Data Model)
2016 INCF Working Group on NIDM (NeuroImaging Data Model)
2015 INCF Working Group on NIDM (NeuroImaging Data Model)