INCF was formed in 2005 and has since worked to develop and promote standards, tools, and infrastructure for neuroscience researchers. Here is a summary of our activities of the last 10 years.
Between 2006 and 2013, the INCF has organized 22 scientific workshops on various topics, such as technical issues related to neuroscience databasing, tool development, and modeling of the nervous system. Each workshop had invited participants, selected on the basis of their expertise in the particular area of the workshop. Each workshop delivered a formal report with recommendations to serve as the basis for further activities initiated by INCF.
In our first two phases (2006-2010, 2011-2015), INCF operated scientific Programs in four areas: Digital Brain Atlasing, Ontologies of Neural Structures, Standards for Data Sharing, and Multi-scale Modeling. Programs were preceded by workshops which gathered experts in the respective field to give updates on current state of the art and identify barriers to sharing and collaboration. Recommendations from the workshops formed the basis of each Program's activities. Each Program had an Oversight Committee, overseeing its general direction, and one or several Task Forces carrying out most of the activities and development.
A great success of these endeavours was the coordinated efforts of many scientists in coming together as a community to resolve issues and deliver solutions.
Key Program deliverables include:
Program on Digital Brain Atlasing
- Waxholm Space (WHS), a a coordinate-based reference space of the rodent brain
- A hub-based Digital Atlasing Infrastructure (DAI) which links WHS to key community mouse atlases
- Scalable Brain Atlas, a web-based display engine for brain atlases, imaging data, and topologies
Program on Multi-Scale Modelling
- NineML, a general model description language
- The Multi-Simulation Coordinator (MUSIC), which allows allows large-scale neuron simulators and other applications to communicate during runtime
- The Connection Set Algebra (CSA) for unambiguous description of connectivity in neuronal network models
- A computational neuroscience ontology developed to provide standard semantic annotation models.
Program on Standards for Data Sharing
- A proposed HDF5 standard for storing electrophysiology data (included in Neurodata Without Borders)
- An ontology for experimental neurophysiology (OEN)
- A simple sharing tool ('the one-click tool') for neuroimaging DICOM/NIfTI data
- Inventory of resources and general recommendations on how to incorporate data sharing in neuroimaging experiments with human subjects
- NeuroVault, a database for storing and distributing statistical maps of the human brain from PET and fMRI
- The Neuroimaging Informatics Data Model (NI-DM), a framework for the generation, storage, and query of metadata including provenance information
- The Neuroimaging Analysis Pipeline (Nipype), a framework that combines standard interfaces to current most used neuroimaging software and execution engines
- The Brain Imaging Data Structure, BIDS, a simple and easy to adopt way of organizing neuroimaging and behavioral data.
Program on Ontologies for Neural Structures
- CUMBO, a reference framework for classifying general mammal nervous system structures
- NeuroLex, a structural neuroscience lexicon built on Neuron Registry and CUMBO
- The start of a project to develop a community-based encyclopedia for neuroscience, the KnowledgeSpace
- The Neuron Registry, a standard set of relations and values used to describe neurons
Training and education
From 2010 onward, following a series of workshops on training needs in neuroinformatics, INCF also established several activities to support training and education. These activities were overseen by the INCF Training Committee. The committee organized an introductory neuroinformatics course each year, ran a framework for financial support to other neuroinformatics courses, and supported the INCF participation in the Google Summer of Code program.
Workshop on promoting data sharing in dementia research
INCF and OECD partnered to organize the workshop "Promoting data sharing in dementia research" which was held 20 – 21 September 2015 in Stockholm, Sweden. The workshop aimed to bring together policy-makers, funders, and leading scientists to consider the barriers to data sharing in relation to dementia research and to begin to identify practical steps that can be taken to advance data sharing in this. The program, aims and scope, and all presentations are available for download.