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INCF Scientific Programs

INCF Scientific Programs

From 2007 to the end of 2015, INCF’s activities were focused around four scientific Programs. The first program, the Program for Multiscale Modelling (MSM), was launched in 2007. Two more scientific Programs, the Program for Ontologies of Neural Structures (PONS) and the Program on Digital Brain Atlasing (DBA) were launched in 2008, and the Program for Standards in Data Sharing was launched in 2009.

The launch of an INCF Program was a multi-step process, which started with a topical workshop with leading experts in the subject area. The aim of each workshop was to identify problems in the targeted field, and identify suitable actions to address them. The invited attendees were carefully selected to represent the diversity and breadth of the field. Each meeting generated a report describing the current state of art, listing the most urgent problems and giving recommendations to INCF on how to address these problems.

Each Program formed an Oversight Committee (mainly senior field experts) and one or more Task Forces (mainly early career researchers). The progress of each Task Force was reported regularly to its Oversight Committee, which provided advice and guidance as needed. The Oversight Committee was also responsible for promoting the Task Force outcomes within their community.

The Multiscale Modelling Program

Aim: to improve interoperability and reproducibility of neural simulations.

At the time of the founding of the MSM program,computational modeling had been identified as a potentially useful method for working with neuroscience data, making it possible to integrate datasets with different time scales and length scales, and letting researchers generate and test hypotheses before experiments. However, there were several barriers:

  • There was no way to share models that made their outputs easy to reproduce, especially not across platforms, and no way to publish the results in a way that made re-implementation and replication of results possible.
  • Several widely used simulators existed, but none of them were interoperable. 
  • Simulating big or complex models required access to large-scale computation. 

The assembled Task Force collected key developers from nearly all simulator projects, to collaborate on the development of a markup language for describing models (NineML) and an ontology for computational neuroscience (CNO). For large-scale modelling, the MUSIC tool was developed to link between different simulations, and the Connection Set Algebra was created to describe connections and connection patterns in a compact way.

The Program on Standards for Data Sharing (DASH)

Aim: to develop metadata and data standards for reproducible (neuroscience) research.

In 2009, INCF launched its scientific Program on Data Sharing. The aim of the program was to develop generic standards for data sharing and tools to facilitate the recording, sharing, reporting, and use of metadata in neuroscience. The program formed two Task Forces focused on barriers to the sharing of data in their field: the Electrophysiology Task Force and the Neuroimaging Task Force. The early activities of the Neuroimaging Task Force were focused on identifying and addressing barriers to data sharing in neuroimaging, and to engage the larger neuroimaging community in the data sharing issue. Eventually, these efforts crystallized into two main projects - the neuroimaging data model NIDM and the brain imaging data standard BIDS.

The Electrophysiology Task Force developed a set of requirements for storing electrophysiology data that were later used in the development of the Neuroscience Without Borders: Neurophysiology (NWB) data format for electrophysiology data.

The Program for Ontologies of Neural Structures (PONS)

Aim: to establish consistent naming and classification for all neural structures.

The goal of the PONS program was to create a machine-processable terminology/ontology for describing neural structures across scale. In close association with the INCF Programs on Digital Brain Atlasing and Standards for Datasharing, the Program on Ontologies of Neural Structures (PONS) worked to establish a structured lexicon of terms describing neural structures and their relationships at multiple levels of granularity.  The program also initiated the KnowledgeSpace, a  data-driven encyclopedia and search engine for the neuroscience community.

The Digital Brain Atlasing Program (DBA)

Aim: to coordinate and improve the impact of atlasing projects, with a focus on the rodent brain.

Digital brain atlases are essential tools in neuroscience research. They function as references and analytical tools, and provide stable integration frameworks as a basis for investigations of normal and abnormal brain structure and function.  The key aim of this program was to coordinate and improve the impact of atlasing projects, with a focus on the rodent brain.

The program developed three associated services: the Scalable Brain Atlas, the Digital Atlasing Infrastructure, and the Waxholm Space standard for brain atlases.