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INCF workshop reports and publications

 

Traumatic brain injury: progress and challenges in prevention, clinical care, and research
Year of publication : 2022
A decade of GigaScience: the importance of community organizations for open and FAIR efforts in neuroinformatics
Year of publication : 2022

Neuroscience has undergone a significant transformation over the past decade, becoming an increasingly open and FAIR discipline. I provide personal perspectives on the importance of two community organizations, FORCE11: The Future of Research Communications and e-Scholarship and INCF: The International Neuroinformatics Coordinating Facility in providing the intellectual and community environment where ideas and open sharing of data and code were incubated and tried.

Maryann. E. Martone

Is Neuroscience FAIR? A Call for Collaborative Standardisation of Neuroscience Data
Year of publication : 2022

In this perspective article, we consider the critical issue of data and other research object standardisation and, specifically, how international collaboration, and organizations such as the International Neuroinformatics Coordinating Facility (INCF) can encourage that emerging neuroscience data be Findable, Accessible, Interoperable, and Reusable (FAIR). As neuroscientists engaged in the sharing and integration of multi-modal and multiscale data, we see the current insufficiency of standards as a major impediment in the Interoperability and Reusability of research results. We call for increased international collaborative standardisation of neuroscience data to foster integration and efficient reuse of research objects.

Jean-Baptiste Poline, David N. Kennedy, Friedrich T. Sommer, Giorgio A. Ascoli, David C. Van Essen, Adam R. Ferguson, Jeffrey S. Grethe, Michael J. Hawrylycz, Paul M. Thompson, Russell A. Poldrack, Satrajit S. Ghosh, David B. Keator, Thomas L. Athey, Joshua T. Vogelstein, Helen S. Mayberg, and Maryann E. Martone

PET-BIDS, an extension to the brain imaging data structure for positron emission tomography
Year of publication : 2022
Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data
Year of publication : 2022
Integrating the BIDS Neuroimaging Data Format and Workflow Optimization for Large-Scale Medical Image Analysis
Year of publication : 2022
qMRI-BIDS: An extension to the brain imaging data structure for quantitative magnetic resonance imaging data
Year of publication : 2022
Curation of BIDS (CuBIDS): A workflow and software package for streamlining reproducible curation of large BIDS datasets
Year of publication : 2022
ASL-BIDS, the brain imaging data structure extension for arterial spin labeling
Year of publication : 2022
The Neurodata Without Borders ecosystem for neurophysiological data science
Year of publication : 2022
Vibrational Spectroscopy for the Triage of Traumatic Brain Injury Computed Tomography Priority and Hospital Admissions
Year of publication : 2022
Discrepancy between disability and reported well-being after traumatic brain injury.
Year of publication : 2022
Concomitant spine trauma in patients with traumatic brain injury: Patient characteristics and outcomes.
Year of publication : 2022
Clustering identifies endotypes of traumatic brain injury in an intensive care cohort: a CENTER-TBI study
Year of publication : 2022
Measurement invariance of six language versions of the post-traumatic stress disorder checklist for DSM-5 in civilians after traumatic brain injury
Year of publication : 2022
Recommendations for repositories and scientific gateways from a neuroscience perspective
Year of publication : 2022

Digital services such as repositories and science gateways have become key resources for the neuroscience community, but users often have a hard time orienting themselves in the service landscape to find the best fit for their particular needs. INCF has developed a set of recommendations and associated criteria for choosing or setting up and running a repository or scientific gateway, intended for the neuroscience community, with a FAIR neuroscience perspective.

Malin Sandström, Mathew Abrams, Jan G. Bjaalie, Mona Hicks, David N. Kennedy, Arvind Kumar, Jean-Baptiste Poline, Prasun K. Roy, Paul Tiesinga, Thomas Wachtler & Wojtek J. Goscinski 

Brainhack: Developing a culture of open, inclusive, community-driven neuroscience
Year of publication : 2021
Teaching Computation in Neuroscience: Notes on the 2019 Society for Neuroscience Professional Development Workshop on Teaching
Year of publication : 2021

William Grisham, Mathew Abrams, Walt E Babiec, Adrienne L Fairhall, Robert E Kass, Pascal Wallisch, Richard Olivo

Revisiting Diversity, Equity, and Inclusion Commitments and Instituting Lasting Actionable Changes in the Faculty for Undergraduate Neuroscience
Year of publication : 2021

Lorenz S Neuwirth, Princy S Quadros-Mennella, Yuan Yuan Kang, Monica L Linden, Marc Nahmani, Mathew Abrams, Melanie P Leussis, Kurt R Illig

Core principles for the implementation of the neurodata without borders data standard
Year of publication : 2021
Development of prognostic models for Health-Related Quality of Life following traumatic brain injury
Year of publication : 2021
Brain Temperature Influences Intracranial Pressure and Cerebral Perfusion Pressure After Traumatic Brain Injury: A CENTER-TBI Study
Year of publication : 2021
Primary versus early secondary referral to a specialized neurotrauma center in patients with moderate/severe traumatic brain injury: a CENTER TBI study
Year of publication : 2021
The burden of traumatic brain injury from low-energy falls among patients from 18 countries in the CENTER-TBI Registry: A comparative cohort study.
Year of publication : 2021
Questionnaires vs Interviews for the Assessment of Global Functional Outcomes After Traumatic Brain Injury
Year of publication : 2021
Extended Coagulation Profiling in Isolated Traumatic Brain Injury: A CENTER-TBI Analysis
Year of publication : 2021
Relationship of admission blood proteomic biomarkers levels to lesion type and lesion burden in traumatic brain injury: A CENTER-TBI study
Year of publication : 2021
A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility
Year of publication : 2021

There is great need for coordination around standards and best practices in neuroscience to support efforts to make neuroscience a data-centric discipline. Major brain initiatives launched around the world are poised to generate huge stores of neuroscience data. At the same time, neuroscience, like many domains in biomedicine, is confronting the issues of transparency, rigor, and reproducibility. Widely used, validated standards and best practices are key to addressing the challenges in both big and small data science, as they are essential for integrating diverse data and for developing a robust, effective, and sustainable infrastructure to support open and reproducible neuroscience. However, developing community standards and gaining their adoption is difficult. The current landscape is characterized both by a lack of robust, validated standards and a plethora of overlapping, underdeveloped, untested and underutilized standards and best practices. The International Neuroinformatics Coordinating Facility (INCF), an independent organization dedicated to promoting data sharing through the coordination of infrastructure and standards, has recently implemented a formal procedure for evaluating and endorsing community standards and best practices in support of the FAIR principles. By formally serving as a standards organization dedicated to open and FAIR neuroscience, INCF helps evaluate, promulgate, and coordinate standards and best practices across neuroscience. Here, we provide an overview of the process and discuss how neuroscience can benefit from having a dedicated standards body.

Mathew Birdsall Abrams, Jan G. Bjaalie, Samir Das, Gary F. Egan, Satrajit S. Ghosh, Wojtek J. Goscinski, Jeffrey S. Grethe, Jeanette Hellgren Kotaleski, Eric Tatt Wei Ho, David N. Kennedy, Linda J. Lanyon, Trygve B. Leergaard, Helen S. Mayberg, Luciano Milanesi, Roman Mouček, J. B. Poline, Prasun K. Roy. Stephen C. Strother, Tong Boon Tang, Paul Tiesinga, Thomas Wachtler, Daniel K. Wójcik, Maryann E. Martone

The genetics-BIDS extension: Easing the search for genetic data associated with human brain imaging
Year of publication : 2020
NWB Query Engines: Tools to Search Data Stored in Neurodata Without Borders Format
Year of publication : 2020
iEEG-BIDS, extending the Brain Imaging Data Structure specification to human intracranial electrophysiology
Year of publication : 2019
Steyerberg EW et al. Case-mix, care pathways, and outcomes in patients with traumatic brain injury in CENTER-TBI: a European prospective, multicentre, longitudinal, cohort study. Lancet Neurol. 2019 Oct;18(10):923-934.
Year of publication : 2019
Maas AIR et al. Traumatic brain injury: integrated approaches to improve prevention, clinical care, and research. Lancet Neurol. 2017 Dec;16(12):987-1048
Year of publication : 2017
Shenkin SD et al. Improving data availability for brain image biobanking in healthy subjects: Practice-based suggestions from an international multidisciplinary working group. Neuroimage. 2017 Jun;153:399-409
Year of publication : 2017
Eglen SJ et al. Toward standard practices for sharing computer code and programs in neuroscience. Nat Neurosci. 2017 May 25;20(6):770-773
Year of publication : 2017
Grisham W el al. Proposed Training to Meet Challenges of Large-Scale Data in Neuroscience. Front Neuroinform. 2016 Jul 18;10:28
Year of publication : 2016
Christian Haselgrove et al. A simple tool for neuroimaging data sharing. Front Neuroinform. 2014; 8: 52.
Year of publication : 2014
iNeuro Conference Report
Year of publication : 2014

Preparing a workforce to meet the challenges of large-scale neuroscience data and producing curricula and resources for large-scale neuroscience data analysis

Place: Arlington, VA

Amunts K et al. Interoperable atlases of the human brain. Neuroimage. 2014 Oct 1;99:525-32.
Year of publication : 2014
INCF Program on Digital Brain Atlasing workshop: Towards a multi-modal human brain atlas
Year of publication : 2013

Aim:  To assess the current state of the human brain mapping field and atlas generation to determine the requirements and challenges to the development of a multi-modal human brain atlas.

Place: Seattle, Washington

INCF Workshop on Genetic Disease Models of Psychiatric and Neurological Diseases
Year of publication : 2013

Aim: Evaluate the consilience between murine models and human disease, with an emphasis on neurological and psychiatric diseases that have high prevalence and burden.

Place:Utrecht, The Netherlands

INCF Program on Multiscale Modeling Workshop: From Cellular/Network Models to Tissue Simulation
Year of publication : 2013

To assess the current state of the field and available software infrastructure for tissue modeling from within the field of neuroscience and other fields in order to broadly define an outline of the development needed. 

Place: Stockholm, Sweden

INCF Program on Standards for Data Sharing: New perspectives on workflows and data management for the analysis of electrophysiological data
Year of publication : 2013

Aim: The presentations and discussions of the workshop focused on three major issues related to workflows in electrophysiology: (i) the development of data structures and software libraries that enable interfacing of data from various sources and integration of methods for data manipulation and analysis, (ii) documentation and provenance tracking solutions to support reproducible analysis processes able to cope with the required levels of flexibility and data size, and (iii) workflow management systems that allow automatic and extensible processing of complex analysis workflows, in particular on high performance computers.

Place: Jülich, Germany

Poline JB et al. Data sharing in neuroimaging research. Front Neuroinform. 2012 Apr 5;6:9
Year of publication : 2012
INCF Lithuanian Workshop on Neuroscience and Information Technology
Year of publication : 2012

Objective: The aim of this workshop was to discuss the strategies for forming the Lithuanian Neuroinformatics Node and becoming a member of INCF. The workshop was organized by Dr. Aušra Saudargiene (Department of Informatics, Vytautas Magnus University, Kaunas, and Faculty of Natural Sciences, Vilnius University, Lithuania) and INCF.

Place: Kaunas, Lithuania

INCF Canadian Neuroinformatics Workshop - A satellite Symposium of the CAN 2012 Meeting
Year of publication : 2012

Objective: build the Canada neuroinformatics community, enabling Canadian scientists from diverse neuroinformatics-related fields to gather, exchange knowledge and discuss whether there was community desire for Canada to join the INCF.

Place: Vancuver, Canada

1st INCF Workshop on Validation of Data-Analysis Methods
Year of publication : 2012

Objective: Using tested and proven methods and algorithms for data analysis is an essential prerequisite for reproducible research. For many types of data analysis in neuroscience, however, there are no established measures or test data for quality assessment and comparison of methods. In this two-day workshop, we investigated the needs for concerted efforts to address validation of other analysis methods for different types of data. 

Place: Stockholm, Sweden

INCF Workshop on Multiscale Data Integration for Neuroinformatics
Year of publication : 2012

Aim: Share techniques and experiences from research groups working on whole brain data integration and modeling in different species. This includes issues including metadata annotation, standard vocabularies and ontologies, reference coordinate spaces and methods for performing analysis and data integration of large multiscale datasets. The outcome will help set the agenda for key developments in required standards and technologies to facilitate the integration of data in the fly, rodent and human brains.

Place: Stockholm, Sweden

1st INCF Workshop on Development of a Community-Based Neuroscience Encyclopedia
Year of publication : 2012

Aim: This encyclopedia should provide a semantically organized forum that is built on the latest appropriate technologies and resources for the neuroscience community to develop and maintain ontologies with clear definitions and links to relevant literature, data, models and other resources.

Place: San Diego, United States

INCF Program on Digital Brain Atlasing: Increasing Community Adoption of WHS
Year of publication : 2012

Aim: Asses and review the current state of rodent atlasing and atlasing tools, and to within this context identify possible barriers to community adoption of the INCF-developed Waxholm Space and its underlying Digital Atlasing Infrastructure.

Place: Stockholm, Sweden

Hawrylycz M et al. Digital atlasing and standardization in the mouse brain. PLoS Comput Biol. 2011 Feb 3;7(2):e1001065
Year of publication : 2011
1st INCF Workshop on Cyberinfrastructure for neuroinformatics
Year of publication : 2011

Objective: INCF recently started efforts to establish a cyberinfrastructure for neuroinformatics, including federated filesystems and object models for sharing neuroscientific data, and standards for workflows. The goal of this workshop is to discuss the development of an international federated dataspace for large-scale heterogeneous data.

Place: Stockholm, Sweden

2nd and 3rd INCF Workshops on Needs for Training in Neuroinformatics: Extended and Short Course Provision
Year of publication : 2009

Theme: What are the issues arising when providing extended and short courses in neuroinformatics? How could the INCF facilitate training? In Workshop 2, delegates concentrated on developing the list of subject areas where neuroinformatics training is needed. In Workshop 3, there was discussion on both the stumbling blocks encountered when designing and running short courses and what new short courses are required. Ways in which INCF can be involved were identified, and specific recommendations on the coordination of existing material, validation of courses and funding of short training workshops were colllected and listed in this report.

Place: Pilsen, Czech Republic

1st INCF Workshop on Neuroinformatics in Genetic Animal Models for Brain Diseases
Year of publication : 2009

Objective: Discuss the use and benefits of applying neuroinformatics at each step of building, evaluating and using genetic animal models for human brain diseases. Participants include both neuroinformaticians and experimentalists, with representatives from the mouse/rodent, fly, zebrafish and non-human primate research communities.

Place: Stockholm, Sweden

1st INCF Workshop on Needs for Training in Neuroinformatics
Year of publication : 2008

Objective: Provide an overview of the current state of neuroinformatics training and to make recommendations for future training provisions. 

Place: Edinburgh, UK

1st INCF Workshop on Mouse and Rat Brain Digital Atlasing Systems
Year of publication : 2007

Objective: To survey current activities and plans related to mouse and rat brain digital atlasing systems and to produce a broad international inventory of resources and ongoing efforts. To review the range of techniques that are being used to build, normalize, segment, and label atlases and to examine what aspects of this technical work are redundant, compatible, and compliant across platforms. To forge an international network to foster increased collaboration and interoperability across national, linguistic, and funding barriers and to examine how to promote international collaborations in the future and to improve the impact of atlasing projects in the near term (5 years) while reducing costs and redundancy of these efforts.

Place: Stockholm, Sweden

1st INCF Workshop on NeuroImaging Database Integration
Year of publication : 2007

Objective: Map existing neuroimaging databases, particularly databases containing primary data, and to identify mechanisms that could facilitate integrated use of such databases, including possible fusion of databases.

Place: Stockholm, Sweden

1st INCF Workshop on Global Portal Services for Neuroscience
Year of publication : 2007

Objective: Map out existing portal services for neuroscience, identify their features and future plans, and outline opportunities for synergistic developments. 

Place: Stockholm, Sweden

1st INCF Workshop on Neuroanatomical Nomenclature and Taxonomy
Year of publication : 2007

Objective: Agree on a general strategy for developing a systematic, useful, and scientifically appropriate framework for neuroanatomical nomenclature. 

Place: Stockholm, Sweden

1st INCF Workshop on Sustainability of Neuroscience Databases
Year of publication : 2007

Objective: Discuss issues related to sustainability of neuroscience databases, to identify problems, to discuss solutions or approaches to these problems, and to formulate recommendations to the INCF. 

Place: Stockholm, Sweden

1st INCF Workshop on Large-Scale Modeling of the Nervous System
Year of publication : 2006

Objective: Survey current demands and ongoing activities and plans relating to development of tools for scalable neural network simulations. 

Place: Stocholm, Sweden