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Platform provides accurate, machine-executable computational models of how the brain gives rise to the mind. Enables researchers to quickly get a sense of the alignment of their model(s) to neural and behavioral measurements, and provides these models to experimentalists to prototype new experiments and make sense of biological data. All code is open-source and community members may choose to make their data or model weights fully public.
Proper citation: Brain Score (RRID:SCR_027769) Copy
http://thehumanbrainproject.com
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 16, 2013. The resource redirects to its parent, OSSP. Project seeking to increase the transparency and accessibility of the scientific research process by connecting researchers with an additional source of funding - microinvestments received from the broader online community. In exchange for these public investments, researchers will maintain research logs detailing the play-by-play progress made in their project, as well as publishing all of their data in a public database under a science commons license. These research projects, in turn, will serve to continually update a research-based neuroscience-based human brain & body curriculum.
Proper citation: Human Brain Project (RRID:SCR_013655) Copy
http://kimlab.io/brain-map/atlas/
Website to visualize and share anatomical labels. Franklin and Paxinos (FP) based anatomical labels in Allen Common Coordinate Framework (CCF). Cell type specific transgenic mice and MRI atlas were used to adjust and further segment labels. New segmentations were created in dorsal striatum using cortico-striatal connectivity data. Anatomical labels were digitized based on Allen ontology, and web-interface was created for easy visualization. These labels provide resource to isolate and identify mouse brain anatomical structures. Open source data sharing will facilitate further refinement of anatomical labels and integration of data interpretation within single anatomical platform.
Proper citation: Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas (RRID:SCR_019267) Copy
Seattle based independent, nonprofit medical research organization dedicated to accelerating the understanding of how human brain works. Provides free data and tools to researchers and educators and variety of unique online public resources for exploring the nervous system. Integrates gene expression data and neuroanatomy, along with data search and viewing tools, these resources are openly accessible via the Allen Brain Atlas data portal. Provides Allen Mouse Brain, Allen Spinal Cord Atlas, Allen Developing Mouse Brain Atlas, Allen Human Brain Atlas,Allen Mouse Brain Connectivity Atlas, Allen Cell Type Database, The Ivy Glioblastoma Atlas Project (Ivy GAP), The BrainSpan Atlas of the Developing Human Brain.
Proper citation: Allen Institute for Brain Science (RRID:SCR_006491) Copy
Debian is Linux distribution composed of free and open source software, developed by community supported Debian Project, which was established by Ian Murdock on August 16, 1993.Debian comes with over 59000 packages (precompiled software that is bundled up in nice format for easy installation on your machine), package manager (APT), and other utilities that make it possible to manage thousands of packages on thousands of computers as easily as installing single application.
Proper citation: Debian (RRID:SCR_006638) Copy
https://juaml.github.io/julearn
Software library of easy testing ML models directly from pandas DataFrames, while keeping the flexibility of using scikit-learn’s models.
Proper citation: Julearn (RRID:SCR_024881) Copy
Community registry of software tools and data resources for life sciences. Tools and data services registry as community effort to document bioinformatics resources. Registry of software and databases, facilitating researchers from across spectrum of biological and biomedical science. When adding tools to registry, information including URL, contact information, resource function, field its relevant in, and its primary publication are required. Development is supported by ELIXIR - the European Infrastructure for Biological Information.
Proper citation: bio.tools (RRID:SCR_014695) Copy
https://github.com/openMetadataInitiative/openMINDS
The openMINDS metadata framework comprises: schema specifications for multiple, interlocked metadata models for Linked Data, instance libraries for serviceable, well defined terms and constructs, as well as supportive tooling. openMINDS is developed as open source project by Open Metadata Initiative on GitHub. The framework is distributed over multiple, interlinked GitHub projects with one main GitHub repository for central access and maintenance.
Proper citation: openMINDS metadata framework (RRID:SCR_023173) Copy
https://github.com/openMetadataInitiative/openMINDS_instances
Software application to provide well defined metadata instances for selected schemas of the openMINDS metadata framework.
Proper citation: openMINDS_instances (RRID:SCR_027358) Copy
A multi-modal multivariate pattern analysis of neuroimaging data in Matlab / GNU Octave. Links to examples, exercises, and information for developers are available on the main page.
Proper citation: CoSMoMVPA (RRID:SCR_014519) Copy
http://www.nitrc.org/projects/openwalnut/
Open source tool for multi-modal medical and brain data visualization. It is a tool for the scientific user and a powerful framework for the visualization researcher. It is written in Standard C++ and uses a number of portable libraries (e.g. Qt, Boost and OpenSceneGraph). It runs on common GNU/Linux operating systems, Mac OSX and Windows.
Proper citation: OpenWalnut (RRID:SCR_014157) Copy
https://sourceforge.net/projects/bva-io/
Software package for interfacing the Brain Vision Analyser data files (load/save) for ongoing development of Matlab routines . This package is also compatible with the EEGLAB software, and may be uncompressed in the plugin folder of this software.
Proper citation: BVA import/export EEGLAB plugin (RRID:SCR_016333) Copy
A web-compliant application that allows connectomics visualization by converting datasets to web-optimized tiles, delivering volume transforms to client devices, and providing groups of users with connectome annotation tools and data simultaneously via conventional internet connections. Viking is an extensible tool for connectomics analysis and is generalizable to histomics applications.
Proper citation: Viking Viewer for Connectomics (RRID:SCR_005986) Copy
http://ncmir.ucsd.edu/downloads/montaging_plugins.shtm
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. 02111-1307, USA. Sponsors: ImageJ Mosaic Plug-Ins software presented here was produced at the National Center for Microscopy and Imaging Research at San Diego, which is supported by the National Institutes of Health (NIH) through a National Center for Research Resources program grant P41 RR04050.
Proper citation: National Center for Microscopy and Imaging Research: ImageJ Mosaic Plug-ins (RRID:SCR_001935) Copy
https://github.com/singerlabgt/BrainWAVE
Code to program and run flicker stimulation on BrainWAVE stimulator device. This brain oscillation stimulating software can be adapted across subjects and integrated into variety of experimental designs like electrophysiology, neuroimaging, EEG, MRI. Flexible method for noninvasive stimulation of brain rhythms across species. Used to measure effects of rhythmic brain activity on behavior.
Proper citation: BrainWAVE (RRID:SCR_024396) Copy
https://github.com/openMetadataInitiative/openMINDS_computation
Software repository is part of the open Metadata Initiative for Neuroscience Data Structures (openMINDS). It extends openMINDS core, by providing schema-templates for adding metadata for simulation, data analysis and visualization.
Proper citation: openMINDS computation metadata model (RRID:SCR_026249) Copy
https://github.com/openMetadataInitiative/openMINDS_specimenPrep
Software repository is part of the open Metadata Initiative for Neuroscience Data Structures (openMINDS). It extends openMINDS, by providing metadata schemas for in-depth descriptions of specimen preparations (surgery, tissue slicing, etc.).
Proper citation: openMINDS specimenPrep metadata model (RRID:SCR_026252) Copy
Open-source software package for the analysis of neural data. Chronux routines may be employed in the analysis of both point process and continuous data, ranging from preprocessing, exploratory and confirmatory analysis. The current release is implemented as a MATLAB library. Chronux offers several routines for computing spectra and coherences for both point and continuous processes. In addition, it also offers several general purpose routines that were found useful such as a routine for extracting specified segments from data, or binning spike time data with bins of a specified size. Since the data can be continuous valued, point process times, or point processes that are binned, methods that apply to all these data types are given in routines whose names end with ''''c'''' for continuous, ''''pb'''' for binned point processes, and ''''pt'''' for point process times. Thus, mtspectrumc computes the spectrum of continuous data, mtspectrumpb computes a spectrum for binned point processes, and mtspectrumpt compute spectra for data consisting of point process times. Hybrid routines are also available and similarly named - for instance coherencycpb computes the coherency between continuous and binned point process data.
Proper citation: Chronux (RRID:SCR_005547) Copy
https://broadinstitute.github.io/warp/docs/Pipelines/BuildIndices_Pipeline/README
Software workflow is an open-source, cloud-optimized pipeline developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN) and the BRAIN Initiative Cell Atlas Network (BICAN).
Proper citation: BuildIndices (RRID:SCR_027630) Copy
https://scicrunch.org/scicrunch/data/source/nlx_154697-12/search?q=*
A virtual database of several model resources including: CellML Model Repository, ModelDB, Open Source Brain, SimTK, and ModelRun.
Proper citation: Integrated Models (RRID:SCR_001481) Copy
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