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http://www.nimh.nih.gov/research-funding/training/index.shtml
A portal to the National Institute of Mental Health''s Research Training, Career Development, and Related Programs. Topics cover Resources for Applicants, Individual Fellowship Programs, Individual Career Development Programs, Institutional Training Programs, Additional Career Development/Training-Related Opportunities, and Training Programs to Increase Workforce Diversity.
Proper citation: NIMH Resources for Research Training and Career Development (RRID:SCR_005624) Copy
Realistic simulated MEG datasets ranging from basic sensory to oscillatory sets that mimic functional connectivity; as well as basic visual, auditory, and somatosensory empirical sets. The simulated sets were created for the purpose of testing analysis algorithms across the different MEG systems when the truth is known. MEG baseline recordings were obtained from 5 healthy participants, using three MEG systems: VSM/CTF Omega, Elekta Neuromag Vectorview, 4-D Magnes 3600. Simulated signals were embedded within the CTF and Neuromag 306 baseline recordings (4-D to be added). Participant MRIs are available. Averaged simulation files are available as netcdf files. Neuromag 306 averaged simulations are also available in fif format. Also available: single trials of data where the simulated signal is jittered about a mean value, continuous fif files where the simulated signal is marked by a trigger, and simulations with oscillations added to mimic functional connectivity.
Proper citation: MEGSIM (RRID:SCR_002420) Copy
http://senselab.med.yale.edu/odormapdb
OdorMapDB is designed to be a database to support the experimental analysis of the molecular and functional organization of the olfactory bulb and its basis for the perception of smell. It is primarily concerned with archiving, searching and analyzing maps of the olfactory bulb generated by different methods. The first aim is to facilitate comparison of activity patterns elicited by odor stimulation in the glomerular layer obtained by different methods in different species. It is further aimed at facilitating comparison of these maps with molecular maps of the projections of olfactory receptor neuron subsets to different glomeruli, especially for gene targeted animals and for antibody staining. The main maps archived here are based on original studies using 2-deoxyglucose and on current studies using high resolution fMRI in mouse and rat. Links are also provided to sites containing maps by other laboratories. OdorMapDB thus serves as a nodal point in a multilaboratory effort to construct consensus maps integrating data from different methodological approaches. OdorMapDB is integrated with two other databases in SenseLab: ORDB, a database of olfactory receptor genes and proteins, and OdorDB, a database of odor molecules that serve as ligands for the olfactory receptor proteins. The combined use of the three integrated databases allows the user to identify odor ligands that activate olfactory receptors that project to specific glomeruli that are involved in generating the odor activity maps.
Proper citation: Olfactory Bulb Odor Map DataBase (OdorMapDB) (RRID:SCR_007287) Copy
Community site to make brain imaging research easier that aims to build software that is clearly written, clearly explained, a good fit for the underlying ideas, and a natural home for collaboration.
Proper citation: Neuroimaging in Python (RRID:SCR_013141) Copy
https://www.delaneycare.org/index.php
The Collaboratory of AIDS Researchers for Eradication (CARE) is a consortium of scientific experts in the field of HIV latency from several U.S. and European academic research institutions as well as Merck Research Laboratories working together to find a cure for HIV.
Proper citation: Collaboratory of AIDS Researchers for Eradciation (CARE) (RRID:SCR_013681) Copy
http://hbatlas.org/pages/publications
A research paper with supplementary materials reporting the generation and analysis of exon-level transcriptome and associated genotyping data. The experiment represented both males and females of multiple ethnicities and examines gene regulation and expression in different areas of the brain. A data set on the human brain transcriptome as well as insights into the transcriptional foundations of human neurodevelopment is provided.
Proper citation: Spatio-temporal transcriptome of the human brain (RRID:SCR_013743) Copy
http://www.nitrc.org/projects/nusdast
A repository of schizophrenia neuroimaging data collected from over 450 individuals with schizophrenia, healthy controls and their respective siblings, most with 2-year longitudinal follow-up. The data include neuroimaging data, cognitive data, clinical data, and genetic data.
Proper citation: Northwestern University Schizophrenia Data and Software Tool (NUSDAST) (RRID:SCR_014153) Copy
https://health.uconn.edu/worm-lab/track-a-worm/
Open source system for quantitative assessment of C. Elegans locomotory and bending behavior. Used for quantitative behavioral analyses to understand circuit and gene bases of behavior. Constantly records and analyzes position and body shape of freely moving worm at high magnification.
Proper citation: Track-A-Worm (RRID:SCR_018299) Copy
Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values.
Proper citation: piNET (RRID:SCR_018693) Copy
Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics.
Proper citation: EpiModel (RRID:SCR_018539) Copy
https://github.com/aplbrain/saber
Library of containerized tools and workflow deployment system for enabling processing of large neuroimaging datasets. Provides canonical neuroimaging workflows specified in standard workflow language (CWL), integration with workflow execution engine (Airflow), imaging database (bossDB), and parameter database (Datajoint) to deploy workflows at scale, and tools to automate deployment and optimization of neuroimaging pipelines.
Proper citation: Scalable Analytics for Brain Exploration Research (RRID:SCR_018812) Copy
https://openwetware.org/wiki/RAVE
Open source software tool for reproducible analysis and visualization of intracranial EEG data. Used for analysis of intracranial electroencephalogram data, including data collected using strips and grids (electrocorticography, ECoG) and depth electrodes (stereotactic EEG).
Proper citation: RAVE (RRID:SCR_019040) Copy
https://github.com/r3fang/SnapATAC
Software package for analyzing scATAC-seq datasets.Used to dissects cellular heterogeneity in unbiased manner and map trajectories of cellular states. Can process data from up to million cells. Incorporates existing tools into comprehensive package for analyzing single cell ATAC-seq dataset.
Proper citation: SnapATAC (RRID:SCR_020981) Copy
http://kim.bio.upenn.edu/software/pivot.shtml
Software R package for interactive analysis and visualization of transcriptomics data. Operating systems are macOS, Linux, Windows.
Proper citation: PIVOT software (RRID:SCR_017210) Copy
http://www.brainimagelibrary.org
Repository for confocal microscopy brain imaging data. Data archives that have been established by BRAIN Initiative Data Sharing. National public resource enabling researchers to deposit, analyze, mine, share and interact with large brain image datasets. Operated as partnership between Biomedical Applications Group at Pittsburgh Supercomputing Center, Center for Biological Imaging at University of Pittsburgh and Molecular Biosensor and Imaging Center at Carnegie Mellon University. Provides persistent centralized repository for brain microscopy data.
Proper citation: Brain Image Library (RRID:SCR_017272) Copy
BossDB (Brain Observatory Storage Service and Database) is a cloud-based ecosystem for the storage and management of public large-scale volumetric neuroimaging and connectomics datasets. This includes volumetric Electron Microscopy and X-Ray Micro/Nanotomography data with support for multi-channel image data, segmentations, annotations, meshes, and connectomes. BossDB integrates with community resources for data access, processing, visualization, and analysis, and includes an API that enables metadata management, rendering, datatype conversions, and ingest.
Proper citation: Brain Observatory Storage Service and Database (BossDB) (RRID:SCR_017273) Copy
https://github.com/SciCrunch/NIF-Ontology/tree/neurons/ttl
An ontology for describing the complex phenotypes of neurons.
Proper citation: Neuron Phenotype Ontology (RRID:SCR_017403) Copy
Portal for visualization and analysis of multi omic data in public and private domains. Enables upload, visualization and analysis of scRNA-seq data.
Proper citation: gene Expression Analysis Resource (RRID:SCR_017467) Copy
https://github.com/PriceLab/TReNA
Methods for reconstructing transcriptional regulatory networks.
Proper citation: TReNA (RRID:SCR_017458) Copy
http://compbio.mit.edu/ChromHMM/
Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations.
Proper citation: ChromHMM (RRID:SCR_018141) Copy
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