Tools   Select Another Resource Report Type

http://download.ant-neuro.com/matlab/

Software as an EEGLAB tool used for LIBEEP recordings.

Proper citation: Libeep EEGLAB plugin (RRID:SCR_016334) Copy   

•   Source: SciCrunch Registry

https://github.com/BioDepot/nbdocker

Software tool as Jupyter Notebook extension for Docker. Each Docker container encapsulates its individual computing environment to allow different programming languages and computing environments to be included in one single notebook, provides user to document code as well as computing environment.

Proper citation: nbdocker (RRID:SCR_017159) Copy   

•   Source: SciCrunch Registry

https://github.com/pachterlab/kb_python

Software Python package that wraps kallisto and bustools single-cell RNA-seq workflow. Used for single-cell RNA-seq pre-processing. Simplifies downloading and running of kallisto and bustools programs. Consists of kb ref and kb count commands. kb ref builds or downloads species specific index for pseudo alignment of reads and must be run prior to kb count and it runs kallisto index. kb count runs kallisto and bustools programs and is used for pre-processing of data from variety of single-cell RNA-seq technologies, and for number of different workflows (e.g. production of gene count matrices, RNA velocity analyses, etc.).

Proper citation: kb_python (RRID:SCR_018213) Copy   

•   Source: SciCrunch Registry

http://www.duke.edu/web/gpcr-assay/index.html

Describes data from and access to permanent cell lines containing beta-arrestin fluorescent protein biosensors. This assay Bank provides plasmids, cells lines, and resulting data to the NIDA/NIH funded research community in order to better understand and combat addiction.

Proper citation: Addiction Research GPCR Assay Bank (RRID:SCR_002895) Copy   

•   Source: SciCrunch Registry

http://sleep.alleninstitute.org

Collection of gene expression data in mouse brain for five different conditions of sleep and wakefulness to understand sleep deprivation and dynamic changes underlying sleep and wake cycles. Platform to generate cellular resolution expression data.

Proper citation: Allen Institute for Brain Science Sleep Study (RRID:SCR_002983) Copy   

•   Source: SciCrunch Registry

http://www.nih.gov/science/brain/

Project aimed at revolutionizing understanding of human brain, to show how individual cells and complex neural circuits interact, enable rapid progress in development of new technologies and data analysis tools to treat and prevent brain disorders. BRAIN Initiative encourages collaborations between neurobiologists and scientists from disciplines such as statistics, physics, mathematics, engineering, and computer and information sciences. Institutes and centers contributing to NIH BRAIN Initiative support those research efforts.

Proper citation: BRAIN Initiative (RRID:SCR_006770) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/guide/sitemap/

The National Center for Biotechnology Information''s listing of resources. Sort by alphabetical character, Databases, Downloads, Submissions, Tools and How-To; or by Topic: Chemicals & Bioassays; Data & Software; DNA & RNA; Domains & Structures; Genes & Expression; Genetics & Medicine; Genomes & Maps; Homology; Literature; Proteins; Sequence Analysis; Taxonomy; Training & Tutorials; Variation.

Proper citation: NCBI Resource List (RRID:SCR_005628) Copy   

•   Source: SciCrunch Registry

http://www.nsgportal.org/

Web portal that allows free access to supercomputing resources for large scale modeling and data processing. Portal facilitates access and use of National Science Foundation (NSF) High Performance Computing (HPC) resources by neuroscientists.

Proper citation: Neuroscience Gateway (RRID:SCR_008915) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

Software tool to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files for directional, non-directional or paired-end sequencing. Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for Reduced Representation Bisulfite Sequencing data.

Proper citation: Trim Galore (RRID:SCR_011847) Copy   

•   Source: SciCrunch Registry

http://spark.apache.org/

Software tool as a unified analytics engine for large scale data processing. An open source distributed general purpose cluster computing framework.

Proper citation: Apache Spark (RRID:SCR_016557) Copy   

•   Source: SciCrunch Registry

http://databiosphere.org

Project whose goal is to provide Data Environments to the biomedical community. The Data Biosphere works to create a user experience around key modular components — each having discrete capabilities and clear rules of interaction, and each served by multiple alternative implementations.

Proper citation: Data Biosphere (RRID:SCR_016154) Copy   

•   Source: SciCrunch Registry

https://github.com/TeamMacLean/atacr

Software that analyzes count data from RNA-capture-seq and ATAC-capture-seq experiments. Using BioConductor RangedSummarizedExperiment objects, atacr implements a set of helper functions and quality control plots specific to the analysis of counts of reads in windows across genomes.

Proper citation: atacr (RRID:SCR_016286) Copy   

•   Source: SciCrunch Registry

https://drugs.ncats.io/

Portal of NCATS (the National Center for Advancing Translational Sciences) for drug development information including:US approved drugs, marketed drugs, investigational drugs. Provides manually curated data supplied by the FDA and private companies. Provides drugs marketing and regulatory status, drug ingredient definitions, biological activity and clinical use.

Proper citation: Inxight (RRID:SCR_016490) Copy   

•   Source: SciCrunch Registry

https://nels.bioinfo.no

Web portal for the administration of Norwegian e-Infrastructure for Life Sciences. Enables Norwegian life scientists and their international collaborators to store, share, archive, and analyse their genomics scale data. NeLS is one of the packages of the ELIXIR.NO project.

Proper citation: NeLS (RRID:SCR_016301) Copy   

•   Source: SciCrunch Registry

https://www.ruhr-uni-bochum.de/mpc/software/ProCon/index.html.en

Java based conversion tool for conversion of data from Proteomics files or a LIMS (Laboratory Information Management System) database into standard formats. Used to support wet-lab scientists in creating proteomics data files ready for upload into the public repositories.

Proper citation: ProCon - PROteomics CONversion (RRID:SCR_016363) Copy   

•   Source: SciCrunch Registry

https://knightadrc.wustl.edu/professionals-clinicians/request-center-resources/

Provides on request resources including Data: clinical and cognitive measures as well as MRI and amyloid imaging scans; Tissue: frozen brain tissue, paraffin brain sections, antemortem CSF, DNA, fibroblast, dermal fibroblasts, plasma (fasting and non-fasting) and iPSC; Participants: eligible participants may be invited to enroll in research of other investigators after appropriate review. Researchers can use the request portal to review Center guidelines and policies; view available data and tissue; access data tables and codebooks; and submit request for resources.

Proper citation: Washington University School of Medicine Knight ADRC Request Center Resources Core Facility (RRID:SCR_025254) Copy   

•   Source: SciCrunch Registry

https://marmotgraph.org

Knowledge graph system developed for managing and organizing rich metadata objects, initially for the Human Brain Project (HBP) and now extended to be a more generic, domain-agnostic solution. It is associated with CSCS (Swiss National Supercomputing Centre) and aims to provide a comprehensive toolset and API for working with knowledge graphs.

Proper citation: MarmotGraph (RRID:SCR_027452) Copy   

•   Source: SciCrunch Registry

https://www.bwhneurosciences.org/neurotechnology-studio/

Offers advanced instrumentation and expert support to advance understanding of brain function and brain disease by providing researchers with access to cutting-edge technologies. Provides access to advanced instrumentation for optical microscopy, genomics, metabolic imaging and other technologies, as well as image analysis software. Provides expert support and training, data quality and interpretation.

Proper citation: Brigham and Women’s Hospital NeuroTechnology Studio Core Facility (RRID:SCR_027687) Copy   

•   Source: SciCrunch Registry

http://www.concepthub.org/wiki/Main_Page

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 18, 2016. A database built up with software and services that maintains multiple versions of terminologies, map sets, and values sets concurrently. HDD Access has superseded Concept Hub.

Proper citation: Concept Hub (RRID:SCR_013586) Copy   

•   Source: SciCrunch Registry

https://www.digitalpsych.org/mindlamp1.html

Core collects data to capture and consider the real-time lived experiences of patients. Uses open-source digital platform and mobile app for neuropsychiatric research and clinical care, to monitor, support, and improve brain health by collecting real-time data (like location, activity, heart rate via sensors), conducting digital assessments (surveys, cognitive tests), and delivering interventions (meditation, journaling, psychoeducation) to patients and clinicians. It helps study behavioral patterns, track symptoms, and personalize mental health treatment through features organized around Learn, Assess, Manage, and Prevent.

Proper citation: BIDMC Division of Digital Psychiatry LAMP platform Core Facility (RRID:SCR_027767) Copy   

•   Source: SciCrunch Registry