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https://www.ncbi.nlm.nih.gov/projects/mutagene/
Software tool to explore and analyze mutagenic factors leading to tumors to decipher cancer genetic heterogeneity.
Proper citation: MutaGene (RRID:SCR_016574) Copy
Instrument for cell sorting by BD Biosciences where positive air pressure forces sample cell through an optically gel-coupled cuvette . Hydrodynamic focusing guides particles in a single-file stream through the cuvette, where laser light intercepts the stream at the sample interrogation point.Fluorescence activated cell sorting instrument. Flow cytometer as high speed fixed alignment benchtop cell sorter. Enables multicolor analysis of up to 13 fluorescent markers and two scatter parameters at time.
Proper citation: BD Biosciences: FACSAria III Cell Sorter (RRID:SCR_016695) Copy
http://emg.nysbc.org/redmine/projects/appion/wiki/Appion_Home
Software package for processing and analysis of EM images. Appion is integrated with Leginon data acquisition but can also be used stand-alone after uploading images (either digital or scanned micrographs) or particle stacks using a set of provided tools.
Proper citation: Appion Package (RRID:SCR_016734) Copy
Web tool to import raw cDNA sequences, clean sequences, build sequence contigs, perform SignalP analysis, BLAST contigs against numerous BLAST databases, and view the results. Automates large scale cDNA sequence analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: dCAS (RRID:SCR_016612) Copy
https://www.bioconductor.org/packages/release/workflows/html/RnaSeqGeneEdgeRQL.html
Software to study analysis of an RNA-Seq experiment using the Rsubread and edgeR packages. The workflow starts from read alignment and continues on to data exploration, to differential expression and, finally, to pathway analysis. The analysis includes plots, GO and KEGG analyses, and the analysis of a expression signature as generated by a prior experiment.
Proper citation: RnaSeqGeneEdgeRQL (RRID:SCR_016699) Copy
http://grigoriefflab.janelia.org/ctffind4
Software tool for finding CTFs of electron micrographs. Program used for the estimation of objective lens defocus parameters from transmission electron micrographs. The program CTFFIND3 is an updated version of the program CTFFIND2. For micrographs collected on photographic film and scanned in use CTFFIND 3. For images from CCDs or direct detectors use CTFFIND 4.
Proper citation: CTFFIND (RRID:SCR_016732) Copy
https://bioinformatics.niaid.nih.gov/nglycpred/
Web based server to discriminate between glycosylated and non-glycosylated N-X-(T/S) sequons by incorporating structural information and patterns.
Proper citation: NGlycPred (RRID:SCR_016610) Copy
https://github.com/NeurophysVis/SpectraVis
Web based neuroscience application for analyzing task-related functional networks over time and frequency. Interactive visualization tool for exploring functional brain connectivity.
Proper citation: SpectraVis (RRID:SCR_016691) Copy
https://bioinformatics.niaid.nih.gov/hasp
Web server to visualize phylogenetic, biochemical, and immunological hemagglutinin data in the three-dimensional context of homology models. Database and structural visualization platform for comparative models of influenza A hemagglutinin proteins.
Proper citation: HASP (RRID:SCR_016615) Copy
https://sleepdata.org/datasets/ccshs
Portal for population based pediatric cohorts studied with objective sleep studies. Includes children with in-home sleep studies, acoustic reflectometry, anthropometry, spirometry, blood pressure (BP), and neuropsychology (NP) and behavioral assessments. Signals recorded include EEG, ECG, EOG, EMG, SpO2, airflow (thermocouple) nasal pressure, respiratory effort, position, plethysmography, light, HR.
Proper citation: Cleveland Children's Sleep and Health Study (RRID:SCR_016584) Copy
http://www.indecbiosystems.com/imagingworkbench/default.asp
Software for multichannel dynamic fluorescence image acquisition and analysis by INDEC BioSystems.
Proper citation: Imaging WorkBench (RRID:SCR_016589) Copy
https://sleepdata.org/datasets/bestair/
Portal for sleep study to address challenges in conducting future large-scale trials of sleep apnea treatment. Includes data from sleep apnea patients with cardiovascular disease or risk factors. Signals included in the polysomnography (PSG) montage are ECG, SpO2, airflow, nasal pressure, position, pulse, respiratory effort, snore, tidal volume.
Proper citation: Best Apnea Interventions for Research (BestAIR) sleep study (RRID:SCR_016583) Copy
https://pachterlab.github.io/kallisto/about
Software tool for quantifying abundances of transcripts from RNA-Seq data or target sequences using high-throughput sequencing reads.
Proper citation: kallisto (RRID:SCR_016582) Copy
http://www.nichd.nih.gov/research/supported/pages/tbi.aspx
The National Center for Medical Rehabilitation Research (NCMRR) established a multi-center network of sites that are working together to design clinical intervention protocols and measures of outcome for TBI. Through rigorous patient evaluation, using common protocols and interventions designed for multiple points of care����??including the accident scene, emergency room, intensive care unit, rehabilitation and long-term follow-up����??the NCMRR TBI Clinical Trials Network can study the required numbers of patients to provide answers more rapidly than individual centers acting alone. This interdisciplinary research Network is designed to evaluate the relationship among acute care practice, rehabilitation strategies, and the long-term functional outcome of TBI patients����??that is, to identify which intervention variables result in improvements in long-term outcomes. Taking advantage of the network model structure has allowed TBI research to progress toward a number of clinical research goals. Specifically, the NCMRR wants to highlight two major achievements to date. First, the TBI Network created a profile of its typical patient to determine the number of patients with different clinical features who might be eligible for future studies and to help estimate recruitment times necessary. Second, Network researchers are developing clinical treatment guidelines and procedures for all points in the continuum of care, including TBI Clinical Trials Network Guidelines for surgical care, systems-based protocol for severe and moderate TBI patients, deep-vein thrombosis prophylaxis procedures, and rehabilitation guidelines for physical therapy, speech-language pathology, occupational therapy, and neuropsychology.
Proper citation: Traumatic Brain Injury Clinical Trials Network (RRID:SCR_013165) Copy
https://confluence.crbs.ucsd.edu/display/NIF/OntoQuestMain
An ontology management module to perform ontology-based search over data sources. This management system permits a user to store, search and navigate any number of OWL-structured ontologies. Ontoquest may also be accessed through a variety of web services via the Neuroscience Information Framework.
Proper citation: OntoQuest (RRID:SCR_013281) Copy
http://www.mi.med.osaka-u.ac.jp/gpetview/gpetview.html
GpetView is light-weight image viewer based on Gtk+ library. The supported image format is ANALYZE(TM) format (Mayo Foundation ). GpetView can run on Unix-systems, such as Linux, Solaris, IRIX, Mac OS-X etc. From Version 2.0, GpetView can also run on Win32 system, if you have installed Glib and Gtk+(2.x). Glib andGtk+ can be found at http://www.gtk.org. For Windows users, you can find Gtk+ libraries at http://gladewin32.sourceforge.net/modules/news/ GpetView has the following features: * very light-weight * view images as transverse, coronal, or sagittal * change color-map (support Analyze lkup file) * zoom images * ROI (Region-Of-Interest) with shapes of circle, ellipse, rectangle, polygon and automatic edge detection * Image histogram and profile Sponsors: This resource is supported by Osaka University. Keywords: Image, Viewer, Software, Transverse, Coronal, Sagittal, Map, Histogram,
Proper citation: Gtk-based Analyze Image Viewer (RRID:SCR_013282) Copy
The American Association of Neurological Surgeons is dedicated to advancing the specialty of neurological surgery and serving as the spokes organization for all practitioners of the specialty of neurosurgery, in order to provide the highest quality of care to our patients. :Founded in 1931 as the Harvey Cushing Society, the American Association of Neurological Surgeons (AANS) is a scientific and educational association with over 7,400 members worldwide. The AANS is dedicated to advancing the specialty of neurological surgery in order to provide the highest quality of neurosurgical care to the public. All Active members of the AANS are board certified by the American Board of Neurological Surgery, the Royal College of Physicians and Surgeons of Canada, or the Mexican Council of Neurological Surgery, A.C. Neurosurgery is the medical specialty concerned with the prevention, diagnosis, treatment and rehabilitation of disorders that affect the spinal column, spinal cord, brain, nervous system and peripheral nerves. For more information on what neurosurgeons do, visit our public pages at : :www.NeurosurgeryToday.org : : :. Visitors to our Web site can find Member Counts under membership including demographic details.
Proper citation: American Association of Neurological Surgeons (RRID:SCR_013209) Copy
http://www.bioconductor.org/packages//2.10/bioc/html/HiTC.html
Software package to explore high-throughput ''C'' data such as 5C or Hi-C.
Proper citation: HiTC (RRID:SCR_013175) Copy
http://sourceforge.net/projects/conifer/
Uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes.
Proper citation: CoNIFER (RRID:SCR_013213) Copy
http://rdxplorer.sourceforge.net/
A computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage.
Proper citation: RDXplorer (RRID:SCR_013290) Copy
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