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http://www.feinsteininstitute.org/Feinstein/Feinstein+HomePage

The Feinstein Institute for Medical Research is the research branch of the North Shore-Long Island Jewish Health System. Biomedical research has been a vital aspect of its two academic medical centers North Shore University Hospital and Long Island Jewish Medical Center since their establishment in the early 1950''s. Through its connection to the hospital system, the Institute bridges the gap between biomedical research and patient care, accessing hundreds of thousands of patients in the health system''s 15 hospitals, four long-term care facilities, three trauma centers, six home health agencies and dozens of outpatient facilities. Institute scientists collaborate with clinicians throughout the system to shed light on basic biological processes underlying disease. This knowledge is used to develop new therapies and diagnostics. Currently, more than 800 scientists and investigators are conducting research in oncology, immunology and inflammation, genetics, psychiatry, neurology, pediatrics, surgery, urology, obstetrics/gynecology and many other specialties. In 2008, the Feinstein received funding from the National Institutes of Health in excess of $28 million, and an additional $10 million from other federal sources. Total annual research funding from all sources exceeded $44 million in 2008. We stand at the threshold of an extraordinary time in medicine. Over the last 100 years, biomedical science has progressed very rapidly. Advances coming from the integration of genomics, proteomics and bioinformatics into the biomedical toolkit hold the promise that this transformation will continue well into the 21st century. The Feinstein Institute for Medical Research is a growing force in research innovation, education and progress.

Proper citation: Feinstein Institute for Medical Research (RRID:SCR_004470) Copy   

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http://www.mprc.umaryland.edu/mbc.asp

The Maryland Brain Collection (MBC), a resource of the Maryland Psychiatric Research Center (MPRC), is dedicated to promoting research with brain tissue obtained post-mortem from individuals with schizophrenia or related disorders. The primary goal of the MBC is to provide high-quality tissue, along with comprehensive clinical information, for hypothesis-driven research. The MBC is not conceptualized as a Brain Bank with open access but is maintained and funded through collaborative research. The Maryland Brain Collection is managed by researchers at the Maryland Psychiatric Research Center (MPRC). MPRC scientists are dedicated to understanding the causes and improving the treatment of mental illness. The Maryland Brain Collection is associated with the Office of the Chief Medical Examiner for the State of Maryland and other donor sources. MPRC scientists collaborate with scientists from around the world to understand how abnormalities in brain tissue relate to mental illness. The purpose of the MBC is to study the following: Schizophrenia, Bipolar Disorder, Depression, Suicide/Teen suicide, Substance Abuse.

Proper citation: Maryland Brain Collection (RRID:SCR_004384) Copy   

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http://rarediseasesnetwork.epi.usf.edu/index.htm

The Rare Diseases Clinical Research Network (RDCRN) was created to facilitate collaboration among experts in many different types of rare diseases. Our goal is to contribute to the research and treatment of rare diseases by working together to identify biomarkers for disease risk, disease severity and activity, and clinical outcome, while also encouraging development of new approaches to diagnosis, prevention, and treatment. The Rare Diseases Clinical Research Network (RDCRN) is made up of 19 distinctive consortia that are working in concert to improve availability of rare disease information, treatment, clinical studies, and general awareness for both patients and the medical community. The RDCRN also aims to provide up-to-date information for patients and to assist in connecting patients with advocacy groups, expert doctors, and clinical research opportunities.

Proper citation: Rare Diseases Clinical Research Network (RRID:SCR_004372) Copy   

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http://www.usidnet.org/

Research consortium to advance scientific research in the primary immune deficiency diseases (PIDD) and: * Assemble and maintain a registry of patients with primary immunodeficiency diseases to provide a minimum estimate of the prevalence of each disorder in the United States. Provide a comprehensive clinical picture of each disorder and act as a resource for clinical and laboratory research. * Establish a multifaceted mentoring program to introduce new investigators into the field and stimulate interest and research in primary immune deficiency diseases. * Establish an advisory/review committee to maintain a cell/DNA Repository of biologic material from well-characterized PIDD patients for the advancement of scientific research USIDNET operates a large database of patient information for your use. The purpose and scope of this project is to assemble and maintain a registry of residents with primary immunodeficiency diseases. The project was started with the Registry of U.S. Residents with Chronic Granulomatous Disease. Since then, the registry has been expanded and now collects data on all primary immunodeficiency disorders. The following are just a few of the diseases housed in the registry: Chronic Granulomatous Disease, Common Variable Immunodeficiency Disease, DiGeorge Anomaly, Hyper IgM Syndrome, Leukocyte Adhesion Defect, Severe Combined Immunodeficiency Disease, Wiskott-Aldrich Syndrome, X-Linked Agammaglobulinemia Physicians who would like to register their patients or access the registry are encouraged to contact Onika Davis or Lamar Hamilton, USIDNET team, at odavis (at) primaryimmune.org, or lhamilton (at) primaryimmune.org

Proper citation: USIDNET: US Immunodeficiency Network (RRID:SCR_004672) Copy   

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http://em.emory.edu/protect/index.cfm

Recently, our team completed an NINDS-funded, Phase IIa double-blinded, placebo-controlled pilot clinical trial that examined the pharmacokinetics, safety, and activity of progesterone, a steroid found to have powerful neuroprotective effects in multiple animal models of brain injury. Our pilot study demonstrated a 50% reduction in death among severe TBI patients and less disability among moderate TBI patients treated with progesterone. Based on these promising results and supportive preclinical data, we are conducting a large, phase III clinical trial (ProTECT III) to definitively assess the safety and efficacy of this treatment for adults with moderate to severe acute TBI. The study is slated to begin August 2008. WHY Progesterone: Although progresterone is widely considered a sex steroid, it is also a potent neurosteroid. Progesterone is naturally synthesized in the CNS. A large and growing body of animal studies indicate that early administration of progesterone after TBI reduces cerebral edema, neuronal loss, and behavioral deficits in laboratory animals. Certain properties of progesterone make it an ideal therapeutic candidate. First, in contrast to most drugs tested to date, progesterone rapidly enters the brain and reaches equilibrium with the plasma within an hour of administration. Second, unlike other experimental agents, progesterone has a long history of safe use in humans. Finally, the findings of our pilot clinical trial (presented in the Preliminary Data Section, below) indicate that progesterone has consistent and predictable pharmacokinetic properties, is unlikely to produce harm, and may be efficacious for treating acute TBI in humans.

Proper citation: ProTECT (RRID:SCR_004531) Copy   

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http://krasnow1.gmu.edu/cn3/hippocampus3d/

Data files for a high resolution three dimensional (3D) structure of the rat hippocampus reconstructed from histological sections. The data files (supplementary data for Ropireddy et al., Neurosci., 2012 Mar 15;205:91-111) are being shared on the Windows Live cloud space provided by Microsoft. Downloadable data files include the Nissl histological images, the hippocampus layer tracings that can be visualized alone or superimposed to the corresponding Nissl images, the voxel database coordinates, and the surface rendering VRML files. * Hippocampus Nissl Images: The high resolution histological Nissl images obtained at 16 micrometer inter-slice distance for the Long-Evans rat hippocampus can be downloaded or directly viewed in a browser. This dataset consists of 230 jpeg images that cover the hippocampus from rostral to caudal poles. This image dataset is uploaded in seven parts as rar files. * Hippocampus Layer Tracings: The seven hippocampus layers ''ML, ''GC'', ''HILUS'' in DG and ''LM'', ''RAD'', ''PC'', ''OR'' in CA were segmented (traced) using the Reconstruct tool which can be downloaded from Synapse web. This tool outputs all the tracings for each image in XML format. The XML tracing files for all these seven layers for each of the above Nissl images are zipped into one file and can be downloaded. * Hippocampus VoxelDB: The 3D hippocampus reconstructed is volumetrically transformed into 16 micrometer sized voxels for all the seven layers. Each voxel is reported according to multiple coordinate systems, namely in Cartesian, along the natural hippocampal dimensions, and in reference to the canonical brain planes. The voxel database file is created in ascii format. The single voxel database file was split into three rar archive files. Please note that the three rar archive files should be downloaded and decompressed in a single directory in order to obtain the single voxel data file (Hippocampus-VoxelDB.txt). * 3D Surface Renderings: This is a rar archive file with a single VRML file containing the surface rendering of DG and CA layers. This VRML file can be opened and visualized in any VRML viewer, e.g. the open source software view3dscene. * 3D Hippocampus Movie: This movie contains visualization of the 3D surface renderings of CA (blue) and DG (red) inner and outer boundaries; neuronal embeddings of DG granule and CA pyramidal dendritic arbors; potential synapses between CA3b interneuron axon and pyramidal dendrite, and between CA2 pyramidal axon and CA pyramidal dendrites.

Proper citation: Hippocampus 3D Model (RRID:SCR_005083) Copy   

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http://www.stanford.edu/group/brainsinsilicon/neurogrid.html

A specialized hardware platform that will perform cortex-scale emulations while offering software-like flexibility. With sixteen 12x14 sq-mm chips (Neurocores) assembled on a 6.5x7.5 sq-in circuit board that can model a slab of cortex with up to 16x256x256 neurons - over a million! The chips are interconnected in a binary tree by 80M spike/sec links. An on-chip RAM (in each Neurocore) and an off-chip RAM (on a daughterboard, not shown) softwire vertical and horizontcal cortical connections, respectively. It provides an affordable option for brain simulations that uses analog computation to emulate ion-channel activity and uses digital communication to softwire synaptic connections. These technologies impose different constraints, because they operate in parallel and in serial, respectively. Analog computation constrains the number of distinct ion-channel populations that can be simulatedunlike digital computation, which simply takes longer to run bigger simulations. Digital communication constrains the number of synaptic connections that can be activated per secondunlike analog communication, which simply sums additional inputs onto the same wire. Working within these constraints, Neurogrid achieves its goal of simulating multiple cortical areas in real-time by making judicious choices.

Proper citation: Neurogrid (RRID:SCR_005024) Copy   

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http://drugcentral.org/

Database of drug information created and maintained by the Division of Translational Informatics at University of New Mexico. It provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, and pharmacologic action.

Proper citation: DrugCentral (RRID:SCR_015663) Copy   

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http://bioinformatics.hungry.com/clearcut/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023.Software as a stand-alone reference implementation for the Relaxed Neighbor Joining (RNJ) algorithm. Used in distance-based phylogenetic tree reconstruction method to process large sequence datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Clearcut (RRID:SCR_016059) Copy   

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https://www.immport.org/home

Data sharing repository of clinical trials, associated mechanistic studies, and other basic and applied immunology research programs. Platform to store, analyze, and exchange datasets for immune mediated diseases. Data supplied by NIAID/DAIT funded investigators and genomic, proteomic, and other data relevant to research of these programs extracted from public databases. Provides data analysis tools and immunology focused ontology to advance research in basic and clinical immunology.

Proper citation: The Immunology Database and Analysis Portal (ImmPort) (RRID:SCR_012804) Copy   

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http://i2b2.cchmc.org/

A data warehouse that integrates information on patients from multiple sources and consists of patient information from all the visits to Cincinnati Children''''s between 2003 and 2007. This information includes demographics (age, gender, race), diagnoses (ICD-9), procedures, medications and lab results. They have included extracts from Epic, DocSite, and the new Cerner laboratory system and will eventually load public data sources, data from the different divisions or research cores (such as images or genetic data), as well as the research databases from individual groups or investigators. This information is aggregated, cleaned and de-identified. Once this process is complete, it is presented to the user, who will then be able to query the data. The warehouse is best suited for tasks like cohort identification, hypothesis generation and retrospective data analysis. Automated software tools will facilitate some of these functions, while others will require more of a manual process. The initial software tools will be focused around cohort identification. They have developed a set of web-based tools that allow the user to query the warehouse after logging in. The only people able to see your data are those to whom you grant authorization. If the information can be provided to the general research community, they will add it to the warehouse. If it cannot, they will mark it so that only you (or others in your group with proper approval) can access it.

Proper citation: i2b2 Research Data Warehouse (RRID:SCR_013276) Copy   

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http://cole-trapnell-lab.github.io/monocle-release/docs/

Software package for analyzing single cell gene expression, classifying and counting cells, performing differential expression analysis between subpopulations of cells, and reconstructing cellular trajcectories. Works well with very large single-cell RNA-Seq experiments containing tens of thousands of cells or more. Used in computational analysis of gene expression data in single cell gene expression studies to profile transcriptional regulation in complex biological processes and highly heterogeneous cell populations.

Proper citation: Monocle2 (RRID:SCR_016339) Copy   

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https://bioconductor.org/packages/release/bioc/html/MAST.html

Software as an open source package for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.

Proper citation: MAST (RRID:SCR_016340) Copy   

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http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html

Software tool as a framework for modeling the sequences of short sequence motifs based on the maximum entropy principle (MEP). Used for sequence motifs such as those involved in RNA splicing.

Proper citation: MAxEntScan (RRID:SCR_016707) Copy   

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https://www.niaid.nih.gov/

National Institute of Allergy and Infectious Diseases is a leading research institution to understand, treat, and prevent infectious, immunologic, and allergic diseases.

Proper citation: NIAID (RRID:SCR_016598) Copy   

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https://niaid.github.io/spice/

Software application for data mining and visualization. Used for analyzes of large FLOWJO data sets from polychromatic flow cytometry and organizing the normalized data graphically.

Proper citation: SPICE (RRID:SCR_016603) Copy   

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https://sleepdata.org/datasets/cfs

Portal for family based study of sleep apnea. Contains data for quantifying the familial aggregation of sleep apnea. The polysomnographic (PSG) montage signals: EEG, ECG, EOG, EMG, SpO2, plethysmography, airflow (thermistor), nasal pressure, respiratory effort, position, snore.

Proper citation: Cleveland Family Study (RRID:SCR_016585) Copy   

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https://github.com/gelles-brandeis/CoSMoS_Analysis

Software tools for analyzing co-localization single-molecule spectroscopy image data.

Proper citation: CoSMoS_Analysis (RRID:SCR_016896) Copy   

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http://www.bx.psu.edu/~giardine/vision/

International project to analyze mouse and human hematopoiesis, and provide a tractable system with clear clinical significance and importance to NIDDK. Collection of information from the flood of epigenomic data on hematopoietic cells as catalogs of validated regulatory modules, quantitative models for gene regulation, and a guide for translation of research insights from mouse to human.

Proper citation: ValIdated Systematic IntegratiON of epigenomic data (RRID:SCR_016921) Copy   

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https://panoramaweb.org/project/home/begin.view?

Repository software for targeted mass spectrometry assays from Skyline. Targeted proteomics knowledge base. Public repository for quantitative data sets processed in Skyline. Facilitates viewing, sharing, and disseminating results contained in Skyline documents.

Proper citation: PanoramaWeb (RRID:SCR_017136) Copy   

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