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http://www.jhu.edu/

Johns Hopkins University is private research university in Baltimore, Maryland. Founded in 1876, university was named for its first benefactor, American entrepreneur, abolitionist, and philanthropist Johns Hopkins.

Proper citation: Johns Hopkins University; Maryland; USA (RRID:SCR_010247) Copy   

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http://www.hopkins-abxguide.org/

Concise, clinically useful information for diagnosing, managing and treating infectious diseases in adults; however it does cover some pediatric topics including vaccines. It is designed for primary care providers and other non-infectious disease specialists as a tool that can be used at the point of care to assist in prescribing antibiotics.

Proper citation: ABX Guide (RRID:SCR_008214) Copy   

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https://www.ctsacentral.org/

National consortium of medical research institutions working together to transform the local, regional, and national environment to increase the efficiency and speed of clinical and translational research across the country. Consortium members share a common vision to reduce the time it takes for laboratory discoveries to become treatments for patients, to engage communities in clinical research efforts and to train clinical and translational researchers. This consortium includes 60 medical research institutions located throughout the nation, linking them together to energize the discipline of clinical and translational science. The CTSA consortium has five Strategic Goals: * National Clinical and Translational Research Capability * The Training and Career Development of Clinical and Translational Scientists * Consortium-Wide Collaborations * The Health of our Communities and the Nation * T1 Translational Research

Proper citation: Clinical and Translational Science Awards Consortium (RRID:SCR_008339) Copy   

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http://www.adgenetics.org/

Consortium to conduct genome-wide association studies (GWAS) to identify genes associated with an increased risk of developing late-onset Alzheimer''''s disease (LOAD). The goal of the ADGC is to identify genetic variants associated with risk for AD. It plans to do this through the following collaborative goals: # Identify genes responsible for AD susceptibility # Identify AD sub-phenotype genes rate-of-progression plaque / tangle load / distribution biomarker variability # Generate a genetic data resource for the AD research community Data generated by ADGC is available at the following website: https://www.niagads.org/content/alzheimers-disease-genetics-consortium-adgc-collection

Proper citation: Alzheimers Disease Genetics Consortium (RRID:SCR_004004) Copy   

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http://eaglep.case.edu/iamdgc_web/

Consortium aiming to identify the remaining genetic risk variants for Age-related Macular Degeneration (AMD). To increase the statistical power needed to identify genes that have small, yet significant contributions to AMD, the consortium is conducting a meta-analysis on 15 Genome Wide Association Studies (GWAS) pooled from consortium members representing over 8,000 patients with advanced AMD (dry type, neovascular, or both) and 50,000 controls. In addition to verifying known genes, the consortium identified 19 new gene variants. The genes identified in these studies function in the immune system, cholesterol transport and metabolism, and formation and maintenance of connective tissue. This study provides a nearly complete picture of genetic heritability for AMD.

Proper citation: International AMD Genetics Consortium (RRID:SCR_004009) Copy   

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http://www.bioconductor.org/packages/release/bioc/html/CoGAPS.html

Software that infers biological processes which are active in individual gene sets from corresponding microarray measurements. It achieves this inference by combining a MCMC matrix decomposition algorithm (GAPS) with a novel statistic inferring activity on gene sets.

Proper citation: CoGAPS (RRID:SCR_001479) Copy   

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http://ccb.jhu.edu/software/ASprofile/

A suite of programs for extracting, quantifying and comparing alternative splicing (AS) events from RNA-seq data.

Proper citation: ASprofile (RRID:SCR_001833) Copy   

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http://sourceforge.net/projects/blox/

A quantitative medical imaging and visualization program for use on brain MR, DTI, and MRS data. Programming Language: Java, JavaScript, Scheme

Proper citation: Blox (RRID:SCR_006667) Copy   

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https://jhuccs1.us/gpcrc/

Perform clinical, epidemiological, and therapeutic research in gastroparesis and provide an infrastructure that can rapidly and efficiently design and conduct clinical trials for effective medical, surgical, or other interventions to improve treatment of patients with gastroparesis. The GpCRC studies comprise well characterized individuals with diabetic, surgical, and idiopathic gastroparesis.

Proper citation: Gastroparesis Clinical Research Consortium (RRID:SCR_006673) Copy   

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https://mcp.bs.jhmi.edu/

Provides leadership in biomedical research on animal and human diseases and assists with the health and humane care of research animals within the institution.

Proper citation: Johns Hopkins School of Medicine Department of Molecular and Comparative Pathobiology (RRID:SCR_008297) Copy   

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http://ccb.jhu.edu/software/FLASH/

Open source software tool to merge paired-end reads from next-generation sequencing experiments. Designed to merge pairs of reads when original DNA fragments are shorter than twice length of reads. Can improve genome assemblies and transcriptome assembly by merging RNA-seq data.

Proper citation: FLASH (RRID:SCR_005531) Copy   

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http://ccb.jhu.edu/software/glimmer/index.shtml

A software system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.

Proper citation: Glimmer (RRID:SCR_011931) Copy   

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http://www.scienceexchange.com/facilities/johns-hopkins-university

An Portal, Core facility

Proper citation: Johns Hopkins University Labs and Facilities (RRID:SCR_012375) Copy   

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http://direct2experts.org

An on-going project and collaboration tool where biomedical researchers can access to expertise and related resources across institutions, regardless of local platforms and tools. Users can work with participating institutions in order to connect to their existing research networking tools. Biomedical institutions that wish to participate must have a mature, deployed research networking tool and can commit resources to assessments.

Proper citation: DIRECT2experts (RRID:SCR_013958) Copy   

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http://neurodata.io/

Project portal dedicated to understand animal and machine intelligence and repository of data and tools. Suite of tools to analyze and graph imaging data. Image and data repository for large, publicly available neuro-specific data files and images. Contains tools for analytics, databases, cloud computing, and Web-services applied to both big neuroimages and big neurographs.

Proper citation: neurodata (RRID:SCR_014264) Copy   

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https://diabetescenters.org/centers

Diabetes Research Centers (DRC) is an integrated program of diabetes, endocrinology and metabolism research.

Proper citation: Diabetes Research Centers (RRID:SCR_014535) Copy   

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http://www.nitrc.org/projects/dots/

A fast, scalable tool developed at the Johns Hopkins University to automatically segment the major anatomical fiber tracts within the human brain from clinical quality diffusion tensor MR imaging. With an atlas-based Markov Random Field representation, DOTS directly estimates the tract probabilities, bypassing tractography and associated issues. Overlapping and crossing fibers are modeled and DOTS can also handle white matter lesions. DOTS is released as a plug-in for the MIPAV software package and as a module for the JIST pipeline environment. They are therefore cross-platform and compatible with a wide variety of file formats.

Proper citation: DOTS WM tract segmentation (RRID:SCR_009459) Copy   

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http://www.jhu.edu/lschramm/spinalindex.htm

Serial histological sections of rat spinal cord at the lumbar and thoracic levels. Serial sections of rat spinal cord cut in the horizontal and sagittal planes. Also transverse and sagittal section series of the postnatal thoracic spinal cord immunolabeled for SMI-32.

Proper citation: Schramm Lab Spinal Cord Atlases (RRID:SCR_003265) Copy   

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http://www.hprd.org

Database that represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. All the information in HPRD has been manually extracted from the literature by expert biologists who read, interpret and analyze the published data.

Proper citation: HPRD - Human Protein Reference Database (RRID:SCR_007027) Copy   

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http://www.roselab.jhu.edu/coil/

The Protein Coil Library is a library of protein structure fragments derived from the Protein Data Bank (PDB). The fragments in this library are those fragments in the PDB that cannot be classified as either alpha-helix or beta-strand. Three-dimensional structures as well as side-chain and backbone torsion angles are stored in the database. The Protein Coil Library allows rapid and comprehensive access to non-alpha-helix and non-beta-strand fragments contained in the Protein Data Bank (PDB). The library contains both sequence and structure information together with calculated torsion angles for both the backbone and side chains. Several search options are implemented, including a query function that uses output from popular PDB-culling servers directly. Additionally, several popular searches are stored and updated for immediate access. The library is a useful tool for exploring conformational propensities, turn motifs, and a recent model of the unfolded state. The library stores the complete torsion angle descriptions for the fragments as well as the three dimensional structures of the fragments themselves. The goal of extracting and pre-calculating this data is to allow for more straightforward investigation of peptide structure without the background of secondary structure elements. In addition to searching by PDB ID, it is possible to download a particular size class, perform a batch search of PDB/chain ID''s, or download precompiled lists of PDB ID''s of interest (PDB Select, etc.). For users interested in browsing the entire database at once or maintaining their own locally-updated copy of the library, FTP access instructions are also provided. The files stored in the coil library FTP site or returned after a batch search are organized heirarchically by PDB ID. This is done to reduce filesystem access times and fascilitate searches using the UNIX find utility. At the lowest directory level in the heirarchy, files are further sorted by fragment length. As a result, the number of files in a particular directory is generally less then 50, yielding relatively fast access on UNIX/Linux filesystems. The heirarchical organization is based on the middle two letters of the PDB ID. For example, hen egg lysozyme, which has a PDB ID of 1HEL, will be located in the directory h/he/. At the final level, fragments of varying sizes are stored in directories that correspond to their fragment length. Again, using lysozyme as an example, any seven-residue fragments, if they exist, will reside in the directory h/he/7/. Similarly, seven-residue fragments from 2HEX and 1HE0 will also be in this location. Sponsors: The Protein Coil Library is funded by Johns Hopkins University.

Proper citation: The Protein Coil Library (RRID:SCR_008233) Copy   

•   Source: SciCrunch Registry