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Tissue bank that specifically provides human tissue and cell samples for research purposes. It offers PBMCs, whole blood, solid tumor tissues, circulating tumor cells, and a variety of other bio-specimens.
Proper citation: Conversant Biologics Inc. (RRID:SCR_010675) Copy
A software platform which enables users to conduct genetic engineering with genomic manipulation tools (provided in the platform). Genome Compiler includes multiple DNA synthesis providers, lab facility services, and advanced bioinformatics tools and genetic repositories. Data can be imported from VectorNTI, SnapGene, ApE, Clone Manager, and others. The Gibson Assembly and Restriction Ligation methods are supported by Genome Compiler.
Proper citation: GenomeCompiler (RRID:SCR_013988) Copy
Interactive database of software tools for analysis of long read sequencing data.Catalogue of long-read sequencing data analysis tools. Catalogue of downstream analysis tools of real and synthetic long-read technologies.
Proper citation: long-read-tools (RRID:SCR_019116) Copy
http://arch.library.northwestern.edu/
Arch is an open access repository for the research and scholarly output of Northwestern University. Log in with your NetID to deposit, describe, and organize your research for public access and long-term preservation. We'll use our expertise to help you curate, share, and preserve your work.
Proper citation: Arch (RRID:SCR_023130) Copy
Software application to organize and store in structured format signaling information published in scientific literature. Information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. Each relationship is linked to literature reporting experimental evidence. Each node is annotated with chemical inhibitors that modulate its activity. Signaling information is mapped to human proteome. SIGNOR 2.0 stores manually annotated causal relationships between proteins and other biologically relevant entities including chemicals, phenotypes, complexes, etc with compliance to FAIR data principles.
Proper citation: SIGNOR (RRID:SCR_018485) Copy
https://www.rarediseasesnetwork.org/cms/create/researchers/biorepository
Biorepository of samples collected from patients with ALS, ALS-frontotemporal dementia (ALS-FTD), primary lateral sclerosis (PLS), progressive muscular atrophy (PMA), hereditary spastic paraplegia (HSP) and multisystem proteinopathy (MSP). Used by Consortium members and the scientific community to advance therapeutic development through study of the relationship between clinical phenotype and underlying genotype, and also through the discovery and development of biomarkers.
Proper citation: CReATE (RRID:SCR_016436) Copy
A National NIH Center for Biomedical Computing that focuses on physics-based simulation of biological structures and provides open access to high quality simulation tools, accurate models and the people behind them. It serves as a repository for models that are published (as well as the associated code) to create a living archive of simulation scholarship. Simtk.org is organized into projects. A project represents a research endeavor, a software package or a collection of documents and publications. Includes sharing of image files, media, references to publications and manuscripts, as well as executables and applications for download and source code. Simulation tools are free to download and space is available for developers to manage, share and disseminate code.
Proper citation: Simtk.org (RRID:SCR_002680) Copy
https://school.wakehealth.edu/departments/pathology/comparative-medicine/vervet-research-colony
NIH funded national research resource to provide biomedical research community with access to US born, known age, pedigreed, genomically sequenced, pathogen free Caribbean origin vervet monkeys also known as African green monkeys. Provides access to animals, extensive multisystem clinical phenotyping, sample and data repositories, expertise in use of nonhuman primate models for translational studies, serves as platform for training veterinarians and other professionals in biomedical research, husbandry, clinical care, and the colony behavioral management.
Proper citation: Wake Forest Vervet Research Colony (RRID:SCR_006678) Copy
Bioinformatics platform for storing, organizing, processing, and sharing genomic and other biomedical big data. Designed to make it easier for bioinformaticians to develop analyses, developers to create genomic web applications and IT administers to manage large-scale compute and storage genomic resources. Designed to run on top of cloud operating systems such as Amazon Web Services and OpenStack. Currently, there are implementations that work on AWS and Xen+Debian/Ubuntu. Functionally, Arvados has two major sets of capabilities: (a) data management and (b) compute management.
Proper citation: Arvados (RRID:SCR_002223) Copy
http://ireceptor.irmacs.sfu.ca/
Data discovery platform that facilitates curation, analysis and sharing of antibody/B-cell and T-cell receptor repertoires from multiple labs and institutions. Used to increase value of data through sharing with community. Platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories.
Proper citation: iReceptor (RRID:SCR_022294) Copy
https://www.ngdc.noaa.gov/mgg/curator/
A repository of geologic material from sea floor and lakebed cores, grabs, and dredges archived by participating institutions.
Proper citation: Index to Marine and Lacustrine Geologic Samples (RRID:SCR_009430) Copy
http://fcon_1000.projects.nitrc.org/indi/enhanced/
Dataset of 1000 characterized community-ascertained participants using state-of-the-art multiband imaging-based resting state fMRI (R-fMRI) and diffusion tensor imaging (DTI), genetics, and a deep phenotyping protocol from a large cross-sectional sample of brain development, maturation and aging (ages 6 - 85 yrs). The Center for Magnetic Resonance Research (CMRR), University of Minnesota, provided the NKI-RS effort with the latest version of the Multiband EPI sequence (Xu et al. 2012) and associated image reconstruction algorithms, enabling the acquisition of state-of-the-art imaging datasets for this large-scale imaging effort. The enhanced NKI-RS expands upon the phenotypic protocol of the original NKI-RS and captures a broad range of behavioral and cognitive phenomenology relevant to psychiatric health and illness. The validity and value of assessments were evaluated by consulting leaders in the field of psychiatric phenotyping.
Proper citation: NKI-RS Enhanced Sample (RRID:SCR_010461) Copy
Network evaluating consensus-based common data elements (CDE) for traumatic brain injury (TBI) and psychological health (TBI-CDE, www.commondataelements.ninds.nih.gov/TBI.aspx) while extensively phenotyping a cohort of TBI patients across the injury spectrum from concussion to coma. Institutions that participate in the TBI Network will be able to track the outcomes of patients through a 3, 6 and 12-month followup program and compare outcomes with other participating institutions. For the three acute care centers, patients were enrolled that presented to the emergency department within 24 hours of head injury and required computed tomography (CT). For the rehabilitation center, referrals from acute hospitals were enrolled. Patients were consented to participate in components: clinical profile; blood draws for measurement of proteomic and genomic markers; 3T MRI within 2 weeks; three-month Glasgow Outcome Scale-Extended (GOS-E); and six-month TBI-CDE Core outcome assessments. A web-enabled database, imaging repository, and biospecimen bank was developed using the TBI-CDE recommendations. A total of 605 patients were enrolled. Of these subjects, 88% had a GCS 13-15, 5% had a GCS 9-12, and 7% had a GCS of 8 or less. Three-month GOS-E''s were obtained for 78% of the patients. Comprehensive 6-month outcome measures, including PTSD assessment, are ongoing until September 2011. Blood specimens were collected from 450 patients. Initial CTs for 605 patients and 235 patients with 3T MRI studies were transferred to an imaging repository. The TRACK TBI Network will provide qualified institutions access to a web-based version of key forms in tracking TBI outcomes for Quality Improvement and institutional benchmarking.
Proper citation: TRACK TBI Network (RRID:SCR_004723) Copy
https://github.com/openMetadataInitiative/openMINDS_specimenPrep
Software repository is part of the open Metadata Initiative for Neuroscience Data Structures (openMINDS). It extends openMINDS, by providing metadata schemas for in-depth descriptions of specimen preparations (surgery, tissue slicing, etc.).
Proper citation: openMINDS specimenPrep metadata model (RRID:SCR_026252) Copy
https://petab.readthedocs.io/en/latest/
Repository contains PEtab specifications and additional documentation. Data format for specifying parameter estimation problems in systems biology. SBML and TSV based data format for parameter estimation problems in systems biology. Human- and computer- readable format for representing parameter estimation problems in systems biology.
Proper citation: PEtab (RRID:SCR_026915) Copy
DataLad data distribution. Super dataset collating DataLad datasets from various sources including OpenNeuro, CRCNS, etc., to provide unified access to over 200TB of neural data.
Proper citation: datasets.datalad.org (RRID:SCR_019089) Copy
A microarray data warehouse integrated with a software platform for microarray data analysis. It can be used as a LIMS for DNA chip experiments, also. Unlike other microarray data repositories, it entirely dispenses with free-text format, instead holding all the information in a format ready for statistical analysis.
Proper citation: M-CHiPS (RRID:SCR_010944) Copy
http://metpetdb.rpi.edu/metpetweb/
Database / data repository for metamorphic petrology that is being designed and built by a global community of metamorphic petrologists in collaboration with computer scientists at Rensselaer Polytechnic Institute as part of the National Cyberinfrastructure Initiative.
Proper citation: MetPetDB (RRID:SCR_002208) Copy
http://web.bioinformatics.ic.ac.uk/eqtlexplorer/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. An eQTL visualization tool that allows users to mine and understand data from a repository of genetical genomics experiments (entry from Genetic Analysis Software)
Proper citation: EQTL EXPLORER (RRID:SCR_001123) Copy
https://github.com/sridevi96/NeuroDevTime
Software code for age prediction in fetal brain and organoid single cell data. This repository contains cell type agnostic models to predict the developmental age of brain cell types from single cell RNAseq data. Code contains 4 jupyter notebooks, which apply pretrained models to predict neurodevelopmental age of cell types in new human fetal brain and organoid datasets.
Proper citation: NeuroDevTime (RRID:SCR_026651) Copy
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