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https://www.embrys.jp/embrys/html/About.html
Data collection of gene expression patterns mapped in whole-mount mouse embryo (ICR strain) of mid-gestational stages (Embryonic Day 9.5, 10.5, 11.5), in which most striking dynamics in pattern formation and organogenesis is observed. Collection of gene expression patterns of transcription factors (TFs) and TF-related factors such as transcription cofactors. Genes were extracted from databases including RIKEN Transcription Factor Database and Panther Classification System.
Proper citation: EMBRYS (RRID:SCR_006689) Copy
HTAN is National Cancer Institute funded Cancer Moonshot initiative to construct 3-dimensional atlases of dynamic cellular, morphological, and molecular features of human cancers as they evolve from precancerous lesions to advanced disease.Provides three dimensional atlases of cancer transitions for diverse set of tumor types. Efforts to map healthy organs and previous large-scale cancer genomics approaches focused on bulk sequencing at single point in time. Data portal for Human Tumor Atlas Network. Data available on HTAN Portal is open access. Certain data types with potential for re-identification are available in restricted access through dbGAP.
Proper citation: Human Tumor Atlas Network (RRID:SCR_023364) Copy
Integrated healthcare biobank that operates under certified conditions and strict SOPs. Enables biomedical and translational researchers to perform their analyses using high quality biospecimens and data to generate reliable and reproducible research data. Core offers modular biobanking portfolio that can cover workflow from blood collection to storage, including all pre-analytical steps and their documentation. Offers spectrum of additional services ranging from DNA/RNA extraction and virtual microscopy to entire management of sample and data flow for national and international research consortia. Provides secure conventional and automated storage of samples at various temperatures as well as secure data management.
Proper citation: Charite University and Berlin Institute for Health Research Central Biobank Core Facility (RRID:SCR_023495) Copy
https://github.com/linnarsson-lab/loom-viewer
Software tool for sharing, browsing and visualizing single-cell data stored in the Loom file format.
Proper citation: loom-viewer (RRID:SCR_016683) Copy
Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron.
Proper citation: MRIcron (RRID:SCR_002403) Copy
Ensembl SARS-Cov2 data portal.
Proper citation: Ensembl Covid-19 (RRID:SCR_024704) Copy
https://cab.spbu.ru/software/spades/
Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: SPAdes (RRID:SCR_000131) Copy
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
This page contains the Influenza Surveillance Report during 2008-2009 Influenza Season Week 15, ending April 18, 2009.
Proper citation: FluView: A Weekly Influenza Surveillance Report (RRID:SCR_001118) Copy
Project aimed at making neuroimaging data sets of brain freely available to scientific community. By compiling and freely distributing neuroimaging data sets, future discoveries in basic and clinical neuroscience are facilitated.
Proper citation: Open Access Series of Imaging Studies (RRID:SCR_007385) Copy
http://mousespinal.brain-map.org/about.html
Platform for exploring spinal cord at cellular and molecular levels. Map of gene expression for adult and juvenile mouse spinal cord. Provides map of normal mouse when used to compare gene expression in diseased or injury models. Interactive database of gene expression mapped across all anatomic segments of mouse spinal cord at postnatal days 4 and 56. Indexed set of images based on RNA in situ hybridization data, searchable and sortable by gene, age, expression, cervical, thoracic, lumbar, sacral, and coccygeal segments.
Proper citation: Allen Mouse Spinal Cord Atlas (RRID:SCR_007418) Copy
Collection of transmembrane protein datasets containing experimentally derived topology information from the literature and from public databases. Web interface of TOPDB includes tools for searching, relational querying and data browsing, visualisation tools for topology data.
Proper citation: Topology Data Bank of Transmembrane Proteins (RRID:SCR_007964) Copy
https://epilepsy.uni-freiburg.de/freiburg-seizure-prediction-project
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 29,2025. Electroencephalogram (EEG) data recorded from invasive and scalp electrodes. The EEG database contains invasive EEG recordings of 21 patients suffering from medically intractable focal epilepsy. The data were recorded during an invasive pre-surgical epilepsy monitoring at the Epilepsy Center of the University Hospital of Freiburg, Germany. In eleven patients, the epileptic focus was located in neocortical brain structures, in eight patients in the hippocampus, and in two patients in both. In order to obtain a high signal-to-noise ratio, fewer artifacts, and to record directly from focal areas, intracranial grid-, strip-, and depth-electrodes were utilized. The EEG data were acquired using a Neurofile NT digital video EEG system with 128 channels, 256 Hz sampling rate, and a 16 bit analogue-to-digital converter. Notch or band pass filters have not been applied. For each of the patients, there are datasets called ictal and interictal, the former containing files with epileptic seizures and at least 50 min pre-ictal data. the latter containing approximately 24 hours of EEG-recordings without seizure activity. At least 24 h of continuous interictal recordings are available for 13 patients. For the remaining patients interictal invasive EEG data consisting of less than 24 h were joined together, to end up with at least 24 h per patient. An interdisciplinary project between: * Epilepsy Center, University Hospital Freiburg * Bernstein Center for Computational Neuroscience (BCCN), Freiburg * Freiburg Center for Data Analysis and Modeling (FDM).
Proper citation: Electroencephalogram Database: Prediction of Epileptic Seizures (RRID:SCR_008032) Copy
http://locustdb.genomics.org.cn/
The migratory locust (Locusta migratoria) is an orthopteran pest and a representative member of hemimetabolous insects. Its transcriptomic data provide invaluable information for molecular entomology study of the insect and pave a way for comparative studies of other medically, agronomically, and ecologically relevant insects. This first transcriptomic database of the locust (LocustDB) has been developed, building necessary infrastructures to integrate, organize, and retrieve data that are either currently available or to be acquired in the future. It currently hosts 45,474 high quality EST sequences from the locust, which were assembled into 12,161 unigenes. This database contains original sequence data, including homologous/orthologous sequences, functional annotations, pathway analysis, and codon usage, based on conserved orthologous groups (COG), gene ontology (GO), protein domain (InterPro), and functional pathways (KEGG). It also provides information from comparative analysis based on data from the migratory locust and five other invertebrate species, such as the silkworm, the honeybee, the fruitfly, the mosquito and the nematode. LocustDB also provides information from comparative analysis based on data from the migratory locust and five other invertebrate species, such as the silkworm, the honeybee, the fruitfly, the mosquito and the nematode. It starts with the first transcriptome information for an orthopteran and hemimetabolous insect and will be extended to provide a framework for incorporation of in-coming genomic data of relevant insect groups and a workbench for cross-species comparative studies.
Proper citation: Migratory Locust EST Database (RRID:SCR_008201) Copy
Open source object relational database system that uses and extends SQL language combined with many features that safely store and scale the most complicated data workloads. PostgreSQL runs on all major operating systems.
Proper citation: PostgreSQL (RRID:SCR_021067) Copy
Abstract and indexing database with full text links that is produced by Elsevier Co. Combines expertly curated abstract and citation database with enriched data and linked scholarly literature across wide variety of disciplines.
Proper citation: Scopus (RRID:SCR_022559) Copy
https://github.com/clinwiki-org/clinwiki
Clinical trials database.
Proper citation: ClinWiki (RRID:SCR_021297) Copy
Network of healthcare organizations, together with data partners in Brazil, South Korea, and Japan, to bring clinical facts on more than 250 million patients around the world. Federated model so users of this data are ensured new patients, observations, and results every day, all harmonized to standard terminology like ICD-10 and LOINC without any data wrangling required at the point of care. The raw data is not available to authors of papers and papers in medicine are being retracted.
Proper citation: trinetx (RRID:SCR_022760) Copy
http://www.clcbio.com/products/clc-main-workbench/
A suite of software for DNA, RNA and protein sequence data analysis. The software allows for the analysis and visualization of Sanger sequencing data as well as gene expression analysis, molecular cloning, primer design, phylogenetic analyses, and sequence data management.
Proper citation: CLC Main Workbench (RRID:SCR_000354) Copy
http://www.cs.cmu.edu/~schneide/tut5/node42.html
A model evaluation method for training someone to read data. There are three methods: the holdout method, K-fold cross validation, and leave-one-out cross validation.
Proper citation: Cross Validation (RRID:SCR_000702) Copy
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