Tag: workflows

GENCODE is a scientific project in genome research and part of the ENCODE (ENCyclopedia Of DNA Elements) scale-up project. The GENCODE consortium was initially formed as part of the pilot phase of the ENCODE project to identify and map all protein-co ...

The Open Data Commons for Traumatic Brain Injury (DC-TBI) was created by the TBI community to mitigate dark data in TBI research. The ODC-TBI also aims to increase transparency with individual-level data, enhance collaboration, facilitate advanced an ...

The EuroPhenome project provides access to raw and annotated mouse phenotyping data generated from primary pipelines such as EMPReSSlim and secondary procedures from specialist centres. Mutants of interest can be identified by searching the gene or t ...

Recent cancer pharmacogenomic studies profiled large panels of cell lines against hundreds of approved drugs and experimental chemical compounds. The overarching goal of these screens is to measure sensitivity of cell lines to chemical perturbations, ...

The Resource of Asian Primary Immunodeficiency Diseases (RAPID) is a repository of molecular alterations in primary immunodeficiency diseases (PID). It hosts information on sequence variations and expression at the mRNA and protein levels of all gene ...

The Chemotion-repository is a repository for chemistry research data. The repository was founded at the Karlsruhe Institute of Technology (KIT) in Germany as a project funded by the German Research Foundation. The repository is domain specific, offer ...

Open access database for rodent cognition data integration and sharing

The WorkflowHub is a registry of scientific workflows.

BioImage Informatics Index (BIII) is a bioimaging resource that describes software tools, training materials and imaging datasets with the aim of helping researchers find, identify and propagate image analysis tools or workflows. BIII aims to help bi ...

A community resource of quantitative mass spectrometry-based proteomics datasets. MassIVE.quant is an extension of the Mass Spectrometry Interactive Virtual Environment (MassIVE) to provide the opportunity for large-scale deposition of data from qua ...

The eQTL Catalogue aims to provide uniformly processed gene expression and splicing QTLs from all available public studies on human. Quantitative trait loci (QTL) are genomic variants that are significantly associated to a measurable phenotype. This ...

TarDB is a database for conserved miRNA targets, degradome supported miRNA targets and miRNA-triggered phasiRNAs in plants. TarDB is a plant miRNA target repository, which is based on cross-species conservation filter, degradome PARE-seq, and small R ...

Versatile databases for genomic sequencing and lab management. LabxDB comes with ready-to-use databases. Data is stored in PostgreSQL. LabxDB provides web-browser GUI and a programmatic API for intregration into pipelines. LabxDB for high-throughpu ...

PPNID: a manually curated reference database and identification tool for plant-parasitic nematode.

Online Crowd-Sourced HR-MS Database for Suspect and Non-targeted Screening of New Psychoactive Substances.

Advancing a comprehensive database of bacterial plasmids.

The webTWAS integrates large number of GWAS summary level data for disease, and this number will be constantly increasing according to our timely curation. The webTWAS calculates the causal genes using single tissue expression imputation (MetaXcan an ...

An End-to-End Deep Learning-Based Workflow for Biomedical Knowledge Graph Extraction, Optimization and Applications.

Human Antigen Receptor Consortium (huARdb) is a comprehensive database of single cell immune profiling and V(D)J T cell and B cell analysis, enhanced with advanced visualization of single-cell data.

The Use of LipidIMMS Analyzer for Lipid Identification in Ion Mobility-Mass Spectrometry-Based Untargeted Lipidomics. Questions: zhouzw AT sioc.ac.cn, jiangzhu AT sioc.ac.cn. © Zhu lab , Interdisciplinary Research Center on Biology and Chemistry (I ...

COVID-19 preVIEW is a tool for semantic search to explore COVID-19 research preprints.

A data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information. The main web resource to explore human mitochondrial variability data and their pathological correlation. HmtVar is a manually-curate ...

PSnpBind is a large database of protein–ligand complexes covering a wide range of binding pocket mutations and small molecules’ landscape. This database can be used as a source of data for different types of studies, for example, developing machine l ...

Fusarium graminearum Genome Database (FGDB) is a comprehensive genome database on one of the most devastating fungal plant pathogens of wheat and barley. FGDB provides information on two gene sets independently derived by automated annotation of the ...

Unique data of 323,899 blood tests pre- and post-implementation of a computerised order entry system with key clinical pathway time-points for all blood tests. Data on date/time of requests, laboratory processing times and reported results.

Database of standardized mouse morphology data for morphometric meta-analyses.

An automated approach to spectral unmixing of fluorescent biological images.

Computational tools and libraries for CRISPR/Cas9-derived RNA-guided engineered nucleases (RGENs).

Comprehensive drug discovery and genomic research workbench, knowledgebase and data management system.

BMSS2 is a unified database-driven modelling package for systematic model selection and identifiability analysis.

A generic integrated web-based workflow system to evaluate genotype-phenotype correlations in human mitochondrial diseases.

English-Chinese Cancer Parallel Corpus (ECParaCorp) is a database involving information of 6 cancers in three different themes: cancer prevention, cancer screening and cancer treatment.

The Biomedical Research Hub (BRH) is a cloud-based and multifunctional web interface that provides a secure environment for discovery and analysis of scientific results and data.

FinaleDB (FragmentatIoN AnaLysis of cEll-free DNA DataBase) is a comprehensive cell-free DNA (cfDNA) fragmentation pattern database to host uniformly processed and quality controlled paired-end cfDNA WGS datasets.

Rapid development of cloud-native intelligent data pipelines for scientific data streams using the HASTE Toolkit. Client for the HASTE Storage Engine. Smart middleware for working with a variety of storage media with Scientific Computing datasets. ...

AREAdata is a worldwide climate dataset averaged across spatial units at different scales through time. It is a PearseLab data resource where you can download daily estimates of climate/environmental data which have been averaged across different lev ...

An Online Platform for Automated NGS Data Analysis and Sharing. CSI NGS Portal is an online platform for fully automated NGS data analysis and sharing . CSI NGS Portal uses a single, randomly generated, persistent, secure and http-only browser cookie ...

DODO is a graph database to facilitate access and interaction with disease and phenotype ontologies. The aim of DODO is to allow an easier way to interact and explore disease ontologies and their identifiers. The database is build on Neo4j and incorp ...

A database for exploring N6-methyladenosine methylome. REPIC (RNA Epitranscriptome Collection) is a database dedicated to provide a new resource to investigate potential functions and mechanisms of N6-adenosine methylation (m6A) modifications. Curre ...

Simple containerised setup of a custom Ensembl database and web server for any species. Forked from molluscdb/molluscdb-plugin. Example configurations to set up custom Ensembl sites using GenomeHubs. GenomeHubs example configuration and demo scrip ...