tools

Discover optimal ontology annotations

ssuhr@ebi.ac.uk — Fri, 26 Feb 2016 16:49:14 +0000

Identifying suitable mouse disease models by integrating phenotypic and genotype data

ssuhr@ebi.ac.uk — Thu, 25 Feb 2016 16:26:19 +0000

Identify human candidate disease genes - GenoBridge

ssuhr@ebi.ac.uk — Mon, 15 Feb 2016 13:15:30 +0000

GenoBridge

The fundamental genetic similarity between mice and humans allows researchers to infer a human gene's function based on studies with laboratory mice. Identifying essential clues on gene function provided by model organisms has proved to be a powerful approach to gain knowledge on both human disease and mammalian biology.

Simple and versatile biobank sample information federation: MIABIS Connect

ssuhr@ebi.ac.uk — Fri, 18 Dec 2015 13:21:37 +0000

MIABIS Connect

Finding biosamples with specific characteristics across different biobanks is challenging because each biobank manages sample information differently. Together with the sensitive nature of large amounts of biosample information, this makes it difficult to pull information together for example in a central place where a researcher can browse and discover groups of samples that might be suitable for a given research project.

Determine the coordination geometry of metals in biological macromolecules

ssuhr@ebi.ac.uk — Wed, 25 Mar 2015 16:52:01 +0000

Metals are essential for the structure and function of many proteins and nucleic acids. The geometric arrangement of the atoms that coordinate a metal in a biological macromolecule is an important determinant of the specificity and role of that metal. FindGeo quickly finds and determines the coordination geometry of selected, or all, metals in a given structure.

Investigate functional relationships between metal-binding macromolecules

ssuhr@ebi.ac.uk — Wed, 25 Mar 2015 16:34:59 +0000

MetalS2 facilitates the investigation of the functional relationships between metal-dependent enzymes and metal-binding macromolecules in general.

Structural analysis of metal sites in biological macromolecules

ssuhr@ebi.ac.uk — Wed, 25 Mar 2015 15:57:44 +0000

MetalPDB supports the structural analysis of metal sites in biological macromolecules and reveals structurally similar or equivalent sites occurring in other macromolecules based on structural information contained in the Protein Data Bank (PDB).

Evaluating the effect of drugs by integrating clinical trials data and genomic information

ssuhr@ebi.ac.uk — Wed, 25 Mar 2015 14:01:45 +0000

The Clinical Trials Information Mediator supports researchers by providing insight into the effect of drugs on patients based on clinical trials data and genomic information.

Visualising ontologies and locating terms in a query interface

ssuhr@ebi.ac.uk — Wed, 25 Mar 2015 13:32:05 +0000

The PLATO ontology tree viewer is a plugin that supports visualization of terms in an ontology. Nodes can be expanded and collapsed as needed.

Manage cross-references between digital entities with different identifiers

ssuhr@ebi.ac.uk — Wed, 25 Mar 2015 09:37:55 +0000

myEquivalents is a system to manage cross-references between digital entities with different identifiers. It can help organisations maintaining data to manage their cross-references and aids finding multiple descriptions of the same biomedical entities.

Visualise health consequences of mutations in protein structures

ssuhr@ebi.ac.uk — Wed, 18 Mar 2015 10:38:53 +0000

PLan-Variants

This pilot web service bridges the disciplines of clinical genetics and structural biology by displaying the health consequences of mutations as annotations on a protein structure.

Unlocking data from mouse disease models: diabetes ontology

ssuhr@ebi.ac.uk — Wed, 11 Mar 2015 14:08:29 +0000

The BioMedBridges diabetes-specific ontology enables users to integrate mouse disease model and human data resources while taking into account the different temporal stages of human disease.

Supporting researchers sharing sensitive data: identifying requirements

ssuhr@ebi.ac.uk — Thu, 05 Mar 2015 14:04:07 +0000

Legal and Ethical Requirements Assessment Tool - LAT

Uncertainty about ethical and legal requirements with respect to sensitive data – such as personally identifiable data – is one of the most important barriers to data sharing. Aimed at researchers with limited or no background or experience with these formal requirements, this tool aims to clarify if and how sensitive data can be shared, or when additional actions or expert advice are needed.

Unlocking biomolecule volume data

ssuhr@ebi.ac.uk — Thu, 05 Feb 2015 15:46:30 +0000

Information on the structure of macromolecules is important for biology and medicine because the function of many important biological processes can be directly linked to macromolecular structure or changes therein. For example, structural information on how a drug is bound to a target may yield vital clues on how to optimize its structure to promote more efficient binding. The BioMedBridges shape-matching software - which will be incorporated into a web-based shape-matching service - will enable the wealth of low-resolution volume data in the EMDB and PDB resources to be searched based on their shape, providing entirely new perspectives on the relationships between structures.

Sharing protein engineering knowledge

ssuhr@ebi.ac.uk — Thu, 05 Feb 2015 10:25:40 +0000

PiMS

PiMS is a laboratory information management system for use in recombinant protein production laboratories; to manage the stages from the selected target protein to the production of soluble protein. PiMS development is part of a larger vision to provide a unified and extensible set of software tools for structural biology, offering seamless data transfer and a consistent user experience, from target selection to the interpretation of the structure.