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1.  SpeckTackle: JavaScript charts for spectroscopy 
Background
Spectra visualisation from methods such as mass spectroscopy, infrared spectroscopy or nuclear magnetic resonance is an essential part of every web-facing spectral resource. The development of an intuitive and versatile visualisation tool is a time- and resource-intensive task, however, most databases use their own embedded viewers and new databases continue to develop their own viewers.
Results
We present SpeckTackle, a custom-tailored JavaScript charting library for spectroscopy in life sciences. SpeckTackle is cross-browser compatible and easy to integrate into existing resources, as we demonstrate for the MetaboLights database. Its default chart types cover common visualisation tasks following the de facto ‘look and feel’ standards for spectra visualisation.
Conclusions
SpeckTackle is released under GNU LGPL to encourage uptake and reuse within the community. The latest version of the library including examples and documentation on how to use and extend the library with additional chart types is available online in its public repository.
Electronic supplementary material
The online version of this article (doi:10.1186/s13321-015-0065-7) contains supplementary material, which is available to authorized users.
doi:10.1186/s13321-015-0065-7
PMCID: PMC4432097  PMID: 25984241
JavaScript; Charting library; Spectroscopy
2.  SpeckTackle: JavaScript charts for spectroscopy 
Background
Spectra visualisation from methods such as mass spectroscopy, infrared spectroscopy or nuclear magnetic resonance is an essential part of every web-facing spectral resource. The development of an intuitive and versatile visualisation tool is a time- and resource-intensive task, however, most databases use their own embedded viewers and new databases continue to develop their own viewers.
Results
We present SpeckTackle, a custom-tailored JavaScript charting library for spectroscopy in life sciences. SpeckTackle is cross-browser compatible and easy to integrate into existing resources, as we demonstrate for the MetaboLights database. Its default chart types cover common visualisation tasks following the de facto ‘look and feel’ standards for spectra visualisation.
Conclusions
SpeckTackle is released under GNU LGPL to encourage uptake and reuse within the community. The latest version of the library including examples and documentation on how to use and extend the library with additional chart types is available online in its public repository.
Electronic supplementary material
The online version of this article (doi:10.1186/s13321-015-0065-7) contains supplementary material, which is available to authorized users.
doi:10.1186/s13321-015-0065-7
PMCID: PMC4432097  PMID: 25984241
JavaScript; Charting library; Spectroscopy
3.  The MetaboLights repository: curation challenges in metabolomics 
MetaboLights is the first general-purpose open-access curated repository for metabolomic studies, their raw experimental data and associated metadata, maintained by one of the major open-access data providers in molecular biology. Increases in the number of depositions, number of samples per study and the file size of data submitted to MetaboLights present a challenge for the objective of ensuring high-quality and standardized data in the context of diverse metabolomic workflows and data representations. Here, we describe the MetaboLights curation pipeline, its challenges and its practical application in quality control of complex data depositions.
Database URL: http://www.ebi.ac.uk/metabolights
doi:10.1093/database/bat029
PMCID: PMC3638156  PMID: 23630246
5.  MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data 
Nucleic Acids Research  2012;41(Database issue):D781-D786.
MetaboLights (http://www.ebi.ac.uk/metabolights) is the first general-purpose, open-access repository for metabolomics studies, their raw experimental data and associated metadata, maintained by one of the major open-access data providers in molecular biology. Metabolomic profiling is an important tool for research into biological functioning and into the systemic perturbations caused by diseases, diet and the environment. The effectiveness of such methods depends on the availability of public open data across a broad range of experimental methods and conditions. The MetaboLights repository, powered by the open source ISA framework, is cross-species and cross-technique. It will cover metabolite structures and their reference spectra as well as their biological roles, locations, concentrations and raw data from metabolic experiments. Studies automatically receive a stable unique accession number that can be used as a publication reference (e.g. MTBLS1). At present, the repository includes 15 submitted studies, encompassing 93 protocols for 714 assays, and span over 8 different species including human, Caenorhabditis elegans, Mus musculus and Arabidopsis thaliana. Eight hundred twenty-seven of the metabolites identified in these studies have been mapped to ChEBI. These studies cover a variety of techniques, including NMR spectroscopy and mass spectrometry.
doi:10.1093/nar/gks1004
PMCID: PMC3531110  PMID: 23109552
6.  MetaboLights: towards a new COSMOS of metabolomics data management 
Metabolomics  2012;8(5):757-760.
Exciting funding initiatives are emerging in Europe and the US for metabolomics data production, storage, dissemination and analysis. This is based on a rich ecosystem of resources around the world, which has been build during the past ten years, including but not limited to resources such as MassBank in Japan and the Human Metabolome Database in Canada. Now, the European Bioinformatics Institute has launched MetaboLights, a database for metabolomics experiments and the associated metadata (http://www.ebi.ac.uk/metabolights). It is the first comprehensive, cross-species, cross-platform metabolomics database maintained by one of the major open access data providers in molecular biology. In October, the European COSMOS consortium will start its work on Metabolomics data standardization, publication and dissemination workflows. The NIH in the US is establishing 6–8 metabolomics services cores as well as a national metabolomics repository. This communication reports about MetaboLights as a new resource for Metabolomics research, summarises the related developments and outlines how they may consolidate the knowledge management in this third large omics field next to proteomics and genomics.
doi:10.1007/s11306-012-0462-0
PMCID: PMC3465651  PMID: 23060735
Metabolomics; Databases; ISA-Tab; ISA commons

Results 1-6 (6)