A5057780150- Research Data Management Practices
- Scientific Computing and Data Management
- Biomedical Text Mining and Ontologies
- Semantic Web and Ontologies
- Bioinformatics and Genomic Networks
- Gene Regulatory Network Analysis
- Microbial Metabolic Engineering and Bioproduction
- Data Quality and Management
- Genetics, Bioinformatics, and Biomedical Research
- Distributed and Parallel Computing Systems
- Simulation Techniques and Applications
- Geological Modeling and Analysis
- Image Processing and 3D Reconstruction
- Library Science and Information Systems
- Data Management and Algorithms
- Genomics and Phylogenetic Studies
- Cancer Genomics and Diagnostics
- Data Stream Mining Techniques
- Gene expression and cancer classification
- Data Mining Algorithms and Applications
- Advanced Data Storage Technologies
- COVID-19 diagnosis using AI
- Business Process Modeling and Analysis
- Computational Drug Discovery Methods
- Genomics and Rare Diseases
University of Manchester
2017-2025
Bluebird Bio (France)
2023
Wellcome Trust
2010-2023
European Bioinformatics Institute
2013-2023
Ontario Institute for Cancer Research
2022
Milliman (United States)
2022
Manado State University
2022
University of Southampton
1997-2019
Health Information Management
2019
SIB Swiss Institute of Bioinformatics
2015
Abstract Motivation: Molecular biotechnology now makes it possible to build elaborate systems models, but the biology community needs information standards if models are be shared, evaluated and developed cooperatively. Results: We summarize Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is software-independent language describing common research in many areas of computational biology, including cell...
BioModels (http://www.ebi.ac.uk/biomodels/) is a repository of mathematical models biological processes. A large set curated to verify both correspondence the process that model seeks represent, and reproducibility simulation results as described in corresponding peer-reviewed publication. Many submitted database are annotated, cross-referencing its components external resources such records, terms from controlled vocabularies ontologies. comprises two main branches: one composed derived...
The FAIR principles have been widely cited, endorsed and adopted by a broad range of stakeholders since their publication in 2016. By intention, the 15 guiding do not dictate specific technological implementations, but provide guidance for improving Findability, Accessibility, Interoperability Reusability digital resources. This has likely contributed to adoption principles, because individual stakeholder communities can implement own solutions. However, it also resulted inconsistent...
Abstract The notion that data should be Findable, Accessible, Interoperable and Reusable, according to the FAIR Principles, has become a global norm for good stewardship prerequisite reproducibility. Nowadays, guides policy actions professional practices in public private sectors. Despite such endorsements, however, Principles are aspirational, remaining elusive at best, intimidating worst. To address lack of practical guidance, help with capability gaps, we developed Cookbook, an open,...
Recent trends within computational and data sciences show an increasing recognition adoption of workflows as tools for productivity reproducibility that also democratize access to platforms processing know-how. As digital objects be shared, discovered, reused, benefit from the FAIR principles, which stand Findable, Accessible, Interoperable, Reusable. The Workflows Community Initiative's Working Group (WCI-FW), a global open community researchers developers working with across disciplines...
The Minimum Information Required in the Annotation of Models Registry (http://www.ebi.ac.uk/miriam) provides unique, perennial and location-independent identifiers for data used biomedical domain. At its core is a shared catalogue collections, each which an individual namespace created, extensive metadata recorded. This allows generation Uniform Resource Identifiers (URIs) to uniquely identify any record collection. Moreover, various services are provided facilitate creation resolution...
Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora databases tools deployed, technically complex diverse implementations, across spectrum disciplines. The corpus documentation resources is fragmented Web, with much redundancy, has lacked common standard information. outcome scientists must often struggle find, understand, compare use best for...
In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such depends on the discipline science humble bricks mortar that make integration possible; identifiers a core component this infrastructure. Drawing our experience work by other groups, we outline 10 lessons have learned about identifier qualities best practices facilitate large-scale integration. Specifically, propose actions...
BioModels is a reference repository hosting mathematical models that describe the dynamic interactions of biological components at various scales. The resource provides access to over 1,200 described in literature and 140,000 automatically generated from pathway resources. Most model are cross‐linked with external resources facilitate interoperability. A large proportion manually curated ensure reproducibility simulation results. This tutorial presents BioModels' content, features,...
Abstract Most biomedical data repositories issue locally-unique accessions numbers, but do not provide globally unique, machine-resolvable, persistent identifiers for their datasets, as required by publishers wishing to implement citation in accordance with widely accepted principles. Local may however be prefixed a namespace identifier, providing global uniqueness. Such “compact identifiers” have been used informatics support resource identification local identifier assignment. We report...
The COVID-19 pandemic has highlighted the need for FAIR (Findable, Accessible, Interoperable, and Reusable) data more than any other scientific challenge to date. We developed a flexible, multi-level, domain-agnostic FAIRification framework, providing practical guidance improve FAIRness both existing future clinical molecular datasets. validated framework in collaboration with several major public-private partnership projects, demonstrating delivering improvements across all aspects of...
The main goals and challenges for the life science communities in Open Science framework are to increase reuse sustainability of data resources, software tools, workflows, especially large-scale data-driven research computational analyses. Here, we present key findings, procedures, effective measures recommendations generating establishing sustainable resources based on collaborative, cross-disciplinary work done within EOSC-Life (European Cloud Life Sciences) consortium. Bringing together...
The FAIR principles describe characteristics intended to support access and reuse of digital artifacts in the scientific research ecosystem. Persistent, globally unique identifiers, resolvable on Web, associated with a set additional descriptive metadata, are foundational data. Here we some basic exemplars for their design, use orchestration other system elements achieve FAIRness objects.
Computing accurate nucleic acid melting temperatures has become a crucial step for the efficiency and optimisation of numerous molecular biology techniques such as in situ hybridization, PCR, antigene targeting, microarrays. MELTING is free open source software which computes enthalpy, entropy temperature acids. 4.2 was able to handle several types hybridization DNA/DNA, RNA/RNA, DNA/RNA provided corrections due presence sodium. The program can use either an approximative approach or more...
Commentary28 December 2015Open Access The evolution of standards and data management practices in systems biology Natalie J Stanford Corresponding Author Manchester Institute Biotechnology, University Manchester, UK School Computer Science, Search for more papers by this author Katherine Wolstencroft Leiden Advanced University, Leiden, Netherlands Martin Golebiewski Heidelberg Theoretical Studies, Heidelberg, Germany Renate Kania Nick Juty European Molecular Biology Laboratory,...
The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of community standards and formats computational systems biology related fields. This report summarizes topics activities fourth edition annual COMBINE meeting, held Paris during September 16-20 2013, attended by a total 96 people. pioneered first day devoted modeling approaches biology, which attracted broad audience scientists thanks panel renowned speakers. During subsequent days,...
Summary: Cytochrome bd’ has been implicated in having an important role microaerobic nitrogen fixation the enteric bacterium Klebsiella pneumoniae , where it is expressed under all conditions that permit diazotrophy. In this paper sequence of genes encoding terminal oxidase ( cydAB ) and characterization a cyd mutant are reported. The deduced amino acid sequences support proposal His 19, 186 Met 393 provide three four axial ligands to Fe haems complex. nitrogen-fixing ability was severely...