BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

Background: Quantitative models of biochemical and cellular systems are used to answer a variety of questions in the biological sciences. The number of published quantitative models is growing steadily thanks to increasing interest in the use of models as well as the development of improved software systems and the availability of better, cheaper computer hardware. To maximise the benefits of this growing body of models, the field needs centralised model repositories that will encourage, facilitate and promote model dissemination and reuse. Ideally, the models stored in these repositories should be extensively tested and encoded in community-supported and standardised formats. In addition, the models and their components should be cross-referenced with other resources in order to allow their unambiguous identification. Description: BioModels Database http://www.ebi.ac.uk/biomodels/ is aimed at addressing exactly these needs. It is a freely-accessible online resource for storing, viewing, retrieving, and analysing published, peer-reviewed quantitative models of biochemical and cellular systems. The structure and behaviour of each simulation model distributed by BioModels Database are thoroughly checked; in addition, model elements are annotated with terms from controlled vocabularies as well as linked to relevant data resources. Models can be examined online or downloaded in various formats. Reaction network diagrams generated from the models are also available in several formats. BioModels Database also provides features such as online simulation and the extraction of components from large scale models into smaller submodels. Finally, the system provides a range of web services that external software systems can use to access up-to-date data from the database. Conclusions: BioModels Database has become a recognised reference resource for systems biology. It is being used by the community in a variety of ways; for example, it is used to benchmark different simulation systems, and to study the clustering of models based upon their annotations. Model deposition to the database today is advised by several publishers of scientific journals. The models in BioModels Database are freely distributed and reusable; the underlying software infrastructure is also available from SourceForge https://sourceforge.net/projects/biomodels/ under the GNU General Public License

Expansion of the BioCyc collection of pathway/genome databases to 160 genomes

The BioCyc database collection is a set of 160 pathway/genome databases (PGDBs) for most eukaryotic and prokaryotic species whose genomes have been completely sequenced to date. Each PGDB in the BioCyc collection describes the genome and predicted metabolic network of a single organism, inferred from the MetaCyc database, which is a reference source on metabolic pathways from multiple organisms. In addition, each bacterial PGDB includes predicted operons for the corresponding species. The BioCyc collection provides a unique resource for computational systems biology, namely global and comparative analyses of genomes and metabolic networks, and a supplement to the BioCyc resource of curated PGDBs. The Omics viewer available through the BioCyc website allows scientists to visualize combinations of gene expression, proteomics and metabolomics data on the metabolic maps of these organisms. This paper discusses the computational methodology by which the BioCyc collection has been expanded, and presents an aggregate analysis of the collection that includes the range of number of pathways present in these organisms, and the most frequently observed pathways. We seek scientists to adopt and curate individual PGDBs within the BioCyc collection. Only by harnessing the expertise of many scientists we can hope to produce biological databases, which accurately reflect the depth and breadth of knowledge that the biomedical research community is producing

RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics.

Web services application programming interface (API) was developed to provide a programmatic access to the regulatory interactions accumulated in the RegPrecise database (http://regprecise.lbl.gov), a core resource on transcriptional regulation for the microbial domain of the Department of Energy (DOE) Systems Biology Knowledgebase. RegPrecise captures and visualize regulogs, sets of genes controlled by orthologous regulators in several closely related bacterial genomes, that were reconstructed by comparative genomics. The current release of RegPrecise 2.0 includes >1400 regulogs controlled either by protein transcription factors or by conserved ribonucleic acid regulatory motifs in >250 genomes from 24 taxonomic groups of bacteria. The reference regulons accumulated in RegPrecise can serve as a basis for automatic annotation of regulatory interactions in newly sequenced genomes. The developed API provides an efficient access to the RegPrecise data by a comprehensive set of 14 web service resources. The RegPrecise web services API is freely accessible at http://regprecise.lbl.gov/RegPrecise/services.jsp with no login requirements

KEGG for representation and analysis of molecular networks involving diseases and drugs

Most human diseases are complex multi-factorial diseases resulting from the combination of various genetic and environmental factors. In the KEGG database resource (http://www.genome.jp/kegg/), diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system. Disease information is computerized in two forms: pathway maps and gene/molecule lists. The KEGG PATHWAY database contains pathway maps for the molecular systems in both normal and perturbed states. In the KEGG DISEASE database, each disease is represented by a list of known disease genes, any known environmental factors at the molecular level, diagnostic markers and therapeutic drugs, which may reflect the underlying molecular system. The KEGG DRUG database contains chemical structures and/or chemical components of all drugs in Japan, including crude drugs and TCM (Traditional Chinese Medicine) formulas, and drugs in the USA and Europe. This database also captures knowledge about two types of molecular networks: the interaction network with target molecules, metabolizing enzymes, other drugs, etc. and the chemical structure transformation network in the history of drug development. The new disease/drug information resource named KEGG MEDICUS can be used as a reference knowledge base for computational analysis of molecular networks, especially, by integrating large-scale experimental datasets

Integration of environmental data in BIM tool & linked building data

Environmental assessment is a critical need to ensure building sustainability. In order to enhance the sustainability of building, involved actors should be able to access and share not only information about the building but also data about products and especially their environmental assessment. Among several approaches that have been proposed to achieve that, semantic web technologies stand out from the crowd by their capabilities to share data and enhance interoperability in between the most heterogeneous systems. This paper presents the implementation of a method in which semantic web technologies and particularly Linked Data have been combined with Building Information Modelling (BIM) tools to foster building sustainability by introducing products with their environmental assessment in building data during the modelling phase. Based on Linked Building Data (LBD) vocabularies and environmental data, several ontologies have been generated in order to make both of them available as Resource Description Framework (RDF) graphs. A database access plugin has been developed and installed in a BIM tool. In that way, the LBD generated from the BIM tool contains, for each product a reference to its environmental assessment which is contained in a triplestore

Peer to peer (P2P) and cloud computing on infrastructure as a service (IaaS) performance analysis

The resources of information technology and the availability of services on non-cloud network systems are limited. This constitutes problems for companies, especially in the efficient management of information technology. The high investment in infrastructure procurement is an obstacle in building centralized systems, including the adoption of cloud computing through Infrastructure as a Service (IaaS), as an elective solution. This research aims to analyze the performance of cloud servers on IaaS services using the parameters of cloud service availability, resource utilization, and throughput transfer which were implemented in companies engaged in the toll road concession sector. Furthermore, the results are expected to be a reference in supporting company decisions/policies related to cloud system adoption. The methodology involved the Network Development Life Cycle (NDLC), a system constituted by 6 (six) stages of management, namely user, proxy server, database, web service, monitoring service, and Remote Desktop Protocol (RDP). The results of cloud service availability indicate that the cloud system provides service availability (system interface, broad network access, and resource pooling). Furthermore, cloud systems have a significant performance on resource utilization (CPU) and throughput transfer parameters, while non-cloud systems only excel in response time and resource utilization (Memory) parameters. The overall result analysis based on this research scenario showed that the cloud system provides services according to user needs and has a better speed in data transmission, but has shortcomings in response time

Spectral Library of European Pegmatites, Pegmatite Minerals and Pegmatite Host-Rocks The GREENPEG Project Database

Abstract. The GREENPEG spectral database contains the spectral signature, obtained through reflectance spectroscopy studies, of European pegmatites and minerals, as well as their host rocks. Samples include Nb-Y-F (NYF) and Li-Cs-Ta (LCT)-type pegmatites and host rocks from pegmatite locations in Austria, Ireland, Norway, Portugal, and Spain. The database contains the reflectance spectra (raw and with continuum removed), sample photographs, and main absorption features automatically extracted by a self-proposed Python routine. Whenever possible, spectral mineralogy was interpreted based on the continuum-removed spectra. A detailed description of the database, its content and structure, the measuring instrument, and interoperability with Geographic Information Systems (GIS) is available in this database report. Moreover, examples of how the data can be used and interpreted are also provided. The advantages and added value of the presented dataset reside on its European scale with representative samples from pegmatites with distinct genesis, mineralogy, structure, and host rocks that can be used as a reference for pegmatite exploration at a global scale through satellite image processing, for example. The reported spectral mineral assemblages can also be of interest when considering resource estimation or ore processing. Thus, it is expected that this open dataset, available on the Zenodo platform https://doi.org/10.5281/zenodo.6518319 (Cardoso-Fernandes et al., 2022), will be a reference for distinct types of users ranging from academia to industry. </jats:p

Immunome database for marsupials and monotremes

Background: To understand the evolutionary origins of our own immune system, we need to characterise the immune system of our distant relatives, the marsupials and monotremes. The recent sequencing of the genomes of two marsupials (opossum and tammar wallaby) and a monotreme (platypus) provides an opportunity to characterise the immune gene repertoires of these model organisms. This was required as many genes involved in immunity evolve rapidly and fail to be detected by automated gene annotation pipelines.Description: We have developed a database of immune genes from the tammar wallaby, red-necked wallaby, northern brown bandicoot, brush-tail possum, opossum, echidna and platypus. The resource contains 2,235 newly identified sequences and 3,197 sequences which had been described previously. This comprehensive dataset was built from a variety of sources, including EST projects and expert-curated gene predictions generated through a variety of methods including chained-BLAST and sensitive HMMER searches. To facilitate systems-based research we have grouped sequences based on broad Gene Ontology categories as well as by specific functional immune groups. Sequences can be extracted by keyword, gene name, protein domain and organism name. Users can also search the database using BLAST.Conclusion: The Immunome Database for Marsupials and Monotremes (IDMM) is a comprehensive database of all known marsupial and monotreme immune genes. It provides a single point of reference for genomic and transcriptomic datasets. Data from other marsupial and monotreme species will be added to the database as it become available. This resource will be utilized by marsupial and monotreme immunologists as well as researchers interested in the evolution of mammalian immunity

arrayMap: A Reference Resource for Genomic Copy Number Imbalances in Human Malignancies

Background: The delineation of genomic copy number abnormalities (CNAs) from cancer samples has been instrumental for identification of tumor suppressor genes and oncogenes and proven useful for clinical marker detection. An increasing number of projects have mapped CNAs using high-resolution microarray based techniques. So far, no single resource does provide a global collection of readily accessible oncoge- nomic array data. Methodology/Principal Findings: We here present arrayMap, a curated reference database and bioinformatics resource targeting copy number profiling data in human cancer. The arrayMap database provides a platform for meta-analysis and systems level data integration of high-resolution oncogenomic CNA data. To date, the resource incorporates more than 40,000 arrays in 224 cancer types extracted from several resources, including the NCBI's Gene Expression Omnibus (GEO), EBIs ArrayExpress (AE), The Cancer Genome Atlas (TCGA), publication supplements and direct submissions. For the majority of the included datasets, probe level and integrated visualization facilitate gene level and genome wide data re- view. Results from multi-case selections can be connected to downstream data analysis and visualization tools. Conclusions/Significance: To our knowledge, currently no data source provides an extensive collection of high resolution oncogenomic CNA data which readily could be used for genomic feature mining, across a representative range of cancer entities. arrayMap represents our effort for providing a long term platform for oncogenomic CNA data independent of specific platform considerations or specific project dependence. The online database can be accessed at http://www.arraymap.org.Comment: 17 pages, 5 inline figures, 3 tables, supplementary figures/tables split into 4 PDF files; manuscript submitted to PLoS ON

An Embedded Biometric Sensor for Ubiquitous Authentication

Communication networks and distributed technologies move people towards the era of ubiquitous computing. An ubiquitous environment needs many authentication sensors for users recognition, in order to provide a secure infrastructure for both user access to resources and services and information management. Today the security requirements must ensure secure and trusted user information to protect sensitive data resource access and they could be used for user traceability inside the platform. Conventional authentication systems, based on username and password, are in crisis since they are not able to guarantee a suitable security level for several applications. Biometric authentication systems represent a valid alternative to the conventional authentication systems providing a flexible einfrastructure towards an integrated solution supporting the requirement for improved inter-organizational functionality. In this work the study and the implementation of a fingerprintsbased embedded biometric system is proposed. Typical strategies implemented in Identity Management Systems could be useful to protect biometric information. The proposed sensor can be seen as a self-contained sensor: it performs the all elaboration steps on board, a necessary requisite to strengthen security, so that sensible data are securely managed and stored inside the sensor, without any data leaking out. The sensor has been prototyped via an FPGA-based platform achieving fast execution time and a good final throughput. Resources used, elaboration times of the sensor are reported. Finally, recognition rates of the proposed embedded biometric sensor have been evaluated considering three different databases: the FVC2002 reference database, the CSAI/Biometrika proprietary database, and the CSAI/Secugen proprietary database. The best achieved FAR and FRR indexes are respectively 1.07% and 8.33%, with an elaboration time of 183.32 ms and a working frequency of 22.5 MHz