Enrichment of metabolic routes through Big Data

The Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway is a database that contains a graphical representation of cellular processes. Cellular processes are basic systems involving biochemical reactions at the cellular level such as transport, catabolism, metabolism, growth and cell death. The KEGG Pathway information is shown through the use of graphs, in which the molecular interactions between genes, processes and chemical compounds are represented. This paper proposes to perform Data Analytics using the Big Data Analytics Life Cycle methodology to enrich the metabolic pathways of the KEGG Pathway database by applying the Target Fishing technique

Global proteomics analysis of the response to starvation in <i>C. elegans</i>

Periodic starvation of animals induces large shifts in metabolism but may also influence many other cellular systems and can lead to adaption to prolonged starvation conditions. To date, there is limited understanding of how starvation affects gene expression, particularly at the protein level. Here, we have used mass-spectrometry-based quantitative proteomics to identify global changes in the Caenorhabditis elegans proteome due to acute starvation of young adult animals. Measuring changes in the abundance of over 5,000 proteins, we show that acute starvation rapidly alters the levels of hundreds of proteins, many involved in central metabolic pathways, highlighting key regulatory responses. Surprisingly, we also detect changes in the abundance of chromatin-associated proteins, including specific linker histones, histone variants, and histone posttranslational modifications associated with the epigenetic control of gene expression. To maximize community access to these data, they are presented in an online searchable database, the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd/)

Exploring Black Holes

Introduction: Students discover the properties of black holes based on their understanding of gravity and velocity. They also analyze astronomical images from the Hubble Space Telescope and Sloan Digital Sky Survey. Through an experiment, they define escape velocity. Then they extend this idea to a black hole, which is an object with an escape velocity equal to the speed of light. In the final activity, students become astronomers in charge of a new database of super-massive black holes. Their job is to evaluate new claims to decide if they are valid. They design an evaluation rubric and apply their new understanding of black holes to make their decisions. They also use real scientific data from Dr. Karl Gebhardt's black hole database.McDonald Observator

Towards the architecture of an instructional multimedia database

The applicability of multimedia databases in education may be extended if they can serve multiple target groups, leading to affordable costs per unit for the user. In this contribution, an approach is described to build generic multimedia databases to serve that purpose. This approach is elaborated within the ODB Project ('Instructional Design of an Optical DataBase'); the term optical refers to the use of optical storage media to hold the audiovisual components. The project aims at developing a database in which a hypermedia encyclopedia is combined with instructional multimedia applications for different target groups at different educational levels. The architecture of the Optical Database will allow for switching between application types while working (for instance from tutorial instruction via the encyclopedia to a simulation and back). For instruction, the content of the database is thereby organized around so-called standard instruction routes: one route per target group. In the project, the teacher is regarded as the manager of instruction.\ud \ud From that perspective, the database is primarily organized as a teaching facility. Central to the research is the condition that the architecture of the Optical Database has to enable teachers to select and tailor instruction routes to their needs in a way that is perceived as logical and easy to use

IPAVS: Integrated Pathway Resources, Analysis and Visualization System

Integrated Pathway Resources, Analysis and Visualization System (iPAVS) is an integrated biological pathway database designed to support pathway discovery in the fields of proteomics, transcriptomics, metabolomics and systems biology. The key goal of IPAVS is to provide biologists access to expert-curated pathways from experimental data belonging to specific biological contexts related to cell types, tissues, organs and diseases. IPAVS currently integrates over 500 human pathways (consisting of 24 574 interactions) that include metabolic-, signaling- and disease-related pathways, drug–action pathways and several large process maps collated from other pathway resources. IPAVS web interface allows biologists to browse and search pathway resources and provides tools for data import, management, visualization and analysis to support the interpretation of biological data in light of cellular processes. Systems Biology Graphical Notations (SBGN) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway notations are used for the visual display of pathway information. The integrated datasets in IPAVS are made available in several standard data formats that can be downloaded. IPAVS is available at: http://ipavs.cidms.org

MetaCyc: a multiorganism database of metabolic pathways and enzymes

MetaCyc is a database of metabolic pathways and enzymes located at . Its goal is to serve as a metabolic encyclopedia, containing a collection of non-redundant pathways central to small molecule metabolism, which have been reported in the experimental literature. Most of the pathways in MetaCyc occur in microorganisms and plants, although animal pathways are also represented. MetaCyc contains metabolic pathways, enzymatic reactions, enzymes, chemical compounds, genes and review-level comments. Enzyme information includes substrate specificity, kinetic properties, activators, inhibitors, cofactor requirements and links to sequence and structure databases. Data are curated from the primary literature by curators with expertise in biochemistry and molecular biology. MetaCyc serves as a readily accessible comprehensive resource on microbial and plant pathways for genome analysis, basic research, education, metabolic engineering and systems biology. Querying, visualization and curation of the database is supported by SRI's Pathway Tools software. The PathoLogic component of Pathway Tools is used in conjunction with MetaCyc to predict the metabolic network of an organism from its annotated genome. SRI and the European Bioinformatics Institute employed this tool to create pathway/genome databases (PGDBs) for 165 organisms, available at the website. These PGDBs also include predicted operons and pathway hole fillers

Identification of Design Principles

This report identifies those design principles for a (possibly new) query and transformation language for the Web supporting inference that are considered essential. Based upon these design principles an initial strawman is selected. Scenarios for querying the Semantic Web illustrate the design principles and their reflection in the initial strawman, i.e., a first draft of the query language to be designed and implemented by the REWERSE working group I4