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Found 10 result(s)
The FAIRDOMHub is built upon the SEEK software suite, which is an open source web platform for sharing scientific research assets, processes and outcomes. FAIRDOM (Web Site) will establish a support and service network for European Systems Biology. It will serve projects in standardizing, managing and disseminating data and models in a FAIR manner: Findable, Accessible, Interoperable and Reusable. FAIRDOM is an initiative to develop a community, and establish an internationally sustained Data and Model Management service to the European Systems Biology community. FAIRDOM is a joint action of ERA-Net EraSysAPP and European Research Infrastructure ISBE.
HumanCyc provides an encyclopedic reference on human metabolic pathways. It provides a zoomable human metabolic map diagram, and it has been used to generate a steady-state quantitative model of human metabolism. 2016: Subscriptions are now required to access HumanCyc. For more information on obtaining a subscription, click here: http://www.phoenixbioinformatics.org/biocyc#product-biocyc-subscription
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KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies
The MG-RAST server is an open source system for annotation and comparative analysis of metagenomes. Users can upload raw sequence data in fasta format; the sequences will be normalized and processed and summaries automatically generated. The server provides several methods to access the different data types, including phylogenetic and metabolic reconstructions, and the ability to compare the metabolism and annotations of one or more metagenomes and genomes. In addition, the server offers a comprehensive search capability. Access to the data is password protected, and all data generated by the automated pipeline is available for download in a variety of common formats. MG-RAST has become an unofficial repository for metagenomic data, providing a means to make your data public so that it is available for download and viewing of the analysis without registration, as well as a static link that you can use in publications. It also requires that you include experimental metadata about your sample when it is made public to increase the usefulness to the community.
OpenWorm aims to build the first comprehensive computational model of the Caenorhabditis elegans (C. elegans), a microscopic roundworm. With only a thousand cells, it solves basic problems such as feeding, mate-finding and predator avoidance. Despite being extremely well studied in biology, this organism still eludes a deep, principled understanding of its biology. We are using a bottom-up approach, aimed at observing the worm behaviour emerge from a simulation of data derived from scientific experiments carried out over the past decade. To do so we are incorporating the data available in the scientific community into software models. We are engineering Geppetto and Sibernetic, open-source simulation platforms, to be able to run these different models in concert. We are also forging new collaborations with universities and research institutes to collect data that fill in the gaps All the code we produce in the OpenWorm project is Open Source and available on GitHub.
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SILVA is a comprehensive, quality-controlled web resource for up-to-date aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains alongside supplementary online services. In addition to data products, SILVA provides various online tools such as alignment and classification, phylogenetic tree calculation and viewer, probe/primer matching, and an amplicon analysis pipeline. With every full release a curated guide tree is provided that contains the latest taxonomy and nomenclature based on multiple references. SILVA is an ELIXIR Core Data Resource.
The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive linkouts from our data pages to other Arabidopsis resources.