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Found 5 result(s)

OpenWorm

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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.

TreeGenes

A forest tree genome database

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TreeGenes is a genomic, phenotypic, and environmental data resource for forest tree species. The TreeGenes database and Dendrome project provide custom informatics tools to manage the flood of information.The database contains several curated modules that support the storage of data and provide the foundation for web-based searches and visualization tools. GMOD GUI tools such as CMAP for genetic maps and GBrowse for genome and transcriptome assemblies are implemented here. A sample tracking system, known as the Forest Tree Genetic Stock Center, sits at the forefront of most large-scale projects. Barcode identifiers assigned to the trees during sample collection are maintained in the database to identify an individual through DNA extraction, resequencing, genotyping and phenotyping. DiversiTree, a user-friendly desktop-style interface, queries the TreeGenes database and is designed for bulk retrieval of resequencing data. CartograTree combines geo-referenced individuals with relevant ecological and trait databases in a user-friendly map-based interface. ---- The Conifer Genome Network (CGN) is a virtual nexus for researchers working in conifer genomics. The CGN web site is maintained by the Dendrome Project at the University of California, Davis.

InnateDB

A Knowlede Resource for Innate Immunity Interactions & Pathways

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InnateDB is a publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures an improved coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralised resource. The database can be mined as a knowledgebase or used with our integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response.

ZFMK Biodiversity Data Center

ZFMK Natural History Collections - occurrence data

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The ZFMK Biodiversity Data Center is aimed at hosting, archiving, publishing and distributing data from biodiversity research and zoological collections. The Biodiversity Data Center handles and curates data on: - The specimens of the institutes collection, including provenance, distribution, habitat, and taxonomic data. - Observations, recordings and measurements from field research, monitoring and ecological inventories. - Morphological measurements, descriptions on specimens, as well as - Genetic barcode libraries, and - Genetic and molecular research data associated with specimens or environmental samples. For this purpose, suitable software and hardware systems are operated and the required infrastructure is further developed. Core components of the software architecture are: The DiversityWorkbench suite for managing all collection-related information. The Digital Asset Management system easyDB for multimedia assets. The description database Morph·D·Base for morphological data sets and character matrices.

Leiden Open Variation Database

LOVD

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LOVD portal provides LOVD software and access to a list of worldwide LOVD applications through Locus Specific Database list and List of Public LOVD installations. The LOVD installations that have indicated to be included in the global LOVD listing are included in the overall LOVD querying service, which is based on an API.