B-VegAna (Vegetation edition and Analysis) is an integrated software package oriented towards the storage, management and analysis of ecological data. The package consists of several programs which can be run independently. It includes ten applications (Fagus, Quercus, Ginkgo, Yucca, Zamia, Taxus, Webherb, Wisteria WMS, Welwitschia and Araucaria). The first seven applications offer the opportunity for any user to manage biodiversity data in many interesting ways with an unified interface and data format, the last three apps provide webservices. After almost nine years of development they have become solid tools with a clearly defined added value. Examples for available applications are: (1) Ginkgo - multivariate analysis tool. Oriented mainly towards ordination and classification of ecological data, stressing methods based on symmetric matrices. (2) Quercus - a relevé table editor. It handles relevé data allowing the user to perform phytosociological works. (3) Fagus - floristic records editor. It can handle data coming from field surveys, bibliographic sources or collections. (4) Yucca - a cartographic plotting tool, that enables the user to plot taxa or syntaxa distributions. Taxon, syntaxon or bibliographic thesauri can be edited within the programs. ... [Information of the supplier, modified]
Biodiverse is a tool for the spatial analysis of diversity using indices based on taxonomic, phylogenetic and matrix-based (e.g. genetic distance) relationships, as well as related environmental and temporal variations. Biodiverse supports four processes: 1. linked visualisation of data distributions in geographic, taxonomic, phylogenetic and matrix spaces; 2. spatial moving window analyses including richness, endemism, phylogenetic diversity and beta diversity; 3. spatially constrained agglomerative cluster analyses; and 4. randomisations for hypothesis testing. Biodiverse is open-source and supports user developed extensions. It can be used both through a graphical user interface (GUI) and through user written scripts. Currently more than 170 indices are supported. ... [Information of the supplier]
Bioinformatics is devoted to advancing the scientific understanding of living systems through computation. The Bioinformatics and Biological Computing Unit promotes and supports the adoption, use, and development of bioinformatics tools for advancing biological research. The BBCU server is dedicated to various bioinformatics analyses. Listed here you'll find local resources (tools and databases). Other listed resources (tools and databases) are available on the internet. ... [Information of the supplier, modified]
bioKepler is a Kepler suite facilitating rapid development and scalable distributed execution of bioinformatics workflows in Kepler while simplifying access to a wide range of bioinformatics tools executed locally or distributedly. bioKepler contains a set of Kepler actors, called “bioActors”, that are specialized for running bioinformatics tools at scale along with Kepler directors for distributed data-parallel (DDP) execution on Hadoop and Stratosphere engines. ... [Information of the supplier]
BioMart is a community-driven project to provide unified access to distributed research data to facilitate the scientific discovery process. The BioMart project provides free software and data services to the international scientific community in order to foster scientific collaboration and facilitate the scientific discovery process. The project adheres to the open source philosophy that promotes collaboration and code reuse. ... [Information of the supplier]
BioNLP is an initiative by the Center for Computational Pharmacology (CCP) at the University of Colorado Denver Health Sciences Center to create and distribute code, software, and data for applying natural language processing techniques to biomedical texts. There are many projects associated with BioNLP. The aim of the CCP is to provide novel algorithms and knowledge-based tools for the analysis and interpretation of high-throughput molecular biology data and for information extraction from and management of the biomedical literature. ... [Information of the supplier]
Bioperl is a toolkit of perl modules useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl. Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as CVS modules in our repository. ... [Information of the supplier]
BioStor provides tools for extracting, annotating, and visualising literature from the Biodiversity Heritage Library (and other sources). It builds on ideas developed for bioGUID (see doi:10.1186/1471-2105-10-S14-S5). The main purpose of BioStor is to find articles in the Biodiversity Heritage Library. To get started you can read the guide to using BioStor, or go directly to the Reference Finder. You can also use BioStor to find references from within EndNote and Zotero. If you use the Firefox web browser you could install the OpenURL Referrer add on, which will add the same functionality to sites that support support COinS, such as Mendeley. ... [Information of the supplier]
BiSciCol (Biological Science Collections) Tracker is a funded NSF collaborative project with the goal of building an infrastructure designed to tag and track scientific collections and all of their derivatives. Scientific collections created and used in basic research are an integral part of our scientific infrastructure. Individual specimens in these collections serve as the anchor for an expanding array of information that grows and changes with time about the specimen and the group that the specimen represents. Unfortunately, as we all know, specimens and subsamples are scattered geographically across institutions. Taxonomic, genomic, geospatial, and other information about the specimens is also scattered across independent computer systems and on paper, and are very difficult to access or synthesize. Current data sharing systems such as DigIR are one-way channels and do not allow for quick and easy two-way linking of information or updates as new knowledge is gained. The BiSciCol team will take the appropriate next steps to address a community-wide challenge facing the biological collections community – linking and tracking scientific collection objects (specimens, sequences, images, etc.) and their digital metadata across multiple institutional collections with heterogeneous information management systems. In current distributed data systems (e.g., GBIF, MANIS, HerpNET, ORNIS), information is passed one-way from data providers to users. No mechanism exists to tag or annotate collection objects and link information to other collection objects or data records and back to the original collections. Our deliverables include 1) develop a tracking and annotation system based on globally unique identifiers (GUIDs) and ontological relationships; 2) deploy this system and others in a Virtual Information Appliance (VIA) as a Virtual Machine (VM); and 3) document and implement a set of use cases and practices, based on characteristic physical and digital workflows in the community. ... [Information of the supplier]
Bluejay is a set of Java(TM) objects for the processing, display and querying of XML encoded linear scale data. The main subject for analysis in our implementation are genetic and protein sequences, where features fall somewhere on the linear molecules. Bluejay is growing with the goal of creating a graphical genetic data viewer with point-and-click data mining capabilities, such as those available through your standard Web browser. If the image to the left was animated when you first loaded this document, you should have all you need. Otherwise click on the image to obtain the Java Runtime Environment. Please see the publications for more details on Bluejay. ... [Information of the supplier]