Difference between revisions of "Glossary of Tools"

From iDigBio
Jump to: navigation, search
(update link Audubon Core)
(add CalPhotos missing info)
Line 197: Line 197:
|valign="top"|CalPhotos is a collection of photos of plants, animals, fossils, people, and landscapes from around the world. A variety of organizations and individuals have contributed photographs to CalPhotos. Please be aware that these various contributors maintain copyright and follow the usage guidelines provided with each image.

Revision as of 14:32, 3 September 2014

Short Name Long Name URL Definition
http://www.a2ia.com/ Handwriting recognition software
ABBYY FineReader Engine
http://www.abbyy.com/ Commercial OCR software that can be used to convert typed and typeface label data from specimens into digital text.
Adobe Acrobat 9 Pro
Batch data extraction from TIFF & JPG formats
Amazon EC2
Amazon Elastic Compute Cloud http://aws.amazon.com/ec2/ Amazon Elastic Compute Cloud (Amazon EC2) is a web service that provides resizable compute capacity in the cloud. It is designed to make web-scale computing easier for developers. Amazon EC2's simple web service interface allows you to obtain and configure capacity with minimal friction. It provides you with complete control of your computing resources and lets you run on Amazon's proven computing environment. Amazon EC2 reduces the time required to obtain and boot new server instances to minutes, allowing you to quickly scale capacity, both up and down, as your computing requirements change. Amazon EC2 changes the economics of computing by allowing you to pay only for capacity that you actually use. Amazon EC2 provides developers the tools to build failure resilient applications and isolate themselves from common failure scenarios.
American Bryological & Lichenological Society
AmphibiaWeb provides access to information on amphibian declines, natural history, conservation, and taxonomy.
ADW Animal Diversity Web http://animaldiversity.ummz.umich.edu/site/index.html Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology at the University of Michigan. Data include descriptions, still images, video, and audio.
Australian Plant Census
Database of the accepted scientific names for the Australian vascular flora, both native and introduced, and lists synonyms and misapplications for these names
Application Programming Interface
An Application Programming Interface provides a means for software components to interact with each other and generally hides the underlying complexity of the component or system providing the API. The iDigBio API is documented at iDigBio API
Australian Plant Names Index
Plant names and their usage in the scientific literature, whether as a current name or synonym
Aradidae Database
http://www.esri.com/products/index.html State-of-the-art, industry standard geographical information system software built by ESRI.
Arctos http://arctos.database.museum/home.cfm Arctos is an ongoing effort to integrate access to specimen data, collection-management tools, and external resources on the internet. Nearly all that is known about a specimen can be included in Arctos, and, except for some data encumbered for proprietary reasons, data are open to the public. Arctos is a multidisciplinary collection management information system for natural history. It integrates access to diverse types of collections (paleontology, entomology, botany, ornithology, mammalogy, herpetology) and data types, including specimen records, observations, tissues, parasites, stomach contents, fieldnotes and other documents, and media such as images and audio recordings. It also integrates data with projects and publications that either contribute to the collections or that use data from the collections.
ALA Atlas of Living Austrailia
Audubon Core http://terms.tdwg.org/wiki/Audubon_Core The Audubon Core is a set of vocabularies designed to represent metadata for biodiversity multimedia resources and collections. These vocabularies aim to represent information that will help to determine whether a particular resource or collection will be fit for some particular biodiversity science application before acquiring the media. Among others, the vocabularies address such concerns as the management of the media and collections, descriptions of their content, their taxonomic, geographic, and temporal coverage, and the appropriate ways to retrieve, attribute and reproduce them.
Automontage http://www.syncroscopy.com/syncroscopy/products.asp A software package produced by Syncroscopy and designed to produce clearly focused digital images with extreme depth-of-field.
Barcode of Life http://www.barcodeoflife.org
In 2003, Paul Hebert, researcher at the University of Guelph in Ontario, Canada, proposed “DNA barcoding” as a way to identify species. Barcoding uses a very short genetic sequence from a standard part of the genome the way a supermarket scanner distinguishes products using the black stripes of the Universal Product Code (UPC). Two items may look very similar to the untrained eye, but in both cases the barcodes are distinct.
BHL - China
Biodiversity Heritage Library China
BHL - Europe
Biodiversity Heritage Library Europe
3 year project, involving 28 major natural history museums, botanical gardens and other cooperating institutions

Bio Portal
Service for registering ontologies
Biological Collection Access Service
Transnational network of biological collections of all kinds. BioCASE enables widespread unified access to distributed and heterogeneous European collection and observational databases using open-source, system-independent software and open data standards and protocols
Biodiversity Information Serving Our Nation (BISON)
An integrated and permanent resource for biological occurrence data from the United States. Product of the U.S. Geological Survey's Biological Informatics Program. BISON allows users to explore and analyze U.S. species occurrence data from participating data providers.
BioGeoMancer http://www.biogeomancer.org/index.html A worldwide collaboration of natural history and geospatial data experts. The primary goal of the project is to maximize the quality and quantity of biodiversity data that can be mapped in support of scientific research, planning, conservation, and management. The project promotes discussion, manages geospatial data and data standards, and develops software tools in support of this mission.
Tool widely acknowledged by a growing user community including leading Austrian museums and universities, as well as public authorities and non-profit organisations. The BioOffice application is used for the registration and documentation of biological collections as well as for archiving and evaluation of project-related data such as cartography of flora and fauna.
BioSharing http://www.biosharing.org/ BioSharing works at the global level to build stable linkages between journals and funders implementing data sharing policies, and well-constituted standardization efforts in the biosciences domain, to expedite the communication and the production of an integrated standards-based framework for the capture and sharing of high-throughput genomics and functional genomic bioscience data. BioSharing works with other organisations to: 1.develop catalogues to centralize bioscience data policies and reporting standards. ◦enrich these progressively by linking to other related portals and resources to serve those seeking information on systems serving or implementing the standards 2.moderate a communication forum for funders and stakeholders. ◦promote mutual support and cross-project activities to ensure the difference among the policies and standards do not impede seamless interoperability of the data.
Manages specimen-based, spatially and taxonomically referenced data for ecologists, conservation biologists, evolutionary biologists, systematists, museums and herbaria.
Biological Science Collections http://biscicol.org
Central African Biodiversity Information Network
Funded for a period of 5 years by the Belgian Cooperation and Development Agency, is the implementation of a network of databases on biodiversity information, in collaboration with several research institutions based in Central Africa (mainly Congo DRC, Rwanda and Burundi). The project is a multidisciplinary initiative involving the different departments and units of RMCA.

CalPhotos is a collection of photos of plants, animals, fossils, people, and landscapes from around the world. A variety of organizations and individuals have contributed photographs to CalPhotos. Please be aware that these various contributors maintain copyright and follow the usage guidelines provided with each image.
Mission to unlock the specimen information held by Canadian university-based biological collections and share this via a network of distributed databases, compatible with other biodiversity information networks like the Canadian Biodiversity Information Facility (CBIF) and the Global Biodiversity Information Facility (GBIF).
Catalogue of Life
Indexing world's known species
Canadian Biodiversity Information Facility
Member of the Global Biodiversity Information Facility (GBIF)
Consortium of California Herbaria
Gateway to information from California vascular plant specimens that are housed in herbaria throughout the state. The database now (October 2011) includes information from more than 1.3 million specimens, all searchable through a single interface.
Cercopoidea Organised On Line
Consortium of European Taxonomic Facilities
Networked consortium of scientific institutions in Europe formed to promote training, research and understanding of systematic biology and palaeobiology,
http://www.collectionsweb.org The website of the Research Coordination Network (RCN) for Building a National Community of Natural History Collections.
CombineZ http://www.broadhurst-family.co.uk/lefteye/MainPages/combinez.htm Freeware stacking software designed to produce a single, clearly focused image with high depth-of-field. Supports batch processing.
Computer aided Identification for Phlebotoma of South America
Consortium of North American Bryothyte Herbaria
Consortium of North American Lichen Herbaria
Darwin Core
The Darwin Core is a body of standards. It includes a glossary of terms (in other contexts these might be called properties, elements, fields, columns, attributes, or concepts) intended to facilitate the sharing of information about biological diversity by providing reference definitions, examples, and commentaries. The Darwin Core is primarily based on taxa, their occurrence in nature as documented by observations, specimens, and samples, and related information. Included are documents describing how these terms are managed, how the set of terms can be extended for new purposes, and how the terms can be used.
Database to Name and Taxa
PostGreSQL relational database conceptual schema
DiGIR Distributed Generic Information Retrieval http://digir.net/ DiGIR is a client/server protocol for retrieving information from distributed resources. It uses HTTP as the transport mechanism and XML for encoding messages sent between client and server. It is an opensource project, originally conceived to be the replacement for the Z39.50 protocol used in the Species Analyst project, but is intended to work with any type of information, not just Natural History collections.
Digital Florida
Public interface for biodiversity (collections, etc.), including web mapping application, for Florida. Initial proof of concept for FLMNH Biodiversity Institute, but no existing funding
Discover Life
Mapping and geographic data analysis; open source GIS.
djatoka http://www.dlib.org/dlib/september08/chute/09chute.html Open source JPEG 2000 image server.
Dryad http://datadryad.org/ Dryad is an international repository of data underlying peer-reviewed articles in the basic and applied biosciences. Dryad enables scientists to validate published findings, explore new analysis methodologies, repurpose data for research questions unanticipated by the original authors, and perform synthetic studies. Dryad is governed by a consortium of journals that collaboratively promote data archiving and ensure the sustainability of the repository. As of Nov 18, 2011, Dryad contained 1090 data packages and 2583 data files, associated with articles in 94 journals.
DSLR Digital Single Lens Reflex Camera http://en.wikipedia.org/wiki/Digital_single-lens_reflex_camera A digital camera, usually with interchangeable lenses, that captures digital images in one or more of a variety of formats.
EOL Encyclopedia of Life http://eol.org/
Open source web application to organize information by the names of living creatures
EOL MCZ database
Estonian eBiodiversity
Europeana: think culture
Europeana enables people to explore the digital resources of Europe's museums, libraries, archives and audio-visual collections. It promotes discovery and networking opportunities in a multilingual space where users can engage, share in and be inspired by the rich diversity of Europe's cultural and scientific heritage.
EXIF Exchangeable Image File Format http://www.exif.org/ A standard for storing image metadata and interchange information in image files, especially those using JPEG compression. Most digital cameras now use the EXIF format. The format is part of the DCF standard created by JEITA to encourage interoperability between imaging devices.
Fauna Europaea
The scientific names of all European land and freshwater animals brought together in one authorative database.
FilteredPush http://etaxonomy.org/mw/FilteredPush http://sourceforge.net/projects/filteredpush/ FilteredPush is an NSF-funded project of the Museum of Comparative Zoology, UC Davis, the Harvard University Herbaria and the UMASS-Boston Biodiversity Informatics Lab to build a platform for distributed annotation of distrtibuted data. It provides feedback to the data provider and any other parties interested in the annotations, based on configurable filters to select notification based on attributes of the annotation or the data. FilteredPush is designed to connect remote sites where annotations can be generated with the authoritative databases of the collections holding the vouchers to which those annotations apply. The name reflects function; Push, as annotations can be pushed from remote corners of the network back to authoritative data sets, Filtered, as the curators of these data sets can filter and reject annotations of their data.
Fulgoromorpha List On the Web
FLOW: a taxonomic and knowledge base dedicated to planthoppers (Insecta, Hemiptera, Fulgoromorpha).
Fuzzy Gazetteer
GBIF Global Biodiversity Information Facility
To encourage free and open access to biodiversity data, via the Internet
GCI Grey Card Index
The Gray Card Index (in part) from the Harvard Gray Herbarium is now incorporated into the International Plant Names Index
GDAL Geospatial Data Abstraction Library http://www.gdal.org/
Geospatial library for PostgreSQL. Required to implement map server and other spatial applications/libraries in PostgreSQL. Translation library for raster (GDAL) and vector (OGR) geospatial data formats.
geneious http://www.geneious.com Geneious is a DNA, RNA and protein sequence alignment, assembly and analysis software platform, integrating bioinformatic and molecular biology tools into a simple interface.
GNIS Geographic Names Information System http://nhd.usgs.gov/gnis.html The Geographic Names Information System (GNIS), developed by the U.S. Geological Survey in cooperation with the U.S. Board on Geographic Names, contains information about physical and cultural geographic features in the United States and associated areas, both current and historical (not including roads and highways). The database holds the Federally recognized name of each feature and defines the location of the feature by state, county, USGS topographic map, and geographic coordinates.

Other feature attributes include names or spellings other than the official name, feature designations, feature class, historical and descriptive information. The database assigns a unique feature identifier, a random number, that is a key for accessing, integrating, or reconciling GNIS data with other datasets. The GNIS is our Nation's official repository of domestic geographic feature names information.

GEOLocate http://www.museum.tulane.edu/geolocate/ Software designed to georeference natural history collections data by interpreting locality data and converting them into specific geographic coordinate pairs, including an estimate of precision based on the point-radius method. GeoLocate may be downloaded as a standalone desktop application, used via a web-based interface, or run as a web service against an existing online database.
Georeferencing Calculator
GEOS Geometry Engine - Open Source http://trac.osgeo.org/geos/
Complete functionality of Java Topology Suite (JTS) in C++
GigaPan http://gigapansystems.com/ A robotic camera harness that allows one of numerous DSLR cameras to take multiple images that can be stitched together to form gigapixel, high-resolution image files.
GNA http://www.globalnames.org/
Infrastructure that manages (the strings that serve as) names can discover, index, organize and interconnect on-line information about organisms and serve the needs of biologists
Google Analytics http://www.google.com/analytics/ Google Analytics is the enterprise-class web analytics solution that gives you rich insights into your website traffic and marketing effectiveness. Powerful, flexible, and easy-to-use features now let you see and analyze your traffic data in an entirely new way.
Google Earth Engine
Google Maps
Grass http://grass.osgeo.org/
GIS software used for geospatial data management and analysis, image processing, graphics/maps production, spatial modeling, and visualization
Hadoop http://hadoop.apache.org/ The Apache Hadoop software library is a framework that allows for the distributed processing of large data sets across clusters of computers using a simple programming model. It is designed to scale up from single servers to thousands of machines, each offering local computation and storage. Rather than rely on hardware to deliver high-avaiability, the library itself is designed to detect and handle failures at the application layer, so delivering a highly-availabile service on top of a cluster of computers, each of which may be prone to failures.
Herbaria@Home http://herbariaunited.org/atHome/
Herbaria@home is a ground-breaking new approach to digitising and documenting the archives of the UK's herbaria. This site provides a web-based method for documenting herbarium sheets. We welcome participation in the project. Volunteers (citizen science) participate to enter label data from Herbarium sheets.
HERBIS Erudite Recorded Botanical Information Synthesizer http://www.herbis.org/ This project offers proof of concept and an initial implementation of 'one-button' specimen imaging and data capture by which clicking the shutter on a digital camera would initiate a sequence that culminates with the population of label data and a specimen image into a structured collection database. The ultimate goal is to reduce the total cost of digital collection data capture by significantly reducing human labor required and total project duration. Significant gains can be achieved by developing appropriate protocols and methodologies, then packaging them as web services. Much of this can be accomplished by applying existing technology to data acquisition bottlenecks. The HERBIS webservice is now located at: http://www3.isrl.illinois.edu/~TeleNature/Herbis/src/web/htdocs/
Herpnet Geo-referencing Guidelines
http://www.herpnet.org/Gazetteer/GeorefResources.htm see link for georeferencing for guidelines/best practices
HUBzero http://hubzero.org/ HUBzero is a platform created by Purdue University with the collaboration of several other intitution and is used to create dynamic web sites for scientific research and educational activities. HUBzero allows users to easily publish research software and related educational materials on the web. It is specificially designed for scientific applications. InvertNet.org is built on this platform.
Hymenoptera Online
Hymenoptera database. These data have been gathered with the collaboration of a number of colleagues. Other taxa still need work. If you would like to contribute to the further development and enhancement of this resource, please contact Norman F. Johnson or Luciana Musetti. For technical assistance related to Hymenoptera Online services, please contact Joe Cora. Visit the collection page for the C.A. Triplehorn Insect Collection at the Ohio State University for information on its primary and secondary type holdings as well as databased taxa in the collection.
ICBN International Code on Botanical Nomenclature http://ibot.sav.sk/icbn/main.htm The International Code on Botanical Nomenclature (ICBN) acts as adviser and arbiter for the biological community by generating and disseminating information on the correct use of the scientific names of plants. The ICBN is responsible for producing the International Code of Botanical Nomenclature, a set of rules for the naming of plants and the resolution of nomenclatural problems.
ICR Intelligent Character Recognition http://en.wikipedia.org/wiki/Intelligent_character_recognition An advanced optical character recognition (OCR) or rather more specific handwriting recognition system that allows fonts and different styles of handwriting to be learned by a computer during processing to improve accuracy and recognition levels.
ICZN International Commission on Zoological Nomenclature http://iczn.org/ The International Commission on Zoological Nomenclature (ICZN) acts as adviser and arbiter for the zoological community by generating and disseminating information on the correct use of the scientific names of animals. The ICZN is responsible for producing the International Code of Zoological Nomenclature, a set of rules for the naming of animals and the resolution of nomenclatural problems.
IdentificationKey web service
IdentifyLife is a global, collaborative project providing ways to identify the world's living organisms.
iDigBio Collections
Web application for scientific collections management developed initially for FLMNH collections. Designed to provide ontological flexibility and extensibility through use of triplestores rather than traditional table management. Manages collections, taxonomy, locations, loans, etc.
Index Kewensis
Indexing names of seed plants at the level of genus and species published since 1753, now totalling over one million records.
International Legume Database & Information Service
International project which maintains a database of plants in the family Fabaceae (Leguminosae) and provides services to scientists and other people interested in these plants, including this web-site for access to the database

ImageMagick http://www.imagemagick.org/script/index.php ImageMagick is a software suite to create, edit, compose, or convert bitmap images. It can read and write images in a variety of formats (over 100) including DPX, EXR, GIF, JPEG, JPEG-2000, PDF, PhotoCD, PNG, Postscript, SVG, and TIFF. ImageMagick can be used to resize, flip, mirror, rotate, distort, shear and transform images, adjust image colors, apply various special effects, or draw text, lines, polygons, ellipses and Bezier curves.
Index Fungorum
Global fungal nomenclator coordinated and supported by the Index Fungorum Partnership (CABI, CBS, Landcare Research-NZ), contains names of fungi (including yeasts, lichens, chromistan fungal analogues, protozoan fungal analogues and fossil forms) at all ranks

IPNI International Plant Names Index http://ipni.org/ The International Plant Names Index (IPNI) is a database of the names and associated basic bibliographical details of seed plants, ferns, and lycophytes. Its goal is to eliminate the need for repeated reference to primary sources for basic bibliographic information about plant names. The data are freely available and are gradually being standardized and checked. IPNI is the product of a collaboration between The Royal Botanic Gardens, Kew, The Harvard University Herbaria, and the Australian National Herbarium.
IPT GBIF Integrated Publishing Toolkit The IPT is an open source software server written in Java that allows users to publish and share biodiversity datasets through the Global Biodiversity Information Facility network (GBIF). Designed for interoperability, it enables the publishing of content in databases or text files using open standards; namely the Darwin Core and the Ecological Metadata Language.
Open source web application that makes it easy to share three types of biodiversity-related information: primary taxon occurrence data, taxon checklists, and general metadata about data sources
ITIS Integrated Taxonomic Information System http://www.itis.gov/ Authoritative, searchable taxonomic information on plants, animals, fungi, and microbes of North America and the world, including synonymous and accepted names.
JSON JavaScript Object Notation http://www.json.org/ JSON is a lightweight data-interchange format. It is easy for humans to read and write. It is easy for machines to parse and generate. It is based on a subset of the JavaScript Programming Language, Standard ECMA-262 3rd Edition - December 1999. JSON is a text format that is completely language independent but uses conventions that are familiar to programmers of the C-family of languages, including C, C++, C#, Java, JavaScript, Perl, Python, and many others. These properties make JSON an ideal data-interchange language.
JSTOR Plant Science (now Global Plants)
JSTOR Plant Science (now Global Plants) is an online environment that provides access to foundational content vital to plant science - plant type specimens, taxonomic structures, scientific literature, and related materials. This new environment includes over a million type specimens, paintings, drawings, correspondence, and supporting materials. By 2013, they expect to have over 2.2 million type specimens available, making JSTOR Plant Science the largest collection of its kind in the world. These materials are now truly global in scope representing over 200 partners in 50 countries on 5 continents.
Java Topology Suite
API for modelling and manipulating 2-dimensional linear geometry. It provides numerous geometric predicates and functions. JTS conforms to the Simple Features Specification for SQL published by the Open GIS Consortium.
KE EMu KE Software Electronic Museum http://www.kesoftware.com/emu This is a commercial software product provided by KE Software used by many biological collections. KE Software's Electronic Museum management system, EMu, is a collections management system for all museums, from the small to the very large. Engineered to manage all types of collections, EMu is suited to: Cultural collections, Anthropology, Archaeology, Science and Technology; Paintings, Drawings, Prints, Sculpture and 3-dimensional objects, Decorative Art, Performing Art, Photography, Textiles and Digital Objects; Natural History collections, including Zoology, Earth Sciences, Palaeobiology, Botany, Horticulture and Physical Anthropology; and Special collections, Digital Assets, Historical Societies and Archives.
KML Keyhole Markup Language http://code.google.com/apis/kml/ Keyhole Markup Language (KML) is an XML notation for expressing geographic annotation and visualization within Internet-based, two-dimensional maps and three-dimensional Earth browsers. KML was developed for use with Google Earth, which was originally named Keyhole Earth Viewer. It was created by Keyhole, Inc, which was acquired by Google in 2004. KML is an international standard of the Open Geospatial Consortium. Google Earth was the first program able to view and graphically edit KML files. Other projects such as Marble have also started to develop KML support.
XML C parser and toolkit developed for the Gnome project
Lifemapper uses all of the online geospatial species occurrence data to create distribution maps and, notably, goes one step further to predict where an individual species should exist based on where it is documented to live.
Les Insectes Comestibles d'Afrique de L'Ouest et Centrale sur Internet
Global access to knowledge about life on Earth.
MaNIS Mammal Networked Information System http://www.manisnet.org/ With support from the National Science Foundation, seventeen North American institutions and their collaborators developed the Mammal Networked Information System. The original objectives of MaNIS were to 1) facilitate open access to combined specimen data from a web browser, 2) enhance the value of specimen collections, 3) conserve curatorial resources, and 4) use a design paradigm that can be easily adopted by other disciplines with similar needs. As an NSF-funded initiative, MaNIS achieves these objectives while avoiding the need for long-term, external maintenance of the network and centralized data management.
MANTIS MantisBT http://www.mantisbt.org/ MantisBT is a free popular web-based insect tracking system. It is written in the PHP scripting language and works with MySQL, MS SQL, and PostgreSQL databases and a webserver. MantisBT has been installed on Windows, Linux, Mac OS, OS/2, and others. Almost any web browser should be able to function as a client. It is released under the terms of the GNU General Public License (GPL).
Map of Life
Map window GIS
Open source GIS
MapReduce http://hadoop.apache.org/mapreduce/ Hadoop MapReduce is a programming model and software framework for writing applications that rapidly process vast amounts of data in parallel on large clusters of compute nodes.
Minimum Information for Biological and Biomedical Investigations
MIBBI is managed by a mix of community representatives and invited domain experts. The Portal exists to promote extant projects to the wider community (and each other) and to link to relevant resources. The Foundry is a project to synthesize reporting guidlines from various communities into a suite of orthogonal standards. Discussion lists, teleconferences, open-access development and meetings ensure openess and accountability.
Missouri Botanical Garden
Oldest botanical garden in continuous operation and a National Historic Landmark.
Morphbank Morphbank :: Biological Imaging http://www.morphbank.net/index.php Morphbank :: Biological Imaging is a continuously growing database of images that scientists use for international collaboration, research and education. Images deposited in Morphbank :: Biological Imaging document a wide variety of research including: specimen-based research in comparative anatomy, morphological phylogenetics, taxonomy and related fields focused on increasing our knowledge about biodiversity. The project receives its main funding from the Biological Databases and Informatics program of the National Science Foundation (Grant DBI-0446224). Morphbank :: Biological Imaging was established in 1998 by a Swedish-Spanish-American group of entomologists and is currently housed at the School of Computational Science (SCS) at Florida State University. The project has grown immensely since its beginnings and presently includes a team of 15 biologists, computer scientists, and information scientists who are working on developing the software. Morphbank :: Biological Imaging is dedicated to using open-source software and is a Fair Use Web Site. The software used in the current Morphbank :: Biological Imaging system includes PHP, ImageMagick, MySQL, Apache, Java, and JavaScript.
Ontology management tool
Moss Bug Base (MBB)
mx http://mx.phenomix.org/index.php/Main_Page
mx (preferred reference all lowercase) is a Ruby-based platform that consists of a Ruby on Rails (RoR) application and various supporting gems/libraries. Initially conceived and developed as a collaborative web-based content management system for biosystematists mx now has a wide range of functionality much of which can broadly categorized under the umbrella of biodiversity informatics.

Runs web-based, can run locally as well.

Open Source relational database
NCSA The National Center for Supercomputing Applications http://www.ncsa.illinois.edu/ The National Center for Supercomputing Applications (NCSA), located at the University of Illinois at Urbana-Champaign, provides powerful computers and expert support that help thousands of scientists and engineers across the country improve our world. With the computing power available at NCSA, researchers simulate how galaxies collide and merge, how proteins fold and how molecules move through the wall of a cell, how tornadoes and hurricanes form, and other complex natural and engineered phenomena.
NIMBUS Nimbus Platform and Infrastructure http://www.nimbusproject.org/ An integrated set of tools that deliver the power and versatility of infrastructure clouds to scientific users. Nimbus Platform allows you to combine Nimbus, OpenStack, Amazon, and other clouds. Nimbus Infrastructure is an open source EC2/S3-compatible Infrastructure-as-a-Service implementation specifically targeting features of interest to the scientific community such as support for proxy credentials, batch schedulers, best-effort allocations, and others.
Document analysis and OCR system, featuring pluggable layout analysis, pluggable character recognition, statistical natural language modeling, and multi-lingual capabilities
ODBC Open Database Connectivity http://en.wikipedia.org/wiki/ODBC ODBC is a standard C interface for accessing database management systems (DBMS). The designers of ODBC aimed to make it independent of database systems and operating systems. An application can use ODBC to query data from a DBMS, regardless of the operating system or DBMS it uses. ODBC accomplishes DBMS independence by using an ODBC driver as a translation layer between the application and the DBMS. The application uses ODBC functions, and the driver passes the query to the DBMS.
Opening up Europe’s natural history heritage for Europeana
Project which would provide this multimedia content with specific biological and multilingual functionality to a wide European cultural audience through EUROPEANA was proposed
Commercial high end data management system
ORNIS http://www.ornisnet.org/home Over 5 million bird specimens are housed in North American collections, documenting the composition, distribution, ecology, and systematics of the world's estimated 10,000-16,000 bird species. Millions of additional observational records are held in diverse data sets. ORNIS addresses the urgent call for increased access to these data in an open and collaborative manner, and involves development of a suite of online software tools for data analysis and error-checking. This project, funded by the National Science Foundation, expands on existing infrastructure developed for distributed mammal (MaNIS), amphibian and reptile (HerpNet), and fish (FishNet) databases. Improved access to avian data sets will allow predictive uses to reveal patterns and processes of evolutionary and ecological phenomena that have not been apparent heretofore. Along with similar infrastructures for other vertebrate groups, it also will enable detailed and synthetic knowledge of the earth's biodiversity for tracking climate change, emerging diseases (e.g., West Nile Virus), and other conservation challenges for species in the 21st century.
OWL Web Ontology Language http://en.wikipedia.org/wiki/Web_Ontology_Language The Web Ontology Language (OWL) is a family of knowledge representation languages for authoring ontologies.
Paleobiology Database
Provide global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data
PaleoPortal The Paleontology Portal http://www.paleoportal.org/ This site is a resource for anyone interested in paleontology, from the professional in the lab to the interested amateur scouting for fossils to the student in any classroom. Many resources are gathered into this single entry "portal" to paleontological information on the Internet.
PhenoBlast http://aquila.bio.nyu.edu/cgi-bin/rnaidb/browse/phenoblast.cgi A database of phenotypic signatures, providing access to results from RNAi interference studies in C. elegans.
Phenoscape http://phenoscape.org A scalable infrastructure that enables linking descriptive phenotype observations across different fields of biology by the semantic similarity of their free-text descriptions.
Photoshop http://www.photoshop.com Highly sophisticated image editing software, the gold standard from Adobe.
Photosimile http://ortery.com/products/photosimile5000-professional-multi-row-360-degree-photography-device.php A 28" x 28" x 28" daylight-balanced photography studio that includes a compatible Canon Rebel SLR camera and powerful system control software, Photosimile 5000 facilitates the creation of professional still photos, 360-degree, hemispherical and full spherical product animations.

Driven by software, the system allows users to control all camera and studio settings. This is a fully automated, precise image capture and efficient image processing tool.

Planting Science
Learning and research resource, bringing together students, plant scientists, and teachers from across the nation
PLANTS Database
Provides standardized information about the vascular plants, mosses, liverworts, hornworts, and lichens of the U.S. and its territories. It includes names, plant symbols, checklists, distributional data, species abstracts, characteristics, images, crop information, automated tools, onward Web links, and references.
Provides cloud database and computing services for the taxonomical, ecological, phylogenetical, etc. research
Adds support for geographic objects to the PostgreSQL object-relational database. Required to implement map server and other spatial applications/libraries in PostgreSQL.
Open Source relational database
Cartographic Projections library for PostgreSQL. Required to implement map server and other spatial applications/libraries in PostgreSQL
Psyl'list http://www.hemiptera-databases.com/psyllist/ Psyl'list is an online database dedicated to jumping plant lice. The aim of this ongoing project is primarily to make up for the absence of world catalogue for Psylloidea, in organizing taxonomic data and providing easy access to the published taxonomic data that is already available but scattered in the literature. Informations about geographical distribution and host-plants are partly available for some species and will be complemented continuously.
Quantum GIS Open source GIS
Tropical Plant Database
Provides accurate and factual information on the important plants of the Amazon Rainforest
RDF Resource Description Framework http://www.w3.org/RDF/ RDF is a standard model for data interchange on the Web. RDF has features that facilitate data merging even if the underlying schemas differ, and it specifically supports the evolution of schemas over time without requiring all the data consumers to be changed. RDF extends the linking structure of the Web to use URIs to name the relationship between things as well as the two ends of the link (this is usually referred to as a triple). Using this simple model, it allows structured and semi-structured data to be mixed, exposed, and shared across different applications. This linking structure forms a directed, labeled graph, where the edges represent the named link between two resources, represented by the graph nodes. This graph view is the easiest possible mental model for RDF and is often used in easy-to-understand visual explanations.
Recorder 6
Tool for those entering, collating and exchanging records of species and habitats. Fast and accurate import of data from a variety of sources and different formats, flexible reporting framework, and mapping facilities to enter, view and query data.
Re:discovery http://www.rediscov.com/ Re:discovery is a museum and archival collections management software package that documents and maintains object and digitally-based collections. An internet component allows institutions to share their collections with the public. Re:discovery may be used by archivists, registrars, collections managers, curators, archaeologists, slide librarians, educators, and researchers. It is currently in use at close to 500 sites in the United States and Canada.
REST REpresentational State Transfer http://en.wikipedia.org/wiki/Representational_state_transfer Representational state transfer (REST) is a style of software architecture for distributed hypermedia systems such as the World Wide Web. The REST architectural style was developed in parallel with HTTP/1.1, based on the existing design of HTTP/1.0. The largest implementation of a system conforming to the REST architectural style is the World Wide Web. REST exemplifies how the Web's architecture emerged by characterizing and constraining the macro-interactions of the four components of the Web, namely origin servers, gateways, proxies, and clients, without imposing limitations on the individual participants. As such, REST essentially governs the proper behavior of participants.
Royal Museum for Central Africa
As a research institute, the RMCA leads several scientific projects. Some 85 scientists and 150 students and trainees conduct research on an ever-changing continent of countless communities, lush forests, stark deserts, and unrivalled wildlife
ScioQualis https://scioqualis.com:1443/Default.aspx A Natural History Collections Management Software in the Cloud.
ScioTR http://www.sciotr.com/ A new touch-enabled Windows 8 app which integrates Optical Character Recognition (OCR), Natural Language Parsing (NLP), Model Strategies and crowdsourcing to provide an efficent workflow for capturing highly-structured data from images.
Scratchpads http://scratchpads.eu/ Scratchpads is a social networking tool to build, share, and publish information on the diversity of life. It is part of the EU funded ViBRANT project, and the NERC funded e-Monocot project. As part of these initiatives a new version of the Scratchpads will be released in January 2012.
Southwest Environmental Information Network
Gateway to distributed data resources of interest to the environmental research community in Arizona and beyond.
Survey of Economic Plants for Arid and Semi-Arid Lands
Database and enquiry service about useful "wild" and semi-domesticated plants of tropical and subtropical drylands, developed and maintained at the Royal Botanic Gardens, Kew.

SOAP Simple Object Access Protocol http://en.wikipedia.org/wiki/SOAP SOAP is a protocol specification for exchanging structured information in the implementation of Web Services in computer networks. It relies on Extensible Markup Language (XML) for its message format, and usually relies on other Application Layer protocols, most notably Hypertext Transfer Protocol (HTTP) and Simple Mail Transfer Protocol (SMTP), for message negotiation and transmission. SOAP can form the foundation layer of a web services protocol stack, providing a basic messaging framework upon which web services can be built.
Species 2000
Species 2000 Europa
Specify http://specifysoftware.org/content/welcome-specify-6 The NSF-funded Specify Software Project offers Specify 6.5 and allied applications for museum and herbarium research data processing. Specify 6 handles specimen information for computerizing collection holdings, for tracking specimen and tissue management transactions, and for mobilizing species occurrence data to the Internet. Specify runs on Windows, Mac OS X, and Linux computers; it is free and open source licensed. Specify 6.5 was released in September, 2013.
Society for the Preservation of Natural History Collections
SQL Structured Query Language http://en.wikipedia.org/wiki/SQL SQL is a programming language designed for managing data in relational database management systems (RDBMS). Originally based upon relational algebra and tuple relational calculus, its scope includes data insert, query, update and delete, schema creation and modification, and data access control. SQL became a standard of the American National Standards Institute (ANSI) in 1986, and of the International Organization for Standards (ISO) in 1987. Since then the standard has been enhanced several times with added features. However, issues of SQL code portability between major RDBMS products still exist due to lack of full compliance with, or different interpretations of the standard.
http://symbiota.org, http://taxonbytes.org/symbiota/
The Symbiota Software Project is working towards building a library of webtools to aid biologists in establishing specimen based virtual floras and faunas.
Synthesis of Systematics Resources
4 year project which began in September 2009 comprises 20 European natural history museums, Universities and botanic gardens. It aims to create an integrated European infrastructure for researchers in the natural sciences. SYNTHESYS is split into three activities: Access, Networking and Joint Research Activities
SysTax database system comprises: concept-based botanical and zoological systematics, literature, Botanic Gardens, Herbaria, and Zoological Collections, addresses, multimedia data (pictures, sound files and video sequences).
TACC Texas Advanced Computing Center http://www.tacc.utexas.edu/ The Texas Advanced Computing Center (TACC) at The University of Texas at Austin is one of the leading centers of computational excellence in the United States. The center's mission is to enable discoveries that advance science and society through the application of advanced computing technologies.
TAPIR TDWG Access Protocol for Information Retrieval http://www.tdwg.org/activities/tapir/ TAPIR specifies a standardized, stateless, HTTP transmittable, XML-based request and response protocol for accessing structured data that may be stored on any number of distributed databases of varied physical and logical structure. TAPIR combines and extends features of the BioCASe and DiGIR protocols to create a new and more generic means of communication between client applications and data providers using the Internet.
Implements the TAPIR protocol (stateless, HTTP transmittable, XML-based request and response protocol for accessing structured data that may be stored on any number of distributed databases of varied physical and logical structure)
Implements the TAPIR protocol (stateless, HTTP transmittable, XML-based request and response protocol for accessing structured data that may be stored on any number of distributed databases of varied physical and logical structure). Only tabular (denormalized) data can be served.
TDWG Biodiversity Information Standards Taxonomic Database Working Group http://www.tdwg.org/ TDWG is a not for profit scientific and educational association that is affiliated with the International Union of Biological Sciences. TDWG was formed to establish international collaboration among biological database projects. TDWG promoted the wider and more effective dissemination of information about the world's heritage of biological organisms for the benefit of the world at large. Biodiversity Information Standards (TDWG) now focuses on the development of standards for the exchange of biological/biodiversity data.
OCR engine developed at HP (1985-1995), one of the top 3 engines in the 1995 UNLV Accuracy test
TNRS Taxonomic Name Resolution Service http://tnrs.iplantcollaborative.org/
Service that receives taxonomic names, and reports back the best name according to an authoritative source, in this case TROPICOS. The ability to 'reconcile' alternative names for the same species and return a preferred name can 'normalize' taxonomy in biodiversity databases that currently use different names
TOLKIN The Tree of Life Knowledge and Information Network http://www.tolkin.org/ TOLKIN is an information management and analytical web application to provide informatics support for phylodiversity and biodiversity research projects. As a web-based application, TOLKIN is able to support collaborative projects by providing shared access to a variety of data on voucher specimens, taxonomy, bibliography, morphology, DNA samples, and sequences
Repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. Relational database designed to manage and explore information on phylogenetic relationships.
TROPICOS http://www.tropicos.org/ Tropicos was originally created for internal research but has since been made available to the world's scientific community. All of the nomenclatural, bibliographic, and specimen data accumulated in the Missouri Botanical Garden's electronic databases during the past 25 years are publicly available here. This system has over 1.2 million scientific names and 3.9 million specimen records.
uBio/ClassificationBank http://www.ubio.org/index.php?pagename=servers
"taxonomic concept server" focused on accurately representing subjective taxonomic opinion in the form of classifications and checklists. These classifications may vary considerably in both scope and precision. ClassificationBank draws upon NameBank elements to form the uBio Taxonomic Name Server.
"biological name server" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context. NameBank defines and serves nomenclatural concepts as XML objects
UNITE is a relational database built on a MySQL platform running on a Red Hat Linux Apache web server. Molecular key for fungi, fungal rDNA ITS sequence database
Universal Chalcidoidea Database
Vascular Plants of Canada
Comprehensive database of all vascular plants reported in Canada, Greenland (Denmark) and Saint Pierre and Miquelon (France). VASCAN is literature-based, though recent additions are sometimes specimen-based.
Vernon Systems
Vernon Systems Limited develops two collections management systems for museums and galleries: Vernon CMS, a world leading desktop system for medium-to-large organisations, and eHive, a hosted web-based system for small museums, individual collectors and consortiums
VertNet http://vertnet.org/index.php VertNet is a collaborative effort, bringing together the expertise of biodiversity scientists and informatics experts. The team, led by the University of California Berkeley, includes the University of Colorado, Tulane University, and the University of Kansas. The project will integrate will several targeted biodiversity and collection management applications:

AmphibiaWeb, Animal Diversity Web, Arctos, DataONE, Encyclopedia of Life, GEOLocate, Map of Life and Specify.

Virtual Biodiversity Research and Access Network for Taxonomy http://vbrant.eu/
Virtual Biodiversity Research and Access Network for Taxonomy (ViBRANT) is a European Union FP7 funded project starting in December 2010 that will support the development of virtual research communities involved in biodiversity science. Our goal is to provide a more integrated and effective framework for those managing biodiversity data on the Web.

ViBRANT provides:

1) A virtual research environment (Scratchpads) where users can safely store, share and manage their research information.
2) Analytical services for users to build identification keys and phylogenetic trees.
3) A publication platform for users to automatically compile biodiversity science manuscripts from their research database.
4) A portal for users to centrally access publicly accessible biodiversity research information and literature.
4) Training, helping research communities to use these tools and services. 5) A standards compliant technical architecture that can be sustained by biodiversity research community.

Open source semantic web application to enable the discovery of research and scholarship across disciplines at that institution and beyond
VMWare http://www.vmware.com/ A company providing virtualization software founded in 1998 and based in Palo Alto, California, USA. The company was acquired by EMC Corporation in 2004, and operates as a separate software subsidiary. The company is most notable for its hypervisors virtual machine managers (VMM), one of many hardware virtualization techniques that allow multiple operating systems, termed guests, to run concurrently on a host computer.
World Checklist
International collaborative programme that provides the latest peer reviewed and published opinions on the accepted scientific names and synonyms of selected plant families.
Windows Azure http://www.microsoft.com/windowsazure/ Windows Azure and SQL Azure enable users to build, host, and scale applications in Microsoft datacenters. They require no up-front expenses, no long term commitment, and enable users to pay only for the resources used.
WSDL Web Services Description Language http://www.w3.org/TR/wsdl WSDL is an XML format for describing network services as a set of endpoints operating on messages containing either document-oriented or procedure-oriented information. The operations and messages are described abstractly, and then bound to a concrete network protocol and message format to define an endpoint. Related concrete endpoints are combined into abstract endpoints (services). WSDL is extensible to allow description of endpoints and their messages regardless of what message formats or network protocols are used to communicate.
Xen Xen hypervisor http://xen.org/ The Xen hypervisor, the powerful open source industry standard for virtualization, offers a powerful, efficient, and secure feature set for virtualization of x86, x86_64, IA64, ARM, and other CPU architectures. It supports a wide range of guest operating systems including Windows, Linux, Solaris, and various versions of the BSD operating systems. Xen powers most public cloud services and many hosting services, such as Amazon Web Services, Rackspace Hosting, and Linode.
XML Extensible Markup Language http://www.w3.org/XML/ Extensible Markup Language (XML) is a simple, very flexible text format derived from SGML (ISO 8879). Originally designed to meet the challenges of large-scale electronic publishing, XML is also playing an increasingly important role in the exchange of a wide variety of data on the Web and elsewhere.
XSEDE Extreme Science and Engineering Discovery Environment https://www.xsede.org/home The Extreme Science and Engineering Discovery Environment (XSEDE) is the most advanced, powerful, and robust collection of integrated advanced digital resources and services in the world. It is a single virtual system that scientists can use to interactively share computing resources, data, and expertise. Scientists and engineers around the world use these resources and services things like supercomputers, collections of data, and new tools. XSEDE, and the experts who lead the program, will make these resources easier to use and help more people use them. The five-year, $121-million project is supported by the National Science Foundation. It replaces and expands on the NSF TeraGrid project. More than 10,000 scientists used the TeraGrid to complete thousands of research projects, at no cost to the scientists. That same sort of work only in more detail, generating more new knowledge and improving our world in an even broader range of fields continues with XSEDE.
Zoomify http://www.zoomify.com/ A popular web-based image viewer that allows easy panning and zooming.
https://www.zooniverse.org/ The Zooniverse is home to the internet's largest, most popular and most successful citizen science projects.