Facilities

 

Missouri Botanical Garden

New York Botanical Garden

National Herbarium (US), Smithsonian Institution, Washington DC.

Missouri Botanical Garden (MO)

The full facilities of the Missouri Botanical Garden are available to Biocultural Collections (BC) and to the workshop participants.  The most important of these include the herbarium, the library, the computer facilities (below) and Ridgway Center.  The workshop can be held in the Ridgway Center, the visitor and education center of the Garden.  Joint sessions can be held in the Shoenberg Auditorium, with continental seating and a fully equipped audio-visual room; and breakout sessions can take place in various adjoining classrooms.  The Ridgway Center is ADA compatible, with a restaurant, a gallery, floral display hall, and smaller ancillary rooms that allow meetings, break-out rooms, meals, displays, and informal social events associated with the workshop.  The Garden grounds and buildings immediately outside the Ridgway Center have incomparable floral collections and displays representing the tropics, temperate zones, Japan, China, an English woodland, and taxonomic collections etc.  This will allow participants to escape the classroom atmosphere during breaks to roam the grounds and relax.  Catering St. Louis is now the Garden's exclusive catering company. They operate the Garden Cafe, the excellent restaurant located in the Ridgway Building on the Garden grounds.

Herbarium

The Missouri Botanical Garden, described in detail in the proposal and on-line (www.mobot.org) currently holds a collection of more than 5.5 million vascular plants and 500,000 moss collections. The general herbarium is now divided between two buildings with room to grow for the next 14 years; it will accommodate an anticipated growth rate of 120–150,000 specimens per year. The moss collection was moved in 1999 and its capacity doubled so that there is room for a similar proportional increase. About 50 researchers work at MO either on or off campus. Several are stationed abroad to undertake research projects and collecting activities. Each curator at MO has an office equipped with stereo-microscope and computers with access to the Internet, the local network, and the centralized database TROPICOS. Additional computers are available for students, technical personal, and visitors with identical software facilities. MO is taking the lead in several of the largest floristic projects in the world, e.g., the Flora of China, The Flora of North America, and the Flora Mesoamericana, along with several smaller flora and checklist projects. MO is a renowned research institution with a 140-year history of taking care of natural history collections.

Library

MO’s library contains more than 112,000 volumes of monographs and journals. More than 2,000 current periodicals are received through subscription or exchange. The main emphasis of the collection is on plant taxonomic literature, current and retrospective, collected in all languages. The ethno- and economic botany collection is significant ranging from rare books (890,000 pages available at www.botanicus.org) to the most recent publications, professionally curated by Dr. Linda Oestry, as student of Dr. Jack Harlan.  The reference collection contains more than 3,000 volumes of reference works, including dictionaries, encyclopedias, handbooks, indexes, and bibliographies. The Sturtevant PreLinnaean Collection includes works from 1474 to 1753. E. Lewis Sturtevant, a botanist and agriculturist, donated 463 volumes to MO in 1892. The collection contains many herbals and other works that are among the earliest attempts to classify plants systematically. The collection now includes more than 1,100 volumes. The Linnaean Collection contains more than 900 volumes by Carl Linnaeus, revisions of his works, and his students’ works. The Post-1753 rare book collection contains more than 2,000 books. Examples of holdings include most editions of Michaux's and Nuttall's North American Sylva. Darwin’s works in various editions, including the first printing of the first edition of On the Origin of Species is also included, as well as George Engelmann’s botanical works, accounts of many pre-1850 voyages and explorations, and the first octavo edition of Audubon’s Birds of America. The folio collection of more than 1,000 volumes includes among its works Banks’ Floralegium, a limited edition of 738 engravings made from eighteenth-century copper plates that record the botanical discoveries made on Captain Cook’s first voyage. The Ewan Collection, purchased in 1986, includes the research materials, personal papers, and 5,000 books assembled by Joseph Ewan. The collection is especially strong in the history of natural history, biography, and exploration, and it includes many rare or unique items. The Steere Collection consists of more than 1,000 titles on mosses and was purchased in 1977. MO’s bryology holdings comprise one of the world’s finest bryological literature collections. The map and atlas collections contain more than 7,000 items, including topographic, vegetation, and climatologic maps, with the emphasis on South America, southern Africa, and Missouri. The microfiche collections contain more than 40,000 fiches. Included are the type-specimen collections of more than 30 herbaria and the Plant Taxonomic Literature Microfiche Collection of 5,000 titles based on Taxonomic Literature (second edition).

Database and Computer facilities

Missouri Botanical Garden currently utilizes a database system called Tropicos to store information on plant names and specimens.  Tropicos currently contains records for over 1 million plant names and over 3.5 million plant specimens.  Our proposal is to expand the Tropicos database to include ethno/economic information to existing entries and using the expanded database to add additional specimen and name records of ethno/economic significance.

MBG maintains its production plant taxonomic database, TROPICOS, on two servers: an IBM RS/6000 Model 7013-580 minicomputer with 128 megabytes of RAM and over 100 gigabytes of hard disk space and a Sun Microsystems E3000 dual-CPU minicomputer with one gigabyte of RAM and over 65 gigabytes of hard disk space. TROPICOS will soon be migrated to a Hewlett Packard DL580 3-Ghz dual-CPU server with 4 gigabytes of RAM and 2 Gbps fiber-channel Storage Area Network. The main MBG website, www.mobot.org, runs on a Hewlett Packard DL380 3-Ghz server with 1 gigabyte of RAM, dual gigabit ethernet connections, and 288 gigabyte RAID5 array. The Librarydatabase is maintained on a Hewlett Packard AlphaServer with one gigabyte of RAM and 18 gigabytes of hard disk space. All servers are networked with a Gigabit Ethernet server room infrastructure and can support several hundred users from inside and outside MBG. A fiber-optic backbone connects Fast-Ethernet switches across the MBG campus. A dual T-1 (3.1 Mbps) Internet connection, connected via a Linux/Checkpoint firewall and Cisco routers, enables international access to the databases and the web site. The staff uses Windows-based personal computers connected to the network for access both to the databases and for outside access. A combination of SUN SPARCStations and Windows workstations are used at the Garden for GIS (ArcView and ArcInfo) and digital imaging applications. TROPICOS contains a wide variety of information on vascular plants and bryophytes collected by MBG staff, as well as a great wealth of information incorporated from other databases through collaborative agreements. The system currently employs IBM Informix and Microsoft SQL Server relational database engines. Currently there are about one million names and associated data available on the system and around two million specimen records. This information is accessible at http://www.tropicos.org for vascular plants and http://mobot.mobot.org/W3T/Search/most.html for mosses.

Mechanisms for quality control of data entry at MO are multiple:  Business rules have been built into the system to assure that data entered meet requirements.  Names are selected from authority files, TDWG authors, and BPH and TL2 journal titles.  Trained botanists are hired for data entry.  Taxonomic specialists vet entries in their groups.  Georeferencing (latitude/longitude) is included in the specimen database with fields for coordinates; locations are vetted by regional floral experts.  Mapping capabilities are included in Tropicos.  For this proposal, the post-doc coordinating the project will also oversee data entry. 
Capacity for expansion is unlimited and MO is fully committed to the permanent maintenance of Tropicos, with 25 years of data basing and institutional commitment already demonstrated.  All data entered into Tropicos is immediately available and searchable over the Internet. 
The TROPICOS database consists of a wide variety of data on plants collected by MO staff, as well as a great wealth of information incorporated from other databases through collaborative agreements. Currently there are over 1 million names and associated data available on the system and just over 3.5 million specimen records. The information can be displayed and mapped via the Web at www.tropicos.org .


The New York Botanical Garden (NY) 

The New York Botanical Garden was founded in 1895.  Its scientific programs, facilities, and research collections are indispensable resources for global research and exploration of plant and fungal diversity. 

Information Technology. The Garden has a 500-user institutional network supporting a variety of operating systems including Windows, Mac and Unix.  It includes over 50 fileservers for departmental applications and files, the on-line Library catalog, image storage, the Virtual Herbarium, network backup facilities, E-mail and various NYBG web sites.  We have recently added a 50 mbps primary internet connection with automatic failover to a secondary T1. Network core switching is accomplished via a Cisco 6500 (about to be upgraded and a second 6500 added) with edge switching  via Cisco 3500s. Wireless coverage is available in select locations, including the Pfizer Laboratory. An institutional storage area network providing 20+ terabytes of user storage, scalable to 200+ terabytes, is scheduled for August delivery. A 256-node Linux compute cluster has been proposed to the NSF in support of computational genomics. Recent major projects include development of an online ecommerce Shop website, an online registration capability for the Education Division, and a Garden-wide POS and Web-based ticketing system. Every workstation in the Science Division has access to the institutional network and to the Internet..  The Microsoft Office suite of programs (including word processing, database, spreadsheet and presentation software) is available on all institutional PC's.  Every staff member in the Herbarium is assigned or has access to a workstation and there are 10 additional computers available for use by visitors and interns.
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Herbarium. The William and Lynda Steere Herbarium contains approximately 7,200,000 specimens of plants and fungi.  It is the largest herbarium in the Western Hemisphere, and one of the five largest herbaria in the world. The geographical emphasis of acquisitions has always been the New World.  May 2002 marked the grand opening of the new, state-of-the-art facility designed to house this distinguished research collection and visiting scholars who consult it. The new collections building is a five-story, 70,000 ft² facility constructed as an addition to the Museum Building. In these new quarters, the herbarium has room for growth through at least 2020.  Funds for this approximately $40 million facility were raised from state local and federal funds as well as private sources.  A grant from the National Science Foundation helped to purchase herbarium cabinets, microscopes and computers for the facility.  Nine study rooms are available adjacent to the collections.  Study rooms are supplied with microscopes, herbarium cabinets, computer equipment and access to the Internet and to NYBG institutional databases, e.g., the Virtual Herbarium and the On-line Catalog of the LuEsther T. Mertz Library. Additional study spaces, with microscope and computers, are available in collection range area of the herbarium as well.

Virtual Herbarium. This is the electronic gateway to the collections of the William and Lynda Steere Herbarium. The goals of the Virtual Herbarium are to make specimen data available electronically for use in biodiversity research projects; to reduce shipping of actual specimens for projects where digital representations will suffice for study; and to reunite data elements (e.g., photographs and drawings, manuscripts, published works, microscopic preparations, gene sequences) derived from a specimen with the catalog record for that specimen. The digital collections of the Virtual Herbarium, comprising approximately 930,000 herbarium specimens and 120,000 high-resolution specimen images(as of July 24,2006), are updated daily as the Garden pursues the goal of digitizing all of its 7,200,000 plant and fungi specimens. Associated with the Virtual Herbarium specimen database are two other databases: Index Herbariorum, which is a directory of the world’s 3000+ herbaria, and the Index to American Botanical Literature, which is a bibliography of approximately 62,000 references to articles published since 1995 about plants and fungi in North and South America, Central America and the West Indies.

The database engine supporting the Virtual Herbarium, the Garden uses KE Emu, developed by K E Software.  The database engine underlying KE Emu is KE Texpress, an object oriented database management system. KE Texpress is an open systems, non-proprietary database engine with support for many popular software standards, including SQL, ODBC, HTML, Visual Basic, C/C++, Java and JavaScript.  It uses client/server architecture with Microsoft Windows 95, 98, NT and 2000 Client workstations connected to Unix or Windows NT/2000 servers. 

KE Emu allows for easy sharing of data and linking to other on-line databases, for example, The NYBG Virtual Herbarium is linked via the DiGIR software to the GBIF data portal.  NYBG is a charter member of the EMU Natural History Users Group, which works to advise KE Software on enhancements that meet the need of large natural history museum collections and the scholars who use it.

The Virtual Herbarium was moved to an enhanced server in June 2008. In addition to increased speed for data entry and retrieval, the new server allows for the replication of data to avoid downtime during the nightly reindexing process.

There are several options for searching a Virtual Herbarium catalog.  The Quick Search option is similar to a “Google” box, where search terms can be entered in any order without punctuation.    The Detailed Search option will allow geography-based queries, and also will allow a more structured query on a variety of fields than is possible with the Quick Search.  The Checklist feature lets the user see what taxa are included in the catalog. The lists are arranged by family, and within a family, by genus and then by species. The names are hyperlinked, and clicking on the link initiates a search of all records with that name.   When a search is launched, matching records are sought, and if found, these are displayed in the Search Results table.   The data displayed are a subset of the information captured for all specimens, and include an image thumbnail, the taxonomic name, the collector, the collection location, the type status, and the barcode ID.  

Selecting a record from those listed in the Search Results table invokes the Specimen Details page, which displays all the information that is included on the specimen label, supplemented sometimes by interpretive notes added by the cataloger, and multimedia attachments that relate to the specimen. The taxonomic name is hyperlinked to the Taxonomy Details Page that always includes the name of the plant (binomial plus authority), and sometimes also includes the citation for the original place of publication for the species, synonyms, and a description of the species.  The Person Details includes the name of the person (abbreviated and full), birth and death dates of the person, if known, groups of organisms studied by the person (e.g., Bryophytes, Pteridophytes), the person’s role (e.g., Author, Determiner, Collector, or some combination of these); other details as available, e.g., for collectors, countries or regions where collections were made (generally not an exhaustive list), and other biographical details about the person or their research activities.

The specimen, taxonomic, and person records may be supplemented by images, documents (e.g., Microsoft Word documents, .pdf files), or links to other websites.  The images that appear on the Specimens Detail page are thumbnail images. Clicking on the image will reveal the full size image of the specimen. In addition to specimen images, there may be images of the plant in the living condition; micrographs derived from some part of the specimen, or images of notes, drawings, field book entries or correspondence relating to the specimen.  The collection location of a specimen is displayed on a Google Map, if geocoordinates are available.)

Users have the option to download Search Results on a page-by-page basis, or, for up to 1000 results, to download all results at one time. The data are downloaded in the CSV (comma separated values) format, and can be easily imported into a spreadsheet or database program. Data downloads larger that 1000 records, or download requests that include information beyond that included in the Search Results table, are available by special request. A project is currently underway to allow a user to download records in the KML format for display as a map layer in Google Earth.

NYBG is committed to making Virtual Herbarium data exportable in any format required for other biodiversity projects.   Data are served currently to the GBIF Data Portal (www.gbif.org) and speciesLink using the DiGIR protocol, and Searches using engines such as Google index individual Virtual Herbarium records, and these are linked through the Detailed Results page.   As explained on The Virtual Herbarium website page entitled, “How to link to our data (http://sciweb.nybg.org/science2/hcol/howtolink.asp), it is very simple to construct URLs that will link to searches against the Virtual Herbarium.  This page explains how the URL is made, which parameters are available for searching, and gives examples of values to use for those parameters. These data will also be available through the GBIF Data Portal.
 

Digitization Laboratory. The new Herbarium Digitization Laboratory opened in October 2005. This 787-ft2 facility contains four digitization stations and one lab manager’s workstation. The digitization stations, which are separated from one another by light-impervious, retractable screens, surround a central work counter that doubles as a conference table. Each digitization station consists of a camera and light stand attached to a dedicated computer. One specimen digitization bay contains an Eyelike Precision M22 Digital camera mounted on a TTI Repro-graphic workstation, attached to a Macintosh G5 computer. This camera captures raw images in the range of 64 to 490 megabytes.  A second station contains a Canon EOS-IDS Mark II, and a third has a Kodak instant capture digital camera; both of these are attached to Bencher light stands and are connected to Pentium 4 PC computers. The size of raw images captured by these cameras is 6 megabytes. The fourth station consists of two book scanners, each with book cradle and each attached to a Pentium 4 computer.   All computers in the lab are attached to the NYBG intranet; raw images captured by the Digitization Laboratory cameras are stored in the Archivas Content-Addressed-Storage system. Additional equipment includes several flatbed and photographic slide scanners. Three specimen scanning stations (using a Herbscan apparatus) have been added to the Garden’s specimen digitization arsenal since March 2007.  The Herbarium Digitization Laboratory, which is overseen by Digitization Manager Nestor Pérez-Molière is available for use by specimen cataloging projects, scientific research projects by staff and graduate students, library digitization projects, and undergraduate internships.

Library. With more than 1.25 million print and non-print items, the international botanical community considers The LuEsther T. Mertz Library of the New York Botanical Garden one of the most important research collections in the world, holding more then 260,000 volumes of books and journals.  The Library collects comprehensively in systematic and floristic botany, with particular strengths in studies of the Western Hemisphere, the focus of NYBG’s scientific research program.  Since the establishment of the Library in 1897, other major research and academic libraries in the New York metropolitan area have deferred to it for developing and maintaining collections of literature in botany, horticulture, landscape design, and the history of gardening, making the Mertz Library the reference plant library of record in the metropolitan region.  The Library’s on-line public access catalogue, CATALPA (CATAlog for Library Public Access) presents full bibliographic descriptions, subject headings, and author and title entries for its entire collection of books and journals.  It is accessible to users worldwide over the Internet with a web browser.

Geographic Information Systems (GIS) Laboratory.  The New York Botanical Garden’s Geographic Information Systems Laboratory supports the Garden’s current botanical research and conservation programs by expanding and enhancing analytical capabilities through GIS, training science staff and graduate students in spatial analysis tools, and providing services such as publication-quality maps and analyses to the Garden’s scientific staff and collaborators around the world.  The GIS Laboratory also leads a spatially-based research program aimed at addressing urgent issues in biodiversity conservation, for example, identifying those plant species at greatest risk of extinction, and the geographic areas that are critical for their preservation.  Research draws on the important data resources of the Garden, particularly specimen records in the C.V. Starr Virtual Herbarium.

Equipment in the Lab includes six computer workstations equipped with ArcGIS, ArcInfo, Geoda Google Earth and Google Earth Pro software, a UMAX color scanner, a large-format color printer, color laserjet printer, and a SMARTBoard Interactive Whiteboard, used for demonstrations and training.  The GIS Laboratory draws data from numerous regional sources, and global sources such as the Digital Chart of the World and ESRI Data and Maps (including global imagery shaded relief and elevation data) and is building a digital library of GIS data relevant to botanical science and conservation.


National Herbarium (US), Smithsonian Institution, Washington DC.

Research:
Programmed research activities in the Department of Botany focus on plant systematics in the broadest sense: taxonomy, nomenclature, investigations into comparative anatomy and morphology, molecular systematics, cytology, palynology, phytogeography, ecology, evolutionary theory and economic botany.  Numerous floristic studies are under way, while other research projects are aimed at elucidating evolutionary development, phylogeny, and the broad questions of classification.

Collections:
The United States National Herbarium is a major facility within the Department.  The worldwide representation of plants is comprised of about 5 million specimens.  This herbarium ranks among the best in the world and is especially rich in material from North America, and New world tropics, with additional strengths in the Pacific Islands, the Philippines, and the Indian subcontinent.

Many of the plant groups represented in this collection rank among the best in the world.  Flowering plant families of Acanthaceae, Asteraceae, Bromeliaceae, Gesneriaceae, Melastomataceae, and Poaceae have benefited from a long history of research and study.  Other flowering plant families that enjoy active support include Araceae, Araliaceae, Commelinaceae, Euphorbiaceae, Onagraceae, Passifloraceae, Sapindaceae, sea grasses, Sterculiaceae, and Zingiberales.

The cryptogamic collections rank as premier collections.  The lichen herbarium is one of the best and well curated collections in the world, number more than ¼ million specimens from worldwide localities.  The collection of ferns and fern allies also rates as particularly significant, both in terms of size and historical importance.  Collections of algae and related groups represent an important resource for the study of tropical and subtropical marine taxa, and temperate freshwater groups.

The all-important Type Collection contains more than 100,000 verified type specimens whose data and images are available electronically through the Department’s website.  Other collection resources include a 45,000 specimen wood collection, and microslide reference collections for wood anatomy, pollen and spores.

Infrastructure:
The Department of Botany and the United States National Herbarium occupies over 72,000 square feet of environmentally controlled space for collections, libraries, labs and personnel.  Major improvements to the heating, ventilating and air conditioning systems are under way, and a longer term space analysis within the building has identified a planned 25% expansion of space dedicated to the programmatic needs of the Department of Botany.

Microtechnical and molecular laboratories, equipped with state-of-the-art technologies, are staffed and maintained for use by researcher and visiting scientists.  These facilities support current research that interrelates metabolic, ecological, and anatomical mechanisms in elucidating evolutionary and biosystematics processes, as well as analyses using isozymes and DNA-based genetic markers.

A greenhouse complex measuring more than 8500 square feet supports a diversity of living research materials for all manner of study.

The capacity within the Department of Botany, the National Museum of Natural History and the Smithsonian Institution to provide IT support services, massive storage for digital objects, and web delivery options for collections accessibility is both sufficient for the current need and can support significant expansion.