Saved report templates can now be registered and shared with all users using the Report Manager tool. The manager lists the report templates registered for the opened table with the report names and descriptions. Database users can then select and run registered reports, by-passing the report designer. Users with appropriate permissions can design and register reports in the manager. Registered templates (represented by XML instructions) are incorporated into your database and thus there is no need to locate and share the actual .mrt template files. If 'Shared' is selected, a report will be listed and available to all users. Otherwise, the template will only be listed for the user that created it. Existing .mrt files or files you have received from another project can be imported and thus registered in the manager. Report templates can also be exported to .mrt files for exchanging with other users/projects.
Users without the appropriate permissions can only run registered report templates. Click on the image to see further options.
The BRAHMS ‘WebConnect’ module has now been completed allowing users to create and design websites directly from BRAHMS using the tools provided on the Publish Online menu. You can develop web pages using the full flexibly of HTML, CSS and JavaScript (including JQuery) and selectively upload data and images to your website for taxa; collection events; specimens; seed accessions and their tests; and living collections.
When uploading data, you can choose to upload new records, changed records or otherwise restrict to tagged. Each record in the relevant BRAHMS tables has fields that indicate who uploaded the data and when. By comparing the upload and last modified dates, the system is able to restrict uploading to records that have been changed since their last upload.
Procedures are now provided to create new RDE files from pre-designed project templates - simplifying the file creation process for RDE users. There is no limit to the number of templates you can create.
Projects can now pre-design RDE templates for different categories of data capture and locate these templates in a shared folder designated via a new RDE setup option. The new setup options also allow the database manager/admin to restrict access to the RDE file Creation Wizard on a user by user basis. Users creating new RDE files can now choose a project template to copy from the RDE file template list. Access to the RDE file Creation Wizard can thus be limited to database managers. Using the Wizard, new templates can be defined and added to the shared RDE templates folder.
One of the latest data analysis tools added to BRAHMS is for 'Multi-Column Analysis'. The tool enables you to select two or more data columns in the opened table and it then provides a total for each set or records that have the same data values for these selected columns. This tool has useful applications for all databases. For example, in Collection Events, if you were to choose the fields Family, Country and Year, the totals will be the number of records per different Family + Country + Year combination. In the same table, if you were to choose Collector + Country + Genus + Species, the list would show the number of different species collected by each collector per country. The same tool can also be used to identify and mark up duplicated record entries./
You can select any columns to include in the analysis. By default the results are sorted by count. You can apply filters and sorts to the results data grid. In the above example, we can see that the collector Walters, T. made 89 collections of Agathis lanceolata in New Caledonia.
Recognising the growing importance of international regulations that control the collection and distribution of bio-materials, this version includes extended features to link collections to legal agreements/permits and, optionally, to align these within a selected legal framework.
New functions are also added for exporting entire databases to XML; the ability to transfer databases between data stores; to view all literature links and transaction details across the system; and to manage date time storage more effectively for projects editing data across time zones. Fixes are provided for all reported bugs including those relating to the management of custom fields. The full release notes are published on: https://herbaria.plants.ox.ac.uk/bol/brahms/software/revisions. The BRAHMS manual is updated.
The default legal/permit values as provided can be edited under System > Options > Management > Legal Setup.
A database export tool is now available - allowing you to export an entire database to a folder of XML files. These data can subsequently be imported to another database using the existing Import tool. Using this function, you can transfer your database(s) from any data store to any other store. For example, you could move a database from SQLite or MSSQL Server to PostgreSQL - or in the other direction. This function is added to 8.0.10.
The new data export/transfer tool exports all data including configuration settings.
v8.09 was published 31 October. This is a substantial update with new features and improvements across the system. In addition to an upgraded Seed Module, improved personal name management and overhauled RDE to BRAHMS transfers, there are new tools for date filters, multi-column analysis, Darwin Core archive (DwC) exports, map tagging, GIS links and query sharing.
RDE transfers to BRAHMS are faster and have improved progress feedback. Using the internal ArcGIS mapper, map tagging can now be used to select multiple points for editing or any other purpose.
The full release notes are published on: https://herbaria.plants.ox.ac.uk/bol/brahms/software/revisions.
A major revision to the BRAHMS Seed Manager Module was published mid-September and is now being tested for live use. This module, developed collaboratively with the Millennium Seed Bank Partnership (MSBP) at Kew, has broad curation and research applications for projects that collect, store, test and distribute seed. Included are options for recording detailed seed passport data, seed cleaning and processing, calculations for seed weights and counts, X-ray, tetrazolium and germination testing. For germination tests, results can be scored across replicates for any number of test days with selected observation intervals, leading to the final calculations for germination and viability%. The test scoring form can be conveniently used on a lab bench tablet.
Entering seed weight calculations and germination test observations
A BRAHMS app for botanic gardens has been launched. The app runs on Android and iOS tablets or similar devices. An internet signal is not required - thus it can be used in remote, offline areas. As with BRAHMS desktop, data can viewed and queried in flexible data grids. The app provides functions for stock quantity and status checks, requesting labels, plant moves, verifications, adding notes and adding other general events and requests, for example for propagation. Plants can be geo-referenced using the in-build mapping capabilities. Images can be taken and auto-linked to plant records. If online, you can use dynamic weblinks to check details and images for the current plant name. Data from the app are returned to BRAHMS desktop where you can update the relevant plant records. Further details are provided on the App for Botanic Gardens page.
The garden app speeds up stock checks and related data gathering activities
Dynamic links to the GBIF and JSTOR sites (JSTOR requires licence agreement) to check data against the selected data grid taxon name have been added - the weblinks update as you browse through your data.
Dynamic links to various handy web sites are provided on the Weblink toolbar
The BRAHMS software was updated to v8.08 14 June 2021. The full release notes are published on https://herbaria.plants.ox.ac.uk/bol/brahms/software/revisions.
BRAHMS can now be fully connected to PostgreSQL databases, providing a further option for storing large datasets. This addition will be included in v8.08 which will be published later in April. A data connections wizard for PostreSQL has also been added allowing you to create new PG databases directly from BRAHMS.
PostgreSQL is a free and open-source relational database management system emphasizing extensibility and SQL compliance.
Two revisions for BRAHMS were published during March this year with a substantial number of new features across the system as well as resolving reported snags. The full release notes are published on https://herbaria.plants.ox.ac.uk/bol/brahms/software/revisions.
The multi-value search tool, available in all tables, enables you to copy or enter a list of values to locate and tag records in the currently opened table. For example, you may have a list of species names, collector numbers, publication years, plant accession IDs, barcodes or transaction IDs that you wish to locate. Rather than searching for these one by one, the data items can be manually added to the multi-value search area or pasted in from a list you may have - e.g. a list of values in a Word doc or an Excel column.
The multi-value search option allows you to search for a list of data values.
Version 8.04, released 12 December 2020, includes new features across the system. Changes include the addition of new database indexes that improve overall system efficiency; alterations to the way that RDE data files are imported - now faster and providing additional data analysis feedback; improvements to data grid filtering, especially when querying on numeric values; a range of refinements and additions across the living collection module including a more explicit mechanism to define and control the printing of garden labels; and extensions to mapping tools in RDE files. All reported bugs have been fixed.
The full release notes are published on https://herbaria.plants.ox.ac.uk/bol/brahms/software/revisions.
An example showing multi-parameter character and numeric filtering using the data grid filter row.
Version 8.03 includes features for more efficient sign-in and other system level set-up options; new tagging, filtering and reporting features; additional options for taxonomy and botanic garden management. All reported bugs have been fixed.
The full release notes are published on https://herbaria.plants.ox.ac.uk/bol/brahms/software/revisions.
Version 8.02 brings together many new features and enhancements – as well as resolving bugs as reported. The release notes are published in the v 8.02 release notes document.
A right-click on data grids now provides quick access to many of the commonly used toolbar options.
Earlier this year, Kew Gardens adopted BRAHMS to manage their living collections. Kew has two main public garden sites, one at Kew in London and the other at Wakehurst Place further south in Sussex, also the home to Kew's Millennium Seed Bank. Working closely with Kew horticultural and IT staff, functionality in BRAHMS has been extended to manage Kew's extensive living plant collections with many new features and functions added, based on their long established horticultural practices.
The Royal Horticultural Society (RHS) has announced their adoption of BRAHMS to manage their extensive plant names backbone as well their network of gardens and herbarium collections. Using the expertise of RHS in this area, a new approach that helps manage the complexity of cultivated plant names has been built into BRAHMS. More details are provided in the news item: Oxford teams up with The Royal Horticultural Society to develop innovative plant data management.
The latest BRAHMS system published 10 July. As well as wrapping up all reported issues, v8.01 includes new plant propagation features as part of the Living Collection module. Propagation activities for seed, cuttings and grafts have been streamlined into a more flexible structure which caters for standard production propagation as well as more detailed experimental work. Plant records can now be generated directly from propagation with a tracking system recording the propagation history of each plant.
The latest update to BRAHMS includes a handy User Notification function. This can be used by system administrators to broadcast a message to active users on a networked system. The primary function is to advice users to log out for a software upgrade – with an option to auto-shutdown BRAHMS after a specified number of minutes. Raw phenology data can now be recorded against plant records for any registered trait (flowering, fruiting, leaf flush, etc.) and these data can be summarised by month in table or graph form. Another handy new addition is the ability to sort records in any table that includes species names using Natural Species Sort order.
User notifications can be broadcasted by the System Administrator.
Raw phenology data can now be recorded against plant records for any registered trait.
The name list of the right-side uses Natural Species Sort order.
BRAHMS data grids look rather like Excel worksheets – the data are presented in rows and columns. How does this work in databases with millions of records in a single table? The answer lies in data virtualization. As you scroll up or down the data grid, BRAHMS pulls data from your data store as needed. In fact, the system gathers a little more data than you see at any one time, probably about three screens worth of data - and this helps to provide a seamless flow of data as you scroll up and down the data grids.
In the latest BRAHMS update, the efficiency of data virtualization has been increased. And some handy new instant sort and filter functions have been added. One of these allows users to quickly sort on those records added or last modified most recently. Another allows individual users to filter on the records that they have added or edited.
New quick sort options are provided to bring the last modified or last added records to the top of the table.
A package of updates has been introduced to the living collection module. These include new features for configuring accession and plant ID numbering; adding clonal and non-clonal plant records; deading and resurrecting plants; plant name verification; improved control for name changes; an upgraded stock control system; and the requesting and printing of engraved or standard labels.
One of the new options for botanic gardens provides greater control over changing plant status - deading and resurrecting.
The living collection plants form has a new Identification tab providing greater control over plant naming and for editing plant-voucher links.
If a name is confirmed, a confirmation event is auto-added to the plant Events table including the date and confirmation person. Name change options also allow the separation of clones to a new accession where there is an identification discrepancy for plants derived from the same accession.
On the Plant Vouchers tab, options are provided to list, link and unlink vouchers. This plant has 5 vouchers collected over several years and with different flowering/fruiting status. Here, a filter has been set on the calculated field #VoucherTotal to show plants with >= 3 vouchers. A plant may have multiple vouchers of different categories (herbarium specimens, DNA samples and similar) added over time.
Database manager(s) can now control in more detail the permissions a given user has in a given database. Access can be provided on a module by module basis. Within each module, the user may have Read Only or Read and Modify access. If modify access is provided, the user may selectively be allowed to add records, mark records for deletion, and then to delete records.
User permissions showing a range of settings. Click on the above image to zoom in...
As well as listing and mapping plants by garden area/location from the main plants table, you can now do this directly from the gardens locations table using some handy new form options. With the locations form opened, you can dynamically list or map plants from the current location, browsing through the locations table to update the display. Maps can be restricted to plants that have a Live status or equivalent. You can also map plants for all tagged locations. The next revision will include options to plot KML/KMZ areas defining garden zones and areas.
Plant lists and maps dynamically update as you browse through your locations table
It's often necessary to adjust a map point position based on a distance measurement, for example where a collection event locality note say '20km west along route 249'. Or perhaps to know how far one sample site is from another e.g. in a marine sample site, forest or a botanic garden. This can be done using the internal Map Point Editor Distance Measurements option. Distances can be calculated in different units and if appropriate, an adjusted point can be auto-added to your data grid.
After drawing a polyline, a right-click on the map will update the data grid map reference. Click on the above image to zoom in...
The internal Map Point Editor, dynamically connected to your data grids, has been extended with a location search tool. Localities can be searched for by name or part of a name, adding a region or country to help improve the results listed. Clicking on the suggested locations list adds a blue suggestion marker to the map. A right-click on the map adds the map reference to the data grid. The location search is very similar to that provided in e.g. Google Earth.
The newly added location search option extends the value of the Map Point Editor. Click on the above image to zoom in...
Tagged records in the main species table can now be passed to the Taxonomic Name Resolution Service (TNRS) for analysis/verification. This tool is available from the main Taxa menu when the species table is opened.
The TNRS tool provides a handy way to check taxa names against a number of authorities. Click on the above image to zoom in...
The most recent updates to BRAHMS include some cool new features for editing and managing data and images.
The Image Import tool allows you to import any list of images (file names or URLs) from an Excel .xlsx file, register the images in your image library and link the images to the correct record within your database using one or more data match fields. In the BRAHMS manual, refer to the section Images > Importing images and image links from Excel.
The Find/Replace options works in text fields in RDE and the main database tables. The option is described in the BRAHMS manual section Adding and Editing data > Find and Replace.
The Tag Transfer option has been expanded to transfer tags either to child records or parent records. Thus, if you have tagged a selection of collection events, perhaps using a map filter, you can then use these tags to tag the relevant species, genera, family records in their respective tables. On the other hand, you could tag some species and use these to tag all related collections, specimens, seed accessions, plants and more…
When licensed users update their BRAHMS software, the system now offers to auto-update the structure any connected databases – assuming structural changes are needed. The version of your current database is compared with that of the new software and any required updates are carried out accordingly. If there have been multiple software revisions since your last update, the necessary updates are carried out sequentially. You need to be online to use the auto-update option.
All database updates are now managed by your updated software
The BRAHMS manual has been substantially updated with new sections on Licensing; Installation; Software Updates; Data Stores and Connections; Database Management; User Accounts and Permissions; and Setup and Language. A separate installation guide has also been prepared. Meanwhile, toolbars have been updated to make these ever more intuitive while incorporating a growing number of functions.
Toolbars have been revised to optimise efficiency and layout. Options are grouped into context sensitive tab areas, dynamically enabled.
The September updates to BRAHMS include improved data links to ArcMAP, QGIS and Google Earth; a new central manager for lookup values; a new procedure to import data directly from Excel into any BRAHMS table; and dynamic website creation and editing.
BRAHMS now passes many more data fields including record GUIDs to ArcMAP and QGIS allowing you to check data against locality names and set map themes. Data edited in your GIS can be used to update locality data in BRAHMS.
WebConnect provides tools to add and format web pages and link pages into website menu options. You can set individual pages to require a login, typically used to search sensitive data. The right side of the screen displays and updates your live web site as you edit.
The BRAHMS online Millennium Seed Bank Partnership Data Warehouse has been updated and now stores data on over 144,000 seed accessions with linked wild origin and germination test results. Also added are some 6000 x-ray images of seed, these contributing to the viability testing. Registration and login is required to explore these data. For information on gaining access to the Data Warehouse, please contact Naomi Carvey [N.Carvey @ kew.org]
Top: Xray images are used to assess seed viability. Lower: Interactive cluster map showing seed collection locations.
You can now link directly to ArcMap/ArcGIS and QGIS, assuming you have access to these GIS packages, creating new map projects or open existing ones. If the saved project includes the BRAHMS map point output file as a data layer, this will plot the tagged or filtered data you have selected together with whatever other layers are saved to the map project. Note that the BRAHMS internal ArcGIS mapper requires no installation - but you do need to be online.
Dynamic links have been added to the World Flora Online website with the pages updating as you browse through your data grid.
A range of new developments has been incorporated into BRAHMS v8 during the last month. 1. New data verification tools are available throughout the system. Unlike v7, a given record may have multiple verification entries, tracking verification status category, by who, when and optional comments. Records can be tagged based on their latest verification status, for example records where the map references require checking or those that have doubtful determinations. 2. The transfer of data from Excel to RDE has been speeded up. 3. RDE to BRAHMS imports now maintain the import log in the RDE manager itself as a permanent data transfer reference. 4. There are further configuration control options for data grids, for example, adding vertical grid lines. 5. The record Zoom window has been extended with options to show all fields or only those with data and to navigate to a column by double-clicking on a zoom window field name. 6. Living collection event records are now importing from RDE with options to update plant status, label requirements and annotations.
The Zoom option provides a handy summary of the entire record and also allows you to navigate to any column by double-clicking on the Zoom window field name
A new short guide Getting started with BRAHMS v8 has been prepared with some 25 illustrated tasks, many with video links. The tasks focus on topics such as opening and docking tables, sorting, lookups, defining data views, querying, exporting, editing data and a selection of mapping and reporting features.
BRAHMS v8 users can be assigned access and permission rights to a selected database project. Permissions are edited by the system administrator or database manager. A permission set can be created/saved and can subsequently be assigned to other users. Permissions influence the following features: A) The modules or components of modules that a user sees (modules can be completely hidden); B) Where access is provided, this can be set as Create, Read, Update and Delete (CRUD); Read and Modify; or Read Only. C) Additional non-module related access features can be edited such as the ability to merge records or edit map points.
Left, this permission set may be suitable for a transaction manager; right, an example for visitors with read-only access.
A new map point editor has been added to v8 allowing you to dynamically select map points for collection events, garden plants and the like - with great precision, speeding up all geo-referencing activities. The editor is available in RDE and in your main tables. With auto-save enable, a right click on the map auto-updates the data grid values. Various options are provided to control the map units used, zoom levels and base map selection.
In BRAHMS v8, you can now open and coordinate multiple windows including grids, forms, dynamic weblinks and maps. These windows update as you change grid records.
The first full release of BRAHMS v8 was published on 21 August 2018. You can obtain a copy of the full system for evaluation together with an introductory guide from the OUI evaluation website. The guide provides a series of tasks with links to demonstration data. It introduces a range of topics for botanists, zoologists and others working with Natural History data explaining also how you can import your own plant or animal data.
Video clips demonstrating a range of functions in BRAHMS v8 are gradually be uploaded to https://herbaria.plants.ox.ac.uk/bol/brahms/software/v8videos . These cover wide range of topics from Adding a new user to Mapping and printing labels from a Rapid Data Entry file.
BRAHMS version 8 is being launched August 2018.
Adding to the existing report features, we have connected BRAHMS v8 to a reporting suite that effectively replaces the functions of Text and Visual reporting in v7. As with the ArcGIS API, links to Stimulsoft Reporting have been fully embedded in BRAHMS v8. This new reporter, which comes licensed with BRAHMS, provides almost limitless power to generate lists, master detail reports, labels, charts, cross-tabs and more. You can print, send to documents, attach as email or publish online. Stimulsoft report wizards are provided and there are guides and videos available online for those wanting to stretch their report design legs. Some ready to use examples are provided with BRAHMS, together with some start up notes. For those familiar with v7 reporting, there are many familiar features such as a visual designer; report bands for headers, data, footers and summaries; and text formatting and style setting. Although not needed, you can refer to the full reporter user manual.
The new reporting features integrated with v8 include handy wizards to get you started.
BRAHMS v7 users will quickly recognise many of the tools and functions in v8 as well as the broad layout of the menus - making it easier to upgrade. Some of the main differences between v7 and the new system are highlighted here: Changes_in_v8.pdf
Data grids have a handy filter row where you can enter values to filter on multiple columns.
BRAHMS v8 is now approaching publication as we add in the few key remaining core functions and features. One of these is RDE which we have left to the last. RDE (Rapid Data Entry) provides a very efficient mechanism to add to data - or to gather data from external sources such as Excel files. In V8, All RDE files can be editing after transfer to BRAHMS and then used to update your database.
The video clip below shows how you can coordinate Tree Views with the in-built ArcGis mapper. The Tree View of taxa names is set to Filter on selection (lower screen). The map background switches from Dark Grey to World Imagery. Maps auto-update with filters and the current collection event record is highlighted in yellow. Clicking on map points locates the record in the grid, an excellent way to locate map errors. The Extent of Occurrence (EOO) is easily calculated.
The new BRAHMS system v8 is now under trial at the Oxford University Herbaria. The data from v7 have been transferred in full to a MS SQL Server data store. We will test and adjust the system during February, adjusting as necessary and monitoring performance. Some of the new BRAHMS v8 features are documented on the Explore BRAHMS v8 page.
A form designer with new data display options capable of running on smart phones has been added to BRAHMS online. Once logged in to your website and with the form designer opened (option listed under your login options), you can set up one or more forms for the listed data categories (taxa, specimens, living collections, seed), choosing the form fields to include. The fields can be set to search on 'starts with', 'exact match', 'contains' and 'numeric ranges' - as appropriate. The form designer has a test facility within the designer itself. However, the idea is that you then copy the generated HTML code to a new page on your website and here, edit/refine the code to alter form appearance.
The results can be displayed as they are now in lists, grids and/or maps. But you can also choose to display the results as text in pages. These pages, formatted using knockout templates, can be edited by adding your own report templates. Pages can include images. You can set up several forms, each with different search fields and with a different audience in mind - and these pages can then be added to your website via BRAHMS WebConnect. It should be stressed that the sample output provided is only an example of what can be achieved. A little investment in learning to use knockout templates will pay dividends here. Both the form and the results are easily used/displayed on smart phone size screens. Results can be diverted to a new page on your website - or added below the search form.
The Hanoi herbarium BRAHMS online website on a mobile phone showing a search form and the results including options to zoom into images
With support from a UK BBSRC Global Challenges Research Fund (GCRF) grant ‘Strengthening the Botanical Infrastructure of Malawi’, a one week BRAHMS training event with a focus on specimen imaging was held at the National Herbarium and Botanic Garden of Malawi (15 – 19 May).
Further documenting and improving the knowledge of the Malawi flora will make an important contribution to the management and conservation of its forest and agriculture base, as well as contributing to all aspects of taxonomic research. The font of this knowledge is held at the National Herbarium and Botanic Garden (NHBG) in Zomba. Through this project, NHBG will be better placed to provide reliable botanical information for research and natural resources management. The initial target is to barcode, image and enter data from all 80,000+ herbarium specimens and to publish these verified data online.
The database work builds on previous BRAHMS related training provided by Tim Pearce and computing equipment provided by the Shire River Basin Management Program. Donald Mpalika, IT specialist at NHBG, has already established a data network within the herbarium to optimise the efficiency of the data and image related activities, and Dr. Elizabeth Mwafongo, the Senior Scientific Officer at NHBG, is prioritising material for digitisation. Building on these activities, the current acting director of the NHBG, Dr. Zacharia Magombo is now assembling a package of related activity to further support and expand the role of the herbarium and botanic garden with support from the Malawi Ministry of Natural Resources, Energy, Mining and Environment.
The Indian Ocean Commission (IOC), through its European Union (EU)-funded Biodiversity Program, held a 3 day BRAHMS data management workshop for the herbaria of the Western Indian Ocean (WIO) region. This took place just before the annual African Botanical congress (AETFAT) which this year was held in Nairobi, Kenya. Participants from the Comoros, Kenya, Madagascar, Mauritius and Seychelles were able to refine their knowledge in the use of BRAHMS and in particular, look at new ways of rapidly imaging their herbarium specimens.
The IOC project is supporting the development of a regional botanical network for the Western Indian Ocean region. The islands of this region are marked by a very high rate of endemism. BRAHMS Online will allow individual institutions to publish data online and make their herbaria visible to the wider botanical community, attracting both funding and researchers to their institutes. A pilot project gathering all data and images for the Orchid family has already been completed – this is now being extended to cover all plant families represented in the region’s herbaria.
As part of the IGAD Biodiversity Management Programme, a regional conservation initiative covering seven countries of the Horn of Africa region, an intensive herbarium specimen imaging project has commenced at the East African Herbarium (EA), National Museums of Kenya (NMK) in Nairobi and in the key herbaria of Ethiopia. The EA herbarium is the largest in Tropical East Africa with some 1.2 million specimens. Specimen images are being captured at 4 imaging stations using high resolution Nikon D750 cameras with 50mm lenses mounted on Manfrotto tripods with NanGuang 3 LED photo lighting. Similar equipment is being used in Ethiopia at the National Herbarium (ETH), the Ethiopian Biodiversity Institute (EBI) and at the Haramaya University herbarium. Activities are soon to be extended to the University of Khartoum herbarium (KHU) in Sudan and at Makerere University herbarium in Uganda.
Lawrence Monda, NMK IT manager has set up a BRAHMS network operating from an NMK server allowing multiple users to log in using Remote Access. A similar set up is being implemented in Ethiopia by Fiseha Getachew. Approximate imaging speed is 3 specimens per minute per camera station. Data entry is supported using the new Rapid Data Entry ‘data from label images’ procedure with links to taxon and location dictionaries. The entire process including procedures for data capture from the label images is described in the BRAHMS support article Guidelines for specimen image capture and image based data entry.
A milestone has been reached with the first release of an entirely new generation of the botanical data management system known as BRAHMS. The alpha release, published today, 22 March, takes advantage of the latest data management technologies, creating new opportunities for curation and research for projects running in over 80 countries. For more information, refer to our preliminary guide at http://herbaria.plants.ox.ac.uk/bol/Content/Software/v8/BRAHMSv8alpha.pdf . If you are interested in evaluating v8, please contact the BRAHMS project.
Vietnam has a highly diverse but neglected and heavily threatened flora, and most of the specimens and associated data have been effectively inaccessible. With support from the JRS Biodiversity Foundation project Taking the Vietnam Flora from Isolation to Integration, the Institute of Ecology and Biological Resources of Vietnam and New York Botanical Garden have been supporting specimen data and image capture at the Hanoi Herbarium (HN) in Vietnam. These data are gradually being published on the BRAHMS online site http://herbaria.plants.ox.ac.uk/bol/hanoi where you can search on the data and view the images. The initial focus has been on 11 plant families important in the flora of the country.
Some example searches: Some images of the genus Knema ; Ericaceae collections ; Collections from Kon Tum.
A one week BRAHMS course was held at the Ethiopian Biodiversity Institute (EBI) for staff from EBI, the University of Addis Herbarium and the National Botanic Garden. The course covered the full round of activities from data and image capture to building databases, reporting, mapping and publishing online. Looking ahead, with support from the Biodiversity Management Programme (BMP) for the Horn of Africa region project, the plan is to step up digitization and imaging at EBI and ETH and to build a more integrated botanical data infrastructure for the herbaria and botanic gardens. The course, organised by Kirsty Shaw, Head of Ecological Restoration and Tree Conservation at BGCI, was given by Denis Filer, Oxford Plant Sciences with support from Botanic Garden Conservation International (BGCI) and the Darwin Initiative.
BRAHMS 7.9 includes a range of improvements and additions including querying living collections by garden transaction, improved EDITHIST track changes analysis and further options to restrict web uploads, for example redacting CITES taxa. v7.9 also includes a number of new features relating to v8 upgrading. For gardens, new fields added to main species file to indicate species value for taxonomy/evolution; conservation/biodiversity; heritage and landscape; and plants and people. RDE features for rapid barcoding and specimen imaging have been upgraded. News about v8 will be provided here by end of January.
A one week training course was held at The Morton Arboretum in Illinois. This was for staff working in garden curation and propagation and the herbarium team. During this visit, refinements and additions were made to BRAHMS, streamlining day to day garden curation procedures and the coordination between garden and herbarium data. The Morton Arboretum mobile garden app running on Android 7" tablets was demonstrated. The map-based application connects to BRAHMS v8, sending in plant details such as inventory, observations and management requests. The visit was organized by Sai Ravichandran and Matt Lobdell and the various courses were presented by Denis Filer. The visit was funded by the Institute of Museum and Library Services (IMLS) grant. Following this visit, a revised BRAHMS system 7.8.5 has been published and can be downloaded.
In Dushanbe, the capital of Tajikistan, from 19-22 July 2016 Jan and Marjo Wieringa (Naturalis, Leiden), Anneleen Kool and Hugo de Boer (NHM, Oslo) and Abdolbaset Ghorbani (Uppsala University) taught a basic Brahms course. This course brought together botanists from Tajikistan, including those working in the National herbarium (TAD) and some of the smaller regional herbaria. The TAD herbarium will start to digitise their entire herbarium, including images of all sheets, and eventually put their database online using a BOL website. The course was principally about imaging sheets and entering data in RDE files, but also on extracting and analysing data. An interesting challenge has been interpreting hand-written voucher labels in Russian from Soviet times and translating these through Tajik to English. In some cases we opted for transliteration only, and this helped to link collections to collectors. The workshop is a first step in reviving botanical research in Tajikistan and making the invaluable collections of Tajik biodiversity available to the international research community.
A one week BRAHMS course was held at the Red Butte botanic garden, Salt Lake City, the principal botanic garden in Utah, with participants from their various Red Butte garden sections.
Red Butte run BRAHMS networked from Macs linking to a Cloud based Microsoft Virtual Server run by the University of Utah’s data center. The course was organised by Eddy Dawson, Red Butte IT manager and presented by Denis Filer from Oxford Plant Sciences. The course also provided an opportunity to add some new components to the Living Collection module for seasonal progagation (annual plants), perennial plant orders and plant sales. Utah has a high percentage of endemic plants and the garden represents this in their collection.
Annalisa Managlia, curator of the Bologna herbarium (BOLO), Italy, spent 4 days in Oxford to review aspects of their BRAHMS databases and learn about the Oxford curation processes. The Bologna herbarium is one of the oldest in the world with much historical material dating back to the 16th century. Annalisa is currently developing several databases, desktop and online, for old and new material alike. An example: the collections of Ulisse Aldrovandi.
Over the last two years, we’ve invested heavily in updating the Living Collections (LC) module in BRAHMS. This now provides a flexible management service for gardens and arboreta. Day to day curation activities typically include cataloguing new acquisitions, production propagation, planting out, plant maintenance, logging requests for future action, generating files for label etching and the monitoring of garden stock.
The LC module also links through to all the other available BRAHMS components providing a wide range of services and features for research and extension activities if these are wanted. In some cases, recording and calculating conservation status of garden species may be a priority, with reference to the known wild distribution of the garden species. This may involve species mapping and could extend to more formal ‘red listing’ and the use of the Conservation Assessment Module (CAM). Other projects may want to build up detailed profiles of species with taxonomic data, descriptive texts (distribution, name origin, common names, plant uses, etc.). Others may want to record results of propagation experiments on seed germination, cuttings and grafts.
The potential use for research is only limited by the data you have stored. A new initiative at the Oxford Harcourt Arboretum is the continuous recording of ground temperature across the entire site. Data loggers have been installed across the 140 acres, in the formal arboretum, semi natural woodland & meadow areas. The data, which will be linked to plant records in BRAHMS, will be used to look at how temperature influences plant growth and other phenological stages.
Image management is a key part of BRAHMS and as well as gathering and linking images of garden plants and specimens into the database, images can be assembled and published online together with garden catalogues creating a virtual botanic garden. BRAHMS has also teamed up with the Zegami software team in Oxford allowing you to present images using the cool Zegami search features. For example the Morton Arboretum garden plant and herbarium images.
The LC module is being fully integrated into BRAHMS v8 - using the latest technologies for desktop and online data management and presentation with options to store your data in SQLite, PostgreSQL or MSQL Server. Further storage options can be added to v8 by extending the v8 DB connection script.
Development work on V8 started almost 2 years ago. As with a new large building complex, much of the initial work has been preparing the underlying foundations - with not so much to see above ground. But this is changing rapidly now as the presentation layer (user interface) is added.
The key challenge for us has been to develop a system based on the very latest .NET technologies which requires no IT expertise to install; retains all the flexibility and power of v7; and requires minimum learning for anyone familiar with BRAHMS v7. Needless to say, it also has to import everything from v7. A seamless upgrade. V8 is now running demo databases linked to SQLite, PostgreSQL and MSSQL Server. You can choose one or all of these. Our preferred default data source for small to medium sized databases is SQLite as it requires no installation and is completely portable. As with FoxPro, you can copy your database onto a memory stick and even run it from there. Enterprise databases can tap into the full power, speed and security of the larger DBMS options with no limit to size.
In v8, features that are widely used in v7 like record tagging, 2-step record deletion, Zoom, Sigma summaries and column selection are all back in place - but each significantly improved. Zoom windows can be used like custom forms, and their data edited and saved; visible column selections can be dynamically adjusted, saved and shared with others; sigma summaries automatically update as you move column. Record tagging in the main file is no longer ‘all for one and one for all’! Tags, even when viewed in the main files are user specific. One more much demanded improvement to mention here: RDE and extract files have the same structure. In fact, they are stored and managed in the same data table. A feature of BRAHMS 8 that drives home its flexibility is the ability to open multiple spreadsheets simultaneously, drag and dock these to separate areas your of screen or to a separate monitor. Back to that underground phase - we’ve invested heavily in ensuring window control and docking is as flexible as possible.
The current focus is adding in the new query options. These build on what we already have in v7 but are being developed to allow a more or less limitless range of custom queries, all of which can saved and re-used. And this leads us on to some of the more visible outputs such as mapping and reporting, both benefitting from substantial libraries of features within .NET or available via third party solutions.
A BRAHMS training event was given 7–9 July with participants from the five African Indian Ocean nations: Comores, Madagascar, Mauritius, Réunion and Seychelles with an additional participant from Kenya. The event was sponsored by the Indian Ocean Commission (IOC) Biodiversity Program - European Union fund with training provided by Benny Bytebier (Curator, Bews Herbarium, University of KwaZulu-Natal) and Denis Filer, Plant Sciences, University of Oxford. Course logistics were arranged by Chantal Andrianarivo (IOC) and Thierry Pailler (Université de La Réunion) and hosted at the Université de La Réunion Campus du Tampon. The overall project objectives are to facilitate collaboration and data sharing between the regional herbaria. A specific initial objective is to gather data and images of the Orchidaceae from all participating countries and to assemble these on a joint website.
Course participants: Thierry Pailler, REU Herbarium, Uni. La Réunion; Nicole Benech, REU Herbarium, Uni. La Réunion; Jacqueline Lechevin, REU Herbarium, Uni. La Réunion; Ben Antoy Moussa, HKM Herbarium, Univ. Comoros; Andilyiat Mohamed, HKM Herbarium, Univ. Comoros; Harizoly Razafimandimby, TEF Herbarium, FOFIFA, Madagascar; Solo Hery Rapanarivo,TAN Herbarium, PBZT, Madagascar; Mijoro Rakotoarinivo, DBEV Herbarium, Univ. Antananarivo, Madagascar; Charles Morel, SEY Herbarium, Museum of Natural History, Seychelles; James Mougal, Seychelles National Park Authority/Plant Conservation Action Group (PCA), Seychelles; Claudia Baider, MAU Herbarium, The Mauritius Herbarium, Mauritius; B. Hansha Ramsahye, State House, Mauritius; Kersley Pynee, MAU Herbarium, The Mauritius Herbarium, Mauritius; Chandrajyotee Awotorsing, SSR Botanical Gardens, Pamplemousses, Mauritius; Prishnee Bissessur, Univ. Mauritius, Mauritius; Peris Wangari Kamau,EA Herbarium, East African National Herbarium, NMK, Kenya; Chantal Andrianarivo,Commission de l’Océan Indien (COI)/Biodiversity Programme, Mauritius.
For those lucky enough to have QGIS installed, if you have upgraded to BRAHMS 7.6.6, you can create distribution maps with one click. Not to mention all the analysis stuff on offer. When you map data points from BRAHMS, the files MYMAPFILE.DBF and MYMAPFILE.TXT are created in your mapping folder. The txt file can be added to a QGIS map project (together with your other map layers) using (in QGIS) Layer > Add a layer > Add a delimited text layer - or the equivalent toolbar option. If you then save this as a QGIS project, register the project in BRAHMS using Maps > Saved QGIS… projects, you can then select the saved project when mapping and this will always plot the contents of your current MYMAPFILE.
View The Morton Arboretum garden plants in Zegami.
View The Morton Arboretum herbarium specimens in Zegami
For further information, visit the Zegami website or contact Stephen Taylor: stephen.taylor@imm.ox.ac.uk.
A training course was held at and funded by the Forestry Research Institute of Malaysia (FRIM), Kepong, Kuala Lumpur on May 20 - 26. This was primarily for the combined staff of the KEP, SAN and SAR herbaria in Malaysia but also for representatives from Hanoi and Burma (those visits funded by NYBG/JRS Foundation). Amongst the topics covered were managing referenced species descriptive texts from multiple floras; conservation assessments and red listing; mapping to Quantum GIS; diversity analysis; publishing online (including regional networks); storing multiple enumerations for plot data; and managing botanic garden data. The training course, given by Denis Filer, was coordinated by Saw Lang Guan, Director of the Forest Biodiversity Division at FRIM.
The Seed Bank of Armenian Flora hosted a one-week BRAHMS training course 23 - 27 March 2015 for Seed Bank and Herbarium staff at the Institute of Botany of the Armenian Academy of Sciences in Yerevan. The Seed Bank of Armenia Flora has been a Partner in the Millennium Seed Bank Partnership since 2011. Their priority is to collect and conserve ex-situ seeds from the endemic and endangered plants of Armenia. Tim Pearce from RBG Kew Millennium Seed Bank Partnership provided the training.
Left to right: Shushan Ohanyan; Astghik Papikyan; Gayane Shaboyan; Karine Janjughazyan; Arpine Achoyan; Yevgenia Navasardyan; Yekaterina Shcherbakova; Tim Pearce; Araksya Elbakyan; Anush Nersesyan
A one week BRAHMS training event, 16 to 20 February, was held at The Morton Arboretum, Illinois. The event brought garden and herbarium staff together providing an opportunity to fine tune the BRAHMS living collections module and its linkages between garden accessions and plants, herbarium specimens, images and the literature module. Training sessions and discussions were held on file structures; the optimization of data capture for garden accessions, standard inventory data and observations (these also planning for the use of wireless portable devices); and on query, reporting and mapping requirements. Training was provide by Denis Filer and the event was coordinated by Sai Ravichandran who is their director of IT. The Morton Arboretum, together with the MOR herbarium, is one of the foremost botanical gardens in the USA. The Morton family who founded the garden in 1922 were the originators of USA Arbor day. The Arboretum library is a treasure trove of botanical and horticultural books, journals, prints, original art, letters, photographs, landscape plans and drawings. The Arboretum was recently recognized for excellence in ecological restoration.
The World List of Cycads, published under the auspices of the IUCN/SSC Cycad Specialist Group, is a comprehensive reference for cycads including useful information related to cycad taxonomy. The list has a 30 year history in printed form and a continuously updated online version is now available at Cycadlist.org. The World List of Cycads database is managed using BRAHMS and the website is populated using tables exported directly from the BRAHMS database.
News entry provided by Michael Calonje, Cycad Biologist, Montgomery Botanical Center, Miami, USA.
The BRAHMS online system (BOL) has been extensively updated with Version 5 published end of December. The revised online system provides a greater range of options to explore and present data as browsable data grids, reports, richness and point maps and images. BOL now uses bootstrap for all web pages. Websites are responsive and can be used on devices such as tablets and mobile phones. The categories of data that can be uploaded are: taxa; botanical records and their specimens; living collections; seed accessions with their seed test data; and botanical survey plots with their associated data. All categories of data can include images.
A BRAHMS training event (18 - 19 December) was held at the Korea Forest Training Institute. The course was for researchers and graduates, providing general support for botanical research and collection management. The course covered installation, basic DB handling, data entry using RDE, and report template design. The course was organized by the Herbarium (KH) of Korea National Arboretum and was given Prof. Hui Kim, Mokpo National University.
BRAHMS training events (1 – 4 December) were held in Pretoria and Cape Town, South Africa, introducing the BRAHMS Living Collections module to staff from the Harold Porter, Karoo Desert, Kirstenbosch, Kwelera, Lowveld, KwaZulu-Natal, Pretoria and Walter Sisulu National gardens. With some 30 staff on each of the 2 day courses, there was plenty of debate as how best to fine tune BRAHMS to meet all the needs of the South African gardens. During 2015, SANBI will integrate their herbarium and living collections data in to a single, networked database. The courses were organized by Brenda Daly, supported by SANBI and given by Denis Filer.
The Naturalis BRAHMS national herbarium database in the Netherlands now has over 3.3 million specimen and some 540,000 species and infraspecific taxa entries. Funded by a Dutch Government project, they are aiming to upload a total of 4.5 million specimens by the end of 2015. Almost all of the specimens are imaged and the images are linked in BRAHMS using media library URLs. The database is accessed daily by between 10 and 20 users simultaneous using a remote access system on a virtual server located in Leiden. Naturalis are also involved in current developments with BRAHMS v8.
The Morton Arboretum near Chicago, currently migrating their Living Collections and Herbarium data to BRAHMS, has been awarded a grant from the Institute of Museum and Library Service (IMLS) in the US. The grant will help The Morton Arboretum further integrate and cross reference their living collections and herbarium specimens, images and species data. In particular, the grant will be used to develop a mobile application for use on the grounds that will help staff to enter and check data and images and as well as provide mobile devices to access the mobile app developed for field data entry. They will also be developing in BRAHMS a new plant propagation module to monitor requests and tasks received and performed by The Morton Arboretum's propagation team. The Institute of Museum and Library Services is the primary source of federal support for the United States' 123,000 libraries and 35,000 museums. Their mission is to inspire libraries and museums to advance innovation, lifelong learning, and cultural and civic engagement. Their grant making, policy development, and research help libraries and museums deliver valuable services that make it possible for communities and individuals to thrive. To learn more, visit www.imls.gov and follow IMLS on Facebook and Twitter.
Entry provided by Sai Ravichandran, Director, Information Technology, The Morton Arboretum.
BRAHMS course for 15 participants during 18-22 August held at the facilities of the "Comisión Nacional para el Conocimiento y Uso de la Biodiversidad" (CONABIO), in D.F., México. given by Jeanine Vélez Gavilán from MAPR, Puerto Rico. Topics discussed: installation, standard tools, RDE files, RDE to BRAHMS transfers, query, text and visual reports, specimen imaging, mapping and the development websites using BRAHMS Online.
BRAHMS training and system review 14 – 21 June at the National Botanical Resources Institute (NBRI) in Windhoek, Namibia. NBRI has an impressive herbarium (ca. 90,000 specimens), already mostly catalogued in their central database together with official species list. This is now being extended to incorporate images, living collections, conservation assessment work, plot data and possibly their gene bank data. The visit was or Organized by Esmerialda Klaassen and funded through NBRI. Training sessions with Denis Filer from Plant Sciences, Oxford.
A Resource of Rare Value - a short article published about the BRAHMS project in the University of Oxford Blueprint magazine, pages 12-13.
An Atlas of the World's Conifers. An Analysis of their Distribution, Biogeography, Diversity and Conservation Status published by Brill, Netherlands. Aljos Farjon, Royal Botanic Gardens, Kew, UK and Denis Filer, University of Oxford. The first ever atlas of all known conifer species. It is based on locality information of ca. 37,000 collected herbarium specimens held in scientific institutions. Conifer diversity is analysed and presented with a taxonomic and geographic perspective. Distribution patterns are interpreted using the latest information on continental drift, dispersal and phylogeny. The entire dataset supporting the Atlas can be consulted and verified using the Conifer Database online.
Supporting botanical research in the Eastern Amazon region of Brazil. The official launch of the online herbarium database for Embrapa Amazonia Oriental. The Embrapa herbarium (IAN) was the first project to use BRAHMS in Brazil and has been closely involved in its on-going development. The herbarium with over 190,000 specimens, at least 2000 types, a library of 30,000 type photos and a Xylarium with over 8000 wood samples, has excellent facilities for and welcomes visiting researchers. The launch event was also reported on Portal Brasil.
The Gobabeb Research and Training Centre is an internationally recognized institution focusing on research and training in arid environments and is situated south-east of Walvis Bay in the Namib-Naukluft National Park in Namibia.
The staff of the National Herbarium of Namibia (WIND) have recently spent time at the Gobabeb facilities, to support the centre to resurrect the herbarium, a modest yet valuable collection of Namib Desert plants. The services they rendered included the introduction and setting up of BRAHMS, and training in using this tool; physical maintenance of the collection and repair of herbarium specimens; as well as rearranging the collection to be in line with the updated checklist of indigenous and naturalized plants of Namibia. Staff trained included Gobabeb interns as well as students from the University of Namibia (UNAM) and the Polytechnic of Namibia currently doing in-service training. Read more...
