Software



AquaEcology is developing web-based software for the use in the biodiversity research field. Main objective is to support the researcher in collecting, converting and analysing data by providing him with databases and tools, in order to enable him to put the main focus of his work rather on the interpretation and analysis of data than on the management of data.

Currently, AquaEcology offers a portfolio of software products, which are all based on the same philosophy and on a modular structure:

  • biodivDP, an original information system that can be used both for accumulation and dissemination of biodiversity specific data.

  • OrgaCount, a new scientific software specially designed for counting organisms of different taxonomic groups.

The following chapters will give you valuable information on these products.



biodivDP


What is biodivDP?



The software package biodivDP is an original information system that can be used both for accumulation and dissemination of biodiversity specific data. This system has an array of features that makes it suitable to projects of which audience range from specialists to general public. The internal organisation of this system allows packaging of information at various levels of abstractness without affecting the quality of primary data.

biodivDP has a template system for every level of organisation and a true modular structure which considerably ease modifications and additions to its user interface. Because the design is separated from the database interaction, changes in the interface can be done by almost everyone with basic programming skills.

With inclusion of AJAX, biodivDP comes with a new navigation concept: there are no limits on the number of modules loaded in the interface at a given time; this feature provides the user with the possibility of investigating various types of information at the same time.

The flexibility of biodivDP extends beyond technical aspects deeply into the biological realm through a set of features useful both for applications focussing on taxonomic groups, specific habitats, or geographic areas.

biodivDP accepts an unlimited number of taxonomic standards and classification schemas. This feature keeps primary information up to date without a need to reprocess data and also accommodates alternative investigation by users with various levels of education, scientific opinions, or scope. Without additional programming, the data model can be extended with an unlimited number of additional fields to accommodate any standard (Darwin Core, ABCD, custom fields). This flexibility makes the biodivDP system suitable also for projects focussing on monitoring and specimen/ image collections as well as for data providers for OBIS or GBIF.


Features of biodivDP


A most prominent and internationally known example of a project based on a biodivDP application is the biodiversity database PLANKTON*NET:
PLANKTON*NET as an open access repository for plankton-related information with coverage of all types of phytoplankton and zooplankton from marine and freshwater areas is using biodivDP for accumulation and dissemination of its information.
PLANKTON*NET has been set up and is continuously developed in close co-operation with the Alfred Wegener Institute for Polar and Marine Research (AWI) in Bremerhaven and is hosted by the AWI at http://planktonnet.awi.de.



Modular architecture

biodivDP has a true modular structure which considerably ease modifications and additions to its user interface. The interface is organised in different panels that each of its own can load various modules for different objectives: tools and/ or information. The application offers a template system for every level of organisation, making its interface highly customisable according to the user's needs: visibility, position, size of each panel can be controlled by administrator without touching the code. Panels may be sorted and resized by users as well and their preferences are saved automatically.


New navigational concept

biodivDP comes with a new navigational concept: there are no limits on the number of modules loaded in the interface at a given time. This feature makes it possible to investigate various types of information at the same time. For example, a user may simultaneously search the database, investigate details of a record, and enter data in different, parallel opened panels without interrupting any of the tasks with back and forth browser navigation.


Separation of design from function

Each module is represented by two major components: one involved in database query and the other in design of interface. Because design is separated from database interaction, changes in interface can be done by people with only basic programming skills. However, assistance can be provided to interested parties wishing to establish a running biodivDP system. Customised versions and additional tools may be developed to fit each project needs. Just ask for our support.


Data input

biodivDP comes with an array of input tools for entering data about specimens and other related information; these cover for example tools for input of geographical locations, images, image sets, taxon descriptions etc., maintaining at the same time relationships among entities. Data input and editing tools are closely available within the graphical interface facilitating dataset growth and improvement.

The internal organisation of the biodivDP system allows packaging of information at various levels of abstractness without affecting the quality of primary data.

High resolution information about specimens, which is relevant to the scientific community, may be reassembled under various subjects becoming useful for a wider audience.






Biodiversity and taxonomic oriented modules make this software suitable for any taxonomic scope or geographic scale.

Included in biodivDP are modules for displaying information on observations, images, geographic distribution, classifications, taxon & name details, glossary terms, image sets, literature, etc.

The modular structure, the use of new technology, and the new navigation concept allow development of biodivDP beyond the limits of a regular biodiversity website.

In this example, a tool for online annotations of images is integrated within the image detail module. Other project specific tools and modules may be developed and easily integrated within biodivDP.










OrgaCount


Why OrgaCount?



OrgaCount is a new web-based scientific software by AquaEcology specially designed for counting organisms of different taxonomic groups. Current versions are already implemented for phytoplankton analysis. This application may be used for calculation of biovolumes and other statistics used in plankton monitoring.


In contrast to other similar applications, OrgaCount runs in a server environment connected to Internet, but optionally may be used also locally on a pre-configured mobile device. Web-based installations bring several advantages in terms of compatibility, accessibility and update services. An example of this case is the OrgaCount version maintained on AquaEcology server.


One of the striking advantages of a web-based installation is that it will be not dependent on a specific type of operating system and that it can be run from anywhere, where Internet access is available. This makes it possible that many users work simultaneously and on their own system on the same database without additional installation of software.


The OrgaCount database system

  • ensures that assessment data can be centralised in the same database without import/export operations.

  • is accessible via Internet from anywhere in the world; this means that several members of a national or international project may use the same software installation even if laboratories are located in different geographical areas.

  • has its data stored in a reliable database environment based on a non-proprietary format; data may be obtained via the OrgaCount interface, but by most sophisticated users, data can be directly accessed using other specialised data management software or command line tools.

  • runs inside biodivDP which is a content management system that can be used not only for collecting data, but also for dissemination of data, project achievements, web reports and other.

  • has a modular structure; this combined with the used programming environment allows fast development of additional functionality or presentation panels; the current interface may be easily customised to fit the demands of any user or type of project.


Features of OrgaCount


OrgaCount can be used for counting cells and calculating their biovolume using both predefined and adhoc counting strategies. In case of predefined counting strategies, size classes, biovolumes, and other statistical values are defined a priori. In contrast, when using ad hoc counting strategies the size classes and biovolume data are calculated dynamically during the counting session.


OrgaCount can be used concomitantly on projects that use distinct species and size class lists.

All modules of application are organised in a hierarchical tree structure with four levels that allows easy navigation and understanding of relationships among various entities at every level of organisation.

Consequently, counting data are organised hierarchically in projects, dates, samples, and counting sessions. For each level of organisation, functions for showing detailed information and editing. Application modules include fields for standard metadata, but can be extended at any time to an unlimited number of user defined fields.



OrgaCount can be set up individually for most of the included features such as counting & keyboard layout, species list and biovolumes.




Counting layout:

  • OrgaCount comes with an array of user friendly counting layouts. Because counting layouts are defined in HTML templates and are separated from the core of the application, the list of layouts may be easily extended to meet the requirements of various users.

  • Counting layouts as well as other settings may be changed at any time during counting session without interrupting the counting process.

  • Counting layouts may include as items both taxa and size classes. Counts for each of these are kept separately for preserving counting history.

  • For an item, the counting layout may include an icon, the name of taxon & size class, the assigned key button for counting, the count value, counting factor & counting area unit, link for individual settings or for calculating biovolumes in case applying the adhoc counting strategy.

  • Popup panels allow display of additional information, controls for individual settings or interfaces for assessing biovolumes.

  • Each item in the counting layout may be counted using a different counting factor, can be frozen individually, and may include a confidence-in-determination tag.

  • Sets of species & size class items may be defined and saved for the use in counting sessions. These sets of items may be assembled based on taxonomic expertise or seasonal changes in the composition of the sample. OrgaCount allows changing sets of items during the counting process.

'Master' species lists:

  • If new species or size classes are encountered in samples, these may be added to 'master' species lists using specific modules.

Reports:

  • Individual reports may be generated at session and sample levels. They can be printed directly from the interface, or be saved as Excel or CSV files.

Help:

  • For getting familiar with OrgaCount, quick tutorials and help files as well as video demonstrations are included in application.

System requirements:

  • OrgaCount runs in a server environment on a wide variety of operating systems including various versions of Linux and Windows. A web version of this application is offered on the AquaEcology server and is maintained with latest updates and its database backed up regularly.

  • OrgaCount may also run locally from any type of media such as hard drives, compact flash USB sticks or SD cards. Although local versions run in a server environment as well, they do not require any additional software installation.

  • OrgaCount uses mySQL database for storing counting data. This is one of the fastest and most reliable open source database systems on the market. Data produced with this application may be accessed easily beyond current functionality of OrgaCount.

  • Client requirements: For running OrgaCount, you only need a web browser. Firefox 3, Internet Explorer 7, and Opera 9 were among the browsers used for testing OrgaCount.


Licensing OrgaCount


In order to meet the special needs of the customers, OrgaCount offers a very flexible licence system. In the first place, we differentiate between a local installation of OrgaCount on a pre-configured mobile device that can also be used in the field work, and a server-based version. The latter could be installed either on the customer's server or on a secure server from AquaEcology

A server-based installation hosted by AquaEcology has got many advantages:

  • The user might access his date from all over the world, without further software installations, just using an Internet browser.

  • Multiple users can work on the system at the same time and from different places in the world.

  • Optimum support for implementation and usage of the system can be ensured by AquaEcology or other external colleagues.

  • On server hosted by AquaEcology, functions for automatic updates of the software and for backups of data can easily be implemented.


Training


OrgaCount is a complex and comprehensive application. It offers a wide range of functions and possibilities for the user. The user guide as well as the online help functions will assist you in accessing the features of the programme. In order to make the user familiar with OrgaCount in the most efficient way, AquaEcology also provides you with training courses for single participants as well as for groups.

We offer various individual training models:

  • In-house training of single users: One of our training experts will visit your institute/ company/ department and give individual guidance and support to the user.

  • In-house group training: One of our training experts will visit your institute/ company/ department and provide your team with a systematic and detailed overview over the OrgaCount system. Of course, we will regard individual questions and problems.

  • Single or group training in seminar rooms at AquaEcology in Oldenburg. If you arrive from a far location, we will be delighted to assist you in getting a suitable accommodation.


Just contact us; we will inform you and provide you with an appropriate offer.


Further information on OrgaCount


Further comprehensive information on OrgaCount in textual format is available at the OrgaCount website.

A short overview will be given by our OrgaCount flyer as PDF file (about 2 MB):




Our compilation 'Getting Started' shows you very quickly how to use the programme (PDF file, about 550 KB):




Of course, you may also download the comprehensive user guide of OrgaCount as PDF file (about 2.4 MB):




In order to be able to read the flyer, you will need the application Acrobat Reader® it is freely available from the Adobe® website:



OrgaCount can also be tested as a demo version directly on the OrgaCount server.

Just test it and let yourself being convinced of a modern, state-of-the-art software!