DEST - Taxonomy Training

The Royal Swedish Academy of Sciences is greatly acknowledged for sponsoring the international graduate school course on Basics of Taxonomy in 2012.

Course programme description

The course will cover the following topics:

• DELTA
• Digital drawing
• Scientific illustration
• Scientific writing and communication

DELTA (DEscription Language for TAxonomy)

The intention of this DELTA-course is to allow young taxonomists to learn the basics of DELTA and to introduce them to the large potentials of the program, which will allow them to build larger or smaller databases for various organism groups. The program was developed by CSIRO (Commonwealth Scientific & Industrial Research Organisation) in Australia to handle taxonomic data (e.g. all kinds of characters). Although the program has been around for a while, DELTA is still the state of the art tool in modern taxonomy.
In order to optimise the function of the global resources it is important that the local taxonomists have knowledge and training to utilize taxonomic data in an optimal way. Keys, descriptions and fauna lists are lacking a universal standard, which makes it difficult to get an overview of and to compare different sources. It is here DELTA comes in!
It is an advanced computer programme which helps the taxonomist to describe new species and to re-describe previously known species. It has the advantage of standardizing species descriptions that also puts them in an identical format, which makes it possible to use the information in comparative (phylogenetic) studies, something that is often difficult today. DELTA also speeds up and forms a quality control of the data processed by the taxonomist, since all data has to be processed in an identical manner, and all characters for all taxa has to be entered into the program. DELTA databases can then be used to build interactive, illustrated keys that can be distributed over the internet. Access to such keys will be advantageous for experts, general biologists as well as for the layman.
DELTA is freely available from the internet. A major advantage of DELTA is that is exclusive, i.e. that only data that are available in the material that is to be used as a base for a taxonomic key is needed. This is a huge advantage compared to printed keys that are limited by the underlying hierarchical structure. This also makes the keys more easy to use also for non-experts. Available databases in DELTA, are for example, fishes, corals and polychaetes, although some still are under various states of construction (see http://biodiversity.uno.edu/delta/www/data.htm).
DELTA program: http://delta-intkey.com/
Specific aims to achieve in this course.
This course will give an introductory overview on databases in taxonomy, examples of such systems are the OBIS-project (http://www.iobis.org/), Tree of Life (http://tolweb.org/tree/phylogeny.html) and GenBank (http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/). Another important initiative is the Global Biodiversity Information facility (GBIF) (http://www.gbif.org/), aiming to combine various taxonomic databases to a functional unit.  Also a closer look into Biodiversity Information Standards (TDWG) to see what can be coming in the future. The remaining part of the DELTA-part of the course (4-4.5 days) will be to introduce the participants into using the DELTA program.
The participants are encouraged to bring species (or higher level) data of some organism group they are familiar with. About four to seven species is enough with at least five to ten characters (species descriptions and illustrations). The participants will work with their material during the course to build a database by code, score and illustrate their organism group. They will build interactive illustrated keys, making dichotomous keys for printing and generate natural language species descriptions. Also how to produce NEXUS files for use in phylogenetical programs.

Digital drawing

The digital drawing method for scientific illustrations using Adobe Illustrator has become a standard method for taxonomic descriptions in many labs. The great advantages of this method lie in increased speed and the possibility to create such smooth lines that would not be possible using traditional free-hand ink drawing. The resulting vector graphics can be directly processed by most online journals and can be used for printing in journals and digital copies (pdf ’s for proofs and eps files for publication). Using vector paths they are much smaller and have a much higher quality and resolution than bitmap versions. It is also possible to use photos and micrographs as a master for a line drawing. Although the time saved is considerable using the digital drawing method (once mastered), the illustration of complex details like setae still takes most of the time. D’Udekem d’Acoz (pers. comm.) proposed the use of the brushes function of Adobe Illustrator for such structures. In the course I also introduce this idea and expand it into a whole system to make libraries for setae and related structures automatically.

Scientific illustration

The course aims at to understand human perception of illustrations; to be informed about a variety of methods of illustration; and learn how to be a "do-it-yourself-illustrator" based on a limited of methods.
Topics of the course will include:

• Theories behind the use of illustrations for various scientific purposes
• Human perception of illustrations
• Composition, colour theory, choice of illustration method
• Short history of scientific illustrations
• Aids like camera lucida
• Black and white methods like copper graphics, charcoal, pencil and black ink
• Colour methods like water-colour (aquarelle), crayons, coloured pencils, pastel, computer graphics and airbrush)

Beside illustrations of biological specimens, aspects on diagrams, tables, typography and posters will be included. Some of the methods will only be demonstrated and others will be practised.

Scientific writing and communication

Course designed to introduce participants to the details of writing scientific publications. The main emphasis is on the most common form, the "primary scientific paper". The course will explain the current structure of scientific literature, the main features of the scientific information 'industry', and the particular rules, and customs the international scientific community follows when publishing. Particular emphasis will be placed on little taught aspects of the publication process such as how to decide about a suitable forum for scientific paper, as well as practicalities how to prepare and work through the different stages of the publication process (manuscript preparation, submission, dealing with editors and the printing process). Less emphasis will be placed on grammar and the use of English (special aspects of language use and style will be discussed). Principles of preparing figures and tables will be extensively discussed, as well as the important aspects of participating at international conferences (posters, talks, personal interactions).
Main topics are:

• The scientific literature: structure, purpose, prestige, types of publications
• How to write scientific papers: before you begin
• Basic decisions – what, how, when. Gathering intelligence about the unknown
• Parts of an article: IMRAD
• How to write the main parts of a scientific paper
• Supporting parts & their importance
• Figures & tables
• Submitting a manuscript
• Stages to publication: what happens when and where?
• How to handle the stages of publication process
• Other types of papers: Posters. Talks & scientific conferences: how to perform and participate?

Duration course programme
Two weeks

Date
16 - 27 April 2012

Course language
English

Target Audience
MSc students, PhD students as well as for early career researchers

Location
Sven Lovén Centre for Marine Sciences, Kristineberg, Sweden
http://www.loven.gu.se/english/stations/kristineberg

Teachers
DELTA: Dr Matz Berggren, Institution of Marine Ecology, Göteborg University, Sweden & Dr Charles Oliver Coleman, Museum für Naturkunde, Berlin, Germany
Digital drawing: Dr Charles Oliver Coleman, Museum für Naturkunde, Berlin, Germany
Scientific illustration: Prof. Tomas Cedhagen, Department of Marine Ecology, University of Aarhus, Denmark
Scientific writing and communication: Dr Gabor Lövei, Department of Plant Protection, Danish Institute of Agricultural Sciences, Slagelse, Denmark

Registration fee
€ 850 (Euros)
The registration fee includes course attendance, course material (scientific illustration), accommodation and meals.  Participants are responsible for their own travel expenses.

The coordinators of DEST-training are currently seeking external funding in order to waive the participants’ registration fees partly or entirely.

Maximum number of participants
15
Criteria for selection will be scientific merit, motivation and usefulness of the training course for your career.

Registration
Deadline for registration: 15 January 2012.
Participants will receive notification by 1 February 2012 whether accepted to the course.
Course will be cancelled if minimum registration is not reached.

Click here for the registration form.

Payment
Payment details and deadline will be provided upon acceptance to the training.