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Vlaams Instituut voor de Zee

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Voorstel stage-onderwerp 2012-2013
In het Vlaams Marien Datacentrum, een onderdeel van het VLIZ, beheren we verschillende soortenlijsten. Deze worden door taxonomen gecontroleerd en uitgebreid, zie lager voor de urls. Graag werken we in het kader hiervan een stage uit voor een student Bio-Informatica.
WoRMS : http://www.marinespecies.org/ (World Reg. Mar. Species)
ERMs : http://www.marbef.org/data/erms.php (Eur. Reg. Mar. Species)
BeRMs : http://www.marinespecies.org/berms/ (Belgian Reg. Mar. Species)
 
Abstract advanced bachelor of bioinformatics 2019-2020Combining marine species occurrence data into standardized maps for analysing their distribution

A distribution map is being developed which combines the occurrence records of different databases to study the distribution of marine species and to also see the links between these databases.

The project is envisioned as follows. Using R, all the occurrence records are downloaded from the WoRMS, OBIS, EurOBIS, GBIF and IDIGBIO databases. These are then combined in to a MongoDB database, along with the shapefile of Marine Regions (MR) and Marine Ecoregions Of the World (MEOW). Each shapefile contains a list of polygons, which are linked to the occurrence records via their (latitude/longitude) coordinates. The records also contain a date/time value in most cases. Through an R Shiny app the user can choose the location, taxon and a date range as input. The R Shiny app will query the MongoDB database for the right records and polygons, which will then be plotted on a leaflet map as points and polygons. The infrastructure of this distribution map will be added to the Lifewatch R Shiny projects and to the WoRMS distribution map.

In this traineeship the download is still in progress. The code to download the records is written and is now being applied to download all the records. The MongoDB structure has also been determined.

Further steps of the project, which is the R Shiny app and integration into Lifewatch and WoRMS are still to be done.

Abstract 2018-2019: Automation of link updates between taxonomic and genetic databases
WoRMS (www.marinespecies.org) is a website that consists of an authorative and comprehensive list of marine organisms. It is a perfect searchplace for scientists to find potential subjects to perform analysis on. One feature that helps with this search is the links that WoRMS offers to scientists to other scientific sites like the NCBI taxonomy browser (Genbank), European Bioinformatics Institute (EBI), Barcode of Life (BoLD) and many more. This project focusses on the automation of link updates of three different genetic databases in WoRMS using PHP scripting. Taxonomy browser links will be updated much quicker to show a more accurate overview of the number of nucleotides and proteins per organism. EBI links and Elixir MarRef links were added as new link providers. A general workflow was used to make all the links. A series of steps were performed on the downloaded files to prepare them for implementation in a database. when implemented in the database the links could be made. Future versions of the scripts may include more info depending on the user’s demand.
 
Samenvatting eindwerk 2014-2015: OPTIMALISATIE VAN HET ZOOSCAN PROTOCOL VOOR EEN EFFICIËNTERE VERWERKINGVAN ZOÖPLANKTON
The purpose of my internship was to verify the ZooSCAN process and its optimization. It’s a fairly recent technology and a comprehensive check on its operation had not been done yet at the Flanders Marine Institute (VLIZ). Three crucial parts of the process have been thoroughly examined. Initially the focus was on sample preparation. With dilution series the ‘Motodo Plankton Splitter’ is tested. Verification on how many dilutions can be made and still have representative results. The system replicates have been tested in detail and extensively. The final step was to evaluate the learningsets which are used to classify zooplankton. This bachelor thesis can be used as a manual for this infrastructure and enable future users to quickly understand the ZooSCAN. The features are summarized.
Biodiversity research study is ecologically important because zooplankton is an essential part of the marine ecosystem in the North Sea. The ecological quality of these waters is determined inter alia by the concentrations of various species zooplankton. Therefor the zooplankton should be monitored, because it is the basic food of many marine animals, especially for higher trophic levels and specifically to fish. In addition, zooplankton is highly temperature-dependent and thus perfect to capture changes in climate.
The RV Simon Stevin sails on regular basis to collect zooplankton. Collected samples have to be sieved first to extract the medium. If necessary dilutions can be made. Afterwards, the samples are scanned with the ZooSCAN. Computer programs used for investigating are: ImageJ, VueScan and the statistical program Tanagra. The last step is the taxonomic classification for which the computer program Plankton Identifier is used.
Sample preparation has proven to be more efficient with a 200 µm sieve. Zooplankton should be separated from each other on the sample bed before scanning. If sand is present this can best be decanted with glass measuring cups.
The number of converted fragments after dilution should be around 2000. This enables quick and efficient work. If there are very low numbers of zooplankton in the validated groups, the entire process should be repeated. Alternatively two smaller fractions added together can obtain an appropriate dilution.
The existing VLIZ learningset works best if merged with the newly created set. The classification is than better and more time efficient. In the future, vignettes of less common taxa have to be added to the learningset. This will significantly improve the software.

Address

Wandelaarkaai 7
8400 Oostende
+32 [0]59/34 21 30

Contacts

Traineeship supervisor
T'Jampens Roeland
Roeland.TJampens@howest.be
Traineeship supervisor
Bart Vanhoorne
+32 59 34 21 30
bart.vanhoorne@vliz.be
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