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The key to sustainable sea lice control is in the genome.

About LiceBase

Disclaimer

The data, information, and resources, applications, and electronic services on this web site (further called LiceBase) is provided to you by the Sea Lice Research Centre (SLRC) free of charge on a BEST EFFORT basis for the sole purpose of research. There is no warranty for correctness of data and information in LiceBase neither expressed or implied; there is no warranty for the fitness of data, and applications in LiceBase for any particular purpose, including merchantability or commercial application. The owner of LiceBase DISCLAIMS any liability for material or immaterial losses incured by using LiceBase or one of the resources or data provided by this site. 

Data usage policy

The data, information, resources, and services available through this site are owned by the Sea Lice Research Centre and the University of Bergen Norway. The owner of the data and services grants you a non-exclusive, non-transferable, revocable license to use the data and services provided for the purpose of research. Fair usage policy applies. Note that the owner of the data intends to publish the genome assembly, genome annotation, including but not limited to protein coding genes, gene expression, non-coding RNAs, repetitive sequences, and conserved regions.

 

Funding and Organization

 
SFI_logoLiceBase is a database for sea lice genomics. LiceBase provides the genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, Blast functionality and access to related high-thoughput genomics data.
 
Sea lice (Lepeophtheirus salmonis and Caligus spp.) are the major pathogens affecting global salmon farming industry and have a significant impact in many areas. The annual loss has recently been estimated to be more than €300 million and the aquaculture industry relies heavily on a few chemotherapeutants for lice control. Emerging resistance development to these drugs increase the necessity to develop new treatment methods (biological, prophylactic and drugs) and tools to avoid increased loss due to sea lice and to ensure a sustainable salmon farming industry in the future.
 
LiceBase is developed at the Sea Lice Research Centre (SLRC), a centre for research based innovation (CRI) established through the Norwegian Research Council and hosted by University of Bergen. The CRI has a long term funding (5+3 years) from both the research council and the consortium partners (3 academic partners: University of Bergen, Institute of Marine Research, Norwegian School of Veterinary Science, and 5 industrial partners: Elanco Animal Health, EWOS Innovation AS, PatoGen Analyse AS, Marine Harvest ASA, Lerøy Seafood Group ASA). The research is organized in 6 different work packages.

LiceBase - defined as work package 5 of the SLRC - is a system for storing and mining the data from within this and related projects and is aimed to be the preferred site for the global research community for access to genome data on sea lice and other related genomes. The work will involve both development and application of bioinformatics tools to facilitate data representation and analysis (e.g., genome annotation, integration of data from genome-wide functional studies).

​LiceBase is also an international deliverable in work package 3 of the Norwegian Elixir node. ELIXIR Norway is coordinated by the University of Bergen and includes the University of Oslo, the University of Tromsø, the Norwegian University of Science and Technology in Trondheim, and the Norwegian University of Life Sciences at Ås. The Research Council of Norway supports the Node primarily through its program for research infrastructure. LiceBase is integrated with NELS, the Norwegian e-infrastructure for life sciences, which contains several integrated packages geared towards genome scale analyses, provision of web services, and genomics toolboxes.

 

 

People

  • Project leader LiceBase development: Michael Dondrup (admin@licebase.org), Researcher at SLRC and the Department of Informatics, UiB 
  • Scientific programmer: Wei Zhang
  • ​Work package leader (SLRC WP5, Node leader Elixir Norway): Inge Jonassen, Professor at Department of Informatics, UiB

Legal

By using the site with or without authentication you agree to our Privacy Policy and our Terms and Conditions.

Software

For sustainability, we are following a free-open-source software policy for use of software to build LiceBase. We are relying on excellent pieces of  software developed by the Generic Model Organism Database project (GMOD) and other open source projects. We are very grateful for the contributions from countless individuals to free-open-source software we are using, and we are also publishing our modifications to components, if applicable.  

LiceBase is built using Tripal and Drupal. We are using GBrowse as the Genome browser, we have implemented some modifications to allow using SAML-IdP based authentication for single-signon (SSO) between Drupal/Tripal and GBrowse.

Tripal Logo

SimpleSAMLphp is developed by UniNet and used for authetication and SSO.

simplesamlphp logo

For running Blast, we provide an enhanced version of the GBrowse tool BLAST Graphic Viewer.

The source code of adapted components is available here:

Mission Statement

“One of our objectives is to promote the development of more effective, less harmful medicines to combat sea lice,” explains Sigmund Grønmo, Rector of UiB and the proud host of the SLRC.

Most information on this site is now public. This includes the L. salmonis genome, annotation, in-situ hybridizations, and published RNAi experiments. If RNAi experiments are published, they will be made available to public automatically. You will need an account only to deposit data in LiceBase and to see unplished RNAi experiments. If you wish to have a LiceBase account or require further information, please send an email to admin -at- licebase -dot- org.