Leishmaniasis Virtual Laboratory

The Leishmaniasis Virtual Laboratory is an open, collaborative research environment for the molecular surveillance of Leishmania and their vectors. It offers online collaborative and research tools for advancing current knowledge about this neglected disease.

The Lab empowers researchers and public health workers internationally by giving them a single access point to the right tools and most relevant, in-depth data on the parasite and vector responsible for this disease. The Lab is also for international organisations, pharmaceutical companies and public sector workers. They can access it and provide relevant in-depth information or data on the parasite (Leishmania) and the vector (Phlebotomine sandfly) responsible for the disease.

The Leishmaniasis Virtual Lab is accessible from here.

Tools and services at your fingertips

  • The Leish VirtLab gives researchers and public workers an easy, single access point to a a collaborative workspace. Through the Lab you can share sequences and protocols with other researchers and decide who can access your files.
  • Leishmania and sandfly collections - database search built from CLIOC, COLFLEB and ISCIII-WHO-CCL. Cluster & aggregate your results by area.
  • Molecular analysis of DNA sequences - customise pipelines to add your own parameters. Execute your experiments in a large-scale computing infrastructure and interpret the results online.

The Lab is built on top of the EUBrazilCC infrastructure. It is interoperable with the EGI Federated Cloud and provides developers with the tools they need to deploy virtual infrastructures using different frameworks like private clouds, supercomputing and opportunistic desktop resources

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Data Sources

EUBrazil Cloud Connect will retrieve sequences from existing Leishmania and Sand Fly collections such as ISCIII-WHO-CCL collection, COLFLEB and CLIOC, and will present them in an integrated manner to the user. Resources such as PubMed and GenBank will be periodically inspected as well for new records on Leishmaniasis. EUBrazil Cloud Connect eInfrastructure will get occurrence records from biodiversity collections such as speciesLink-COLFLEB.

  • COLFLEB (http://colfleb.fiocruz.br/) The collection of phlebotomine sand flies – COLFLEB - of the Centro de Pesquisas René Rachou located in Belo Horizonte, state of Minas Gerais, was initiated in the 1950s. The collection has approximately 90,000 sand flies specimens distributed across 320 species from South and North America.
  • CLIOC (http://clioc.fiocruz.br/) - The Leishmania collection of the Oswaldo Cruz Institute. The Leishmania collection of the FIOCRUZ – CLIOC is registered in the World Federation for Culture Collections, WFCC, WDCM 731 - is fully computerized, including all process and information data. All the strains are identified at the species level using biochemical methods and most of them have molecular data associated.

CLIOC and COLFLEB are interconnected through the speciesLink network (http://splink.cria.org.br/) and the strain data from CLIOC is available through SIColNet (http://sicol.splink.org.br/index).

  • PubMed (www.ncbi.nlm.nih.gov/pubmed) comprises more than 23 million citations for biomedical literature from MEDLINE, life science journals, and online books. PubMed is a free resource that is developed and maintained by the National Center for Biotechnology Information (NCBI), at the U.S. National Library of Medicine (NLM), located at the National Institutes of Health (NIH).
  • GenBank® (www.ncbi.nlm.nih.gov/genbank/) is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42). GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. These three organizations exchange data on a daily basis. A new release is made every two months.

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End users

The Leishmaniasis Virtual Laboratory (Leish VirtLab) is for researchers, public health workers and related government departments internationally whose work and mission involves leishmaniasis surveillance and research.

The Lab is also for international organisations, pharmaceutical companies and public sector workers. They can access it and provide relevant in-depth information or data on the parasite (Leishmania) and the vector (Phlebotomine sandfly) responsible for the disease.

Usage policy

The Leishmaniasis Virtual Lab offers a dedicated set of tools and services to advance knowledge of Leishmaniasis. It is a single entry point to both the most relevant data sources and powerful computing systems for executing experiments.

Our aim is enable lab users to share their knowledge and results much more effectively. Researchers and field workers from all relevant disciplinary areas are expected to share new insights and exchange knowledge, thus increasing international co-operation on this neglected disease and its devastating effects. Engagement with users will help EU Brazil Cloud Connect to validate the Leish VirtLab.

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Social challenge

Leishmaniasis affects the poorest of the poor

Leishmaniasis is one of the most neglected diseases in the world. It affects the poorest of the poor, mainly in developing countries, such as Latin America, the Euro-Mediterranean basin, North and East Africa and the Indian sub-continent.

  • 350 million people are considered at risk of contracting leishmaniasis.
  • 1.5-2 million new cases occur every year.

Three factors are causing the disease to spread more quickly and widely than ever before: human-made and environmental changes; immune status (essentially because of Leishmania/HIV co-infection); treatment failure and drug resistance.

More effective control of neglected tropical diseases like Leishmaniasis is vital to achieving poverty reduction and spurring social-economic development without waiting for countries to fully develop and living conditions to improve over a potentially long period of time.

Today, we have a poor understanding of the factors exacerbating the spread of Leishmaniasis, which is spreading both northwards and southward, possibly due to environmental and/or climate change and affecting vector species populations. There are several priorities to improving our current knowledge. The correct identification of the etiological agent is key to understanding the likely course of a patient’s medical condition. It is equally important to understand the nature and cause of the disease to improve treatment outcomes.

Investment key to advance our knowledge of this neglected disease

More effective control of neglected tropical diseases like Leishmaniasis is vital to achieving poverty reduction and spurring social-economic development without waiting for countries to fully develop and living conditions to improve over a potentially long period of time.

European and Brazilian research teams in EU Brazil Cloud Connect have collaboratively developed the Leish VirtLab as part of an international drive to advance our knowledge of Leishmaniasis and mitigate its devastating effects on some of the world’s poorest populations.

This investment is fundamental for several reasons. The Leish VirtLab represents an important improvement on the tools and mechanisms currently available for the surveillance of this neglected disease. Making more powerful tools and services available to anyone any time through a single access point is a crucial step towards advancing current knowledge on Leishmaniasis.

Just as importantly, our efforts are helping to increase awareness of the disease and foster further collaboration internationally.

The EU Brazil Cloud Connect team of contributors

Oswaldo Cruz Foundation and the Istituto de Salud Carlos III-WHO Collaborating Centre for Leishmaniasis bring expertise on the disease. Valencia University of Technology and Newcastle University provide technical support for handling and processing data collections. CRIA provides both data on species location and expertise in ecological niche modelling.

From a technical viewpoint, EU Brazil Cloud Connect builds on expertise gained in both European and Brazilian initiatives, as well as earlier EU-Brazil collaborative initiatives on cloud computing, supercomputing and biodiversity.

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