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adali981 edited this page Aug 30, 2021 · 8 revisions

VirusLab is a Web Server for analyzing viral sequences and visualizing and their variants and characteristics. Welcome to the Wiki Page of our project!

Which need are we addressing?

The pandemic outbreak of the coronavirus disease COVID-19, caused by the virus species SARS-CoV2, has created unprecedented attention towards the genetic mechanisms of viruses. The sudden outbreak has also shown that the research community is generally unprepared to face pandemic crises in a number of aspects, including effective visualization services that support virology and biology knowledge discovery. We respond to such urgent need by means of a novel Web Server collecting virus sequences and their properties, so as to facilitate current and future research studies.

What is our background?

Thanks to our previous knowledge in human genomics (documented with our conceptual model focused on human genomics, pipeline for genomic data integration, and database for genomic sequences, searchable through the GenoSurf Web Interface), we have been able to rapidly design corresponding systems for the domain of viral genomics.

In April 2020 we proposed the Viral Conceptual Model (VCM), which was developed by interviewing a variety of experts of the various aspects of virus research (including clinicians,
epidemiological experts, drug and vaccine developers). In August 2020 we produced the corresponding integrated and curated database ViruSurf http://gmql.eu/virusurf/, which integrates viral sequences from NCBI GenBank, RefSeq, COG-UK, NMDC. At the end of this year, we are now proposing VirusLab http://genomic.deib.polimi.it/viruslab/, an instrument to analyze, visualize and inspect viral variants over populations and sub-populations of interest.

What are the assets and novelties of our Web Server?

For many different virus species (now including SARS-CoV-2, SARS-CoV-1, MERS, Dengue, and Ebola), VirusLab Web Server allows to load viral sequences with their metadata and to inspecting their metadata, variants and salient characteristics in friendly visualization screens also providing insights on the comparative distributions of different sub-populations.

The system is stateless but we include a light-weight session management, based on the concept of JSON-session, which allows the user to download and resume sessions as simple JSON files, possibly merging the populations of different sessions into a single one.

The main inputs of VirusLab are:

  • user-input raw sequence files (in FASTQ), plus corresponding metadata in CSV format, for SARS-CoV-2
  • user-input FASTA files (plus corresponding metadata in CSV format) for a variety of different viruses (SARS-CoV-2, SARS-CoV, MERS-CoV, Dengue and Ebola are currently supported);
  • a repository of pre-loaded JSON files that are provided to the user (representing interesting populations from NCBI/COG-UK)
  • any application that can produce a JSON-session correctly formatted file (we provide documentation on how the JSON-session is formed in Upload JSON page)

VirusLab can also be used as an interface to other systems of the same suite, all of which can build the appropriate JSON-session needed from VirusLab. We now provide ViruSurf.

As an additional point, for SARS-CoV-2 virus we can highlight interesting mutations as collected into a Knowledge Base that matches amino acid mutations with known effects discussed in recent literature.

How to navigate this WIKI documentation?

Please use the menu on the top right corner of this WIKI home to navigate this documentation.

Input Management addresses all the ways that can be employed to upload (or select) data to be analyzed with VirusLab.

VirusLab home page explains the structure of the website, specifying the interactions that can be operated among the different screens.

In Demonstrative Examples we provide

Please read our page What we support to learn more about browser compatibility and supported size of input.

- Please be aware! -
Due to the memory usage limitations imposed by this Chrome and Edge browsers,
VirusLab may not work with big input datasets and example projects. 
We strongly advice to switch to Firefox or Safari.

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