Opal 2.x

OBiBa’s core database application for biobanks

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You can Try it !

  • username: administrator
  • password: password

What's new

  • Projects
  • Administration
  • R
  • DataSHIELD

Projects

A project is a repository of data and dictionaries.
In a project, data are imported, exported, analysed, transformed and shared. 

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Project Tables

Formerly known as a datasource.

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Project Tables

A table has a dictionary (variables) and values.
  • Each variable can be edited individually,
  • There is a summary for each value type.

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Project Tables

Derived variable scripts versioning.

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Project Files

A project has its own folder to allow collaborative work.

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Project Reports

Use R and Markdown for reporting.

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Project Tasks

Follow import, export, copy, report tasks.

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Project Permissions

Manage project permissions in one page.

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Project Administration

Description, data storage, key store...

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Administration

Administration was improved to make Opal more dynamic.
  • Data access: users, ...
  • Data management: identifiers, ...
  • Data analysis: R, ...
  • System: databases, JVM...


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Users

  • Users and groups can be added from the web interface,
  • Users can be authenticated by password or certificate.

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Identifiers Mappings

  • Identifiers of any entity type can be mapped,
  • Easier identifiers management.

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R Service

R server can be controlled, even if it runs on a different machine.


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Databases

  • Easier database management,
  • MongoDB for large datasets.


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Java Virtual Machine

  • Memory usage
  • Threads
  • Garbage collector activity


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R

Opal and R in 5 lines.
# Login in opal
library(opal)o <- opal.login('administrator', 'password', 'http://localhost:8080')
# Assign a table to a data.frameopal.assign(o,'D','mica_demo.FNAC')
# Analyse data in the remote R sessionopal.execute(o,"summary(D)")

# Get data into the local R sessionD <- opal.execute(o,"D")
# Terminate remote R sessionopal.logout(o)

DataSHIELD

DataSHIELD process is parallelized.

Was sequential

    

  1. R command is executed on Opal 1
    2. 

  2. ...
    3. 

  3. R command is executed on Opal n
    4. 

  4. Results are combined
    5.
Now is parallel
    

  1. R command is submitted to Opal 1, ..., Opal n
    2. 

  2. R command result is retrieved from Opal 1, ..., Opal n
    3. 

  3. Results are combined
    4.

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