ioChem-BD documentation

License type Documentation Status

Welcome

Find here notes and guides about ioChem-BD platform, how to use it and eventually, how to install it.
Don’t hesitate contacting us at contact@iochem-bd.org if you need further information.

Please consider reading some papers regarding this platform and other related topics:

Álvarez-Moreno, M., de Graaf, C., López, N., Maseras, F., Poblet, J. M., Bo, C.
Managing the Computational Chemistry Big Data Problem: The ioChem-BD Platform.
J. Chem. Inf. Model, 55, 1, 95-103 (2015). https://doi.org/10.1021/ci500593j
Bo, C., Maseras, F. & López, N.
The role of computational results databases in accelerating the discovery of catalysts.
Nat Catal 1, 809–810 (2018). https://doi.org/10.1038/s41929-018-0176-4

About

ioChem-BD relies in an unique software platform which is builded in a modular way to satisfy all the needs: data creation and curation, publishing, storage, indexing data and search engine services.

The main node of the network runs the Find module, which acts as central server and is feed by any new data published in the repositories.
The Find module provides a fast chemical-aware search engine open public service and is hosted at the Barcelona Supercomputer Center (BSC). Also, the first public-access node is provided by BSC.

Other ioChem-BD modules automatize relevant data-extracting processes and transforms raw numerical data into labeled data in a database. It provides the researcher with tools for validating, enriching, publishing and sharing information, as well as tools to access, post-process and visualize data.

Users include computational chemistry research groups worldwide, university libraries and related services, and high performance supercomputer centers.

ioChem-BD function overview diagram

ioChem-BD function overview diagram

Modular architecture

The services available in the repository are actually provided by different modules: Create, Browse and Find. Each one has different objectives in managing chemistry digital assets, and they both complement each other. While there exists one only Find, there are as many Create/Browse modules as nodes in the network.

Create module

This web service is intended for use in private manner. It is fed with user files uploaded via a web browser or from any box running a Linux shell client, see Uploading Content into Create page.

Features:

  • Private interface, content accessed by user permission only
  • Productivity-oriented GUI designed using the zKoss framework
  • Automated document, data graph/chart generation: PDF files of supporting information reports, reaction energy profiles, etc…
  • Search by keywords and administrative metadata
  • Compact and intuitive design
  • Publish user selected data to the companion Browse module
The data is structured inside this module using projects and calculations, like folders and files inside a file system.
Each calculation has to be enclosed inside a project, and a project can be on the root or enclosed inside another project as a subproject.
Data organization is totally left to the user’s own criteria.

Browse module

This web service is intended for public access. It is fed with projects and calculations published from the Create module.
The Browse module uses entities such are Community, Collection and Item to organize the information:

  • Communities are the basis of hierarchy organization

  • Collections are the end point where to publish elements

  • Items are viewable digital assets. An item can be made of a single or a group of files, all of them related to the same calculation:

    • input and output files,
    • graphics,
    • associated documents,
    • and more…

We can make a direct correspondence of elements between Create and Browse organizational elements:

Create entity Browse entity
- Community
Project Collection
Calculation Item

It is up to ioChem-BD’s system administrator to generate users, groups and communities where to publish content. Collections and items are automatically generated during the process of publication from the Create module.