Open your research to the world

ioChem-BD - The Computational Chemistry Results Repository

Central service

Connected nodes

Collections available

Items indexed

One module for each need

Find service

The Central Point of our network of repositories

Features:

Fed by ioChem-BD distributed nodes whenever a new item is published
Advanced indexing of chemical data and metadata
Very fast search engine implemented over Apache Solr and RDKit frameworks
Search by chemical substructure similarity, chemical elements or any text term

Watch it live on the top of this page

Featured technologies

XML-CML

The Chemical Markup Language (CML) is used as the only internal data format. No unformatted nor style information is stored, just raw XML data ready to be further processed.

Jumbo-converters

ioChem-BD takes advantage of our own text-parsing library to convert data from plain text calculations files into CML. We use the same semantics as Jumbo-converters library but more efficiently.

Easy to Customize

With little programming knowledge (jumbo-converters, XSLT) users can customize new file types, define new data to be captured and how it should be visualized, add metadata, and much more.

Create module

Web Service/DesktopApp oriented to handle and manage your files in a daily basis

Features:

Private storage area
Compact and intuitive interface design
Visualization tools
Graph/chart generation,i.e., Reaction Energy Profiles, Orbitals, Spectra, etc ...
Search by keywords, chemical substructure and metadata
REST API interface enables remote interaction and processes automation

Linux shell

A Linux shell client activates specific commands that enable interacting with the Create module from the command line.

This tool is specially crafted to manage long unattended data operations by using simple shell scripts.

Browse module

DSpace based Repository for publishing data generated by the Create module

Features:

DOIs and permanent storage for your published datasets
Plain navigation across datasets collections
Accessible end-points to third-party connectors REST API, RDF, OAI-PMH
Facilitates content syndication, data replication and data harvesting

Institutions running ioChem-BD nodes

Public access

Private access

Institute of Chemical Research of Catalonia

French Alternative Energies and Atomic Energy Commission

Institutional accounts at BSC public server

Berry College
Colorado State University
CSC - IT Center for Science
ETH Zurich
First Mohammed University
Hebrew University of Jerusalem
Hunan Normal University
Indian Institute of Technology, Delhi
Institute of Chemical Research of Catalonia
Irkutsk State University
Lund University
Memorial University of Newfoundland
Norwegian University of Science and Technology (NTNU)
Sastra University
The University of Newcastle, Australia
Universidad Autónoma de Nuevo León
Universidad de Oviedo
Universidad de Sevilla
Universidade de São Paulo
Universidade Federal Rural do Rio de Janeiro
Université des Frère Mentouri Constantine
Université Mohammed Premier
Universitetet Oslo
University of agriculture, Faidalabad, Pakistan
University of Campinas
University of Michigan
University of Prince Edward Island
University of Surrey
Winston-Salem State University
Yarmouk University
More to come...

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To deploy your own ioChem-BD node, please fill the license request form

Please read before applying:

Fill this form if you want to host your own copy of ioChem-BD software and deploy it in your own servers. If your request is approved, you will get a license for running ioChem-BD both Create and Browse modules.
Check hardware and software requirements in the Installation documents.
If you apply for an academic organization license, please use an academic institution e-mail address to prove your affiliation. Do not use email addresses such as Gmail, Yahoo or Outlook accounts.
If you only want to use the ioChem-BD services hosted at the Barcelona Supercomputing Center node (BSC-CNS) as an individual, please fill this other form.
If you have any other question please contact us.

Administrative Information

Institution information

Institution name*

Department *

Country

City *

Address *

Contact Person

Last Name *

First Name *

Position *

Phone *

Email address *

* required

Technical Information

IP Public address *

Fully Qualified Domain Name (optional)

Intended use of the software * Please describe briefly which use will you be willing to give to the software.

I have read and agree to the Terms of Service

To sign up, you must request a new user account

Please read before applying:

Your user account will allow you to access and operate the ioChem-BD services hosted at the Barcelona Supercomputing Center node (BSC-CNS).
As a non-profit organization, BSC-CNS’ policy is to make use of the centre’s resources for research purposes and non-profit aims only. If you intend to use resources for profit purposes, we should establish a commercial agreement, whether you belong to a non-profit or a for-profit organization.
If you apply for an academic organization license, please use an academic institution e-mail address to prove your affiliation. Do not use email addresses such as Gmail, Yahoo or Outlook accounts.
User accounts will be grouped by Institution / Department / ResearchGroup. Please, keep this hierarchy in mind when applying for a new account. Contact your supervisor to avoid future conflicts.
If you want to host your own copy of ioChem-BD software and deploy it in your own servers, please fill this other form to request a copy.
If you have any other question please contact us.

ioChem-BD News

04-09-2017 to 07-09-2017

EUCO-TCC 2017 (Barcelona)

This summer, the ioChem-BD team assisted to the EUCO-TCC congress held at the Institut d'Estudis Catalans, such a magnific place, and city also.
Our staff perform a practical demo to the theoretical chemists that assisted the congress.

During poster session, assistants could get info about @MolecuBot project, which takes advantage of Fireworks workflow software and ioChem-BD platform to build large result datasets

20-09-2016

UAB Seminar

Presented a seminar at the Chemistry Faculty of Universitat Autónoma de Barcelona with the title: ioChem-BD: a digital solution to manage computational chemistry big data.
Later in the afternoon, our staff perform a practical demo to the theoretical chemists.

11-09-2016 to 15-09-2016

EUCHEMS 2016

During the five days the congress lasted, the ioChem-BD team set up a booth where to exhibit the platform and expose its major features.
We received a warm response from all the attendants at the EUCHEMS meeting on Seville.

09-09-2016

ECOSTBio meeting workshop

A hands-on demo of ioChem-BD platform was performed on Krakow (Poland) during the Fifth workshop of ECOSTBio working groups. Our user base keeps growing!

31-06-2016

VALCHEM16

The Reference Network on Theoretical and Computational Chemistry (XQTRC) organization has awarded the ioChem-BD project with the Valchem16 prize. Read more

27-11-2015

ICIQ-FIFC symposium

ioChem-BD platform and its features were exposed on the Spain-Japan Joint Symposium on Theoretical and Computational Chemistry of Complex Systems.

09-11-2015

euroCRIS 2015

ioChem-BD presented at the euroCRIS Strategic Membership Meeting

01-10-2005

ERC - Proof Of Concept accepted

Our chemical software is now part of ERC POC on BigData4Cat project

14-07-2015

ICIQ Hackathon

User Hackathon: All theoretical chemist at ICIQ centre used their ioChem-BD instance at once and continuously, generating a high work load to test software resilience and throughput. Some minor bugs were found (and marked for correction!) but on the whole all tests passed well.

04-02-2015

HPCKP'15

ioChem-BD presented at the HPC Knowledge Meeting'15.

27-01-2015

Web ICIQ

ioChem-BD highlighted at the ICIQ Web site.

23-12-2014

Excelciencia

On the press: Recordando los datos. Article about ioChem-BD at www.excelciencia.org.

03-12-2014

Paper Published

First iochem-BD paper published. J. Chem. Info. Mod. DOI 10.1021/ci500593j

30-11-2014

TSIUC'14

ioChem-BD presented at the TSIUC'14. See the slides.

Changelog

Coming soon

v1.3 under development

Comming features

New computational packages. Priority: CP2K
Multiple bug fixes
Add substructure search functionality using RDKit toolkit

September 21, 2018

v1.2.6 released

Major updates on Create and Browse modules, upgraded UI and improved UX.

Added QuantumEspresso data format. Added connection to the new Find module.

Features

Added QuantumEspresso software package to the captured formats.
Upgraded zKoss libraries to latest v8.5.1.
Refactored CSS stylesheets for better display.
View more ...

November 1, 2017

New service released: ioChem-BD Find

Coded new central service that syndicates calculations from all existing public ioChem-BD Browse modules.

Features

Metadata/term search
Substructure similarity search
Search by atom type

Explore new Find service at the following url: https://www.iochem-bd.org

September 2, 2016

v1.2 released

New features

DOI generation by an extremely easy procedure:click and forget
New computational packages. Priority: Molcas
Improved Orca HTML5 reports
Embargo set/lift feature during dataset publishing process
Additional metadata fields

February 18, 2016

v1.1 released

New features

Freely available for academic institutions worldwide upon EULA agreement
Added new computational package: Orca
Included molden orbital file visualitzation in Create and Browse module, currently for Orca files
New report : Automatic generation of Reaction Energy Profile
Browse module user interface revamped
Creative Commons licensing information on generated content, metadata fields and generated HTML5 resume pages
New update utility. From now on, updates will be applied by using a single shell script
Multiple bug fixes, a bunch of them!

August 4, 2015

v1.0 release

Two major web services: Create and Browse. ioChem-BD software comes to fill the gap between chemical data generation and its publication on papers, journals, and other digital media.

This new tool uses latest standards in data manipulation, curation, discovery and presentation. Not only speeding and leveraging tedious tasks such as data analysis and generation of SI.

Features:

Available services
- Create - Private use only. It allows data curation, manipulation in the form of reports and HTML5 summaries, and publishing to Browse module
- Browse - Intended for public access of all content published from Create module. Users can browse, subscribe and share content
- CAS - Central Authentication Service to manage login/logout current services from a centralized point
Supported computational packages:
- ADF
- Gaussian
- Turbomole
- VASP
Two user report types:
- Supporting information, classical PDF files
- Spin state energies for transition metal complexes

Data managed in a hierarchical manner: Projects/Calculations in Create, Community/Collection/Item in Browse

ioChem-BD services can be feed from two different sources:

Create Web UI: from your web browser you can upload calculations and manage project elements
Create Shell Client: A Linux shell app with +12 commands to manage and batch upload large number of files (fully scriptable)

About

ioChem-BD

is a digital repository aimed to manage and store Computational Chemistry files.
comes to fill the gap between results generation and manuscripts publication, and raise data to 5* quality
was created by the fusion of previous projects:

Developed at Institute of Chemical Research of Catalonia

Developed at Universitat Rovira i Virgili

Goals:

Build a distributed database of computational chemistry results: reduce size and increase value.
Set a common data standard among all quantum chemistry legacy formats (XML - CML)
Become a daily tool in data management, search and manipulation
Redefine workflows: store results and publishing, open-data
Be open to add future functionalities for data manipulation and analysis

DOI

Author

Method

Basis Set

Stoichiometry

Program

Calc. type

Name

Subject

Title

Description

Instutions

One module for each need

Find

Browse

Create

Find service

Featured technologies

XML-CML

Jumbo-converters

Easy to Customize

Create module

Linux shell

Browse module

Institutions running ioChem-BD nodes

Public access

Private access

Institutional accounts at BSC public server

Subscribe to our mailing list

To deploy your own ioChem-BD node, please fill the license request form

Please read before applying:

Administrative Information

Institution information

Contact Person

* required

Technical Information

To sign up, you must request a new user account

Please read before applying:

ioChem-BD News

Changelog

v1.3 under development

Comming features

v1.2.6 released

Features

Bug fixes

New service released: ioChem-BD Find

Features

v1.2 released

New features

v1.1 released

New features

v1.0 release

Features:

About

ioChem-BD

Goals:

Supported by: